| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Abbasi, R., et al.
(författare)
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Observation of anisotropy in the arrival directions of galactic cosmic rays at multiple angular scales with IceCube
- 2011
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 740:1, s. 16-
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Tidskriftsartikel (refereegranskat)abstract
- Between 2009 May and 2010 May, the IceCube neutrino detector at the South Pole recorded 32 billion muons generated in air showers produced by cosmic rays with a median energy of 20 TeV. With a data set of this size, it is possible to probe the southern sky for per-mil anisotropy on all angular scales in the arrival direction distribution of cosmic rays. Applying a power spectrum analysis to the relative intensity map of the cosmic ray flux in the southern hemisphere, we show that the arrival direction distribution is not isotropic, but shows significant structure on several angular scales. In addition to previously reported large-scale structure in the form of a strong dipole and quadrupole, the data show small-scale structure on scales between 15 degrees and 30 degrees. The skymap exhibits several localized regions of significant excess and deficit in cosmic ray intensity. The relative intensity of the smaller-scale structures is about a factor of five weaker than that of the dipole and quadrupole structure. The most significant structure, an excess localized at (right ascension alpha = 122 degrees.4 and declination d = -47 degrees.4), extends over at least 20 degrees in right ascension and has a post-trials significance of 5.3 sigma. The origin of this anisotropy is still unknown.
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| 3. |
- Abbasi, R., et al.
(författare)
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Constraints on the extremely-high energy cosmic neutrino flux with the IceCube 2008-2009 data
- 2011
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 83:9, s. 092003-
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Tidskriftsartikel (refereegranskat)abstract
- We report on a search for extremely-high energy neutrinos with energies greater than 10(6) GeV using the data taken with the IceCube detector at the South Pole. The data was collected between April 2008 and May 2009 with the half-completed IceCube array. The absence of signal candidate events in the sample of 333.5 days of live time significantly improves model-independent limits from previous searches and allows to place a limit on the diffuse flux of cosmic neutrinos with an E-2 spectrum in the energy range 2.0 x 10(6) - 6.3 x 10(9) GeV to a level of E-2 phi <= 3.6 x 10(-8) GeV cm(-2) sec(-1) sr(-1).
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| 4. |
- Abbasi, R., et al.
(författare)
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First search for extremely high energy cosmogenic neutrinos with the IceCube Neutrino Observatory
- 2010
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Ingår i: Physical review. D, Particles, fields, gravitation, and cosmology. - 1550-7998. ; 82:7, s. 072003-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the results of the search for extremely-high energy neutrinos with energies above 10(7) GeV obtained with the partially (similar to 30%) constructed IceCube in 2007. From the absence of signal events in the sample of 242.1 days of effective live time, we derive a 90% C.L. model independent differential upper limit based on the number of signal events per energy decade at E-2 phi(ve+v mu+v tau) similar or equal to 1.4 x 10(-6) GeV cm(-2) sec(-1) sr(-1) for neutrinos in the energy range from 3 x 10(7) to 3 x 10(9) GeV.
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| 5. |
- Abbasi, R., et al.
(författare)
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Limits on Neutrino Emission from Gamma-Ray Bursts with the 40 String IceCube Detector
- 2011
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 106:14, s. 141101-
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Tidskriftsartikel (refereegranskat)abstract
- IceCube has become the first neutrino telescope with a sensitivity below the TeV neutrino flux predicted from gamma-ray bursts if gamma-ray bursts are responsible for the observed cosmic-ray flux above 10(18) eV. Two separate analyses using the half-complete IceCube detector, one a dedicated search for neutrinos from p gamma interactions in the prompt phase of the gamma-ray burst fireball and the other a generic search for any neutrino emission from these sources over a wide range of energies and emission times, produced no evidence for neutrino emission, excluding prevailing models at 90% confidence.
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| 6. |
- Abbasi, R., et al.
(författare)
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Measurement of the anisotropy of cosmic-ray arrival directions with icecube
- 2010
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Ingår i: The Astrophysical Journal Letters. - 2041-8205. ; 718, s. L194-L198
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Tidskriftsartikel (refereegranskat)abstract
- We report the first observation of an anisotropy in the arrival direction of cosmic rays with energies in the multi-TeV region in the Southern sky using data from the IceCube detector. Between 2007 June and 2008 March, the partially deployed IceCube detector was operated in a configuration with 1320 digital optical sensors distributed over 22 strings at depths between 1450 and 2450 m inside the Antarctic ice. IceCube is a neutrino detector, but the data are dominated by a large background of cosmic-ray muons. Therefore, the background data are suitable for high-statistics studies of cosmic rays in the southern sky. The data include 4.3 billion muons produced by downward-going cosmic-ray interactions in the atmosphere; these events were reconstructed with a median angular resolution of 3 degrees and a median energy of similar to 20 TeV. Their arrival direction distribution exhibits an anisotropy in right ascension with a first-harmonic amplitude of (6.4 +/- 0.2 stat. +/- 0.8 syst.) x 10(-4).
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| 7. |
- Abbasi, R., et al.
(författare)
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Search for relativistic magnetic monopoles with the AMANDA-II neutrino telescope
- 2010
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 69:3-4, s. 361-378
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Tidskriftsartikel (refereegranskat)abstract
- We present the search for Cherenkov signatures from relativistic magnetic monopoles in data taken with the AMANDA-II detector, a neutrino telescope deployed in the Antarctic ice cap at the Geographic South Pole. The non-observation of a monopole signal in data collected during the year 2000 improves present experimental limits on the flux of relativistic magnetic monopoles: Our flux limit varies between 3.8x10(-17) cm(-2) s(-1) sr(-1) (for monopoles moving at the vacuum speed of light) and 8.8x10(-16) cm(-2) s(-1) sr(-1) (for monopoles moving at a speed beta=v/c=0.76, just above the Cherenkov threshold in ice). These limits apply to monopoles that are energetic enough to penetrate the Earth and enter the detector from below the horizon. The limit obtained for monopoles reaching the detector from above the horizon is less stringent by roughly an order of magnitude, due to the much larger background from down-going atmospheric muons. This looser limit is however valid for a larger class of magnetic monopoles, since the monopoles are not required to pass through the Earth.
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| 8. |
- Abbasi, R., et al.
(författare)
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All-particle cosmic ray energy spectrum measured with 26 IceTop stations
- 2013
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Ingår i: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 44, s. 40-58
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Tidskriftsartikel (refereegranskat)abstract
- We report on a measurement of the cosmic ray energy spectrum with the IceTop air shower array, the surface component of the IceCube Neutrino Observatory at the South Pole. The data used in this analysis were taken between June and October, 2007, with 26 surface stations operational at that time, corresponding to about one third of the final array. The fiducial area used in this analysis was 0.122 km(2). The analysis investigated the energy spectrum from 1 to 100 PeV measured for three different zenith angle ranges between 0 degrees and 46 degrees. Because of the isotropy of cosmic rays in this energy range the spectra from all zenith angle intervals have to agree. The cosmic-ray energy spectrum was determined under different assumptions on the primary mass composition. Good agreement of spectra in the three zenith angle ranges was found for the assumption of pure proton and a simple two-component model. For zenith angles theta < 30 degrees, where the mass dependence is smallest, the knee in the cosmic ray energy spectrum was observed at about 4 PeV, with a spectral index above the knee of about -3.1. Moreover, an indication of a flattening of the spectrum above 22 PeV was observed.
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| 9. |
- Abbasi, R., et al.
(författare)
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Constraints on high-energy neutrino emission from SN 2008D
- 2011
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 527:4, s. A28-
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Tidskriftsartikel (refereegranskat)abstract
- SN 2008D, a core collapse supernova at a distance of 27 Mpc, was serendipitously discovered by the Swift satellite through an associated X-ray flash. Core collapse supernovae have been observed in association with long gamma-ray bursts and X-ray flashes and a physical connection is widely assumed. This connection could imply that some core collapse supernovae possess mildly relativistic jets in which high-energy neutrinos are produced through proton-proton collisions. The predicted neutrino spectra would be detectable by Cherenkov neutrino detectors like IceCube. A search for a neutrino signal in temporal and spatial correlation with the observed X-ray flash of SN 2008D was conducted using data taken in 2007-2008 with 22 strings of the IceCube detector. Events were selected based on a boosted decision tree classifier trained with simulated signal and experimental background data. The classifier was optimized to the position and a "soft jet" neutrino spectrum assumed for SN 2008D. Using three search windows placed around the X-ray peak, emission time scales from 100-10 000 s were probed. No events passing the cuts were observed in agreement with the signal expectation of 0.13 events. Upper limits on the muon neutrino flux from core collapse supernovae were derived for different emission time scales and the principal model parameters were constrained. While no meaningful limits can be given in the case of an isotropic neutrino emission, the parameter space for a jetted emission can be constrained. Future analyses with the full 86 string IceCube detector could detect up to similar to 100 events for a core-collapse supernova at 10 Mpc according to the soft jet model.
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| 10. |
- Abbasi, R., et al.
(författare)
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First search for atmospheric and extraterrestrial neutrino-induced cascades with the IceCube detector
- 2011
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 84:7, s. 072001-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the first search for atmospheric and for diffuse astrophysical neutrino-induced showers (cascades) in the IceCube detector using 257 days of data collected in the year 2007-2008 with 22 strings active. A total of 14 events with energies above 16 TeV remained after event selections in the diffuse analysis, with an expected total background contribution of 8.3 +/- 3.6. At 90% confidence we set an upper limit of E(2)Phi(90%CL) < 3.6 x 10(-7) GeV.cm(-2).s(-1).sr(-1) on the diffuse flux of neutrinos of all flavors in the energy range between 24 TeV and 6.6 PeV assuming that Phi proportional to E(-2) and the flavor composition of the nu(e):nu(mu):nu(tau) flux is 1:1:1 at the Earth. The atmospheric neutrino analysis was optimized for lower energies. A total of 12 events were observed with energies above 5 TeV. The observed number of events is consistent with the expected background, within the uncertainties.
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