| 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. |
- Burillo, S. G., et al.
(författare)
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Molecular line emission in NGC 1068 imaged with ALMA : I. An AGN-driven outflow in the dense molecular gas
- 2014
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 567, s. 125-
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Tidskriftsartikel (refereegranskat)abstract
- Aims. We investigate the fueling and the feedback of star formation and nuclear activity in NGC 1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy, by analyzing the distribution and kinematics of the molecular gas in the disk. We aim to understand if and how gas accretion can self-regulate.Methods. We have used the Atacama Large Millimeter Array (ALMA) to map the emission of a set of dense molecular gas (n(H2) ' 1056 cm3) tracers (CO(3-2), CO(6-5), HCN(4-3), HCO+(4-3), and CS(7-6)) and their underlying continuum emission in the central r ∼ 2 kpc of NGC 1068 with spatial resolutions ∼0:3000:500 (∼20-35 pc for the assumed distance of D = 14 Mpc). Results. The sensitivity and spatial resolution of ALMA give an unprecedented detailed view of the distribution and kinematics of the dense molecular gas (n(H2) ≈ 1056cm3) in NGC 1068. Molecular line and dust continuum emissions are detected from a r ∼ 200 pc off-centered circumnuclear disk (CND), from the 2.6 kpc-diameter bar region, and from the r ∼ 1:3 kpc starburst (SB) ring. Most of the emission in HCO+, HCN, and CS stems from the CND. Molecular line ratios show dramatic order-of-magnitude changes inside the CND that are correlated with the UV/X-ray illumination by the active galactic nucleus (AGN), betraying ongoing feedback. We used the dust continuum fluxes measured by ALMA together with NIR/MIR data to constrain the properties of the putative torus using CLUMPY models and found a torus radius of 20+6 10 pc. The Fourier decomposition of the gas velocity field indicates that rotation is perturbed by an inward radial flow in the SB ring and the bar region. However, the gas kinematics from r ∼ 50 pc out to r ∼ 400 pc reveal a massive (Mmol ∼ 2:7+0:9 1:2 × 107 M) outflow in all molecular tracers. The tight correlation between the ionized gas outflow, the radio jet, and the occurrence of outward motions in the disk suggests that the outflow is AGN driven. Conclusions. The molecular outflow is likely launched when the ionization cone of the narrow line region sweeps the nuclear disk. The outflow rate estimated in the CND, dM=dt ∼ 63+21 37 M yr1, is an order of magnitude higher than the star formation rate at these radii, confirming that the outflow is AGN driven. The power of the AGN is able to account for the estimated momentum and kinetic luminosity of the outflow. The CND mass load rate of the CND outflow implies a very short gas depletion timescale of ≤1 Myr. The CND gas reservoir is likely replenished on longer timescales by efficient gas inflow from the outer disk. © ESO 2014.
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| 3. |
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| 4. |
- Langerak, A. W., et al.
(författare)
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EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations
- 2012
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 26:10, s. 2159-2171
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Forskningsöversikt (refereegranskat)abstract
- PCR-based immunoglobulin (Ig)/T-cell receptor (TCR) clonality testing in suspected lymphoproliferations has largely been standardized and has consequently become technically feasible in a routine diagnostic setting. Standardization of the pre-analytical and post-analytical phases is now essential to prevent misinterpretation and incorrect conclusions derived from clonality data. As clonality testing is not a quantitative assay, but rather concerns recognition of molecular patterns, guidelines for reliable interpretation and reporting are mandatory. Here, the EuroClonality (BIOMED-2) consortium summarizes important pre- and post-analytical aspects of clonality testing, provides guidelines for interpretation of clonality testing results, and presents a uniform way to report the results of the Ig/TCR assays. Starting from an immunobiological concept, two levels to report Ig/TCR profiles are discerned: the technical description of individual (multiplex) PCR reactions and the overall molecular conclusion for B and T cells. Collectively, the EuroClonality (BIOMED-2) guidelines and consensus reporting system should help to improve the general performance level of clonality assessment and interpretation, which will directly impact on routine clinical management (standardized best-practice) in patients with suspected lymphoproliferations.
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| 5. |
- Van den Bulcke, Jan, et al.
(författare)
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3D tree-ring analysis using helical X-ray tomography
- 2014
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Ingår i: Dendrochronologia. - : Elsevier BV. - 1125-7865 .- 1612-0051. ; 32:1, s. 39-46
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Tidskriftsartikel (refereegranskat)abstract
- The current state-of-the-art of tree-ring analysis and densitometry is still mainly limited to two dimensions and mostly requires proper treatment of the surface of the samples. In this paper we elaborate on the potential of helical X-ray computed tomography for 3D tree-ring analysis. Microdensitometrical profiles are obtained by processing of the reconstructed volumes. Correction of the structure direction, taking into account the angle of growth rings and grain, results in very accurate microdensity and precise ring width measurements. Both a manual as well as an automated methodology is proposed here, of which the MATLAB (c) code is available. Examples are given for pine (Pinus sylvestris L), oak (Quercus robur L) and teak (Tectona grandis L.). In all, the methodologies applied here on the 3D volumes are useful for growth related studies, enabling a fast and non-destructive analysis.
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| 6. |
- Viti, S., et al.
(författare)
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Molecular line emission in NGC 1068 imaged with ALMA II. The chemistry of the dense molecular gas
- 2014
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 570, s. 28-
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Tidskriftsartikel (refereegranskat)abstract
- Aims. We present a detailed analysis of Atacama Large Millimeter/submillimeter Array (ALMA) Bands 7 and 9 data of CO, HCO+, HCN, and CS, augmented with Plateau de Bure Interferometer (PdBI) data of the ~200 pc circumnuclear disc (CND) and the ~1.3 kpc starburst ring (SB ring) of NGC 1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy. We aim to determine the physical characteristics of the dense gas present in the CND, and to establish whether the different line intensity ratios we find within the CND, as well as between the CND and the SB ring, are due to excitation effects (gas density and temperature differences) or to a different chemistry.Methods. We estimate the column densities of each species in local thermodynamic equilibrium (LTE). We then compute large one-dimensional, non-LTE radiative transfer grids (using RADEX) by using only the CO transitions first, and then all the available molecules to constrain the densities, temperatures, and column densities within the CND. We finally present a preliminary set of chemical models to determine the origin of the gas.Results. We find that, in general, the gas in the CND is very dense (>105 cm-3) and hot (T> 150 K), with differences especially in the temperature across the CND. The AGN position has the lowest CO/HCO+, CO/HCN, and CO/CS column density ratios. The RADEX analyses seem to indicate that there is chemical differentiation across the CND. We also find differences between the chemistry of the SB ring and some regions of the CND; the SB ring is also much colder and less dense than the CND. Chemical modelling does not succeed in reproducing all the molecular ratios with one model per region, suggesting the presence of multi-gas phase components.Conclusions. The LTE, RADEX, and chemical analyses all indicate that more than one gas-phase component is necessary to uniquely fit all the available molecular ratios within the CND. A higher number of molecular transitions at the ALMA resolution is necessary to determine quantitatively the physical and chemical characteristics of these components.
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| 7. |
- Wernersson, Erik L. G., et al.
(författare)
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Postprocessing method for reducing phase effects in reconstructed microcomputed-tomography data
- 2013
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Ingår i: Optical Society of America. Journal A. - 1084-7529 .- 1520-8532. ; 30:3, s. 455-461
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Tidskriftsartikel (refereegranskat)abstract
- With increased resolution in x-ray computed tomography, refraction adds increasingly to the attenuation signal. Though potentially beneficial, the artifacts caused by refraction often need to be removed from the image. In this paper, we propose a postprocessing method, based on deconvolution, that is able to remove these artifacts after conventional reconstruction. This method poses two advantages over existing projection-based (preprocessing) phase-retrieval or phase-removal algorithms. First, evaluation of the parameters can be done very quickly, improving the overall speed of the method. Second, postprocessing methods can be applied when projection data is not available, which occurs in several commercial systems with closed software or when projection data has been deleted. It is shown that the proposed method performs comparably to state-of-the-art methods in terms of image quality.
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| 8. |
- Adams, C., et al.
(författare)
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Validation of ACE and OSIRIS ozone and NO2 measurements using ground-based instruments at 80 degrees N
- 2012
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 5:5, s. 927-953
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Tidskriftsartikel (refereegranskat)abstract
- The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80A degrees N, 86A degrees W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80A degrees N. Satellite 14-52 km ozone and 17-40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 +/- 0.2% and -0.2 +/- 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14-52 km satellite and 0-14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1-7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25-52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007-2009 spring-time mean relative difference improved from -5.0 +/- 0.4% to -3.1 +/- 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a +/- 1A degrees latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.
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| 9. |
- Boone, F., et al.
(författare)
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An extended Herschel drop-out source in the center of AS1063: A normal dusty galaxy at z = 6.1 or SZ substructures?
- 2013
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 559, s. L1-
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Tidskriftsartikel (refereegranskat)abstract
- In the course of our 870 μm APEX/LABOCA follow-up of the Herschel Lensing Survey we have detected a source in AS1063 (RXC J2248.7-4431) that has no counterparts in any of the Herschel PACS/SPIRE bands, it is a Herschel "drop-out" with S870=S500 ≥ 0:5. The 870 μm emission is extended and centered on the brightest cluster galaxy, suggesting either a multiply imaged background source or substructure in the Sunyaev-Zel'dovich increment due to inhomogeneities in the hot cluster gas of this merging cluster. We discuss both interpretations with emphasis on the putative lensed source. Based on the observed properties and on our lens model we find that this source may be the first submillimeter galaxy (SMG) with a moderate far-infrared (FIR) luminosity (LFIR. © ESO 2013.
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| 10. |
- Burillo, S. G., et al.
(författare)
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Molecular gas chemistry in AGN. II. High-resolution imaging of SiO emission in NGC 1068: shocks or XDR?
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 519:Article Number: A2
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Tidskriftsartikel (refereegranskat)abstract
- Context. This paper is part of a multi-species survey of line emission from the molecular gas in the circum-nuclear disk (CND) of the Seyfert 2 galaxy NGC 1068. Unlike in other active galaxies, the intensely star-forming regions in NGC 1068 and the CND can be resolved with current instrumentation. This makes this galaxy an optimal test-bed to probe the effects of AGN on the molecular medium at similar to 100 pc scales. Aims. Single-dish observations have provided evidence that the abundance of silicon monoxide (SiO) in the CND of NGC 1068 is enhanced by 3-4 orders of magnitude with respect to the values typically measured in quiescent molecular gas in the Galaxy. We aim at unveiling the mechanism(s) underlying the SiO enhancement. Methods. We have imaged the emission of the SiO(2-1) (86.8 GHz) and CN(2-1) (226.8 GHz) lines in NGC 1068 at similar to 150 pc and 60 pc spatial resolution with the IRAM Plateau de Bure interferometer (PdBI). We have also obtained complementary IRAM 30 m observations of HNCO and methanol (CH3OH) lines. These species are known as tracers of shocks in the Galaxy. Results. SiO is detected in a disk of similar to 400 pc size around the AGN. SiO abundances in the CND of similar to(1-5) x 10(-9) are about 1-2 orders of magnitude above those measured in the starburst ring. The overall abundance of CN in the CND is high: similar to(0.2-1) x 10(-7). The abundances of SiO and CN are enhanced at the extreme velocities of gas associated with non-circular motions close to the AGN (r
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