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- 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. |
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| 3. |
- Dahl-Jensen, D., et al.
(författare)
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Eemian interglacial reconstructed from a Greenland folded ice core
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 493:7433, s. 489-494
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Tidskriftsartikel (refereegranskat)abstract
- Efforts to extract a Greenland ice core with a complete record of the Eemian interglacial (130,000 to 115,000 years ago) have until now been unsuccessful. The response of the Greenland ice sheet to the warmer-than-present climate of the Eemian has thus remained unclear. Here we present the new North Greenland Eemian Ice Drilling ('NEEM') ice core and show only a modest ice-sheet response to the strong warming in the early Eemian. We reconstructed the Eemian record from folded ice using globally homogeneous parameters known from dated Greenland and Antarctic ice-core records. On the basis of water stable isotopes, NEEM surface temperatures after the onset of the Eemian (126,000 years ago) peaked at 8 +/- 4 degrees Celsius above the mean of the past millennium, followed by a gradual cooling that was probably driven by the decreasing summer insolation. Between 128,000 and 122,000 years ago, the thickness of the northwest Greenland ice sheet decreased by 400 +/- 250 metres, reaching surface elevations 122,000 years ago of 130 +/- 300 metres lower than the present. Extensive surface melt occurred at the NEEM site during the Eemian, a phenomenon witnessed when melt layers formed again at NEEM during the exceptional heat of July 2012. With additional warming, surface melt might become more common in the future.
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| 4. |
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| 5. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
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| 7. |
- Jin, J.J., et al.
(författare)
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Comparison of CMAM simulations of carbon monoxide (CO), nitrous oxide (N2O), and methane (CH4) with observations from Odin/SMR, ACE-FTS, and Aura/MLS
- 2009
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 9, s. 3233-3252
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Tidskriftsartikel (refereegranskat)abstract
- Simulations of CO, N2O and CH4 from a coupled chemistry-climate model (CMAM) are compared with satellite measurements from Odin Sub-Millimeter Radiometer (Odin/SMR), Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), and Aura Microwave Limb Sounder (Aura/MLS). Pressure-latitude cross-sections and seasonal time series demonstrate that CMAM reproduces the observed global CO, N2O, and CH4 distributions quite well. Generally, excellent agreement with measurements is found between CO simulations and observations in the stratosphere and mesosphere. Differences between the simulations and the ACE-FTS observations are generally within 30%, and the differences between CMAM results and SMR and MLS observations are slightly larger. These differences are comparable with the difference between the instruments in the upper stratosphere and mesosphere. Comparisons of N2O show that CMAM results are usually within 15% of the measurements in the lower and middle stratosphere, and the observations are close to each other. However, the standard version of CMAM has a low N2O bias in the upper stratosphere. The CMAM CH4 distribution also reproduces the observations in the lower stratosphere, but has a similar but smaller negative bias in the upper stratosphere. The negative bias may be due to that the gravity drag is not fully resolved in the model. The simulated polar CO evolution in the Arctic and Antarctic agrees with the ACE and MLS observations. CO measurements from 2006 show evidence of enhanced descent of air from the mesosphere into the stratosphere in the Arctic after strong stratospheric sudden warmings (SSWs). CMAM also shows strong descent of air after SSWs. In the tropics, CMAM captures the annual oscillation in the lower stratosphere and the semiannual oscillations at the stratopause and mesopause seen in Aura/MLS CO and N2O observations and in Odin/SMR N2O observations. The Odin/SMR and Aura/MLS N2O observations also show a quasi-biennial oscillation (QBO) in the upper stratosphere, whereas, the CMAM does not have QBO included. This study confirms that CMAM is able to simulate middle atmospheric transport processes reasonably well.
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| 9. |
- McIntyre, S., et al.
(författare)
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Global prevalence of cerebral palsy: A systematic analysis
- 2022
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Ingår i: Developmental Medicine and Child Neurology. - : Wiley. - 0012-1622 .- 1469-8749. ; 64:12, s. 1494-1506
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Tidskriftsartikel (refereegranskat)abstract
- Aim To determine trends and current estimates in regional and global prevalence of cerebral palsy (CP). Method A systematic analysis of data from participating CP registers/surveillance systems and population-based prevalence studies (from birth year 1995) was performed. Quality and risk of bias were assessed for both data sources. Analyses were conducted for pre-/perinatal, postnatal, neonatal, and overall CP. For each region, trends were statistically classified as increasing, decreasing, heterogeneous, or no change, and most recent prevalence estimates with 95% confidence intervals (CI) were calculated. Meta-analyses were conducted to determine current birth prevalence estimates (from birth year 2010). Results Forty-one regions from 27 countries across five continents were represented. Pre-/perinatal birth prevalence declined significantly across Europe and Australia (11 out of 14 regions), with no change in postneonatal CP. From the limited but increasing data available from regions in low- and middle-income countries (LMICs), birth prevalence for pre-/perinatal CP was as high as 3.4 per 1000 (95% CI 3.0-3.9) live births. Following meta-analyses, birth prevalence for pre-/perinatal CP in regions from high-income countries (HICs) was 1.5 per 1000 (95% CI 1.4-1.6) live births, and 1.6 per 1000 (95% CI 1.5-1.7) live births when postneonatal CP was included. Interpretation The birth prevalence estimate of CP in HICs declined to 1.6 per 1000 live births. Data available from LMICs indicated markedly higher birth prevalence.
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| 10. |
- McLinden, C. A., et al.
(författare)
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OSIRIS: A Decade of Scattered Light
- 2012
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Ingår i: Bulletin of the American Meteorological Society. - 0003-0007 .- 1520-0477. ; 93:12, s. 1845-1863
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Tidskriftsartikel (refereegranskat)abstract
- Into year 11 of a 2-yr mission, OSIRIS is redefining how limb-scattered sunlight can be used to probe the atmosphere, even into the upper troposphere.
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