| 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. |
- Chang, Tsu Chi, et al.
(författare)
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Electrically Injected GaN-Based Vertical-Cavity Surface-Emitting Lasers with TiO2 High-Index-Contrast Grating Reflectors
- 2020
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Ingår i: ACS Photonics. - : American Chemical Society (ACS). - 2330-4022. ; 7:4, s. 861-866
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate the first electrically injected GaN-based vertical-cavity surface-emitting lasers (VCSELs) with a TiO2 high-index-contrast grating (HCG) as the top mirror. Replacing the top distributed Bragg reflector (DBR) with an HCG offers substantial thickness reduction, polarization-pinning, and setting of the resonance wavelength by the grating parameters. Conventional HCGs are usually suspended in the low refractive index material, such as air, in order to create the largest refractive index contrast. However, the mechanical stability of such structures can be questioned and creating free-hanging GaN-membrane on top of GaN is problematic. We have therefore fabricated TiO2-HCGs resting directly on GaN without an air-gap. No DBR layers are used below the HCG to boost the reflectivity. A VCSEL with an aperture diameter of 10 μm shows a threshold current of 25 mA under pulsed operation at room temperature. The lasing modes locate around 400 nm and are transversely electrically -polarized with a line width of 0.5 nm. The full-width half-maximum beam divergence is 10°. This demonstration of a TiO2-HCG VCSEL offers a new route to achieve polarization pinning and could also allow additional benefits such as postgrowth setting of the resonance wavelength.
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| 4. |
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| 5. |
- Cai, Jing, et al.
(författare)
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Size-segregated particle number and mass concentrations from different emission sources in urban Beijing
- 2020
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:21, s. 12721-12740
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Tidskriftsartikel (refereegranskat)abstract
- Although secondary particulate matter is reported to be the main contributor of PM2.5 during haze in Chinese megacities, primary particle emissions also affect particle concentrations. In order to improve estimates of the contribution of primary sources to the particle number and mass concentrations, we performed source apportionment analyses using both chemical fingerprints and particle size distributions measured at the same site in urban Beijing from April to July 2018. Both methods resolved factors related to primary emissions, including vehicular emissions and cooking emissions, which together make up 76% and 24% of total particle number and organic aerosol (OA) mass, respectively. Similar source types, including particles related to vehicular emissions (1.6 +/- 1.1 mu gm(-3); 2.4 +/- 1.8 x 10(3) cm(-3) and 5.5 +/- 2.8 x 10(3) cm(-3) for two traffic-related components), cooking emissions (2.6 +/- 1.9 mu gm(-3) and 5.5 +/- 3.3 x 10(3) cm(-3)) and secondary aerosols (51 +/- 41 mu gm(-3) and 4.2 +/- 3.0 x 10(3) cm(-3)), were resolved by both methods. Converted mass concentrations from particle size distributions components were comparable with those from chemical fingerprints. Size distribution source apportionment separated vehicular emissions into a component with a mode diameter of 20 nm (traffic-ultrafine) and a component with a mode diameter of 100 nm (traffic-fine). Consistent with similar day- and nighttime diesel vehicle PM2.5 emissions estimated for the Beijing area, traffic-fine particles, hydrocarbon-like OA (HOA, traffic-related factor resulting from source apportionment using chemical fingerprints) and black carbon (BC) showed similar diurnal patterns, with higher concentrations during the night and morning than during the afternoon when the boundary layer is higher. Traffic-ultrafine particles showed the highest concentrations during the rush-hour period, suggesting a prominent role of local gasoline vehicle emissions. In the absence of new particle formation, our re-sults show that vehicular-related emissions (14% and 30% for ultrafine and fine particles, respectively) and cooking-activity-related emissions (32 %) dominate the particle number concentration, while secondary particulate matter (over 80 %) governs PM2.5 mass during the non-heating season in Beijing.
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| 6. |
- Choi, M. J., et al.
(författare)
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An adipocyte-specific defect in oxidative phosphorylation increases systemic energy expenditure and protects against diet-induced obesity in mouse models
- 2020
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Ingår i: Diabetologia. - : Springer. - 0012-186X .- 1432-0428.
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Tidskriftsartikel (refereegranskat)abstract
- Aims/hypothesis: Mitochondrial oxidative phosphorylation (OxPhos) is essential for energy production and survival. However, the tissue-specific and systemic metabolic effects of OxPhos function in adipocytes remain incompletely understood. Methods: We used adipocyte-specific Crif1 (also known as Gadd45gip1) knockout (AdKO) mice with decreased adipocyte OxPhos function. AdKO mice fed a normal chow or high-fat diet were evaluated for glucose homeostasis, weight gain and energy expenditure (EE). RNA sequencing of adipose tissues was used to identify the key mitokines affected in AdKO mice, which included fibroblast growth factor 21 (FGF21) and growth differentiation factor 15 (GDF15). For in vitro analysis, doxycycline was used to pharmacologically decrease OxPhos in 3T3L1 adipocytes. To identify the effects of GDF15 and FGF21 on the metabolic phenotype of AdKO mice, we generated AdKO mice with global Gdf15 knockout (AdGKO) or global Fgf21 knockout (AdFKO). Results: Under high-fat diet conditions, AdKO mice were resistant to weight gain and exhibited higher EE and improved glucose tolerance. In vitro pharmacological and in vivo genetic inhibition of OxPhos in adipocytes significantly upregulated mitochondrial unfolded protein response-related genes and secretion of mitokines such as GDF15 and FGF21. We evaluated the metabolic phenotypes of AdGKO and AdFKO mice, revealing that GDF15 and FGF21 differentially regulated energy homeostasis in AdKO mice. Both mitokines had beneficial effects on obesity and insulin resistance in the context of decreased adipocyte OxPhos, but only GDF15 regulated EE in AdKO mice. Conclusions/interpretation: The present study demonstrated that the adipose tissue adaptive mitochondrial stress response affected systemic energy homeostasis via cell-autonomous and non-cell-autonomous pathways. We identified novel roles for adipose OxPhos and adipo-mitokines in the regulation of systemic glucose homeostasis and EE, which facilitated adaptation of an organism to local mitochondrial stress.
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| 7. |
- 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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| 8. |
- Doi, Yasuo, et al.
(författare)
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The JCMT BISTRO Survey: Magnetic Fields Associated with a Network of Filaments in NGC 1333
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 899:1
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Tidskriftsartikel (refereegranskat)abstract
- We present new observations of the active star formation region NGC 1333 in the Perseus molecular cloud complex from the James Clerk Maxwell Telescope B-Fields In Star-forming Region Observations (BISTRO) survey with the POL-2 instrument. The BISTRO data cover the entire NGC 1333 complex (∼1.5 pc ? 2 pc) at 0.02 pc resolution and spatially resolve the polarized emission from individual filamentary structures for the first time. The inferred magnetic field structure is complex as a whole, with each individual filament aligned at different position angles relative to the local field orientation. We combine the BISTRO data with low- and high- resolution data derived from Planck and interferometers to study the multiscale magnetic field structure in this region. The magnetic field morphology drastically changes below a scale of ∼1 pc and remains continuous from the scales of filaments (∼0.1 pc) to that of protostellar envelopes (∼0.005 pc or ∼1000 au). Finally, we construct simple models in which we assume that the magnetic field is always perpendicular to the long axis of the filaments. We demonstrate that the observed variation of the relative orientation between the filament axes and the magnetic field angles are well reproduced by this model, taking into account the projection effects of the magnetic field and filaments relative to the plane of the sky. These projection effects may explain the apparent complexity of the magnetic field structure observed at the resolution of BISTRO data toward the filament network.
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| 9. |
- Jo, Donghui, et al.
(författare)
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PST-24 : A Zeolite with Varying Intracrystalline Channel Dimensionality
- 2020
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 59:40, s. 17691-17696
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Tidskriftsartikel (refereegranskat)abstract
- Herein we report the synthesis, structure solution, and catalytic properties of PST-24, a novel channel-based medium-pore zeolite. This zeolite was synthesized via the excess fluoride approach. Electron diffraction shows that its structure is built by composite cas-zigzag (cas-zz) building chains, which are connected by double 5-ring (d5r) columns. While the cas-zz building chains are ordered in the PST-24 framework, the d5r columns adopt one of two possible arrangements; the two adjacent d5r columns are either at the same height or at different heights, denoted arrangements S and D, which can be regarded as open and closed valves that connect the channels, respectively. A framework with arrangement D only has a 2D 10-ring channel system, whereas that with arrangement S only contains 3D channels. In actual PST-24 crystals, the open and closed valves are almost randomly dispersed to yield a zeolite framework where the channel dimensionality varies locally from 2D to 3D.
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| 10. |
- Kivipelto, Miia, et al.
(författare)
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World-Wide FINGERS Network : A global approach to risk reduction and prevention of dementia
- 2020
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Ingår i: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 16:7, s. 1078-1094
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Tidskriftsartikel (refereegranskat)abstract
- Reducing the risk of dementia can halt the worldwide increase of affected people. The multifactorial and heterogeneous nature of late-onset dementia, including Alzheimer's disease (AD), indicates a potential impact of multidomain lifestyle interventions on risk reduction. The positive results of the landmark multidomain Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) support such an approach. The World-Wide FINGERS (WW-FINGERS), launched in 2017 and including over 25 countries, is the first global network of multidomain lifestyle intervention trials for dementia risk reduction and prevention. WW-FINGERS aims to adapt, test, and optimize the FINGER model to reduce risk across the spectrum of cognitive decline-from at-risk asymptomatic states to early symptomatic stages-in different geographical, cultural, and economic settings. WW-FINGERS aims to harmonize and adapt multidomain interventions across various countries and settings, to facilitate data sharing and analysis across studies, and to promote international joint initiatives to identify globally implementable and effective preventive strategies.
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