| 1. |
- Barbe, Laurent, et al.
(författare)
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Toward a confocal subcellular atlas of the human proteome
- 2008
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Ingår i: Molecular and cellular proteomics. - 1535-9476 .- 1535-9484. ; 7:3, s. 499-508
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Tidskriftsartikel (refereegranskat)abstract
- Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.
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| 2. |
- Månsdotter, Anna, et al.
(författare)
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Parental share in public and domestic spheres: a population study on gender equality, death, and sickness.
- 2006
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Ingår i: Journal of epidemiology and community health. - : BMJ. - 0143-005X .- 1470-2738. ; 60:7, s. 616-20
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Tidskriftsartikel (refereegranskat)abstract
- STUDY OBJECTIVE: Examine the relation between aspects of gender equality and population health based on the premise that sex differences in health are mainly caused by the gender system. SETTING/ PARTICIPANTS: All Swedish couples (98 240 people) who had their first child together in 1978. DESIGN: The exposure of gender equality is shown by the parents' division of income and occupational position (public sphere), and parental leave and temporary child care (domestic sphere). People were classified by these indicators during 1978-1980 into different categories; those on an equal footing with their partner and those who were traditionally or untraditionally unequal. Health is measured by the outcomes of death during 1981-2001 and sickness absence during 1986-2000. Data are obtained by linking individual information from various national sources. The statistical method used is multiple logistic regressions with odds ratios as estimates of relative risks. MAIN RESULTS: From the public sphere is shown that traditionally unequal women have decreased health risks compared with equal women, while traditionally unequal men tend to have increased health risks compared with equal men. From the domestic sphere is indicated that both women and men run higher risks of death and sickness when being traditionally unequal compared with equal. CONCLUSIONS: Understanding the relation between gender equality and health, which was found to depend on sex, life sphere, and inequality type, seems to require a combination of the hypotheses of convergence, stress and expansion.
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| 3. |
- Achterberg, A., et al.
(författare)
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First Year Performance of the IceCube Neutrino Telescope
- 2006
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Ingår i: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 26:3, s. 155-173
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Tidskriftsartikel (refereegranskat)abstract
- The first sensors of the IceCube neutrino observatory were deployed at the South Pole during the austral summer of 2004-2005 and have been producing data since February 2005. One string of 60 sensors buried in the ice and a surface array of eight ice Cherenkov tanks took data until December 2005 when deployment of the next set of strings and tanks began. We have analyzed these data, demonstrating that the performance of the system meets or exceeds design requirements. Times are determined across the whole array to a relative precision of better than 3 ns, allowing reconstruction of muon tracks and light bursts in the ice, of air-showers in the surface array and of events seen in coincidence by surface and deep-ice detectors separated by up to 2.5 km.
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| 4. |
- Achterberg, A., et al.
(författare)
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Five years of searches for point sources of astrophysical neutrinos with the AMANDA-II neutrino telescope
- 2007
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Ingår i: Physical Review D. Particles, fields, gravitation, and cosmology. - 1550-7998. ; 75:10, s. 102001-
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Tidskriftsartikel (refereegranskat)abstract
- We report the results of a five-year survey of the northern sky to search for point sources of high energy neutrinos. The search was performed on the data collected with the AMANDA-II neutrino telescope in the years 2000 to 2004, with a live time of 1001 days. The sample of selected events consists of 4282 upward going muon tracks with high reconstruction quality and an energy larger than about 100 GeV. We found no indication of point sources of neutrinos and set 90% confidence level flux upper limits for an all-sky search and also for a catalog of 32 selected sources. For the all-sky search, our average (over declination and right ascension) experimentally observed upper limit Phi0=((E/(1 TeV)))gamma·((d Phi)/dE) to a point source flux of muon and tau neutrino (detected as muons arising from taus) is Phinu[sub mu] + [overline nu ][sub mu]0+Phinu[sub tau] + [overline nu ][sub tau]0=11.1× 10-11 TeV-1 cm-2 s-1, in the energy range between 1.6 TeV and 2.5 PeV for a flavor ratio Phinu[sub mu] + [overline nu ][sub mu]0/Phinu[sub tau] + [overline nu ][sub tau]0=1 and assuming a spectral index gamma=2. It should be noticed that this is the first time we set upper limits to the flux of muon and tau neutrinos. In previous papers we provided muon neutrino upper limits only neglecting the sensitivity to a signal from tau neutrinos, which improves the limits by 10% to 16%. The value of the average upper limit presented in this work corresponds to twice the limit on the muon neutrino flux Phinu[sub mu] + [overline nu ][sub mu]0=5.5×10-11 TeV-1 cm-2 s-1. A stacking analysis for preselected active galactic nuclei and a search based on the angular separation of the events were also performed. We report the most stringent flux upper limits to date, including the results of a detailed assessment of systematic uncertainties.
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| 5. |
- Achterberg, A., et al.
(författare)
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Limits on the high-energy gamma and neutrino fluxes from the SGR 1806-20 giant flare of 27 December 2004 with the AMANDA-II detector
- 2006
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:22, s. 221101-
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Tidskriftsartikel (refereegranskat)abstract
- On 27 December 2004, a giant gamma flare from the Soft Gamma-Ray Repeater 1806-20 saturated many satellite gamma-ray detectors, being the brightest transient event ever observed in the Galaxy. AMANDA-II was used to search for down-going muons indicative of high-energy gammas and/or neutrinos from this object. The data revealed no significant signal, so upper limits (at 90% C.L.) on the normalization constant were set: 0.05(0.5) TeV-1 m(-2) s(-1) for gamma=-1.47 (-2) in the gamma flux and 0.4(6.1) TeV-1 m(-2) s(-1) for gamma=-1.47 (-2) in the high-energy neutrino flux.
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| 6. |
- Achterberg, A., et al.
(författare)
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Limits on the Muon Flux from Neutralino Annihilations at the Center of the Earth with AMANDA
- 2006
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Ingår i: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 26:2, s. 129-139
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Tidskriftsartikel (refereegranskat)abstract
- 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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| 7. |
- Achterberg, A., et al.
(författare)
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On the selection of AGN neutrino source candidates for a source stacking analysis with neutrino telescopes
- 2006
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Ingår i: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 26:4-5, s. 282-300
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Achterberg, A., et al.
(författare)
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Search for neutrino-induced cascades from gamma-ray bursts with AMANDA
- 2007
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 664:1, s. 397-410
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Tidskriftsartikel (refereegranskat)abstract
- Using the neutrino telescope AMANDA-II, we have conducted two analyses searching for neutrino-induced cascades from gamma-ray bursts. No evidence of astrophysical neutrinos was found, and limits are presented for several models. We also present neutrino effective areas which allow the calculation of limits for any neutrino production model. The first analysis looked for a statistical excess of events within a sliding window of 1 or 100 s (for short and long burst classes, respectively) during the years 2001-2003. The resulting upper limit on the diffuse flux normalization times E2 for the Waxman-Bahcall model at 1 PeV is 1.6×10-6 GeV cm-2 s-1 sr-1 (a factor of 120 above the theoretical prediction). For this search 90% of the neutrinos would fall in the energy range 50 TeV to 7 PeV. The second analysis looked for neutrino-induced cascades in coincidence with 73 bursts detected by BATSE in the year 2000. The resulting upper limit on the diffuse flux normalization times E2, also at 1 PeV, is 1.5×10-6 GeV cm-2 s-1 sr-1 (a factor of 110 above the theoretical prediction) for the same energy range. The neutrino-induced cascade channel is complementary to the up-going muon channel. We comment on its advantages for searches of neutrinos from GRBs and its future use with IceCube.
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| 9. |
- Amanda Collaboration, -, et al.
(författare)
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Optical Properties of Deep Glacial Ice at the South Pole
- 2006
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Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202 .- 2169-897X. ; 111:D13, s. D13203-
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Tidskriftsartikel (refereegranskat)abstract
- We have remotely mapped optical scattering and absorption in glacial ice at the South Pole for wavelengths between 313 and 560 nm and depths between 1100 and 2350 m. We used pulsed and continuous light sources embedded with the AMANDA neutrino telescope, an array of more than six hundred photomultiplier tubes buried deep in the ice. At depths greater than 1300 m, both the scattering coefficient and absorptivity follow vertical variations in concentration of dust impurities, which are seen in ice cores from other Antarctic sites and which track climatological changes. The scattering coefficient varies by a factor of seven, and absorptivity (for wavelengths less than ∼450 nm) varies by a factor of three in the depth range between 1300 and 2300 m, where four dust peaks due to stadials in the late Pleistocene have been identified. In our absorption data, we also identify a broad peak due to the Last Glacial Maximum around 1300 m. In the scattering data, this peak is partially masked by scattering on residual air bubbles, whose contribution dominates the scattering coefficient in shallower ice but vanishes at ∼1350 m where all bubbles have converted to nonscattering air hydrates. The wavelength dependence of scattering by dust is described by a power law with exponent −0.90 ± 0.03, independent of depth. The wavelength dependence of absorptivity in the studied wavelength range is described by the sum of two components: a power law due to absorption by dust, with exponent −1.08 ± 0.01 and a normalization proportional to dust concentration that varies with depth; and a rising exponential due to intrinsic ice absorption which dominates at wavelengths greater than ∼500 nm.
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| 10. |
- Aspholm, Marina, et al.
(författare)
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SabA is the H. pylori hemagglutinin and is polymorphic in binding to sialylated glycans.
- 2006
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Ingår i: PLoS pathogens. - : Public Library of Science (PLoS). - 1553-7374 .- 1553-7366. ; 2:10
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Tidskriftsartikel (refereegranskat)abstract
- Adherence of Helicobacter pylori to inflamed gastric mucosa is dependent on the sialic acid-binding adhesin (SabA) and cognate sialylated/fucosylated glycans on the host cell surface. By in situ hybridization, H. pylori bacteria were observed in close association with erythrocytes in capillaries and post-capillary venules of the lamina propria of gastric mucosa in both infected humans and Rhesus monkeys. In vivo adherence of H. pylori to erythrocytes may require molecular mechanisms similar to the sialic acid-dependent in vitro agglutination of erythrocytes (i.e., sialic acid-dependent hemagglutination). In this context, the SabA adhesin was identified as the sialic acid-dependent hemagglutinin based on sialidase-sensitive hemagglutination, binding assays with sialylated glycoconjugates, and analysis of a series of isogenic sabA deletion mutants. The topographic presentation of binding sites for SabA on the erythrocyte membrane was mapped to gangliosides with extended core chains. However, receptor mapping revealed that the NeuAcalpha2-3Gal-disaccharide constitutes the minimal sialylated binding epitope required for SabA binding. Furthermore, clinical isolates demonstrated polymorphism in sialyl binding and complementation analysis of sabA mutants demonstrated that polymorphism in sialyl binding is an inherent property of the SabA protein itself. Gastric inflammation is associated with periodic changes in the composition of mucosal sialylation patterns. We suggest that dynamic adaptation in sialyl-binding properties during persistent infection specializes H. pylori both for individual variation in mucosal glycosylation and tropism for local areas of inflamed and/or dysplastic tissue.
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| 11. |
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| 12. |
- Bengtson, Sara H, et al.
(författare)
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Kinin receptor expression during Staphylococcus aureus infection.
- 2006
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Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 108:6, s. 2055-2063
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Tidskriftsartikel (refereegranskat)abstract
- An inappropriate host response to invading bacteria is a critical parameter that often aggravates the outcome of an infection. Staphylococcus aureus is a major human Gram-positive pathogen that causes a wide array of community- and hospital-acquired diseases ranging from superficial skin infections to severe conditions such as staphylococcal toxic shock. Here we find that S aureus induces inflammatory reactions by modulating the expression and response of the B1 and B2 receptors, respectively. This process is initiated by a chain of events, involving staphylococcal-induced cytokine release from monocytes, bacteria-triggered contact activation, and conversion of bradykinin to its metabolite desArg9bradykinin. The data of the present study implicate an important and previously unknown role for kinin receptor regulation in S aureus infections.
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| 13. |
- Berglund, Lisa, et al.
(författare)
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A genecentric Human Protein Atlas for expression profiles based on antibodies
- 2008
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 7:10, s. 2019-2027
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Forskningsöversikt (refereegranskat)abstract
- An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to approximately 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescence-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.
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| 14. |
- Bodin, Örjan, et al.
(författare)
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The value of small size: loss of forest patches and ecological thresholds in southern Madagascar
- 2006
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Ingår i: Ecological Applications. - : the Ecological Society of America. - 1051-0761 .- 1939-5582. ; 16:2, s. 440-451
-
Tidskriftsartikel (refereegranskat)abstract
- Many services generated by forest ecosystems provide essential support for human well-being. However, the vulnerability of these services to environmental change such as forest fragmentation are still poorly understood. We present spatial modeling of the generation of ecosystem services in a human-dominated landscape where forest habitat patches, protected by local taboos, are located in a matrix of cultivated land in southern Madagascar. Two ecosystem services dependent on the forest habitats were addressed: (1) crop pollination services by wild and semidomesticated bees (Apoidea), essential for local crop production of, for example, beans, and (2) seed dispersal services based on the presence of ring-tailed lemurs (Lemur catta). We studied the vulnerability of these ecosystem services to a plausible scenario of successive destruction of the smallest habitat patches. Our results indicate that, in spite of the fragmented nature of the landscape, the fraction of the landscape presently covered by both crop pollination and seed dispersal services is surprisingly high. It seems that the taboo system, though indirectly and unintentionally, contributes to upholding the generation of these services by protecting the forest patches. Both services are, however, predicted to be very vulnerable to the successive removal of small patches. For crop pollination, the rate of decrease in cover was significant even when only the smallest habitat patches were removed. The capacity for seed dispersal across the landscape displayed several thresholds with habitat patch removal. Our results suggest that, in order to maintain capacity for seed dispersal across the landscape and crop pollination cover in southern Androy, the geographical location of the remaining forest patches is more crucial than their size. We argue that in heavily fragmented production landscapes, small forest patches should increasingly be viewed as essential for maintaining ecosystem services, such as agricultural production, and also should be considered in the ongoing process of tripling the area of protected habitats in Madagascar.
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| 15. |
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| 16. |
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| 18. |
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| 19. |
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
- Botner, Olga, et al.
(författare)
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Exotic Physics with IceCube
- 2006
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Ingår i: Proceedings of the first Workshop on Exotic Physics with Neutrino Telescopes, Uppsala, Sweden, 20-22 Sept 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 27. |
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| 28. |
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| 29. |
- Botner, Olga, et al.
(författare)
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First Results from IceCube
- 2006
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Ingår i: Presented by Spencer R. Klein at the Particles and Nuclei Int Conference (PANIC 2005), Santa Fe, New Mexico, USA, 24-28 Oct 2005.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 30. |
- Botner, Olga, et al.
(författare)
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From AMANDA to IceCube
- 2005
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Ingår i: Vth International Conference on Non-Accelerator New Physics.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 31. |
- Botner, Olga, et al.
(författare)
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From AMANDA to IceCube
- 2006
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Ingår i: Presented by Per Olof Hulth for the IceCube Collaboration at the 3rd Int Workshop on NOVE: Neutrino Oscillations in Venice: 50 Years After the Neutrino Experimental Discovery, Venice, Italy 7-10 Febr 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 32. |
- Botner, Olga, et al.
(författare)
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From AMANDA to IceCube: Neutrino Astronomy at the South Pole
- 2006
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Ingår i: Presented by K Filimonov for the IceCube Collaboration at the 9th Conf on the Interactions of Particle and Nuclear Physics (CIPANP 2006), Westin Rio Mar Beach, Puerto Rico, 30 May-3 June 2206.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 33. |
- Botner, Olga, et al.
(författare)
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Getting there: From AMANDA to IceCube
- 2005
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Ingår i: PS International Europhysics Conference on High Energy Physics (HEP-EPS 2005), Lisbon, Portugal, 21-27 July 2005.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 34. |
- Botner, Olga, et al.
(författare)
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IceCube: : Initial Performance
- 2005
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Ingår i: 29th International Cosmic Ray Conference.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 35. |
- Botner, Olga, et al.
(författare)
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IceCube - Neutrino Astronomy at South Pole
- 2006
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Ingår i: Presented at the 2nd Scandinavian Neutrino Workshop (SNOW 2006), Stockholm, Sweden, 2-6 May 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 36. |
- Botner, Olga, et al.
(författare)
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IceCube: Performance, Status and Future
- 2006
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Ingår i: Proceedings of the XIV International Symposium on Very High Energy Cosmic Ray Interactions (ISVHECRI 2006), Weihai, China, 15-22 Aug 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 37. |
- Botner, Olga, et al.
(författare)
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IceCube: The State of the Art
- 2006
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Ingår i: Proceedings of the Vulcano Workshop 2006: Frontier Objetcs in Astrophysics and Particle Physics, Vulcano, Italy 22-27 May 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 38. |
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| 39. |
- Botner, Olga, et al.
(författare)
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IceCube: Toward a km3 Neutrino Telescope
- 2006
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Ingår i: Proceedings of the XX European Cosmic Ray Symposium, Firenze, Italy, 5-8 Sept 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 40. |
- Botner, Olga, et al.
(författare)
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IceTop Status in 2004
- 2005
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Ingår i: Nuclear Physics B 145. ; , s. 327-330
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 41. |
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| 42. |
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| 43. |
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| 44. |
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| 45. |
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| 46. |
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| 47. |
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| 48. |
- Botner, Olga, et al.
(författare)
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Neutrino Astronomy at the South Pole
- 2006
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Ingår i: Presented by D.J. Boersma for the IceCube Collaboration at the Lake Louise Winter Institute on Fundamental Interactions, Lake Louise Alberta, Canada, 17-23 Febr 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 49. |
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| 50. |
- Botner, Olga, et al.
(författare)
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Neutrino Astronomy with IceCube and AMANDA
- 2006
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Ingår i: Proceedings of the XXII Int Conf on Neutrino Physics and Astrophysics, Santa Fe, New Mexico, USA, 13-19 June 2006.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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