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  • 2651.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate.2002In: J. Org. Chem., Vol. 67, p. 1852-1865Article in journal (Refereed)
  • 2652. Acharya, P.
    et al.
    Cheruku, P.
    Chatterjee, S.
    Acharya, S.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J.
    Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes2004In: J. Am. Chem. Soc., Vol. 126, p. 2862-2869Article in journal (Refereed)
  • 2653.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes.2004In: J Am Chem Soc, ISSN 0002-7863, Vol. 126, no 9, p. 2862-9Article in journal (Other scientific)
  • 2654.
    Acharya, P
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, P
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, Sunanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Karthick Babu, S
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, S
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes2004In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 9, p. 2862-2869Article in journal (Refereed)
    Abstract [en]

    To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by (1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK(a) values of the monomeric nucleotide blocks as well as Delta pK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G*(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimics to expand the alphabet of the genetic code.

  • 2655.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Issakson, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Pradeepkumar, P.I.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Experimental Evidences Unequivocally Prove the Role of Stereoelectronics as One of the Major Forces Responsible for the Self-assembly of DNA and RNA.2002In: Collect. Czech. Chem. Commun.: Collection Symposium Series (Chemistry of Nucleic Acid Components), Vol. 5, p. 99-120Article in journal (Refereed)
  • 2656.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Nawrot, B
    Sprinzl, M
    Thibaudeau, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    The strength of the 3 '-gauche effect dictates the structure of 3 '-O-anthraniloyladenosine and its 5 '-phosphate, two analogues of the 3 '-end of aminoacyl-tRNA1999In: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, ISSN 0300-9580, no 7, p. 1531-1536Article in journal (Other scientific)
    Abstract [en]

    Anthranilic acid charged yeast tRNA(Phe) or E. Coli tRNA(Val) are able to form a stable complex with EF-Tu*GTP, hence the 2'- and 3'-O-anthraniloyladenosines and their 5'-phosphate counterparts have been conceived to be the smallest units that are capable

  • 2657.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Plashkevych, O
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Morita, C
    Yamada, S
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.2003In: J Org Chem, ISSN 0022-3263, Vol. 68, no 4, p. 1529-38Article in journal (Other scientific)
  • 2658.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Thibaudeau, C
    Chattopadhyaya, J
    An energetic correlation of ab initio and NMR studies of the 3 '-gauche effect in 3 '-substituted thymidines2001In: NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, ISSN 1525-7770, Vol. 20, no 4-7, p. 1229-1233Article in journal (Refereed)
    Abstract [en]

    A straightforward correlation of our experimental NMR findings on 3'-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the DeltaG(NRM)degrees (298k) of N reversible arrow S equilibrium in nucleoside can be predicted

  • 2659.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Trifonova, A
    Thibaudeau, C
    Foldesi, A
    Chattopadhyaya, J
    The transmission of the electronic character of guanin-9-yl drives the sugar-phosphate backbone torsions in guanosine 3 ',5 '-bisphosphate1999In: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, ISSN 1433-7851, Vol. 38, no 24, p. 3645-3650Article in journal (Refereed)
  • 2660.
    Acharya, P
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Velikian, I
    Acharya, S
    Chattopadhyaya, J
    Molecular modelling of 2 '-OH mediated hydrogen bonding in ribonucleos(t)ides by NMR constrained AM1 and MMX calculations2001In: NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, ISSN 1525-7770, Vol. 20, no 4-7, p. 1211-1217Article in journal (Refereed)
    Abstract [en]

    The intra- and intermolecular hydrogen bonding (DeltaG(298K)degrees approximate to 2 kcal mol(-1)) of 2'-OH in nucleos(t)ides has been reported by the temperature- and concentration-dependent NMR study in conjunction with dihedral dependence of the NMR de

  • 2661.
    Acharya, Parag
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl adenosine (a mimic of 3'-teminal CCAOH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl adenosine, thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

    List of papers
    1. The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
    Open this publication in new window or tab >>The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-phosphate Backbone Torsions in Guanosine 3',5'-bisphosphate.
    Show others...
    1999 In: Angew. Chem. Int. Ed., Vol. 38, no 24, p. 3645-3650Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91143 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    2. The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
    Open this publication in new window or tab >>The RNA Molecular Wire: The pH-Dependent Change in Electronic Character of Adenine-9-yl is Transmitted to Drive the Sugar-Phosphate Backbone Torsions in Adenosine 3', 5'-bisphosphate
    Show others...
    2000 In: J. Phys. Org. Chem., Vol. 13, p. 300-305Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91144 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    3. The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
    Open this publication in new window or tab >>The Strength of the 3'-gauche effect Dictates the Structure of 3'-anthraniloyladenosine and its 5'-phosphate, Two Analogues of the 3'-end of Aminoacyl tRNA
    Show others...
    1999 In: J. Chem. Soc. Perkin 2, p. 1531-1536Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91145 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    4. The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    Open this publication in new window or tab >>The Hydrogen Bonding and Hydration of 2'-OH in Adenosine and Adenosine 3'-ethylphosphate
    2002 In: J. Org. Chem., Vol. 67, no 6, p. 1852-1865Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91146 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    5. A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
    Open this publication in new window or tab >>A Repertoire of Pyridinium-Phenyl-Methyl Cross-Talk through a Cascade of Intramolecular Electrostatic Interactions
    Show others...
    2003 In: J. Org. Chem., Vol. 68, no 4, p. 1529-1538Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91147 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    6. Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    Open this publication in new window or tab >>Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') monophosphates by the Nearest Neighbor Interaction in the Stacked State
    2002 In: J. Am. Chem. Soc., Vol. 124, no 46, p. 13722-13730Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91148 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    7. Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    Open this publication in new window or tab >>Tandem Electrostatic Effect From the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-neighbor Stacking
    2003 In: J. Am. Chem. Soc., Vol. 125, no 8, p. 2094-2100Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91149 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    8. Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Open this publication in new window or tab >>Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Show others...
    2003 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 33, p. 9948-9961Article in journal (Refereed) Published
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91150 (URN)10.1021/ja034651h (DOI)12914458 (PubMedID)
    Available from: 2003-11-26 Created: 2003-11-26 Last updated: 2017-12-14Bibliographically approved
    9. The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
    Open this publication in new window or tab >>The Nucleobases in Single-stranded DNA are Better Stacked and Yet Their Pseudoaromatic Characters are More Poorly Cross-modulated Than in the RNA Counterparts Due to Variable Tandem Nearest-neighbour Electrostatic Interactions
    Show others...
    In: J. Am. Chem. Soc.Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91151 (URN)
    Available from: 2003-11-26 Created: 2003-11-26Bibliographically approved
    10. Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
    Open this publication in new window or tab >>Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
    Show others...
    2004 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 9, p. 2862-2869Article in journal (Refereed) Published
    Abstract [en]

    To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK(a) error (sigma = +/-0.01 to 0.02) by (1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK(a) values of the monomeric nucleotide blocks as well as Delta pK(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G*(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimics to expand the alphabet of the genetic code.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91152 (URN)10.1021/ja0386546 (DOI)14995203 (PubMedID)
    Available from: 2003-11-26 Created: 2003-11-26 Last updated: 2017-12-14Bibliographically approved
  • 2662.
    Acharya, Parag
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, Sandipta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, P
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Amirkhanov, N. V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Földesi, A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions2003In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 33, p. 9948-9961Article in journal (Refereed)
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

  • 2663.
    Acharya, Rupesh
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Object Oriented Design Pattern Extraction From Java Source Code2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In case of software architecture reconstruction, design pattern detection plays a vital role since its presence reflects the point of design decision. Currently most of the studied approaches only focus on the Gang of Four (GOF) design patterns so those tools are not flexible enough to identify other proprietary pattern instances. Moreover, the GOF design pattern can be implemented in various ways which many of the tools suffers to detect. Apart from that not only design pattern is of vital importance for software architecture reconstruction but other patterns like anti-patterns and presence of bad smell code are also equally important. So the approach discussed here is a solution for detecting any pattern instances (not only GOF patterns) from the source code provided that relevant information is extracted during the static analysis phase.

    Our approach is based on the graph pattern matching technique where the source code is modeled as a graph and the pattern to search for is provided as a graph query pattern. For the detection of patterns we focus on structural and behavioral analysis of source code as in the case of a tool called PINOT. The novelty of our approach compared to PINOT is that the choice of behavioral analyzers can be provided as a constraint in the graph query pattern unlike hardcoded in PINOT. Moreover, we can provide more than one constraint in the graph query pattern at node, edge or complete graph level hence, we can compose our query pattern as we want which helps us to specify different kind of new patterns and handle varying implementations of design patterns as well.

  • 2664.
    Acharya, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, P.
    Földesi, A.
    Chattopadhyaya, J.
    Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State2002In: J. Am. Chem. Soc., Vol. 124, p. 13722-13730Article in journal (Refereed)
  • 2665.
    Acharya, S
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Földesi, A
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cross-modulation of physicochemical character of aglycones in dinucleoside (3'-->5') monophosphates by the nearest neighbor interaction in the stacked state.2002In: J Am Chem Soc, ISSN 0002-7863, Vol. 124, no 46, p. 13722-30Article in journal (Other scientific)
  • 2666.
    Acharya, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Barman, J.
    Cheruku, P.
    Chatterjee, S.
    Acharya, P.
    Isaksson, J.
    Chattopadhyaya, J.
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004In: J. Am. Chem. Soc., Vol. 126, p. 8674-8681Article in journal (Refereed)
  • 2667.
    Acharya, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Földesi, A.
    Chattopadhyaya, J.
    The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates2003In: J. Org. Chem., Vol. 68, p. 1906-1910Article in journal (Refereed)
  • 2668.
    Acharya, S
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Földesi, A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    The pK(a) of the internucleotidic 2'-hydroxyl group in diribonucleoside (3'-->5') monophosphates.2003In: J Org Chem, ISSN 0022-3263, Vol. 68, no 5, p. 1906-10Article in journal (Other scientific)
  • 2669.
    Acharya, Sandipta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Some Aspects of Physicochemical Properties of DNA and RNA2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pKa values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pKa values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.

    List of papers
    1. The pKa’s of 2'-Hydroxyl Group in Nucleosides and Nucleotides
    Open this publication in new window or tab >>The pKa’s of 2'-Hydroxyl Group in Nucleosides and Nucleotides
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    2001 In: J. Am. Chem. Soc., Vol. 123, p. 2893-2894Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94240 (URN)
    Available from: 2006-04-07 Created: 2006-04-07 Last updated: 2014-03-03Bibliographically approved
    2. The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates
    Open this publication in new window or tab >>The pKa of the Internucleotidic 2'-Hydroxyl Group in Diribonucleoside (3'→5') Monophosphates
    2003 In: J. Org. Chem., Vol. 68, p. 1906-1910Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94241 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    3. Non-identical electronic characters of the internucleotidic pohosphates in RNA modulate the chemical reactivity of the phosphodiester bonds
    Open this publication in new window or tab >>Non-identical electronic characters of the internucleotidic pohosphates in RNA modulate the chemical reactivity of the phosphodiester bonds
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    2006 In: Org. Biomol. Chem., Vol. 4, p. 928-941Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94242 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    4. Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State
    Open this publication in new window or tab >>Cross-Modulation of Physicochemical Character of Aglycones in Dinucleoside (3'→5') Monophosphates by the Nearest Neighbor Interaction in the Stacked State
    2002 In: J. Am. Chem. Soc., Vol. 124, p. 13722-13730Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94243 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    5. Tandem Electrostatic Effect from the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-Neighbor Interaction
    Open this publication in new window or tab >>Tandem Electrostatic Effect from the First to the Third Aglycon in the Trimeric RNA Owing to the Nearest-Neighbor Interaction
    2003 In: J. Am. Chem. Soc, Vol. 125, p. 2094-2100Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94244 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    6. Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
    Open this publication in new window or tab >>Cross-Modulation of the pKa of Nucleobases in a Single-Stranded Hexameric-RNA Due to Tandem Electrostatic Nearest-Neighbor Interactions
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    2003 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 33, p. 9948-9961Article in journal (Refereed) Published
    Abstract [en]

    The pH titration studies (pH 6.7-12.1) in a series of dimeric, trimeric, tetrameric, pentameric, and hexameric oligo-RNA molecules [GpA (2a), GpC (3a), GpApC (5), GpA(1)pA(2)pC (6), GpA(1)pA(2)pA(3)pC (7), GpA(1)pA(2)pA(3)pA(4)pC (8)] have shown that the pK(a) of N(1)-H of 9-guaninyl could be measured not only from its own deltaH8G, but also from the aromatic marker protons of other constituent nucleobases. The relative chemical shift differences [Deltadelta((N)(-)(D))] between the protons in various nucleotide residues in the oligo-RNAs at the neutral (N) and deprotonated (D) states of the guanine moiety show that the generation of the 5'-(9-guanylate ion) in oligo-RNAs 2-8 reduces the stability of the stacked helical RNA conformation owing to the destabilizing anion(G(-))-pi/dipole(Im(delta)(-)) interaction. This destabilizing effect in the deprotonated RNA is, however, opposed by the electrostatically attractive atom-pisigma (major) as well as the anion(G(-))-pi/dipole(Py(delta)(+)) (minor) interactions. Our studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain. Thus, such specific generation of a charge at a single nucleobase moiety allows us to explore the relative strength of stacking within a single-stranded helix. The pK(a) of 5'-Gp residue from its own deltaH8G in the hexameric RNA 8 is found to be 9.76 +/- 0.01; it, however, varies from 9.65 +/- 0.01 to 10.5 +/- 0.07 along the RNA chain as measured from the other marker protons (H2, H8, H5, and H6) of 9-adeninyl and 1-cytosinyl residues. This nucleobase-dependent modulation of pK(a)s (DeltapK(a) +/- 0.9) of 9-guaninyl obtained from other nucleobases in the hexameric RNA 8 represents a difference of ca. 5.1 kJ mol(-)(1), which has been attributed to the variable strength of electrostatic interactions between the electron densities of the involved atoms in the offset stacked nucleobases as well as with that of the phosphates. The chemical implication of this variable pK(a) for guanin-9-yl deprotonation as obtained from all other marker protons of each nucleotide residue within a ssRNA molecule is that it enables us to experimentally understand the variation of the electronic microenvironment around each constituent nucleobase along the RNA chain in a stepwise manner with very high accuracy without having to make any assumption. This means that the pseudoaromaticity of neighboring 9-adeninyl and next-neighbor nucleobases within a polyanionic sugar-phosphate backbone of a ssRNA can vary from one case to another due to cross-modulation of an electronically coupled pi system by a neighboring nucleobase. This modulation may depend on the sequence context, spatial proximity of the negatively charged phosphates, as well as whether the offset stacking is ON or OFF. The net outcome of this electrostatic interaction between the neighbors is creation of new sequence-dependent hybrid nucleobases in an oligo- or polynucleotide whose properties are unlike the monomeric counterpart, which may have considerable biological implications.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-91150 (URN)10.1021/ja034651h (DOI)12914458 (PubMedID)
    Available from: 2003-11-26 Created: 2003-11-26 Last updated: 2017-12-14Bibliographically approved
    7. Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
    Open this publication in new window or tab >>Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA
    Show others...
    2004 In: J. Am. Chem. Soc., Vol. 126, p. 8674-8681Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94246 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    8. Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern
    Open this publication in new window or tab >>Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern
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    2004 In: Biochemistry, Vol. 43, p. 15996-16010Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94247 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
    9. Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
    Open this publication in new window or tab >>Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
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    2004 In: J. Am. Chem. Soc., Vol. 126, p. 2862-2869Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94248 (URN)
    Available from: 2006-04-07 Created: 2006-04-07Bibliographically approved
  • 2670. Acharya, Sandipta
    et al.
    Barman, Jharna
    Cheruku, Pradeep
    Chatterjee, Subhrangsu
    Acharya, Parag
    Isaksson, Johan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, Jyoti
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004In: J. Am. Chem. Soc., ISSN 0002-7863, Vol. 126, p. 8674-8681Article in journal (Refereed)
  • 2671.
    Acharya, Sandipta
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Barman, Jharna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, Pradeep
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, Subhrangsu
    Acharya, Parag
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Isaksson, Johan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, Jyoti
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Significant pKa perturbation of nucleobases is an intrinsic property of the sequence context in DNA and RNA.2004In: J Am Chem Soc, ISSN 0002-7863, Vol. 126, no 28, p. 8674-81Article in journal (Other scientific)
  • 2672.
    Acharya, Sandipta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Barman, Jharna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Cheruku, Pradeep
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chatterjee, Subhrangsu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Acharya, Parag
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Isaksson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Chattopadhyaya, Jyoti
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Bioorganic Chemistry.
    Significant pKa Perturbation of Nucleobases Is an Intrinsic Property of the Sequence Context in DNA and RNA2004In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 126, no 28, p. 8674-8681Article in journal (Refereed)
  • 2673. Achatz, Johannes Georg
    et al.
    Hooge, Matthew
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Jondelius, Ulf
    Tyler, Seth
    Systematic revision of acoels with 9+0 sperm ultrastructure (Convolutida) and the influence of sexual conflict on morphology2010In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 48, no 1, p. 9-32Article, review/survey (Refereed)
    Abstract [en]

    We have used newly discerned morphological characters as well as molecular-sequence data from 18S and 28S rDNA to revise the families recently designated as the '9+0' acoels - what we call Convolutida. Characters from the ultrastructure of sperm, with their '9+0' axonemes, are useful in delineating the Convolutida, but are either species-specific or too conserved within the group to be used to infer relationships within it. Male genital organs, prostatoid organs, and sagittocysts, on the other hand, give a good phylogenetic signal for reconstructing relationships of such genera as Conaperta, Anaperus, and Achoerus; some features of the reproductive organs correlate with habitat and show how the Convolutida probably originated as epiphytic predators and radiated into the mesopsammon, pelagic, and coral-associated realms. In this revision of the Convolutida we provide revised synopses of its families - which we restrict to the Anaperidae, Convolutidae, and Sagittiferidae - and describe a new species, Polychoerus gordoni, from New Zealand. We transfer the genus Adenopea from the Antroposthiidae to the Convolutidae; Conaperta, Neochildia, and Oxyposthia from the Convolutidae to the Anaperidae; Paranaperus and Praeanaperus from the Anaperidae to the Haploposthiidae. Convoluta aegyptica is synonymized with Convoluta boehmigi, Convoluta lacazii with Convoluta sordida, and the genus Picola (Convolutidae) with Deuterogonaria (Haploposthiidae). Amphiscolops blumi, A. carvalhoi, and A. langerhansi, all of which possess a cellular seminal bursa, are transferred to the genus Heterochaerus. Convoluta elegans and Pseudanaperus tinctus are classified as nomina nuda. We use our findings on the ultrastructure of female genital organs and spermatozoa to show that sexual conflict plays a major role in the evolution of diversity of these structures and that the phylogeny of the Acoela would comprise early forms without female genital organs and hyper- or hypodermal transfer of sperm through advanced forms with ever longer and narrower bursal nozzles and sperm with axial microtubules. Moreover, our results show that the acquisition of endosymbiotic algae happened at least twice within the Acoela.

  • 2674.
    Achcar, JA
    et al.
    Uppsala University, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Faculty of Social Sciences, Department of Information Science.
    Agrawal, MC
    Anand, KN
    Ali, MM
    Ali, MM
    Bagui, SC
    Baker, RD
    Balamurali, S
    Balasooriya, U
    Bansal, AK
    Barry, J
    Bonett, DG
    Box, G
    Carling, K
    Caudill, SB
    Chakraborti, S
    Chatfield, C
    Chatterjee, S
    Cornell, JA
    Cox, D
    Draper, NR
    Ehrenberg, A
    Finney, DJ
    25 years of applied statistics1998In: JOURNAL OF APPLIED STATISTICS, ISSN 0266-4763, Vol. 25, no 1, p. 3-22Article in journal (Refereed)
  • 2675. Achen, M G
    et al.
    Jeltsch, M
    Kukk, E
    Mäkinen, T
    Vitali, A
    Wilks, A F
    Alitalo, K
    Stacker, S A
    Vascular endothelial growth factor D (VEGF-D) is a ligand for the tyrosine kinases VEGF receptor 2 (Flk1) and VEGF receptor 3 (Flt4).1998In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 95, no 2Article in journal (Refereed)
    Abstract [en]

    We have identified a member of the VEGF family by computer-based homology searching and have designated it VEGF-D. VEGF-D is most closely related to VEGF-C by virtue of the presence of N- and C-terminal extensions that are not found in other VEGF family members. In adult human tissues, VEGF-D mRNA is most abundant in heart, lung, skeletal muscle, colon, and small intestine. Analyses of VEGF-D receptor specificity revealed that VEGF-D is a ligand for both VEGF receptors (VEGFRs) VEGFR-2 (Flk1) and VEGFR-3 (Flt4) and can activate these receptors. However. VEGF-D does not bind to VEGFR-1. Expression of a truncated derivative of VEGF-D demonstrated that the receptor-binding capacities reside in the portion of the molecule that is most closely related in primary structure to other VEGF family members and that corresponds to the mature form of VEGF-C. In addition, VEGF-D is a mitogen for endothelial cells. The structural and functional similarities between VEGF-D and VEGF-C define a subfamily of the VEGFs.

  • 2676. Achen, M G
    et al.
    Roufail, S
    Domagala, T
    Catimel, B
    Nice, E C
    Geleick, D M
    Murphy, R
    Scott, A M
    Caesar, C
    Makinen, T
    Alitalo, K
    Stacker, S A
    Monoclonal antibodies to vascular endothelial growth factor-D block its interactions with both VEGF receptor-2 and VEGF receptor-3.2000In: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 267, no 9Article in journal (Refereed)
    Abstract [en]

    Vascular endothelial growth factor-D (VEGF-D), the most recently discovered mammalian member of the VEGF family, is an angiogenic protein that activates VEGF receptor-2 (VEGFR-2/Flk1/KDR) and VEGFR-3 (Flt4). These receptor tyrosine kinases, localized on vascular and lymphatic endothelial cells, signal for angiogenesis and lymphangiogenesis. VEGF-D consists of a central receptor-binding VEGF homology domain (VHD) and N-terminal and C-terminal propeptides that are cleaved from the VHD to generate a mature, bioactive form consisting of dimers of the VHD. Here we report characterization of mAbs raised to the VHD of human VEGF-D in order to generate VEGF-D antagonists. The mAbs bind the fully processed VHD with high affinity and also bind unprocessed VEGF-D. We demonstrate, using bioassays for the binding and cross-linking of VEGFR-2 and VEGFR-3 and biosensor analysis with immobilized receptors, that one of the mAbs, designated VD1, is able to compete potently with mature VEGF-D for binding to both VEGFR-2 and VEGFR-3 for binding to mature VEGF-D. This indicates that the binding epitopes on VEGF-D for these two receptors may be in close proximity. Furthermore, VD1 blocks the mitogenic response of human microvascular endothelial cells to VEGF-D. The anti-(VEGF-D) mAbs raised to the bioactive region of this growth factor will be powerful tools for analysis of the biological functions of VEGF-D.

  • 2677.
    Achenbach, Jan-Ole
    et al.
    Rhein Westfal TH Aachen, Mat Chem, Aachen, Germany.
    Mraz, Stanislav
    Rhein Westfal TH Aachen, Mat Chem, Aachen, Germany.
    Primetzhofer, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Applied Nuclear Physics.
    Schneider, Jochen M.
    Rhein Westfal TH Aachen, Mat Chem, Aachen, Germany.
    Correlative Experimental and Theoretical Investigation of the Angle-Resolved Composition Evolution of Thin Films Sputtered from a Compound Mo2BC Targe2019In: Coatings, ISSN 2079-6412, Vol. 9, no 3, article id 206Article in journal (Refereed)
    Abstract [en]

    The angle-resolved composition evolution of Mo-B-C thin films deposited from a Mo2BC compound target was investigated experimentally and theoretically. Depositions were carried out by direct current magnetron sputtering (DCMS) in a pressure range from 0.09 to 0.98 Pa in Ar and Kr. The substrates were placed at specific angles α with respect to the target normal from 0 to ±67.5°. A model based on TRIDYN and SIMTRA was used to calculate the influence of the sputtering gas on the angular distribution function of the sputtered species at the target, their transport through the gas phase, and film composition. Experimental pressure- and sputtering gas-dependent thin film chemical composition data are in good agreement with simulated angle-resolved film composition data. In Ar, the pressure-induced film composition variations at a particular α are within the error of the EDX measurements. On the contrary, an order of magnitude increase in Kr pressure results in an increase of the Mo concentration measured at α = 0° from 36 at.% to 43 at.%. It is shown that the mass ratio between sputtering gas and sputtered species defines the scattering angle within the collision cascades in the target, as well as for the collisions in the gas phase, which in turn defines the angle- and pressure-dependent film compositions.

  • 2678. Achenbach, Stephan
    et al.
    Friedrich, Matthias G.
    Nagel, Eike
    Kramer, Christopher M.
    Kaufmann, Philip A.
    Farkhooy, Amir
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Respiratory Medicine and Allergology.
    Dilsizian, Vasken
    Flachskampf, Frank A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cardiology.
    CV Imaging: What Was New in 2012?2013In: JACC Cardiovascular Imaging, ISSN 1936-878X, E-ISSN 1876-7591, Vol. 6, no 6, p. 714-734Article in journal (Refereed)
    Abstract [en]

    Echocardiography, single-photon emission computed tomography (SPECT), positron emission tomography (PET), cardiac magnetic resonance, and cardiac computed tomography can be used for anatomic and functional imaging of the heart. All 4 methods are subject to continuous improvement. Echocardiography benefits from the more widespread availability of 3-dimensional imaging, strain and strain rate analysis, and contrast applications. SPECT imaging continues to provide very valuable prognostic data, and PET imaging, on the one hand, permits quantification of coronary flow reserve, a strong prognostic predictor, and, on the other hand, can be used for molecular imaging, allowing the analysis of extremely small-scale functional alterations in the heart. Magnetic resonance is gaining increasing importance as a stress test, mainly through perfusion imaging, and continues to provide very valuable prognostic information based on late gadolinium enhancement. Magnetic resonance coronary angiography does not substantially contribute to clinical cardiology at this point in time. Computed tomography imaging of the heart mainly concentrates on the imaging of coronary artery lumen and plaque and has made substantial progress regarding outcome data. In this review, the current status of the 5 imaging techniques is illustrated by reviewing pertinent publications of the year 2012. 

  • 2679. Achermann, Sheila
    Småsyskonstudier om AST: föräldrarnas upplevelser2016Conference paper (Other academic)
  • 2680. Achermann, Sheila
    et al.
    Bölte, Sven
    Falck-Ytter, Terje
    Intense data collection from infant siblings of children on the autism spectrum: Is it ethical?2016Conference paper (Refereed)
  • 2681. Achermann, Sheila
    et al.
    Bölte, Sven
    Falck-Ytter, Terje
    Parents’ Perspectives on Infant Sibling Studies in Autism Spectrum Disorder2017Conference paper (Refereed)
  • 2682.
    Achermann, Sheila
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Psychology.
    Nyström, Pär
    Gredebäck, Gustaf
    Bölte, Sven
    Falck-Ytter, Terje
    Characterizing Motor Functioning in Infants at Risk for Autism Spectrum Disorder Using Motion Capture Technology2018Conference paper (Refereed)
  • 2683.
    Achieng, Spance Joy
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Law, Department of Law.
    SOFTWARE PATENTS: A study on the patentability of software inventions2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The primary objective of the thesis will be to focus on patent protection of software under the European Patent Convention, by analyzing the different approaches that the European Patent Office has taken into consideration since the mid-1980s. These approaches are derived from the different decisions that emanate from the Technical Boards of Appeal of the European Patent Office. The thesis will examine the most relevant decisions illustrating the juridical tendencies and basis that have been utilized to decide over the patentability of computer programs. The analysis will conclude with the latest approach taken by the Technical Board of the European Patent Office. The study will examine the patentability requirements of inventions in general established within the European Patent Convention. Sources that will be utilized to carry out this research will include case law, legislation, specialized legal commentary; journals and books. The present study sustains that computer programs may be patented as long as they comply with all the general requirements of an invention prescribed under the European Patent Convention together with the condition established by case law called the technical character requirement. Nevertheless, due to the fact that the Technical Boards of Appeal are not bound by previous case law, the current position could keep evolving as it relies on the stance of  the European Patent Office on patentability of computer programs which is seems to be influenced by the changes in the technological world 

  • 2684.
    Achilleos, Antonakis
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    Ethical web design: An audit of municipality websites in Europe2015Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    All municipalities have a website. This thesis examined the websites of 24 towns in 6 EU member countries in terms of their ethical design. This study found that there are websites that are in the stage of providing contact information only, while other are more detailed with advanced techniques allowing openness and participation. The study found also that there is no code of ethics or EU / country laws that regulate the design or content of a municipality website, as far as their ethical aspect is concerned. What is regulated by the EU and the countries of the municipalities studied in this thesis, is the existence and use of cookies in municipality websites.  The study found that due to lack of control, the websites’ ethical design mainly depends on the local authorities’ interest and initiative. Even for cookies where laws exist, citizens are not informed correctly.

  • 2685.
    Achour, Nemer
    Sveriges lantbruksuniversitet.
    Evaluating energy efficiency and emissions of charred biomass used as a fuel for household cooking in rural Kenya2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In sub-Saharan Africa a large share of the energy use utilize biomass as a fuel. In some

    countries more than 90 percent of the energy use is biomass. This energy is primarily used for

    cooking, heating and drying. Cooking food on an open fire or using a traditional stove will

    combust the firewood inefficiently and leads to pollution in the form of particulate matter,

    carbon monoxide and other hazardous pollutants. Indoor pollution has serious health effects

    and especially women and children are affected by this since they spend more time in the

    kitchens compared to men.

    More efficient combustion would lead to less harmful pollution to women and children in

    these rural areas. There are different kinds of stoves on the market and one of them is the

    gasifier stove which allows the biomass to go through pyrolysis in a separate step before

    complete combustion. If the charred biomass is harvested before complete combustion it can

    be saved for later use. This stove will result in cleaner and more energy efficient combustion

    compared to the traditional 3-stone-fire.

    The aim of this study has been to evaluate the charred biomass harvested from this gasifier

    stove in terms of energy use efficiency, emissions and cooking time. The charred biomass was

    compared to conventional charcoal bought at the local market. The charred biomass

    investigated is charred Grevillea prunings from the

    Grevillea Robusta tree, charred coconut

    husks (

    Cocos nucifera) and charred maize cobs (Zea mays). They were tested by cooking a

    meal consisting of two dishes at five different households for different kinds of charred

    biomass and conventional charcoal as a reference.

    Using charred Grevillea prunings gives an energy saving up to 31 percent while charred

    coconut husks gives up to 11 percent energy saved compared to the 3-stone-fire. Charred

    maize cobs was only up to 2 percent more energy efficient than conventional charcoal due to

    its low energy density and fast burning rate. In most cases there was no significant difference

    between the emissions of the different charred fuel types. Only charred maize cobs resulted in

    significantly higher emissions than the other fuels. Household B deviated from the others

    households and had higher emissions. In conclusion the different types of charred biomass are

    good fuels for cooking. Charred maize cobs are less valuable since they require a higher rate

    of refilling of fuel during cooking and do not result in better energy use efficiency compared

    to conventional charcoal.

    There were no significant differences between the different types of charred biomass and

    conventional charcoal in emissions except for a few cases where charred maize cobs had a

    slightly higher level of emission compared to the others. CO

    2- levels were so low that there

    was no risk of harmful concentrations in any way. PM

    2.5-emissions levels were safe, but the

    CO-emissions levels for charred maize cobs were close to levels were symptoms might show.

  • 2686.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    A process-view on the role of resource practices for SME growth2005In: Paper presented at the Interdisciplinary European Conference on Entrepreneurship Research, Amsterdam, February 2005, 2005Conference paper (Other academic)
  • 2687.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Business firm growth: Are we talking about the same thing?2005In: Paper presented at RENT XIX (Research in Entrepreneurship and Small Business), November 17-18, 2005, Naples, Italy, 2005Conference paper (Other academic)
  • 2688.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Investigating Patterns of Development in SMEs2006In: Paper presented at the Academy of Management Annual Meeting, Atlanta, Georgia, August 11-16, 2006, 2006Conference paper (Other academic)
  • 2689.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    One Decade Later: Following Up the ‘Gröna Kvisten’ Prize-winning Growth Firms2006In: Managing Complexity and Change in SMEs: Frontiers in European Research, Cheltenham: Edward Elgar , 2006, p. 10-34Chapter in book (Other (popular science, discussion, etc.))
  • 2690.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    One decade later?: Following up the Gröna kvisten prize-winning high-growth firms2004In: Paper presented at RENT XVIII (Research in Entrepreneurship and Small Business), November 25-26, 2004, Copenhagen, Denmark, 2004Conference paper (Other academic)
  • 2691.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Towards a re-conceptualization of firm growth2004In: Frontiers of entrepreneurship research 2004: proceedings of the twenty-fourth annual Entrepreneurship Research Conference, Babson Park, Mass.: Arthur M. Blank Center for Entrepreneurship, Babson College , 2004Conference paper (Other academic)
  • 2692.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Tracing patterns of growth: A first analysis of the 'Gröna Kvisten' high-growth ventures2005In: Advances in Interdisciplinary European Entrepreneurship research: Vol. 2, Münster: Lit Verlag , 2005, p. 101-132Chapter in book (Other academic)
  • 2693.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Tracing patterns of growth: An analysis of the 'Gröna Kvisten' high-growth ventures2004In: Paper presented at the Interdisciplinary European Conference on Entrepreneurship Research, Regensburg, February 2004, 2004Conference paper (Other academic)
  • 2694.
    Achtenhagen, Leona
    et al.
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Helin, Jenny
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Melin, Leif
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Naldi, Lucia
    Internationella Handelshögskolan, Högskolan i Jönköping, IHH, EMM (Entrepreneurskap, Marknadsföring, Management).
    Tricks of twigs: how the ‘Gröna Kvisten’-winning firms grew big(ger)2005In: Paper presented at the Annual Conference on Corporate Strategy, Vallendar, Germany, March 11-12, 2005, 2005Conference paper (Other academic)
  • 2695. Achterberg, A.
    et al.
    Ackermann, M.
    Adams, J.
    Ahrens, J.
    Andeen, K.
    Atlee, D. W.
    Bahcall, J. N.
    Bai, X.
    Baret, B.
    Barwick, S. W.
    Bay, R.
    Beattie, K.
    Becka, T.
    Becker, J. K.
    Becker, K. -H
    Berghaus, P.
    Berley, D.
    Bernardini, E.
    Bertrand, D.
    Besson, D. Z.
    Blaufuss, E.
    Boersma, D. J.
    Bohm, C.
    Bolmont, J.
    Boeser, S.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Bouchta, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Braun, J.
    Burgess, C.
    Burgess, T.
    Castermans, T.
    Chirkin, D.
    Christy, B.
    Clem, J.
    Cowen, D. F.
    D'Agostino, M. V.
    Davour, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Day, C. T.
    De Clercq, C.
    Demiroers, L.
    Descamps, F.
    Desiati, P.
    DeYoung, T.
    Diaz-Velez, J. C.
    Dreyer, J.
    Dumm, J. P.
    Duvoort, M. R.
    Edwards, W. R.
    Ehrlich, R.
    Eisch, J.
    Ellsworth, R. W.
    Evenson, P. A.
    Fadiran, O.
    Fazely, A. R.
    Feser, T.
    Filimonov, K.
    Fox, B. D.
    Gaisser, T. K.
    Gallagher, J.
    Ganugapati, R.
    Geenen, H.
    Gerhardt, L.
    Goldschmidt, A.
    Goodman, J. A.
    Gozzini, R.
    Grullon, S.
    Gross, A.
    Gunasingha, R. M.
    Gurtner, M.
    Hallgren, A.
    Halzen, F.
    Han, K.
    Hanson, K.
    Hardtke, D.
    Hardtke, R.
    Harenberg, T.
    Hart, J. E.
    Hauschildt, T.
    Hays, D.
    Heise, J.
    Helbing, K.
    Hellwig, M.
    Herquet, P.
    Hill, G. C.
    Hodges, J.
    Hoffman, K. D.
    Hommez, B.
    Hoshina, K.
    Hubert, D.
    Hughey, B.
    Hulth, P. O.
    Hultqvist, K.
    Hundertmark, S.
    Huelss, J. -P
    Ishihara, A.
    Jacobsen, J.
    Japaridze, G. S.
    Johansson, H.
    Jones, A.
    Joseph, J. M.
    Kampert, K. -H
    Karle, A.
    Kawai, H.
    Kelley, J. L.
    Kestel, M.
    Kitamura, N.
    Klein, S. R.
    Klepser, S.
    Kohnen, G.
    Kolanoski, H.
    Koepke, L.
    Krasberg, M.
    Kuehn, K.
    Landsman, H.
    Leich, H.
    Leier, D.
    Leuthold, M.
    Liubarsky, I.
    Lundberg, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Luenemann, J.
    Madsen, J.
    Mase, K.
    Matis, H. S.
    McCauley, T.
    McParland, C. P.
    Meli, A.
    Messarius, T.
    Meszaros, P.
    Miyamoto, H.
    Mokhtarani, A.
    Montaruli, T.
    Morey, A.
    Morse, R.
    Movit, S. M.
    Muenich, K.
    Nahnhauer, R.
    Nam, J. W.
    Niessen, P.
    Nygren, D. R.
    Oegelman, H.
    Olivas, A.
    Patton, S.
    Pena-Garay, C.
    Perez de los Heros, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Piegsa, A.
    Pieloth, D.
    Pohl, A. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Porrata, R.
    Pretz, J.
    Price, P. B.
    Przybylski, G. T.
    Rawlins, K.
    Razzaque, S.
    Resconi, E.
    Rhode, W.
    Ribordy, M.
    Rizzo, A.
    Robbins, S.
    Roth, P.
    Rott, C.
    Rutledge, D.
    Ryckbosch, D.
    Sander, H. -G
    Sarkar, S.
    Schlenstedt, S.
    Schmidt, T.
    Schneider, D.
    Seckel, D.
    Seo, S. H.
    Seunarine, S.
    Silvestri, A.
    Smith, A. J.
    Solarz, M.
    Song, C.
    Sopher, J. E.
    Spiczak, G. M.
    Spiering, C.
    Stamatikos, M.
    Stanev, T.
    Steffen, P.
    Stezelberger, T.
    Stokstad, R. G.
    Stoufer, M. C.
    Stoyanov, S.
    Strahler, E. A.
    Straszheim, T.
    Sulanke, K. -H
    Sullivan, G. W.
    Sumner, T. J.
    Taboada, I.
    Tarasova, O.
    Tepe, A.
    Thollander, L.
    Tilav, S.
    Tluczykont, M.
    Toale, P. A.
    Turcan, D.
    van Eijndhoven, N.
    Vandenbroucke, J.
    Van Overloop, A.
    Veigt, B.
    Wagner, W.
    Walck, C.
    Waldmann, H.
    Walter, M.
    Wang, Y. -R
    Wendt, C.
    Wiebusch, C. H.
    Wikstroem, G.
    Williams, D. R.
    Wischnewski, R.
    Wissing, H.
    Woschnagg, K.
    Xu, X. W.
    Yodh, G.
    Yoshida, S.
    Zornoza, J. D.
    IceCube contributions to the XIV International Symposium on Very High Energy Cosmic Ray Interactions (ISVHECRI 2006) Weihai, China - August 15-222008In: Nuclear physics B, Proceedings supplements, ISSN 0920-5632, E-ISSN 1873-3832, Vol. 175, p. 407-408Article in journal (Refereed)
  • 2696. Achterberg, A.
    et al.
    Ackermann, M.
    Adams, J.
    Ahrens, J.
    Andeen, K.
    Auffenberg, J.
    Bahcall, J. N.
    Bai, X.
    Baret, B.
    Barwick, S. W.
    Bay, R.
    Beattie, K.
    Becka, T.
    Becker, J. K.
    Becker, K. -H.
    Berghaus, P.
    Berley, D.
    Bernardini, E.
    Bertrand, D.
    Besson, D. Z.
    Blaufuss, E.
    Boersma, D. J.
    Bohm, C.
    Bolmont, J.
    Boeser, S.
    Botner, O.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Bouchta, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Braun, J.
    Burgess, C.
    Burgess, T.
    Castermans, T.
    Chirkin, D.
    Christy, B.
    Clem, J.
    Cowen, D. F.
    D'Agostino, M. V.
    Davour, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Day, C. T.
    De Clercq, C.
    Demiroeres, L.
    Descamps, F.
    Desiati, P.
    DeYoung, T.
    Diaz-Velez, J. C.
    Dreyer, J.
    Dumm, J. P.
    Duvoort, M. R.
    Edwards, W. R.
    Ehrlich, R.
    Eisch, J.
    Ellsworth, R. W.
    Evenson, P. A.
    Fadiran, O.
    Fazely, A. R.
    Filimonov, K.
    Foerster, M. M.
    Fox, B. D.
    Franckowiak, A.
    Gaisser, T. K.
    Gallagher, J.
    Ganugapati, R.
    Geenen, H.
    Gerhardt, L.
    Goldschmidt, A.
    Goodman, J. A.
    Gozzini, R.
    Griesel, T.
    Gross, A.
    Grullon, S.
    Gunasingha, R. M.
    Gurtner, M.
    Hallgren, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Halzen, F.
    Han, K.
    Hanson, K.
    Hardtke, D.
    Hardtke, R.
    Hart, J. E.
    Hasegawa, Y.
    Hauschildt, T.
    Hays, D.
    Heise, J.
    Helbing, K.
    Hellwig, M.
    Herquet, P.
    Hill, G. C.
    Hodges, J.
    Hoffman, K. D.
    Hommez, B.
    Hoshina, K.
    Hubert, D.
    Hughey, B.
    Hulth, P. O.
    Huess, J. -P.
    Hultqvist, K.
    Hundertmark, S.
    Inaba, M.
    Ishihara, A.
    Jacobsen, J.
    Japaridze, G. S.
    Johansson, H.
    Jones, A.
    Joseph, J. M.
    Kampert, K. -H.
    Kappes, A.
    Karg, T.
    Karle, A.
    Kawai, H.
    Kelley, J. L.
    Kitamura, N.
    Klein, S. R.
    Klepser, S.
    Kohnen, G.
    Kolanoski, H.
    Pke, L. Ko
    Kowalski, M.
    Kowarik, T.
    Krasberg, M.
    Kuehn, K.
    Labare, M.
    Landsman, H.
    Leich, H.
    Leier, D.
    Liubarsky, I.
    Lundberg, J.
    Luenemann, J.
    Madsen, J.
    Mase, K.
    Matis, H. S.
    McCauley, T.
    McParland, C. P.
    Meli, A.
    Messarius, T.
    Meszaros, P.
    Miyamoto, H.
    Mokhtarani, A.
    Montaruli, T.
    Morey, A.
    Morse, R.
    Movit, S. M.
    Muenich, K.
    Nahnhauer, R.
    Nam, J. W.
    Niessen, P.
    Nygren, D. R.
    Oegelman, H.
    Olivas, A.
    Patton, S.
    Pena-Garay, C.
    De Los Heros, C. Perez
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Piegsa, A.
    Pieloth, D.
    Pohl, A. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Porrata, R.
    Pretz, J.
    Price, P. B.
    Przybylski, G. T.
    Rawlins, K.
    Razzaque, S.
    Resconi, E.
    Rhode, W.
    Ribordy, M.
    Rizzo, A.
    Robbins, S.
    Roth, P.
    Rott, C.
    Rutledge, D.
    Ryckbosch, D.
    Sander, H. -G.
    Sarkar, S.
    Schlenstedt, S.
    Schmidt, T.
    Schneider, D.
    Seckel, D.
    Semburg, B.
    Seo, S. H.
    Seunarine, S.
    Silvestri, A.
    Smith, A. J.
    Solarz, M.
    Song, C.
    Sopher, J. E.
    Spiczak, G. M.
    Spiering, C.
    Stamatikos, M.
    Stanev, T.
    Steffen, P.
    Stezelberger, T.
    Stokstad, R. G.
    Stoufer, M. C.
    Stoyanov, S.
    Strahler, E. A.
    Straszheim, T.
    Sulanke, K. -H.
    Sullivan, G. W.
    Sumner, T. J.
    Taboada, I.
    Tarasova, O.
    Tepe, A.
    Thollander, L.
    Tilav, S.
    Tluczykont, M.
    Toale, P. A.
    Turcan, D.
    Van Eijndhoven, N.
    Vandenbroucke, J.
    Van Overloop, A.
    Viscomi, V.
    Voigt, B.
    Wagner, W.
    Walck, C.
    Waldmann, H.
    Walter, M.
    Wang, Y. -R.
    Wendt, C.
    Wiebusch, C. H.
    Wikstroem, G.
    Williams, D. R.
    Wischnewski, R.
    Wissing, H.
    Woschnagg, K.
    Xu, X. W.
    Yodh, G.
    Yoshida, S.
    Zornoza, J. D.
    Boer, M.
    Cline, T.
    Crew, G.
    Feroci, M.
    Frontera, F.
    Hurley, K.
    Lamb, D.
    Rau, A.
    Rossi, F.
    Ricker, G.
    Von Kienlin, A.
    The search for muon neutrinos from northern hemisphere gamma-ray bursts with AMANDA2008In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 674, no 1, p. 357-370Article in journal (Refereed)
    Abstract [en]

    We present the results of the analysis of neutrino observations by the Antarctic Muon and Neutrino Detector Array (AMANDA) correlated with photon observations of more than 400 gamma-ray bursts (GRBs) in the northern hemisphere from 1997 to 2003. During this time period, AMANDA's effective collection area for muon neutrinos was larger than that of any other existing detector. After the application of various selection criteria to our data, we expect similar to 1 neutrino event and <2 background events. Based on our observations of zero events during and immediately prior to the GRBs in the data set, we set the most stringent upper limit on muon neutrino emission correlated with GRBs. Assuming a Waxman-Bahcall spectrum and incorporating all systematic uncertainties, our flux upper limit has a normalization at 1 PeV of E-2 Phi(nu) <= 6.3 x 10(-9) GeV cm(-2) s(-1) sr(-1), with 90% of the events expected within the energy range of similar to 10 TeV to similar to 3 PeV. The impact of this limit on several theoretical models of GRBs is discussed, as well as the future potential for detection of GRBs by next-generation neutrino telescopes. Finally, we briefly describe several modifications to this analysis in order to apply it to other types of transient point sources.

  • 2697. Achterberg, A.
    et al.
    Ackermann, M.
    Adams, J.
    Ahrens, J.
    Andeen, K.
    Auffenberg, J.
    Bai, X.
    Baret, B.
    Barwick, S. W.
    Bay, R.
    Beattie, K.
    Becka, T.
    Becker, J. K.
    Becker, K. -H
    Beimforde, M.
    Berghaus, P.
    Berley, D.
    Bernardini, E.
    Bertrand, D.
    Besson, D. Z.
    Blaufuss, E.
    Boersma, D. J.
    Bohm, C.
    Bolmont, J.
    Boeser, S.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Bouchta, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Braun, J.
    Burgess, C.
    Burgess, T.
    Castermans, T.
    Chirkin, D.
    Christy, B.
    Clem, J.
    Cowen, D. F.
    D'Agostino, M. V.
    Davour, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Day, C. T.
    De Clercq, C.
    Demiroers, L.
    Descamps, F.
    Desiati, P.
    DeYoung, T.
    Diaz-Velez, J. C.
    Dreyer, J.
    Dumm, J. P.
    Duvoort, M. R.
    Ehrlich, R.
    Eisch, J.
    Ellsworth, R. W.
    Evenson, P. A.
    Fadiran, O.
    Fazely, A. R.
    Filimonov, K.
    Finley, C.
    Foerster, M. M.
    Fox, B. D.
    Franckowiak, A.
    Franke, R.
    Gaisser, T. K.
    Gallagher, J.
    Ganugapati, R.
    Geenen, H.
    Gerhardt, L.
    Goldschmidt, A.
    Goodman, J. A.
    Gozzini, R.
    Griesel, T.
    Grullon, S.
    Grob, A.
    Gunasingha, R. M.
    Gurtner, M.
    Ha, C.
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Halzen, F.
    Han, K.
    Hanson, K.
    Hardtke, D.
    Hardtke, R.
    Hart, J. E.
    Hasegawa, Y.
    Hauschildt, T.
    Hays, D.
    Heise, J.
    Helbing, K.
    Hellwig, M.
    Herquet, P.
    Hill, G. C.
    Hodges, J.
    Hoffman, K. D.
    Hommez, B.
    Hoshina, K.
    Hubert, D.
    Hughey, B.
    Huelb, J. -P
    Hulth, P. O.
    Hultqvist, K.
    Hundertmark, S.
    Inaba, M.
    Ishihara, A.
    Jacobsen, J.
    Japaridze, G. S.
    Johansson, H.
    Jones, A.
    Joseph, J. M.
    Kampert, K. -H
    Kappes, A.
    Karg, T.
    Karle, A.
    Kawai, H.
    Kelley, J. L.
    Kislat, F.
    Kitamura, N.
    Klein, S. R.
    Klepser, S.
    Kohnen, G.
    Kolanoski, H.
    Koepke, L.
    Kowalski, M.
    Kowarik, T.
    Krasberg, M.
    Kuehn, K.
    Labare, M.
    Landsman, H.
    Lauer, R.
    Leich, H.
    Leier, D.
    Liubarsky, I.
    Lundberg, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Luenemann, J.
    Madsen, J.
    Maruyama, R.
    Mase, K.
    Matis, H. S.
    McCauley, T.
    McParland, C. P.
    Meagher, K.
    Meli, A.
    Messarius, T.
    Meszaros, P.
    Miyamoto, H.
    Mokhtarani, A.
    Montaruli, T.
    Morey, A.
    Morse, R.
    Movit, S. M.
    Muenich, K.
    Nahnhauer, R.
    Nam, J. W.
    Nieben, P.
    Nygren, D. R.
    Olivas, A.
    Patton, S.
    Pena-Garay, C.
    Heros, Carlos Pérez de Los
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Piegsa, A.
    Pieloth, D.
    Pohl, Annika C.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Porrata, R.
    Pretz, J.
    Price, P. B.
    Przybylski, G. T.
    Rawlins, K.
    Razzaque, S.
    Redl, P.
    Resconi, E.
    Rhode, W.
    Ribordy, M.
    Rizzo, A.
    Robbins, S.
    Roth, P.
    Rothmaier, F.
    Rott, C.
    Rutledge, D.
    Ryckbosch, D.
    Sander, H. -G
    Sarkar, S.
    Satalecka, K.
    Schlenstedt, S.
    Schmidt, T.
    Schneider, D.
    Seckel, D.
    Semburg, B.
    Seo, S. H.
    Sestayo, Y.
    Seunarine, S.
    Silvestri, A.
    Smith, A. J.
    Song, C.
    Sopher, J. E.
    Spiczak, G. M.
    Spiering, C.
    Stamatikos, M.
    Stanev, T.
    Stezelberger, T.
    Stokstad, R. G.
    Stoufer, M. C.
    Stoyanov, S.
    Strahler, E. A.
    Straszheim, T.
    Sulanke, K. -H
    Sullivan, G. W.
    Sumner, T. J.
    Taboada, I.
    Tarasova, O.
    Tepe, A.
    Thollander, L.
    Tilav, S.
    Tluczykont, M.
    Toale, P. A.
    Tosi, D.
    Turcan, D.
    van Eijndhoven, N.
    Vandenbroucke, J.
    Van Overloop, A.
    de Vries-Uiterweerd, G.
    Viscomi, V.
    Voigt, B.
    Wagner, W.
    Walck, C.
    Waldmann, H.
    Walter, M.
    Wang, Y. -R
    Wendt, C.
    Wiebusch, C. H.
    Wikstroem, G.
    Williams, D. R.
    Wischnewski, R.
    Wissing, H.
    Woschnagg, K.
    Xu, X. W.
    Yodh, G.
    Yoshida, S.
    Zornoza, J. D.
    Detection of atmospheric muon neutrinos with the IceCube 9-string detector2007In: Physical Review D - Particles, Fields, Gravitation and Cosmology, ISSN 1550-7998, Vol. 76, no 2, p. 027101-Article in journal (Refereed)
    Abstract [en]

    The IceCube neutrino detector is a cubic kilometer TeV to PeV neutrino detector under construction at the geographic South Pole. The dominant population of neutrinos detected in IceCube is due to meson decay in cosmic-ray air showers. These atmospheric neutrinos are relatively well understood and serve as a calibration and verification tool for the new detector. In 2006, the detector was approximately 10% completed, and we report on data acquired from the detector in this configuration. We observe an atmospheric neutrino signal consistent with expectations, demonstrating that the IceCube detector is capable of identifying neutrino events. In the first 137.4 days of live time, 234 neutrino candidates were selected with an expectation of 211 +/- 76.1(syst)+/- 14.5(stat) events from atmospheric neutrinos.

  • 2698. Achterberg, A.
    et al.
    Ackermann, M.
    Adams, J.
    Ahrens, J.
    Andeen, K.
    Auffenberg, J.
    Bai, X.
    Baret, B.
    Barwick, S. W.
    Bay, R.
    Beattie, K.
    Becka, T.
    Becker, J. K.
    Becker, K. -H
    Berghaus, P.
    Berley, D.
    Bernardini, E.
    Bertrand, D.
    Besson, D. Z.
    Blaufuss, E.
    Boersma, D. J.
    Bohm, C.
    Bolmont, J.
    Boeser, S.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Bouchta, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Braun, J.
    Burgess, T.
    Castermans, T.
    Chirkin, D.
    Christy, B.
    Clem, J.
    Cowen, D. F.
    D'Agostino, M. V.
    Davour, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Day, C. T.
    De Clercq, C.
    Demirors, L.
    Descamps, F.
    Desiati, P.
    DeYoung, T.
    Diaz-Velez, J. C.
    Dreyer, J.
    Dumm, J. P.
    Duvoort, M. R.
    Edwards, W. R.
    Ehrlich, R.
    Eisch, J.
    Ellsworth, R. W.
    Evenson, P. A.
    Fadiran, O.
    Fazely, A. R.
    Filimonov, K.
    Finley, C.
    Foerster, M. M.
    Fox, B. D.
    Franckowiak, A.
    Franke, R.
    Gaisser, T. K.
    Gallagher, J.
    Ganugapati, R.
    Geenen, H.
    Gerhardt, L.
    Goldschmidt, A.
    Goodman, J. A.
    Gozzini, R.
    Griesel, T.
    Gross, A.
    Grullon, S.
    Gunasingha, R. M.
    Gurtner, M.
    Ha, C.
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Halzen, F.
    Han, K.
    Hanson, K.
    Hardtke, D.
    Hardtke, R.
    Hart, J. E.
    Hasegawa, Y.
    Hauschildt, T.
    Hays, D.
    Heise, J.
    Helbing, K.
    Hellwig, M.
    Herquet, P.
    Hill, G. C.
    Hodges, J.
    Hoffman, K. D.
    Hommez, B.
    Hoshina, K.
    Hubert, D.
    Hughey, B.
    Hulss, J. -P
    Hulth, P. O.
    Hultqvist, K.
    Hundertmark, S.
    Inaba, M.
    Ishihara, A.
    Jacobsen, J.
    Japaridze, G. S.
    Johansson, H.
    Jones, A.
    Joseph, J. M.
    Kampert, K. -H
    Kappes, A.
    Karg, T.
    Karle, A.
    Kawai, H.
    Kelley, J. L.
    Kislat, F.
    Kitamura, N.
    Klein, S. R.
    Klepser, S.
    Kohnen, G.
    Kolanoski, H.
    Koepke, L.
    Kowalski, M.
    Kowarik, T.
    Krasberg, M.
    Kuehn, K.
    Labare, M.
    Landsman, H.
    Lauer, R.
    Leich, H.
    Leier, D.
    Liubarsky, I.
    Lundberg, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Luenemann, J.
    Madsen, J.
    Maruyama, R.
    Mase, K.
    Matis, H. S.
    McCauley, T.
    McParland, C. P.
    Meli, A.
    Messarius, T.
    Meszaros, P.
    Miyamoto, H.
    Mokhtarani, A.
    Montaruli, T.
    Morey, A.
    Morse, R.
    Movit, S. M.
    Muenich, K.
    Nahnhauer, R.
    Nam, J. W.
    Niessen, P.
    Nygren, D. R.
    Oegelman, H.
    Olivas, A.
    Patton, S.
    Pena-Garay, C.
    de los Heros, Carlos Pérez
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Piegsa, A.
    Pieloth, D.
    Pohl, Annika C.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Porrata, R.
    Pretz, J.
    Price, P. B.
    Przybylski, G. T.
    Rawlins, K.
    Razzaque, S.
    Resconi, E.
    Rhode, W.
    Ribordy, M.
    Rizzo, A.
    Robbins, S.
    Roth, P.
    Rothmaier, F.
    Rott, C.
    Rutledge, D.
    Ryckbosch, D.
    Sander, H. -G
    Sarkar, S.
    Satalecka, K.
    Schlenstedt, S.
    Schmidt, T.
    Schneider, D.
    Seckel, D.
    Semburg, B.
    Seo, S. H.
    Sestayo, Y.
    Seunarine, S.
    Silvestri, A.
    Smith, A. J.
    Solarz, M.
    Song, C.
    Sopher, J. E.
    Spiczak, G. M.
    Spiering, C.
    Stamatikos, M.
    Stanev, T.
    Stezelberger, T.
    Stokstad, R. G.
    Stoufer, M. C.
    Stoyanov, S.
    Strahler, E. A.
    Straszheim, T.
    Sulanke, K. -H
    Sullivan, G. W.
    Sumner, T. J.
    Taboada, I.
    Tarasova, O.
    Tepe, A.
    Thollander, L.
    Tilav, S.
    Tluczykont, M.
    Toale, P. A.
    Tosi, D.
    Turcan, D.
    van Eijndhoven, N.
    Vandenbroucke, J.
    Van Overloop, A.
    Viscomi, V.
    Voigt, B.
    Wagner, W.
    Walck, C.
    Waldmann, H.
    Walter, M.
    Wang, Y. -R
    Wendt, C.
    Wiebusch, H.
    Wiedemann, C.
    Wikstrom, G.
    Williams, D. R.
    Wischnewski, R.
    Wissing, H.
    Woschnagg, K.
    Xu, X. W.
    Yodh, G.
    Yoshida, S.
    Zornoza, J. D.
    Multiyear search for a diffuse flux of muon neutrinos with AMANDA-II2007In: Physical Review D - Particles, Fields, Gravitation and Cosmology, ISSN 1550-7998, Vol. 76, no 4, p. 042008-Article in journal (Refereed)
    Abstract [en]

    A search for TeV-PeV muon neutrinos from unresolved sources was performed on AMANDA-II data collected between 2000 and 2003 with an equivalent live time of 807 days. This diffuse analysis sought to find an extraterrestrial neutrino flux from sources with nonthermal components. The signal is expected to have a harder spectrum than the atmospheric muon and neutrino backgrounds. Since no excess of events was seen in the data over the expected background, an upper limit of E-2 Phi(90%C.L.)< 7.4x10(-8) GeV cm(-2) s(-1) sr(-1) is placed on the diffuse flux of muon neutrinos with a Phi proportional to E-2 spectrum in the energy range 16 TeV to 2.5 PeV. This is currently the most sensitive Phi proportional to E-2 diffuse astrophysical neutrino limit. We also set upper limits for astrophysical and prompt neutrino models, all of which have spectra different from Phi proportional to E-2.

  • 2699. Achterberg, A.
    et al.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Bouchta, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Conrad, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Davour, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Lundberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Marciniewski, Pawel
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Pérez de los Heros, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Biermann, P.L.
    On the selection of AGN neutrino source candidates for a source stacking analysis with neutrino telescopes2006In: Astroparticle physics, ISSN 0927-6505, E-ISSN 1873-2852, Vol. 26, no 4-5, p. 282-300Article in journal (Refereed)
    Abstract [en]

    The sensitivity of a search for sources of TeV neutrinos can be improved by grouping potential sources together into generic classes in a procedure that is known as source stacking. In this paper, we define catalogs of Active Galactic Nuclei (AGN) and use them to perform a source stacking analysis. The grouping of AGN into classes is done in two steps: first, AGN classes are defined, then, sources to be stacked are selected assuming that a potential neutrino flux is linearly correlated with the photon luminosity in a certain energy band (radio, IR, optical, keV, GeV, TeV). Lacking any secure detailed knowledge on neutrino production in AGN, this correlation is motivated by hadronic AGN models, as briefly reviewed in this paper.The source stacking search for neutrinos from generic AGN classes is illustrated using the data collected by the AMANDA-II highenergy neutrino detector during the year 2000. No significant excess for any of the suggested groups was found.

  • 2700. Achterberg, A.
    et al.
    Botner, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Bouchta, Adam
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Conrad, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Davour, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Hallgren, Allan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Lundberg, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Marciniewski, Pawel
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Pérez de los Heros, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Zornoza, J. D.
    Limits on the Muon Flux from Neutralino Annihilations at the Center of the Earth with AMANDA2006In: Astroparticle physics, ISSN 0927-6505, E-ISSN 1873-2852, Vol. 26, no 2, p. 129-139Article in journal (Refereed)
    Abstract [en]

    A search has been performed for nearly vertically upgoing neutrino-induced muons with the Antarctic Muon And Neutrino Detector Array (AMANDA), using data taken over the three year period 1997-99. No excess above the expected atmospheric neutrino background has been found. Upper limits at 90% confidence level have been set on the annihilation rate of neutralinos at the center of the Earth, as well as on the muon flux at AMANDA induced by neutrinos created by the annihilation products.

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