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. |
- Aartsen, M. G., et al.
(författare)
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Energy reconstruction methods in the IceCube neutrino telescope
- 2014
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 9, s. P03009-
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Tidskriftsartikel (refereegranskat)abstract
- Accurate measurement of neutrino energies is essential to many of the scientific goals of large-volume neutrino telescopes. The fundamental observable in such detectors is the Cherenkov light produced by the transit through a medium of charged particles created in neutrino interactions. The amount of light emitted is proportional to the deposited energy, which is approximately equal to the neutrino energy for v(e) and v(mu) charged-current interactions and can be used to set a lower bound on neutrino energies and to measure neutrino spectra statistically in other channels. Here we describe methods and performance of reconstructing charged-particle energies and topologies from the observed Cherenkov light yield, including techniques to measure the energies of uncontained muon tracks, achieving average uncertainties in electromagnetic-equivalent deposited energy of similar to 15% above 10 TeV.
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3. |
- Aartsen, M. G., et al.
(författare)
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Observation of High-Energy Astrophysical Neutrinos in Three Years of IceCube Data
- 2014
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 113:10, s. 101101-
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Tidskriftsartikel (refereegranskat)abstract
- A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV-PeV range at the level of 10(-8) GeV cm(-2) s(-1) sr(-1) per flavor and reject a purely atmospheric explanation for the combined three-year data at 5.7 sigma. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year data set, with a live time of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000-TeV event is the highest-energy neutrino interaction ever observed.
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4. |
- Aartsen, M. G., et al.
(författare)
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Search for a diffuse flux of astrophysical muon neutrinos with the IceCube 59-string configuration
- 2014
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:6, s. 062007-
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Tidskriftsartikel (refereegranskat)abstract
- A search for high-energy neutrinos was performed using data collected by the IceCube Neutrino Observatory from May 2009 to May 2010, when the array was running in its 59-string configuration. The data sample was optimized to contain muon neutrino induced events with a background contamination of atmospheric muons of less than 1%. These data, which are dominated by atmospheric neutrinos, are analyzed with a global likelihood fit to search for possible contributions of prompt atmospheric and astrophysical neutrinos, neither of which have yet been identified. Such signals are expected to follow a harder energy spectrum than conventional atmospheric neutrinos. In addition, the zenith angle distribution differs for astrophysical and atmospheric signals. A global fit of the reconstructed energies and directions of observed events is performed, including possible neutrino flux contributions for an astrophysical signal and atmospheric backgrounds as well as systematic uncertainties of the experiment and theoretical predictions. The best fit yields an astrophysical signal flux for nu(mu) + (nu) over bar (mu) of E-2. Phi(E) = 0.25 x 10(-8) GeV cm(-2) s(-1) sr(-1), and a zero prompt component. Although the sensitivity of this analysis for astrophysical neutrinos surpasses the Waxman and Bahcall upper bound, the experimental limit at 90% confidence level is a factor of 1.5 above at a flux of E-2 . Phi(E) = 1.44 x 10(-8) GeV cm(-2) s(-1) sr(-1).
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5. |
- Aartsen, M. G., et al.
(författare)
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Search for neutrino-induced particle showers with IceCube-40
- 2014
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:10, s. 102001-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the search for neutrino-induced particle showers, so-called cascades, in the IceCube-40 detector. The data for this search were collected between April 2008 and May 2009 when the first 40 IceCube strings were deployed and operational. Three complementary searches were performed, each optimized for different energy regimes. The analysis with the lowest energy threshold (2 TeV) targeted atmospheric neutrinos. A total of 67 events were found, consistent with the expectation of 41 atmospheric muons and 30 atmospheric neutrino events. The two other analyses targeted a harder, astrophysical neutrino flux. The analysis with an intermediate threshold of 25 TeV leads to the observation of 14 cascadelike events, again consistent with the prediction of 3.0 atmospheric neutrino and 7.7 atmospheric muon events. We hence set an upper limit of E-2 Phi(lim) <= 7.46 x 10(-8) GeV sr(-1) s(-1) cm(-2) (90% C.L.) on the diffuse flux from astrophysical neutrinos of all neutrino flavors, applicable to the energy range 25 TeV to 5 PeV, assuming an E-nu(-2) spectrum and a neutrino flavor ratio of 1: 1: 1 at the Earth. The third analysis utilized a larger and optimized sample of atmospheric muon background simulation, leading to a higher energy threshold of 100 TeV. Three events were found over a background prediction of 0.04 atmospheric muon events and 0.21 events from the flux of conventional and prompt atmospheric neutrinos. Including systematic errors this corresponds to a 2.7 sigma excess with respect to the background-only hypothesis. Our observation of neutrino event candidates above 100 TeV complements IceCube's recently observed evidence for high-energy astrophysical neutrinos.
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6. |
- Aartsen, M. G., et al.
(författare)
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Search for non-relativistic magnetic monopoles with IceCube
- 2014
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 74:7, s. 2938-
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Tidskriftsartikel (refereegranskat)abstract
- The IceCube Neutrino Observatory is a large Cherenkov detector instrumenting of Antarctic ice. The detector can be used to search for signatures of particle physics beyond the Standard Model. Here, we describe the search for non-relativistic, magnetic monopoles as remnants of the Grand Unified Theory (GUT) era shortly after the Big Bang. Depending on the underlying gauge group these monopoles may catalyze the decay of nucleons via the Rubakov-Callan effect with a cross section suggested to be in the range of to . In IceCube, the Cherenkov light from nucleon decays along the monopole trajectory would produce a characteristic hit pattern. This paper presents the results of an analysis of first data taken from May 2011 until May 2012 with a dedicated slow-particle trigger for DeepCore, a subdetector of IceCube. A second analysis provides better sensitivity for the brightest non-relativistic monopoles using data taken from May 2009 until May 2010. In both analyses no monopole signal was observed. For catalysis cross sections of the flux of non-relativistic GUT monopoles is constrained up to a level of at a 90 % confidence level, which is three orders of magnitude below the Parker bound. The limits assume a dominant decay of the proton into a positron and a neutral pion. These results improve the current best experimental limits by one to two orders of magnitude, for a wide range of assumed speeds and catalysis cross sections.
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7. |
- Aartsen, M. G., et al.
(författare)
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SEARCHES FOR EXTENDED AND POINT-LIKE NEUTRINO SOURCES WITH FOUR YEARS OF ICECUBE DATA
- 2014
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 796:2, s. 109-
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Tidskriftsartikel (refereegranskat)abstract
- We present results on searches for point-like sources of neutrinos using four years of IceCube data, including the first year of data from the completed 86 string detector. The total livetime of the combined data set is 1373 days. For an E-2 spectrum, the observed 90% C. L. flux upper limits are similar to 10(-12) TeV-1 cm(-2) s(-1) for energies between 1 TeV and 1 PeV in the northern sky and similar to 10(-11) TeV-1 cm(-2) s(-1) for energies between 100 TeV and 100 PeV in the southern sky. This represents a 40% improvement compared to previous publications, resulting from both the additional year of data and the introduction of improved reconstructions. In addition, we present the first results from an all-sky search for extended sources of neutrinos. We update the results of searches for neutrino emission from stacked catalogs of sources and test five new catalogs; two of Galactic supernova remnants and three of active galactic nuclei. In all cases, the data are compatible with the background-only hypothesis, and upper limits on the flux of muon neutrinos are reported for the sources considered.
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8. |
- Aartsen, M. G., et al.
(författare)
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Probing the origin of cosmic rays with extremely high energy neutrinos using the IceCube Observatory
- 2013
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11
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Tidskriftsartikel (refereegranskat)abstract
- We have searched for extremely high energy neutrinos using data taken with the IceCube detector between May 2010 and May 2012. Two neutrino-induced particle shower events with energies around 1 PeV were observed, as reported previously. In this work, we investigate whether these events could originate from cosmogenic neutrinos produced in the interactions of ultrahigh energy cosmic rays with ambient photons while propagating through intergalactic space. Exploiting IceCube's large exposure for extremely high energy neutrinos and the lack of observed events above 100 PeV, we can rule out the corresponding models at more than 90% confidence level. The model-independent quasidifferential 90% C. L. upper limit, which amounts to E-2 phi(nu e)+(nu mu)+(nu tau) = 1.2 x 10(-7) GeV cm(-2) s(-1) sr(-1) at 1 EeV, provides the most stringent constraint in the energy range from 10 PeV to 10 EeV. Our observation disfavors strong cosmological evolution of the highest energy cosmic-ray sources such as the Fanaroff-Riley type II class of radio galaxies.
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9. |
- Aartsen, M. G., et al.
(författare)
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First Observation of PeV-Energy Neutrinos with IceCube
- 2013
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:2, s. 021103-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the observation of two neutrino-induced events which have an estimated deposited energy in the IceCube detector of 1.04 +/- 0.16 and 1.14 +/- 0.17 PeV, respectively, the highest neutrino energies observed so far. These events are consistent with fully contained particle showers induced by neutral-current nu(e,mu,tau) ((nu) over bar (e,mu,tau)) or charged-current nu(e) ((nu) over bar (e)) interactions within the IceCube detector. The events were discovered in a search for ultrahigh energy neutrinos using data corresponding to 615.9 days effective live time. The expected number of atmospheric background is 0.082 +/- 0.004(stat)(-0.057)(+0.041)(syst). The probability of observing two or more candidate events under the atmospheric background-only hypothesis is 2.9 x 10(-3) (2.8 sigma) taking into account the uncertainty on the expected number of background events. These two events could be a first indication of an astrophysical neutrino flux; the moderate significance, however, does not permit a definitive conclusion at this time.
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10. |
- Aartsen, M. G., et al.
(författare)
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Measurement of Atmospheric Neutrino Oscillations with IceCube
- 2013
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:8, s. 081801-
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Tidskriftsartikel (refereegranskat)abstract
- We present the first statistically significant detection of neutrino oscillations in the high-energy regime (> 20 GeV) from an analysis of IceCube Neutrino Observatory data collected in 2010 and 2011. This measurement is made possible by the low-energy threshold of the DeepCore detector (similar to 20 GeV) and benefits from the use of the IceCube detector as a veto against cosmic-ray-induced muon background. The oscillation signal was detected within a low-energy muon neutrino sample (20-100 GeV) extracted from data collected by DeepCore. A high-energy muon neutrino sample (100 GeV-10 TeV) was extracted from IceCube data to constrain systematic uncertainties. The disappearance of low-energy upward-going muon neutrinos was observed, and the nonoscillation hypothesis is rejected with more than 5 sigma significance. In a two-neutrino flavor formalism, our data are best described by the atmospheric neutrino oscillation parameters vertical bar Delta m(32)(2)vertical bar = (2.3(-0.5)(+0.6)) x 10(-3) eV(2) and sin(2) (2 theta(23)) > 0.93, and maximum mixing is favored.
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