| 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. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 4. |
- 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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| 5. |
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| 6. |
- 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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| 7. |
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| 8. |
- Davies, Stuart J., et al.
(författare)
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ForestGEO: Understanding forest diversity and dynamics through a global observatory network
- 2021
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207. ; 253
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Tidskriftsartikel (refereegranskat)abstract
- ForestGEO is a network of scientists and long-term forest dynamics plots (FDPs) spanning the Earth's major forest types. ForestGEO's mission is to advance understanding of the diversity and dynamics of forests and to strengthen global capacity for forest science research. ForestGEO is unique among forest plot networks in its large-scale plot dimensions, censusing of all stems ≥1 cm in diameter, inclusion of tropical, temperate and boreal forests, and investigation of additional biotic (e.g., arthropods) and abiotic (e.g., soils) drivers, which together provide a holistic view of forest functioning. The 71 FDPs in 27 countries include approximately 7.33 million living trees and about 12,000 species, representing 20% of the world's known tree diversity. With >1300 published papers, ForestGEO researchers have made significant contributions in two fundamental areas: species coexistence and diversity, and ecosystem functioning. Specifically, defining the major biotic and abiotic controls on the distribution and coexistence of species and functional types and on variation in species' demography has led to improved understanding of how the multiple dimensions of forest diversity are structured across space and time and how this diversity relates to the processes controlling the role of forests in the Earth system. Nevertheless, knowledge gaps remain that impede our ability to predict how forest diversity and function will respond to climate change and other stressors. Meeting these global research challenges requires major advances in standardizing taxonomy of tropical species, resolving the main drivers of forest dynamics, and integrating plot-based ground and remote sensing observations to scale up estimates of forest diversity and function, coupled with improved predictive models. However, they cannot be met without greater financial commitment to sustain the long-term research of ForestGEO and other forest plot networks, greatly expanded scientific capacity across the world's forested nations, and increased collaboration and integration among research networks and disciplines addressing forest science.
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| 9. |
- Hong, Kuo Bin, et al.
(författare)
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Monolithic high-index contrast grating mirror for a GaN-based vertical-cavity surface-emitting laser
- 2021
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Ingår i: Photonics Research. - 2327-9125. ; 9:11, s. 2214-2221
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, a pulsed electrically pumped GaN-based vertical-cavity surface-emitting laser (VCSEL) with one dielectric distributed Bragg reflector and one n-GaN monolithic high-index contrast grating (MHCG) mirror was demonstrated at room temperature. The reflectance of the n-GaN MHCG and cavity mode behaviors of the VCSEL with MHCG for varying n-GaN thickness, MHCG pattern diameter, and current aperture size were numerically investigated. Measured characteristics of the fabricated device showed that the lasing action started at an injection current of 10.2 mA, corresponding to a current density of about 15.1 kA=cm2. Above threshold, the measured slope efficiency was 6.2 × 10−3 W∕A, and the output power was 0.13 mW at 30 mA. Moreover, the measured lasing peak occurring at 403.4 nm and the longitudinal mode spacing of 5.6 nm were in good agreement with simulations. The incorporation of an n-GaN MHCG mirror not only greatly simplified the fabrication but also substantially improved the lasing characteristics in comparison to the previous work applying TiO2 HCG mirrors.
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| 10. |
- Pang, Kanglei, 1993-, et al.
(författare)
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Redirecting configuration of atomically dispersed selenium catalytic sites for efficient hydrazine oxidation
- 2024
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Ingår i: Matter. - 2590-2393 .- 2590-2385. ; 7:2, s. 655-667
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the reconstruction of surface sites is crucial for gaining insights into the true active sites and catalytic mechanisms. While extensive research has been conducted on reconstruction behaviors of atomically dispersed metallic catalytic sites, limited attention has been paid to non-metallic ones despite their potential catalytic activity comparable or even superior to their noble-metal counterpart. Herein, we report a carbonaceous, atomically dispersed non-metallic selenium catalyst that displayed exceptional catalytic activity in the hydrazine oxidation reaction (HzOR) in alkaline media, outperforming the noble-metal Pt catalysts. In situ X-ray absorption spectroscopy (XAS) and Fourier transform infrared spectroscopy revealed that the pristine SeC4 site pre-adsorbs an ∗OH ligand, followed by HzOR occurring on the other side of the OH–SeC4. Theoretical calculations proposed that the pre-adsorbed ∗OH group pulls electrons from the Se site, resulting in a more positively charged Se and a higher polarity of Se–C bonds, thereby enhancing surface reactivity toward HzO/R.
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