| 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. |
- 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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| 3. |
- Pérez-González, P.G.P., et al.
(författare)
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Improving the identification of high-z Herschel sources with position priors and optical/NIR and FIR/mm photometric redshifts
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518:Article Number: L15
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Tidskriftsartikel (refereegranskat)abstract
- We present preliminary results about the detection of high redshift (U)LIRGs in the Bullet cluster field by the PACS and SPIRE instruments within the Herschel Lensing Survey (HLS) Program. We describe in detail a photometric procedure designed to recover robust fluxes and deblend faint Herschel sources near the confusion noise. The method is based on the use of the positions of Spitzer/MIPS 24 mu m sources as priors. Our catalogs are able to reliably (5 sigma) recover galaxies with fluxes above 6 and 10 mJy in the PACS 100 and 160 mu m channels, respectively, and 12 to 18 mJy in the SPIRE bands. We also obtain spectral energy distributions covering the optical through the far-infrared/millimeter spectral ranges of all the Herschel detected sources, and analyze them to obtain independent estimations of the photometric redshift based on either stellar population or dust emission models. We exemplify the potential of the combined use of Spitzer position priors plus independent optical and IR photometric redshifts to robustly assign optical/NIR counterparts to the sources detected by Herschel and other (sub-)mm instruments.
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| 4. |
- Rex, M., et al.
(författare)
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The far-infrared/submillimeter properties of galaxies located behind the Bullet cluster
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518:Article Number: L13
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Tidskriftsartikel (refereegranskat)abstract
- The Herschel Lensing Survey (HLS) takes advantage of gravitational lensing by massive galaxy clusters to sample a population of high-redshift galaxies which are too faint to be detected above the confusion limit of current far-infrared/submillimeter telescopes. Measurements from 100-500 mu m bracket the peaks of the far-infrared spectral energy distributions of these galaxies, characterizing their infrared luminosities and star formation rates. We introduce initial results from our science demonstration phase observations, directed toward the Bullet cluster (1E0657-56). By combining our observations with LABOCA 870 mu m and AzTEC 1.1 mm data we fully constrain the spectral energy distributions of 19 MIPS 24 mu m-selected galaxies which are located behind the cluster. We find that their colors are best fit using templates based on local galaxies with systematically lower infrared luminosities. This suggests that our sources are not like local ultra-luminous infrared galaxies in which vigorous star formation is contained in a compact highly dust-obscured region. Instead, they appear to be scaled up versions of lower luminosity local galaxies with star formation occurring on larger physical scales.
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| 5. |
- Laeng, A., et al.
(författare)
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Validation of MIPAS IMK/IAA V5R_O3_224 ozone profiles
- 2014
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 7:11, s. 3971-3987
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of an extensive validation program of the most recent version of ozone vertical profiles retrieved with the IMK/IAA (Institute for Meteorology and Climate Research/Instituto de Astrofisica de Andalucia) MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) research level 2 processor from version 5 spectral level 1 data. The time period covered corresponds to the reduced spectral resolution period of the MIPAS instrument, i.e., January 2005-April 2012. The comparison with satellite instruments includes all post-2005 satellite limb and occultation sensors that have measured the vertical profiles of tropospheric and stratospheric ozone: ACE-FTS, GOMOS, HALOE, HIRDLS, MLS, OSIRIS, POAM, SAGE II, SCIAMACHY, SMILES, and SMR. In addition, balloon-borne MkIV solar occultation measurements and ground-based Umkehr measurements have been included, as well as two nadir sensors: IASI and SBUV. For each reference data set, bias determination and precision assessment are performed. Better agreement with reference instruments than for the previous data version, V5R_O3_220 (Laeng et al., 2014), is found: the known high bias around the ozone vmr (volume mixing ratio) peak is significantly reduced and the vertical resolution at 35 km has been improved. The agreement with limb and solar occultation reference instruments that have a known small bias vs. ozonesondes is within 7% in the lower and middle stratosphere and 5% in the upper troposphere. Around the ozone vmr peak, the agreement with most of the satellite reference instruments is within 5 %; this bias is as low as 3% for ACE-FTS, MLS, OSIRIS, POAM and SBUV.
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| 6. |
- 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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| 7. |
- Kasai, Y., et al.
(författare)
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Validation of stratospheric and mesospheric ozone observed by SMILES from International Space Station
- 2013
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 6:9, s. 2311-2338
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Tidskriftsartikel (refereegranskat)abstract
- We observed ozone (O3) in the vertical region between 250 and 0.0005 hPa (~ 12–96 km) using the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) on the Japanese Experiment Module (JEM) of the International Space Station (ISS) between 12 October 2009 and 21 April 2010. The new 4 K superconducting heterodyne receiver technology of SMILES allowed us to obtain a one order of magnitude better signal-to-noise ratio for the O3 line observation compared to past spaceborne microwave instruments. The non-sun-synchronous orbit of the ISS allowed us to observe O3 at various local times. We assessed the quality of the vertical profiles of O3 in the 100–0.001 hPa (~ 16–90 km) region for the SMILES NICT Level 2 product version 2.1.5. The evaluation is based on four components: error analysis; internal comparisons of observations targeting three different instrumental setups for the same O3 625.371 GHz transition; internal comparisons of two different retrieval algorithms; and external comparisons for various local times with ozonesonde, satellite and balloon observations (ENVISAT/MIPAS, SCISAT/ACE-FTS, Odin/OSIRIS, Odin/SMR, Aura/MLS, TELIS). SMILES O3 data have an estimated absolute accuracy of better than 0.3 ppmv (3%) with a vertical resolution of 3–4 km over the 60 to 8 hPa range. The random error for a single measurement is better than the estimated systematic error, being less than 1, 2, and 7%, in the 40–1, 80–0.1, and 100–0.004 hPa pressure regions, respectively. SMILES O3 abundance was 10–20% lower than all other satellite measurements at 8–0.1 hPa due to an error arising from uncertainties of the tangent point information and the gain calibration for the intensity of the spectrum. SMILES O3 from observation frequency Band-B had better accuracy than that from Band-A. A two month period is required to accumulate measurements covering 24 h in local time of O3 profile. However such a dataset can also contain variation due to dynamical, seasonal, and latitudinal effects
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| 8. |
- Jones, A., et al.
(författare)
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Technical Note: A trace gas climatology derived from the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) data set
- 2012
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 12:11, s. 5207-5220
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Tidskriftsartikel (refereegranskat)abstract
- The Atmospheric Chemistry Experiment-Fourier Transform Spectrometer (ACE-FTS) aboard the Canadian satellite SCISAT (launched in August 2003) was designed to investigate the composition of the upper troposphere, stratosphere, and mesosphere. ACE-FTS utilizes solar occultation to measure temperature and pressure as well as vertical profiles of over thirty chemical species including O-3, H2O, CH4, N2O, CO, NO, NO2, N2O5, HNO3, HCl, ClONO2, CCl3F, CCl2F2, and HF. Global coverage for each species is obtained approximately over a three month period and measurements are made with a vertical resolution of typically 3-4 km. A quality-controlled climatology has been created for each of these 14 baseline species, where individual profiles are averaged over the period of February 2004 to February 2009. Measurements used are from the ACE-FTS version 2.2 data set including updates for O-3 and N2O5. The climatological fields are provided on a monthly and three-monthly basis (DJF, MAM, JJA, SON) at 5 degree latitude and equivalent latitude spacing and on 28 pressure surfaces (26 of which are defined by the Stratospheric Processes And their Role in Climate (SPARC) Chemistry-Climate Model Validation Activity). The ACE-FTS climatological data set is available through the ACE website.
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| 9. |
- 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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| 10. |
- van Krieken, J. H., et al.
(författare)
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Guideline on the requirements of external quality assessment programs in molecular pathology
- 2013
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Ingår i: Virchows Archiv. - : Springer Science and Business Media LLC. - 0945-6317 .- 1432-2307. ; 462:1, s. 27-37
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Tidskriftsartikel (refereegranskat)abstract
- Molecular pathology is an integral part of daily diagnostic pathology and used for classification of tumors, for prediction of prognosis and response to therapy, and to support treatment decisions. For these reasons, analyses in molecular pathology must be highly reliable and hence external quality assessment (EQA) programs are called for. Several EQA programs exist to which laboratories can subscribe, but they vary in scope, number of subscribers, and execution. The guideline presented in this paper has been developed with the purpose to harmonize EQA in molecular pathology. It presents recommendations on how an EQA program should be organized, provides criteria for a reference laboratory, proposes requirements for EQA test samples, and defines the number of samples needed for an EQA program. Furthermore, a system for scoring of the results is proposed as well as measures to be taken for poorly performing laboratories. Proposals are made regarding the content requirements of an EQA report and how its results should be communicated. Finally, the need for an EQA database and a participant manual are elaborated. It is the intention of this guideline to improve EQA for molecular pathology in order to provide more reliable molecular analyses as well as optimal information regarding patient selection for treatment.
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