| 1. |
- 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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| 2. |
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| 3. |
- Blokland, G. A. M., et al.
(författare)
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Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders
- 2022
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Ingår i: Biological Psychiatry. - : Elsevier BV. - 0006-3223 .- 1873-2402. ; 91:1, s. 102-117
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. Methods: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. Results: Across disorders, genome-wide significant single nucleotide polymorphism–by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10−8), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10−6) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10−7; rs73033497, p = 8.8 × 10−7; rs7914279, p = 6.4 × 10−7), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10−7) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10−7), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10−7) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). Conclusions: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels. © 2021 Society of Biological Psychiatry
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| 4. |
- Brierley, Chris M., et al.
(författare)
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Large-scale features and evaluation of the PMIP4-CMIP6 midHolocene simulations
- 2020
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:5, s. 1847-1872
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Tidskriftsartikel (refereegranskat)abstract
- The mid-Holocene (6000 years ago) is a standard time period for the evaluation of the simulated response of global climate models using palaeoclimate reconstructions. The latest mid-Holocene simulations are a palaeoclimate entry card for the Palaeoclimate Model Intercomparison Project (PMIP4) component of the current phase of the Coupled Model Intercomparison Project (CMIP6) - hereafter referred to as PMIP4-CMIP6. Here we provide an initial analysis and evaluation of the results of the experiment for the mid-Holocene. We show that state-of-the-art models produce climate changes that are broadly consistent with theory and observations, including increased summer warming of the Northern Hemisphere and associated shifts in tropical rainfall. Many features of the PMIP4-CMIP6 simulations were present in the previous generation (PMIP3-CMIP5) of simulations. The PMIP4-CMIP6 ensemble for the mid-Holocene has a global mean temperature change of -0.3 K, which is -0.2K cooler than the PMIP3-CMIP5 simulations predominantly as a result of the prescription of realistic greenhouse gas concentrations in PMIP4-CMIP6. Biases in the magnitude and the sign of regional responses identified in PMIP3-CMIP5, such as the amplification of the northern African monsoon, precipitation changes over Europe, and simulated aridity in mid-Eurasia, are still present in the PMIP4-CMIP6 simulations. Despite these issues, PMIP4-CMIP6 and the mid-Holocene provide an opportunity both for quantitative evaluation and derivation of emergent constraints on the hydrological cycle, feedback strength, and potentially climate sensitivity.
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| 5. |
- Muus, Christoph, et al.
(författare)
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 546-559
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Tidskriftsartikel (refereegranskat)abstract
- Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention. An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.
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| 6. |
- Renoult, Martin, et al.
(författare)
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A Bayesian framework for emergent constraints : case studies of climate sensitivity with PMIP
- 2020
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:5, s. 1715-1735
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we introduce a Bayesian framework, which is explicit about prior assumptions, for using model ensembles and observations together to constrain future climate change. The emergent constraint approach has seen broad application in recent years, including studies constraining the equilibrium climate sensitivity (ECS) using the Last Glacial Maximum (LGM) and the mid-Pliocene Warm Period (mPWP). Most of these studies were based on ordinary least squares (OLS) fits between a variable of the climate state, such as tropical temperature, and climate sensitivity. Using our Bayesian method, and considering the LGM and mPWP separately, we obtain values of ECS of 2.7K (0.6-5.2, 5th-95th percentiles) using the PMIP2, PMIP3, and PMIP4 datasets for the LGM and 2.3K (0.5-4.4) with the PlioMIP1 and PlioMIP2 datasets for the mPWP. Restricting the ensembles to include only the most recent version of each model, we obtain 2.7K (0.7-5.2) using the LGM and 2.3K (0.4-4.5) using the mPWP. An advantage of the Bayesian framework is that it is possible to combine the two periods assuming they are independent, whereby we obtain a tighter constraint of 2.5K (0.8-4.0) using the restricted ensemble. We have explored the sensitivity to our assumptions in the method, including considering structural uncertainty, and in the choice of models, and this leads to 95% probability of climate sensitivity mostly below 5K and only exceeding 6K in a single and most uncertain case assuming a large structural uncertainty. The approach is compared with other approaches based on OLS, a Kalman filter method, and an alternative Bayesian method. An interesting implication of this work is that OLS-based emergent constraints on ECS generate tighter uncertainty estimates, in particular at the lower end, an artefact due to a flatter regression line in the case of lack of correlation. Although some fundamental challenges related to the use of emergent constraints remain, this paper provides a step towards a better foundation for their potential use in future probabilistic estimations of climate sensitivity.
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| 7. |
- Shi, Hao, et al.
(författare)
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Corrosion behavior of Al-containing MAX-phase coatings exposed to oxygen containing molten Pb at 600 degrees C
- 2022
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Ingår i: Corrosion Science. - : Elsevier. - 0010-938X .- 1879-0496. ; 201
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Tidskriftsartikel (refereegranskat)abstract
- Four types of MAX-phase coating samples (Cr2AlC, V2AlC, Ti2AlC, and Ti3AlC2), synthesized via physical vapor deposition and post-annealing of elemental multilayer films, have been investigated toward their potential corrosion protection in 10(-6) wt% oxygen-containing molten Pb for 3200 h at 600 degrees C. Three MAX-phase coatings (Cr2AlC, Ti2AlC, and Ti3AlC2) are corrosion resistant against the molten Pb, via formation of a protective oxide layer. Specifically, various oxide scales formed on each sample: an Al2O3 scale, containing a low amount of Cr2O3 was formed in case of the Cr2AlC coating; a mixed Al2O3 and TiO2 oxide scale was observed for both Ti2AlC and Ti3AlC2 coatings. A more complex mixed oxide layer consisting of VO2, V4O7, and Pb-3(VO4)(2) phases is formed on the V2AlC coating, while the MAX-phase coating was almost entirely consumed. According to their corrosion performance against oxygen containing molten Pb, the order of corrosion resistance is: Cr2AlC > Ti2AlC > Ti3AlC2 > V2AlC.
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| 8. |
- Telloni, Daniele, et al.
(författare)
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Observation and Modeling of the Solar Wind Turbulence Evolution in the Sub-Mercury Inner Heliosphere
- 2022
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Ingår i: Astrophysical Journal Letters. - : Institute of Physics Publishing (IOPP). - 2041-8205 .- 2041-8213. ; 938:2
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Tidskriftsartikel (refereegranskat)abstract
- This letter exploits the radial alignment between the Parker Solar Probe and BepiColombo in late 2022 February, when both spacecraft were within Mercury's orbit. This allows the study of the turbulent evolution, namely, the change in spectral and intermittency properties, of the same plasma parcel during its expansion from 0.11 to 0.33 au, a still unexplored region. The observational analysis of the solar wind turbulent features at the two different evolution stages is complemented by a theoretical description based on the turbulence transport model equations for nearly incompressible magnetohydrodynamics. The results provide strong evidence that the solar wind turbulence already undergoes significant evolution at distances less than 0.3 au from the Sun, which can be satisfactorily explained as due to evolving slab fluctuations. This work represents a step forward in understanding the processes that control the transition from weak to strong turbulence in the solar wind and in properly modeling the heliosphere.
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| 9. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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