340 research outputs found
From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of "supercell statistics", a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number of measurements needed to capture phenotypic differences between healthy and diseased patients, as well as between different diseases that are difficult to diagnose otherwise. We apply our approach to two kinds of single-cell datasets, addressing the diagnosis of a premature aging disorder using images of cell nuclei, as well as the phenotypes of two non-infectious uveitides (the ocular manifestations of Behçet's disease and sarcoidosis) based on multicolor flow cytometry. In the former case, one nuclear shape measurement taken over a group of 30 cells is sufficient to classify samples as healthy or diseased, in agreement with usual laboratory practice. In the latter, our method is able to identify a minimal set of 5 markers that accurately predict Behçet's disease and sarcoidosis. This is the first time that a quantitative phenotypic distinction between these two diseases has been achieved. To obtain this clear phenotypic signature, about one hundred CD8+ T cells need to be measured. Although the molecular markers identified have been reported to be important players in autoimmune disorders, this is the first report pointing out that CD8+ T cells can be used to distinguish two systemic inflammatory diseases. Beyond these specific cases, the approach proposed here is applicable to datasets generated by other kinds of state-of-the-art and forthcoming single-cell technologies, such as multidimensional mass cytometry, single-cell gene expression, and single-cell full genome sequencing techniques.Instituto de Física de Líquidos y Sistemas Biológico
Constraints on the Ultra-High Energy Neutrino Flux from Gamma-Ray Bursts from a Prototype Station of the Askaryan Radio Array
We report on a search for ultra-high-energy (UHE) neutrinos from gamma-ray
bursts (GRBs) in the data set collected by the Testbed station of the Askaryan
Radio Array (ARA) in 2011 and 2012. From 57 selected GRBs, we observed no
events that survive our cuts, which is consistent with 0.12 expected background
events. Using NeuCosmA as a numerical GRB reference emission model, we estimate
upper limits on the prompt UHE GRB neutrino fluence and quasi-diffuse flux from
to GeV. This is the first limit on the prompt UHE GRB
neutrino quasi-diffuse flux above GeV.Comment: 14 pages, 8 figures, Published in Astroparticle Physics Journa
First Constraints on the Ultra-High Energy Neutrino Flux from a Prototype Station of the Askaryan Radio Array
The Askaryan Radio Array (ARA) is an ultra-high energy ( eV) cosmic
neutrino detector in phased construction near the South Pole. ARA searches for
radio Cherenkov emission from particle cascades induced by neutrino
interactions in the ice using radio frequency antennas ( MHz)
deployed at a design depth of 200 m in the Antarctic ice. A prototype ARA
Testbed station was deployed at m depth in the 2010-2011 season and
the first three full ARA stations were deployed in the 2011-2012 and 2012-2013
seasons. We present the first neutrino search with ARA using data taken in 2011
and 2012 with the ARA Testbed and the resulting constraints on the neutrino
flux from eV.Comment: 26 pages, 15 figures. Since first revision, added section on
systematic uncertainties, updated limits and uncertainty band with
improvements to simulation, added appendix describing ray tracing algorithm.
Final revision includes a section on cosmic ray backgrounds. Published in
Astropart. Phys.
An All-Sky Search for Three Flavors of Neutrinos from Gamma-Ray Bursts with the IceCube Neutrino Observatory
We present the results and methodology of a search for neutrinos produced in
the decay of charged pions created in interactions between protons and
gamma-rays during the prompt emission of 807 gamma-ray bursts (GRBs) over the
entire sky. This three-year search is the first in IceCube for shower-like
Cherenkov light patterns from electron, muon, and tau neutrinos correlated with
GRBs. We detect five low-significance events correlated with five GRBs. These
events are consistent with the background expectation from atmospheric muons
and neutrinos. The results of this search in combination with those of
IceCube's four years of searches for track-like Cherenkov light patterns from
muon neutrinos correlated with Northern-Hemisphere GRBs produce limits that
tightly constrain current models of neutrino and ultra high energy cosmic ray
production in GRB fireballs.Comment: 33 pages, 14 figures; minor changes made to match published version
in the Astrophysical Journal, 2016 June 2
Lowering IceCube’s energy threshold for point source searches in the southern sky
Observation of a point source of astrophysical neutrinos would be a "smoking gun" signature of a cosmic-ray accelerator. While IceCube has recently discovered a diffuse flux of astrophysical neutrinos, no localized point source has been observed. Previous IceCube searches for point sources in the southern sky were restricted by either an energy threshold above a few hundred TeV or poor neutrino angular resolution. Here we present a search for southern sky point sources with greatly improved sensitivities to neutrinos with energies below 100 TeV. By selecting charged-current nu(mu) interacting inside the detector, we reduce the atmospheric background while retaining efficiency for astrophysical neutrino-induced events reconstructed with sub-degree angular resolution. The new event sample covers three years of detector data and leads to a factor of 10 improvement in sensitivity to point sources emitting below 100 TeV in the southern sky. No statistically significant evidence of point sources was found, and upper limits are set on neutrino emission from individual sources. A posteriori analysis of the highest-energy (similar to 100 TeV) starting event in the sample found that this event alone represents a 2.8 sigma deviation from the hypothesis that the data consists only of atmospheric background
Improved limits on dark matter annihilation in the Sun with the 79-string IceCube detector and implications for supersymmetry
We present an improved event-level likelihood formalism for including
neutrino telescope data in global fits to new physics. We derive limits on
spin-dependent dark matter-proton scattering by employing the new formalism in
a re-analysis of data from the 79-string IceCube search for dark matter
annihilation in the Sun, including explicit energy information for each event.
The new analysis excludes a number of models in the weak-scale minimal
supersymmetric standard model (MSSM) for the first time. This work is
accompanied by the public release of the 79-string IceCube data, as well as an
associated computer code for applying the new likelihood to arbitrary dark
matter models.Comment: 24 pages, 8 figs, 1 table. Contact authors: Pat Scott & Matthias
Danninger. Likelihood tool available at http://nulike.hepforge.org. v2: small
updates to address JCAP referee repor
The IceCube Neutrino Observatory: Instrumentation and Online Systems
The IceCube Neutrino Observatory is a cubic-kilometer-scale high-energy
neutrino detector built into the ice at the South Pole. Construction of
IceCube, the largest neutrino detector built to date, was completed in 2011 and
enabled the discovery of high-energy astrophysical neutrinos. We describe here
the design, production, and calibration of the IceCube digital optical module
(DOM), the cable systems, computing hardware, and our methodology for drilling
and deployment. We also describe the online triggering and data filtering
systems that select candidate neutrino and cosmic ray events for analysis. Due
to a rigorous pre-deployment protocol, 98.4% of the DOMs in the deep ice are
operating and collecting data. IceCube routinely achieves a detector uptime of
99% by emphasizing software stability and monitoring. Detector operations have
been stable since construction was completed, and the detector is expected to
operate at least until the end of the next decade.Comment: 83 pages, 50 figures; updated with minor changes from journal review
and proofin
The IceCube Neutrino Observatory - Contributions to ICRC 2015 Part II: Atmospheric and Astrophysical Diffuse Neutrino Searches of All Flavors
Papers on atmospheric and astrophysical diffuse neutrino searches of all
flavors submitted to the 34th International Cosmic Ray Conference (ICRC 2015,
The Hague) by the IceCube Collaboration.Comment: 66 pages, 36 figures, Papers submitted to the 34th International
Cosmic Ray Conference, The Hague 2015, v2 has a corrected author lis
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