| 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. |
- Abelev, Betty, et al.
(författare)
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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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Ingår i: 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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Tidskriftsartikel (refereegranskat)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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| 3. |
- Abelev, Betty, et al.
(författare)
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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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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Abelev, Betty, et al.
(författare)
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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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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Barrantes, Alejandro, et al.
(författare)
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Alzheimer’s Disease Amyloid Peptides Interact with DNA, As Proved by Surface Plasmon Resonance
- 2012
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Ingår i: Current Alzheimer Research. - : Bentham eBooks. - 1567-2050 .- 1875-5828. ; 9:8, s. 924-934
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Tidskriftsartikel (refereegranskat)abstract
- According to the amyloid hypothesis, abnormal processing of the β-amyloid precursor protein in Alzheimer's disease patients increases the production of β-amyloid toxic peptides, which, after forming highly aggregated fibrillar structures, lead to extracellular plaques formation, neuronal loss and dementia. However, a great deal of evidence has point to intracellular small oligomers of amyloid peptides, probably transient intermediates in the process of fibrillar structures formation, as the most toxic species. In order to study the amyloid-DNA interaction, we have selected here three different forms of the amyloid peptide: Aβ1-40, Aβ25-35 and a scrambled form of Aβ25-35. Surface Plasmon Resonance was used together with UV-visible spectroscopy, Electrophoresis and Electronic Microscopy to carry out this study. Our results prove that, similarly to the full length Aβ1-42, all conformations of toxic amyloid peptides, Aβ1-40 and Aβ25-35, may bind DNA. In contrast, the scrambled form of Aβ25-35, a non-aggregating and nontoxic form of this peptide, could not bind DNA. We conclude that although the amyloid-DNA interaction is closely related to the amyloid aggregation proneness, this cannot be the only factor which determines the interaction, since small oligomers of amyloid peptides may also bind DNA if their predominant negatively charged amino acid residues are previously neutralized.
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| 6. |
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| 7. |
- García, Oscar, 1963-
(författare)
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Guerrilleros de papel : La representación del guerrillero en seis novelas centroamericanas de los años setenta y ochenta
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of the present study is to analyze and compare the representation of the guerrilla soldier in six contemporary Central American novels. According to Claudio Guillén, the comparison is a dialogue between unity and diversity. It can be defined with the help of two coordinates: a spatial and a temporal. In this study the spatial coordinate includes Nicaragua, Guatemala and El Salvador, and the temporal extends from the mid-seventies to the eighties. The novels written in the seventies are Los compañeros (1976) by Marco Antonio Flores, ¿Te dio miedo la sangre? (1977) by Sergio Ramírez and Caperucita en la zona roja (1977) by Manlio Argueta. The ones written in the eighties are La mujer habitada (1988) by Gioconda Belli, La diáspora (1989) by Horacio Castellanos Moya and El hombre de Montserrat (1994) by Dante Liano. The novels are analyzed from a postcolonial perspective following the ideas of Alfonso de Toro and Santiago Castro-Gómez particularly. The method used is the phenomenological hermeneutics, as proposed by Mario J. Valdés. This implies an analysis performed on four levels: historical, formal, phenomenological and hermeneutic. Two of the key aspects in the analysis are the reader's aesthetic identification with the hero and the postcolonial concept subaltern. The main conclusion is that the representation of the guerrilla soldier in the corpus is very heterogeneous and that almost no protagonist can be considered a subaltern. The reader's identification with the guerrilla soldier ranges from admirative to ironic, though the main type is sympathetic. Hence, the representation may be considered a hybrid, using a term borrowed from anthropologist Néstor García Canclini that opposes binary schemes and essentialist thinking. The guerrilla soldier is regarded as an individual and not as an abstract idea, which indicates that the civil wars in Central America were not just a conflict between two ideologies, but above all a human experience.
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| 8. |
- Garcia Silva, Maria R., et al.
(författare)
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Cloning, characterization, and subcellular localization of a Trypanosoma cruzi argonaute protein defining a new subfamily distinctive of trypanosomatids
- 2010
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Ingår i: Gene. - : Elsevier BV. - 1879-0038 .- 0378-1119. ; 466:1-2, s. 26-35
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Tidskriftsartikel (refereegranskat)abstract
- Over the last years an expanding family of small non-coding RNAs (sRNA) has been identified in eukaryotic genomes which behave as sequence-specific triggers for mRNA degradation, translation repression, heterochromatin formation and genome stability. To achieve their effectors functions, sRNAs associate with members of the Argonaute protein family. Argonaute proteins are segregated into three paralogous groups: the AGO-like subfamily, the PIWI-like subfamily, and the WAGO subfamily (for Worm specific AGO). Detailed phylogenetic analysis of the small RNA-related machinery components revealed that they can be traced back to the common ancestor of eukaryotes. However, this machinery seems to be lost or excessively simplified in some unicellular organisms such as Saccharomyces cerevisiae, Trypanosoma cruzi, Leishmania major and Plasmodium falciparum which are unable to utilize dsRNA to trigger degradation of target RNAs. We reported here a unique ORF encoding for an AGO/PIWI protein in T. cruzi which was expressed in all stages of its life cycle at the transcript as well as the protein level. Database search for remote homologues, revealed the presence of a divergent PAZ domain adjacent to the well supported PIWI domain. Our results strongly suggested that this unique AGO/PIWI protein from T. cruzi is a canonical Argonaute in terms of its domain architecture. We propose to reclassify all Argonaute members from trypanosomatids as a distinctive phylogenetic group representing a new subfamily of Argonaute proteins and propose the generic designation of AGO/PIWI-tryp to identify them. Inside the Trypanosomatid-specific node, AGO/PIWI-tryps were clearly segregated into two paralog groups designated as AGO-tryp and PIWI-tryp according to the presence or absence of a functional link with RNAi-related phenomena, respectively. (C) 2010 Elsevier B.V. All rights reserved.
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| 9. |
- Gómez-Barroso, José Luis, et al.
(författare)
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Prospects of Mobile Search
- 2010
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Search faces (at least) two major challenges. One is to improve efficiency of retrieving relevant content for all digital formats (images, audio, video, 3D shapes, etc). The second is making relevant information retrievable in a range of platforms, particularly in high diffusion ones as mobiles. The two challenges are interrelated but distinct. This report aims at assessing the potential of future Mobile Search. Two broad groups of search-based applications can be identified. The first one is the adaptation and emulation of web search processes and services to the mobile environment. The second one is services exploiting the unique features of the mobile devices and the mobile environments. Examples of these context-aware services include location-based services or interfacing to the internet of things (RFID networks). The report starts by providing an introduction to mobile search. It highlights differences and commonalities with search technologies on other platforms (Chapter 1). Chapter 2 is devoted to the supply side of mobile search markets. It describes mobile markets, presents key figures and gives an outline of main business models and players. Chapter 3 is dedicated to the demand side of the market. It studies users¿ acceptance and demand using the results on a case study in Sweden. Chapter 4 presents emerging trends in technology and markets that could shape mobile search. It is the author's view after discussing with many experts. One input to this discussion was the analysis of on forward-looking scenarios for mobile developed by the authors (Chapter 5). Experts were asked to evaluate these scenarios. Another input was a questionnaire to which 61 experts responded. Drivers, barriers and enablers for mobile search have been synthesised into SWOT analysis. The report concludes with some policy recommendations in view of the likely socio-economic implications of mobile search in Europe. Appears in Collections:Institute for Prospective Technological Studies
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| 10. |
- Le Callet, Patrick, et al.
(författare)
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Qualinet White Paper on Definitions of Quality of Experience : Version 1.2
- 2013
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This White Paper is a contribution of the European Network on Quality of Experience in Multimedia Systems and Services, Qualinet (COST Action IC 1003, see www.qualinet.eu), to the scientific discussion about the term “Quality of Experience” (QoE) and its underlying concepts. It resulted from the need to agree on a working definition for this term which facilitates the communication of ideas within a multidisciplinary group, where a joint interest around multimedia communication systems exists, however approached from different perspectives. Thus, the concepts and ideas cited in this paper mainly refer to the Quality of Experience of multimedia communication systems, but may be helpful also for other areas where QoE is an issue.
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