| 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. |
- Adyari, Bob, et al.
(författare)
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Strong impact of micropollutants on prokaryotic communities at the horizontal but not vertical scales in a subtropical reservoir, China
- 2020
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 721
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Tidskriftsartikel (refereegranskat)abstract
- Micropollutants have become of great concern, because of their disrupting effects on the structure and function of microbial communities. However, little is known about the relative importance of trace micropollutants on the aquatic prokaryotic communities as compared to the traditional physico-chemical characteristics, especially at different spatial dimensions. Here, we investigated free-living (FL) and particle-associated (PA) prokaryotic communities in a subtropical water reservoir, China, across seasons at horizontal (surface water) and vertical (depth-profile) scales by using 16S rRNA gene amplicon sequencing. Our results showed that the shared variances of physico-chemicals and micropollutants explained majority of the spatial variations in prokaryotic communities, suggesting a strong joint effect of the two abiotic categories on reservoir prokaryotic communities. Micropollutants appeared to exert strong independent influence on the core sub-communities (i.e., abundant and wide-spread taxa) than on the satellite (i.e., less abundant and narrow-range taxa) counterparts. The pure effect of micropollutants on both core and satellite sub-communities from FL and PA fractions was similar to 1.5 folds greater than that of physico-chemical factors at the horizontal scale, whereas an opposite effect was observed at the vertical scale. Moreover, eight micropollutants including anti-fungal agents, antibiotics, bisphenol analogues, stimulant and UV-filter were identified as the major disrupting compounds with strong associations with core taxa of typical freshwater prokaryotes. Altogether, we concluded that the ecological disrupting effects of micropollutants on prokaryotic communities may vary along horizontal and vertical dimensions in freshwater ecosystems.
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| 4. |
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| 5. |
- Sun, Gang, et al.
(författare)
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Low-latency and Resource-efficient Service Function Chaining Orchestration in Network Function Virtualization
- 2020
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Ingår i: IEEE Internet of Things Journal. - : IEEE. - 2327-4662. ; 7:7, s. 5760-5772
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Tidskriftsartikel (refereegranskat)abstract
- Recently, network function virtualization (NFV) has been proposed to solve the dilemma faced by traditional networks and to improve network performance through hardware and software decoupling. The deployment of the service function chain (SFC) is a key technology that affects the performance of virtual network function (VNF). The key issue in the deployment of SFCs is proposing effective algorithms to achieve efficient use of resources. In this paper, we propose a service function chain deployment optimization (SFCDO) algorithm based on a breadth-first search (BFS). The algorithm first uses a BFS based algorithm to find the shortest path between the source node and the destination node. Then, based on the shortest path, the path with the fewest hops is preferentially chosen to implement the SFC deployment. Finally, we compare the performances with the greedy and simulated annealing (G-SA) algorithm. The experiment results show that the proposed algorithm is optimized in terms of end-to-end delay and bandwidth resource consumption. In addition, we also consider the load rate of the nodes to achieve network load balancing.
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| 6. |
- Tang, Yumin, et al.
(författare)
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Two Compatible Polymer Donors Enabling Ternary Organic Solar Cells with a Small Nonradiative Energy Loss and Broad Composition Tolerance
- 2020
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Ingår i: Solar RRL. - : Wiley-VCH Verlagsgesellschaft. - 2367-198X. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- High-performance nonfullerene ternary organic solar cells (OSCs) with two polymer donors are less frequently reported because of the limited numbers of efficient polymer donors with good compatibility. Herein, a wide-bandgap polymer P1 with a deep-lying highest occupied molecular orbital (HOMO) level is incorporated as the third component into the benchmark PM6:Y6 binary system to fabricate ternary OSCs. The introduction of P1 not only leads to extended absorption coverage and forms a cascade-like energy level alignment but also shows excellent compatibility with PM6, resulting in a favorable morphology in the ternary blend. More importantly, P1 possesses a deeper HOMO level (-5.6 eV) than most well-known donor polymers, which enables resulting ternary OSCs with an improved open-circuit voltage. As a result, the optimized ternary OSCs with 40 wt% P1 in donors achieve a power conversion efficiency (PCE) of 16.2% with a small nonradiative recombination loss of 0.23 eV, which is among the highest values of ternary OSCs based on two polymer donors. In addition, the ternary OSCs show a broad composition tolerance with a high PCE of over 14% throughout the whole blend ratios. These results provide an effective approach to fabricate efficient ternary OSCs by synergizing two wide-bandgap polymer donors.
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