| 1. |
- Abelev, Betty, et al.
(author)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :11
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Journal article (peer-reviewed)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 2. |
- Abelev, Betty, et al.
(author)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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In: Journal of High Energy Physics. - 1029-8479. ; :7
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Journal article (peer-reviewed)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 3. |
- Abelev, Betty, et al.
(author)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Journal article (peer-reviewed)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 4. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 5. |
- Andersson, Stefan, et al.
(author)
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LUPP : Digitaliseringssamarbete mellan Stiftsbiblioteket vid Linköpings stadsbibliotek och Uppsala universitetsbibliotek
- 2011
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Reports (pop. science, debate, etc.)abstract
- Både Linköpings stadsbibliotek och Uppsala universitetsbibliotek digitaliserar delar av sina samlingar för att kunna erbjuda användarna ett utökat utbud av on-lineresurer. För många innebär digitalisering att ta bilder med en kamera eller skanner och visa bilderna på internet. Det låter enkelt men i själva verket är digitalisering en komplicerad process som kräver stora arbetsinsatser bland annat för att de digitala filerna skall kunna hittas och göras långsiktigt hållbara. LUPP-projektet syftar till att beskriva alla de delar av digitalisering som är nödvändiga för att få ett kvalitativt gott resultat, alltifrån vad man väljer att digitalisera till hur man bör förvara de digitala filerna samt hur man bör visa upp dem.Förutsättningarna att hantera digitalisering är olika för bibliotek av olika storlek och karaktär och för att även få med denna aspekt av digitalisering har ett samarbete inletts mellan de två biblioteken. Projektet presenterar en modell för hur bibliotek av skilda slag kan hantera, och samarbeta kring digitalisering. Syftet är naturligtvis att andra bibliotek med digitaliseringsambitioner, skall kunna dra nytta av modellen och själva tillämpa den för att kunna presentera sina samlingar digitalt.
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| 6. |
- Assimes, Themistocles L., et al.
(author)
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Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies
- 2010
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In: Journal of the American College of Cardiology. - : Elsevier BV. - 0735-1097. ; 56:19, s. 1552-1563
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Journal article (peer-reviewed)abstract
- Objectives We sought to replicate the association between the kinesin-like protein 6 (KIF6) Trp719Arg polymorphism (rs20455), and clinical coronary artery disease (CAD). Background Recent prospective studies suggest that carriers of the 719Arg allele in KIF6 are at increased risk of clinical CAD compared with noncarriers. Methods The KIF6 Trp719Arg polymorphism (rs20455) was genotyped in 19 case-control studies of nonfatal CAD either as part of a genome-wide association study or in a formal attempt to replicate the initial positive reports. Results A total of 17,000 cases and 39,369 controls of European descent as well as a modest number of South Asians, African Americans, Hispanics, East Asians, and admixed cases and controls were successfully genotyped. None of the 19 studies demonstrated an increased risk of CAD in carriers of the 719Arg allele compared with noncarriers. Regression analyses and fixed-effects meta-analyses ruled out with high degree of confidence an increase of >= 2% in the risk of CAD among European 719Arg carriers. We also observed no increase in the risk of CAD among 719Arg carriers in the subset of Europeans with early-onset disease (younger than 50 years of age for men and younger than 60 years of age for women) compared with similarly aged controls as well as all non-European subgroups. Conclusions The KIF6 Trp719Arg polymorphism was not associated with the risk of clinical CAD in this large replication study. (J Am Coll Cardiol 2010;56:1552-63) (C) 2010 by the American College of Cardiology Foundation
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| 7. |
- Bernstein, Joshua G, et al.
(author)
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Spectrotemporal modulation sensitivity as a predictor of speech intelligibility in noise with hearing aids
- 2014
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In: Spectrotemporal modulation sensitivity as a predictor of speech intelligibility in noise with hearing aids.
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Conference paper (peer-reviewed)abstract
- The audiogram predicts less than a third of the variance in speech reception thresholds (SRTs) for hearing-impaired (HI) listeners properly fit with individualized frequency-dependent gain. The remaining variance is often attributed to a combination of su-prathreshold distortion in the auditory pathway and non-auditory factors such as cogni-tive processing. Distinguishing between these factors requires a measure of suprathresh-old auditory processing to account for the non-cognitive contributions. Preliminary re-sults in 12 HI listeners identified a correlation between spectrotemporal modulation (STM) sensitivity and speech intelligibility in noise presented over headphones. The cur-IHCON 2014 27 August 13-17, 2014rent study assessed the effectiveness of STM sensitivity as a measure of suprathreshold auditory function to predict free-field SRTs in noise for a larger group of 47 HI listeners with hearing aids.SRTs were measured for Hagerman sentences presented at 65 dB SPL in stationary speech-weighted noise or four-talker babble. Pre-recorded speech and masker stimuli were played through a small anechoic chamber equipped with a master hearing aid pro-grammed with individualized gain. The output from an IEC711 Ear Simulator was played binaurally through insert earphones. Three processing algorithms were examined: linear gain, linear gain plus noise reduction, or fast-acting compressive gain.STM stimuli consist of spectrally-rippled noise with spectral-peak frequencies that shift over time. STM with a 2-cycle/octave spectral-ripple density and a 4-Hz modulation rate was applied to a 2-kHz lowpass-filtered pink-noise carrier. Stimuli were presented over headphones at 80 dB SPL (±5-dB roving). The threshold modulation depth was estimated adaptively in a two-alternative forced-choice task.STM sensitivity was strongly correlated (R2=0.48) with the global SRT (i.e., the SRTs averaged across masker and processing conditions). The high-frequency pure-tone aver-age (3-8 kHz) and age together accounted for 23% of the variance in global SRT. STM sensitivity accounted for an additional 28% of the variance in global SRT (total R2=0.51) when combined with these two other metrics in a multiple-regression analysis. Correla-tions between STM sensitivity and SRTs for individual conditions were weaker for noise reduction than for the other algorithms, and marginally stronger for babble than for sta-tionary noise.The results are discussed in the context of previous work suggesting that STM sensitivity for low rates and low carrier frequencies is impaired by a reduced ability to use temporal fine-structure information to detect slowly shifting spectral peaks. STM detection is a fast, simple test of suprathreshold auditory function that accounts for a substantial pro-portion of variability in hearing-aid outcomes for speech perception in noise.
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| 8. |
- Buehler, Stefan A., et al.
(author)
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Efficient radiative transfer simulations for a broadband infrared radiometer—Combining a weighted mean of representative frequencies approach with frequency selection by simulated annealing
- 2010
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In: Journal of Quantitative Spectroscopy and Radiative Transfer. - : Elsevier BV. - 0022-4073 .- 1879-1352. ; 111:4, s. 602-615
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Journal article (peer-reviewed)abstract
- We present a method to efficiently simulate the measurements of a broadband infrared instrument. The High Resolution Infrared Radiation Sounder (HIRS) instrument is used as example to illustrate the method. The method uses two basic ideas. Firstly, the channel radiance can be approximated by a weighted mean of the radiance at some representative frequencies, where the weights can be determined by linear regression. Secondly, a near-optimal set of representative frequencies can be found by simulated annealing.The paper does not only describe and analyze the method, it also describes how the method was used to derive optimized frequency grids for the HIRS instruments on the satellites TIROS N, NOAA 6-19, and Metop A. The grids and weights, as well as the optimization algorithm itself are openly available under a GNU public license.
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| 9. |
- Buehler, Stefan, et al.
(author)
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A multi-instrument comparison of integrated water vapour measurements at a high latitude site
- 2012
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In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 12:22, s. 10925-10943
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Journal article (peer-reviewed)abstract
- We compare measurements of integrated water vapour (IWV) over a subarctic site (Kiruna, Northern Sweden) from five different sensors and retrieval methods: Radiosondes, Global Positioning System (GPS), ground-based Fourier-transform infrared (FTIR) spectrometer, ground-based microwave radiometer, and satellite-based microwave radiometer (AMSU-B). Additionally, we compare also to ERA-Interim model reanalysis data. GPS-based IWV data have the highest temporal coverage and resolution and are chosen as reference data set. All datasets agree reasonably well, but the ground-based microwave instrument only if the data are cloud-filtered. We also address two issues that are general for such intercomparison studies, the impact of different lower altitude limits for the IWV integration, and the impact of representativeness error. We develop methods for correcting for the former, and estimating the random error contribution of the latter. A literature survey reveals that reported systematic differences between different techniques are study-dependent and show no overall consistent pattern. Further improving the absolute accuracy of IWV measurements and providing climate-quality time series therefore remain challenging problems.
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| 10. |
- Chasman, Daniel I., et al.
(author)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:24, s. 5329-5343
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Journal article (peer-reviewed)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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