| 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. |
- Yin, X., et al.
(författare)
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Vertical Sandwich Gate-All-Around Field-Effect Transistors with Self-Aligned High-k Metal Gates and Small Effective-Gate-Length Variation
- 2020
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Ingår i: IEEE Electron Device Letters. - : Institute of Electrical and Electronics Engineers Inc.. - 0741-3106 .- 1558-0563. ; 41:1, s. 8-11
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Tidskriftsartikel (refereegranskat)abstract
- A new type of vertical nanowire (NW)/nanosheet (NS) field-effect transistors (FETs), termed vertical sandwich gate-all-around (GAA) FETs (VSAFETs), is presented in this work. Moreover, an integration flow that is compatible with processes used in the mainstream industry is proposed for the VSAFETs. Si/SiGe epitaxy, isotropic quasi-atomic-layer etching (qALE), and gate replacement were used to fabricate pVSAFETs for the first time. Vertical GAA FETs with self-aligned high-k metal gates and a small effective-gate-length variation were obtained. Isotropic qALE, including Si-selective etching of SiGe, was developed to control the diameter/thickness of the NW/NS channels. NWs with a diameter of 10 nm and NSs with a thickness of 20 nm were successfully fabricated, and good device characteristics were obtained. Finally, the device performance was investigated and is discussed in this work. © 2019 IEEE.
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| 4. |
- He, Chengliang, et al.
(författare)
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Near infrared electron acceptors with a photoresponse beyond 1000 nm for highly efficient organic solar cells
- 2020
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Ingår i: Journal of Materials Chemistry A. - : ROYAL SOC CHEMISTRY. - 2050-7488 .- 2050-7496. ; 8:35, s. 18154-18161
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Tidskriftsartikel (refereegranskat)abstract
- Developing near infrared (NIR) organic semiconductors is indispensable for promoting the performance of organic solar cells (OSCs), but addressing the trade-off between voltage and current density thus achieving high efficiency with low energy loss is still an urgent challenge. Herein, NIR acceptors (H1, H2 and H3) with a photoresponse beyond 1000 nm were developed by conjugating dithienopyrrolobenzothiadiazole to 2-(5,6-difluoro-3-oxo-2,3-dihydro-1H-inden-1-ylidene)malononitrileviavaried alkyl thiophene bridges. It was found that the linear outward chains in thiophene bridges could mitigate both the conformation disorder of H3 and the electronic disorder of the PBDB-T:H3 blends, which could help to form a favorable blend morphology, facilitating highly efficient photoelectric conversion in the resultant OSCs. As a result, devices based on PBDB-T:H3 achieve a high efficiency of 13.75% with a low energy loss of 0.55 eV, which is one of the highest efficiencies and the lowest energy loss among OSCs with an optoelectronic response near 1000 nm. This work provides a new design strategy towards NIR acceptors for efficient OSCs and future exploration of functional optoelectronics.
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| 5. |
- Kristan, M., et al.
(författare)
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The Eighth Visual Object Tracking VOT2020 Challenge Results
- 2020
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Ingår i: Computer Vision. - Cham : Springer International Publishing. - 9783030682378 ; , s. 547-601
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2020 is the eighth annual tracker benchmarking activity organized by the VOT initiative. Results of 58 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The VOT2020 challenge was composed of five sub-challenges focusing on different tracking domains: (i) VOT-ST2020 challenge focused on short-term tracking in RGB, (ii) VOT-RT2020 challenge focused on “real-time” short-term tracking in RGB, (iii) VOT-LT2020 focused on long-term tracking namely coping with target disappearance and reappearance, (iv) VOT-RGBT2020 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2020 challenge focused on long-term tracking in RGB and depth imagery. Only the VOT-ST2020 datasets were refreshed. A significant novelty is introduction of a new VOT short-term tracking evaluation methodology, and introduction of segmentation ground truth in the VOT-ST2020 challenge – bounding boxes will no longer be used in the VOT-ST challenges. A new VOT Python toolkit that implements all these novelites was introduced. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net ).
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| 6. |
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| 7. |
- Thomas, Minta, et al.
(författare)
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Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk.
- 2020
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Ingår i: American Journal of Human Genetics. - Cambridge : Elsevier BV. - 0002-9297 .- 1537-6605. ; 107:3, s. 432-444
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Tidskriftsartikel (refereegranskat)abstract
- Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
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| 8. |
- He, Qi, et al.
(författare)
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Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis
- 2020
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 147:9, s. 2634-2644
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Tidskriftsartikel (refereegranskat)abstract
- Intravasation, vascular dissemination and metastasis of malignant tumor cells require their passage through the vascular wall which is commonly composed of pericytes and endothelial cells. We currently decided to investigate the relative contribution of these cell types to B16F10 melanoma metastasis in mice using an experimental model of host Shb gene (Src homology 2 domain containing protein B) inactivation. Conditional inactivation of Shb in endothelial cells using Cdh5-CreERt2 resulted in decreased tumor growth, reduced vascular leakage, increased hypoxia and no effect on pericyte coverage and lung metastasis. RNAseq of tumor endothelial cells from these mice revealed changes in cellular components such as adherens junctions and focal adhesions by gene ontology analysis that were in line with the observed effects on leakage and junction morphology. Conditional inactivation of Shb in pericytes using Pdgfrb-CreERt2 resulted in decreased pericyte coverage of small tumor vessels with lumen, increased leakage, aberrant platelet-derived growth factor receptor B (PDGFRB) signaling and a higher frequency of lung metastasis without concomitant effects on tumor growth or oxygenation. Flow cytometry failed to reveal immune cell alterations that could explain the metastatic phenotype in this genetic model of Shb deficiency. It is concluded that proper pericyte function plays a significant role in suppressing B16F10 lung metastasis.
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| 9. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 10. |
- Li, Xiaofang, et al.
(författare)
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Roles of Acceptor Guests in Tuning the Organic Solar Cell Property Based on an Efficient Binary Material System with a Nearly Zero Hole-Transfer Driving Force
- 2020
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Ingår i: Chemistry of Materials. - : AMER CHEMICAL SOC. - 0897-4756 .- 1520-5002. ; 32:12, s. 5182-5191
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Tidskriftsartikel (refereegranskat)abstract
- Sub-picosecond hole transfer has been recently observed in several narrow band gap nonfullerene small-molecule acceptor (NFA)-based binary blended organic solar cell (OSC) systems operating with negligible energetic driving forces. As the driving forces are near zero, how the added acceptor/donor guests tune the barrier-free hole-transfer dynamics of these systems remains very unclear. In this study, we report a new NFA (BTCT-2Cl) that conducts a sub-picosecond hole transfer (2 ps) for efficient photocurrent generation when pairing with PM6 though the energetic offset is only 0.02 eV. We observe that the added nonfullerene and PCBM components differently tune the charge generation and recombination when selectively exciting BTCT-2Cl. After adding PC71BM, the hole transfer from the host BTCT-2Cl to the host donor is greatly accelerated, with the rate significantly reduced to 0.29 ps and the charge generation becomes more efficient; on the contrary, recombination is prolonged and a larger fill factor is obtained after adding an NFA guest, here, IT-4F. The different tuning on the host binary hole-transfer dynamics is likely related with the phase crystallinity and the domain size changed after adding different acceptor guests. Over 16% efficiency is obtained on the PC71BM-based ternary device that outperforms the host binary and the IT-4F-based ternary solar cells (both showing over 15% efficiencies). The results clearly demonstrate that adding PCBM or NFA guests enables a very effective and different tuning on the hole-transfer rates and the recombination rates between the barrier-free host binary components, hence leading to efficient tuning on the short-circuit current density and fill factor, which outlines new strategies toward designing high-efficiency ternary blended OSC systems.
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