| 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. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 3. |
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| 4. |
- Cao, Hong Min, et al.
(författare)
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A long-lived compact jet in the black hole X-ray binary candidate AT2019wey
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 657
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Tidskriftsartikel (refereegranskat)abstract
- AT2019wey is a transient discovered by the Asteroid Terrestrial-impact Last Alert System survey in December of 2019. Follow-up optical, radio, and X-ray observations led to classification of this source as a Galactic black hole X-ray binary candidate. We carried out one-epoch 6.7 GHz European Very Long Baseline Interferometry Network and two-epoch multi-frequency (1.6, 4.5, 6.7 GHz) Very Long Baseline Array observations within a year after its discovery. These observations reveal a fading and flat-spectrum radio source with no discernible motion. These features suggest the detection of a compact jet. The source appears resolved at milliarcsecond scales, and the source angular size versus frequency trend is consistent with scatter broadening. This allows us to constrain the lower limit of the source distance to 6 kpc if the scattering medium is in a Galactic spiral arm. For a source location at greater than 3 kpc, the estimated upper limit of the peculiar velocity suggests the asymmetric natal kick may have occurred during the black hole formation stage.
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| 5. |
- Ao, Hong, et al.
(författare)
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Orbital climate variability on the northeastern Tibetan Plateau across the Eocene-Oligocene transition
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The first major build-up of Antarctic glaciation occurred in two consecutive stages across the Eocene-Oligocene transition (EOT): the EOT-1 cooling event at similar to 34.1-33.9Ma and the Oi-1 glaciation event at similar to 33.8-33.6Ma. Detailed orbital-scale terrestrial environmental responses to these events remain poorly known. Here we present magnetic and geochemical climate records from the northeastern Tibetan Plateau margin that are dated precisely from similar to 35.5 to 31Ma by combined magneto- and astro-chronology. These records suggest a hydroclimate transition at similar to 33.7Ma from eccentricity dominated cycles to oscillations paced by a combination of eccentricity, obliquity, and precession, and confirm that major Asian aridification and cooling occurred at Oi-1. We conclude that this terrestrial orbital response transition coincided with a similar transition in the marine benthic delta O-18 record for global ice volume and deep-sea temperature variations. The dramatic reorganization of the Asian climate system coincident with Oi-1 was, thus, a response to coeval atmospheric CO2 decline and continental-scale Antarctic glaciation. Marine records indicate a greenhouse to icehouse climate transition at similar to 34 million years ago, but how the climate changed within continental interiors at this time is less well known. Here, the authors show an orbital climate response shift with aridification on the northeastern Tibetan Plateau during this time.
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| 7. |
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| 8. |
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| 9. |
- Cheng, X-P, et al.
(författare)
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Compact Bright Radio-loud AGNs. III. A Large VLBA Survey at 43 GHz
- 2020
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Ingår i: Astrophysical Journal, Supplement Series. - : American Astronomical Society. - 1538-4365 .- 0067-0049. ; 247:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the results from the 43 GHz Very Long Baseline Array (VLBA) observations of 124 compact radio-loud active galactic nuclei (AGNs) that were conducted between 2014 November and 2016 May. The typical dimensions of the restoring beam in each image are about 0.5 mas x 0.2 mas. The highest resolution of 0.2 mas corresponds to a physical size of 0.02 pc for the lowest redshift source in the sample. The 43 GHz very long baseline interferometry (VLBI) images of 97 AGNs are presented for the first time. We study the source compactness on milliarcsecond and submilliarcsecond scales, and suggest that 95 sources in our sample are suitable for future space VLBI observations. By analyzing our data supplemented with other VLBA AGN surveys from the literature, we find that the core brightness temperature increases with increasing frequency below a break frequency similar to 7 GHz, and decreases between similar to 7 and 240 GHz but increases again above 240 GHz in the rest frame of the sources. This indicates that the synchrotron opacity changes from optically thick to thin. We also find a strong statistical correlation between radio and gamma-ray flux densities. Our correlation is tighter than those in the literature derived from lower-frequency VLBI data, suggesting that the gamma-ray emission is produced more cospatially with the 43 GHz VLBA core emission. This correlation can also be extrapolated to the unbeamed AGN population, implying that a universal gamma-ray production mechanism might be at work for all types of AGNs.
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| 10. |
- Cui, Yong, et al.
(författare)
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Single-Junction Organic Photovoltaic Cells with Approaching 18% Efficiency
- 2020
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Ingår i: Advanced Materials. - : WILEY-V C H VERLAG GMBH. - 0935-9648 .- 1521-4095. ; 32:19
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Tidskriftsartikel (refereegranskat)abstract
- Optimizing the molecular structures of organic photovoltaic (OPV) materials is one of the most effective methods to boost power conversion efficiencies (PCEs). For an excellent molecular system with a certain conjugated skeleton, fine tuning the alky chains is of considerable significance to fully explore its photovoltaic potential. In this work, the optimization of alkyl chains is performed on a chlorinated nonfullerene acceptor (NFA) named BTP-4Cl-BO (a Y6 derivative) and very impressive photovoltaic parameters in OPV cells are obtained. To get more ordered intermolecular packing, the n-undecyl is shortened at the edge of BTP-eC11 to n-nonyl and n-heptyl. As a result, the NFAs of BTP-eC9 and BTP-eC7 are synthesized. The BTP-eC7 shows relatively poor solubility and thus limits its application in device fabrication. Fortunately, the BTP-eC9 possesses good solubility and, at the same time, enhanced electron transport property than BTP-eC11. Significantly, due to the simultaneously enhanced short-circuit current density and fill factor, the BTP-eC9-based single-junction OPV cells record a maximum PCE of 17.8% and get a certified value of 17.3%. These results demonstrate that minimizing the alkyl chains to get suitable solubility and enhanced intermolecular packing has a great potential in further improving its photovoltaic performance.
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