| 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. |
- Chen, Chao, et al.
(författare)
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Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients
- 2020
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Ingår i: Aging. - : Impact Journals, LLC. - 1945-4589. ; 12:11, s. 10642-10662
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Tidskriftsartikel (refereegranskat)abstract
- DNA methylation changes during aging, but it remains unclear whether the effect of DNA methylation on lung cancer survival varies with age. Such an effect could decrease prediction accuracy and treatment efficacy. We performed a methylation-age interaction analysis using 1,230 early-stage lung adenocarcinoma patients from five cohorts. A Cox proportional hazards model was used to investigate lung adenocarcinoma and squamous cell carcinoma patients for methylation-age interactions, which were further confirmed in a validation phase. We identified one adenocarcinoma-specific CpG probe, cg14326354PRODH, with effects significantly modified by age (HRinteraction = 0.989; 95% CI: 0.986-0.994; P = 9.18×10-7). The effect of low methylation was reversed for young and elderly patients categorized by the boundary of 95% CI standard (HRyoung = 2.44; 95% CI: 1.26-4.72; P = 8.34×10-3; HRelderly = 0.58; 95% CI: 0.42-0.82; P = 1.67×10-3). Moreover, there was an antagonistic interaction between low cg14326354PRODH methylation and elderly age (HRinteraction = 0.21; 95% CI: 0.11-0.40; P = 2.20×10-6). In summary, low methylation of cg14326354PRODH might benefit survival of elderly lung adenocarcinoma patients, providing new insight to age-specific prediction and potential drug targeting.
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| 3. |
- Chen, Haiyang, et al.
(författare)
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A guest-assisted molecular-organization approach for >17% efficiency organic solar cells using environmentally friendly solvents
- 2021
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Ingår i: Nature Energy. - : NATURE PORTFOLIO. - 2058-7546. ; 6:11, s. 1045-1053
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Tidskriftsartikel (refereegranskat)abstract
- The power conversion efficiencies (PCEs) of laboratory-sized organic solar cells (OSCs), usually processed from low-boiling-point and toxic solvents, have reached high values of over 18%. However, there is usually a notable drop of the PCEs when green solvents are used, limiting practical development of OSCs. Herein, we obtain certificated PCEs over 17% in OSCs processed from a green solvent paraxylene (PX) by a guest-assisted assembly strategy, where a third component (guest) is employed to manipulate the molecular interaction of the binary blend. In addition, the high-boiling-point green solvent PX also enables us to deposit a uniform large-area module (36 cm(2)) with a high efficiency of over 14%. The strong molecular interaction between the host and guest molecules also enhances the operational stability of the devices. Our guest-assisted assembly strategy provides a unique approach to develop large-area and high-efficiency OSCs processed from green solvents, paving the way for industrial development of OSCs. Organic solar cells processed from green solvents are easier to implement in manufacturing yet their efficiency is low. Chen et al. devise a guest molecule to improve the molecular packing, enabling devices with over 17% efficiency.
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| 4. |
- He, Bin, et al.
(författare)
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Worldwide impacts of atmospheric vapor pressure deficit on the interannual variability of terrestrial carbon sinks
- 2022
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Ingår i: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Interannual variability of the terrestrial ecosystem carbon sink is substantially regulated by various environmental variables and highly dominates the interannual variation of atmospheric carbon dioxide (CO2) concentrations. Thus, it is necessary to determine dominating factors affecting the interannual variability of the carbon sink to improve our capability of predicting future terrestrial carbon sinks. Using global datasets derived from machine-learning methods and process-based ecosystem models, this study reveals that the interannual variability of the atmospheric vapor pressure deficit (VPD) was significantly negatively correlated with net ecosystem production (NEP) and substantially impacted the interannual variability of the atmospheric CO2 growth rate (CGR). Further analyses found widespread constraints of VPD interannual variability on terrestrial gross primary production (GPP), causing VPD to impact NEP and CGR. Partial correlation analysis confirms the persistent and widespread impacts of VPD on terrestrial carbon sinks compared to other environmental variables. Current Earth system models underestimate the interannual variability in VPD and its impacts on GPP and NEP. Our results highlight the importance of VPD for terrestrial carbon sinks in assessing ecosystems' responses to future climate conditions.
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| 5. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 6. |
- Kristan, Matej, et al.
(författare)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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Ingår i: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 7. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 8. |
- Wang, Sifan, et al.
(författare)
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Fire carbon emissions over Equatorial Asia reduced by shortened dry seasons
- 2023
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Ingår i: npj Climate and Atmospheric Science. - 2397-3722. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Fire carbon emissions over Equatorial Asia (EQAS) play a critical role in the global carbon cycle. Most regional fire emissions (89.0%) occur in the dry season, but how changes in the dry-season length affect the fire emissions remains poorly understood. Here we show that, the length of the EQAS dry season has decreased significantly during 1979–2021, and the delayed dry season onset (5.4 ± 1.6 (± one standard error) days decade−1) due to increased precipitation (36.4 ± 9.1 mm decade−1) in the early dry season is the main reason. The dry season length is strongly correlated with the length of the fire season. Increased precipitation during the early dry season led to a significant reduction (May: −0.7 ± 0.4 Tg C decade−1; August: −12.9 ± 6.7 Tg C decade−1) in fire carbon emissions during the early and peak fire season. Climate models from the Coupled Model Intercomparison Project Phase 6 project a continued decline in future dry season length in EQAS under medium and high-emission scenarios, implying further reductions in fire carbon emissions.
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| 9. |
- Zhang, Ruyang, et al.
(författare)
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Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects
- 2020
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Ingår i: Chest. - : Elsevier BV. - 0012-3692. ; 158:2, s. 808-819
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Tidskriftsartikel (refereegranskat)abstract
- Background: DNA methylation and gene expression are promising biomarkers of various cancers, including non-small cell lung cancer (NSCLC). Besides the main effects of biomarkers, the progression of complex diseases is also influenced by gene-gene (G×G) interactions. Research Question: Would screening the functional capacity of biomarkers on the basis of main effects or interactions, using multiomics data, improve the accuracy of cancer prognosis? Study Design and Methods: Biomarker screening and model validation were used to construct and validate a prognostic prediction model. NSCLC prognosis-associated biomarkers were identified on the basis of either their main effects or interactions with two types of omics data. A prognostic score incorporating epigenetic and transcriptional biomarkers, as well as clinical information, was independently validated. Results: Twenty-six pairs of biomarkers with G×G interactions and two biomarkers with main effects were significantly associated with NSCLC survival. Compared with a model using clinical information only, the accuracy of the epigenetic and transcriptional biomarker-based prognostic model, measured by area under the receiver operating characteristic curve (AUC), increased by 35.38% (95% CI, 27.09%-42.17%; P = 5.10 × 10–17) and 34.85% (95% CI, 26.33%-41.87%; P = 2.52 × 10–18) for 3- and 5-year survival, respectively, which exhibited a superior predictive ability for NSCLC survival (AUC3 year, 0.88 [95% CI, 0.83-0.93]; and AUC5 year, 0.89 [95% CI, 0.83-0.93]) in an independent Cancer Genome Atlas population. G×G interactions contributed a 65.2% and 91.3% increase in prediction accuracy for 3- and 5-year survival, respectively. Interpretation: The integration of epigenetic and transcriptional biomarkers with main effects and G×G interactions significantly improves the accuracy of prognostic prediction of early-stage NSCLC survival.
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| 10. |
- Huang, Yuting, et al.
(författare)
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Host-Guest Strategy Enabling Nonhalogenated Solvent Processing for High-Performance All-Polymer Hosted Solar Cells
- 2023
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Ingår i: Chinese journal of chemistry. - : WILEY-V C H VERLAG GMBH. - 1001-604X .- 1614-7065. ; 41:9, s. 1066-1074
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Tidskriftsartikel (refereegranskat)abstract
- The power conversion efficiencies (PCEs) of all-polymer solar cells (all-PSCs), usually processed from low-boiling-point and toxic solvents, have reached high values of 18%. However, poor miscibility and uncontrollable crystallinity in polymer blends lead to a notable drop in the PCEs when using green solvents, limiting the practical development of all-PSCs. Herein, a third component (guest) BTO was employed to optimize the miscibility and enhance the crystallinity of PM6/PY2Se-F host film processed from green solvent toluene (TL), which can effectively suppress the excessive aggregation of PY2Se-F and facilitate a nano-scale interpenetrating network morphology for exciton dissociation and charge transport. As a result, TL-processed all-polymer hosted solar cells (all-PHSCs) exhibited an impressive PCE of 17.01%. Moreover, the strong molecular interaction between the host and guest molecules also enhances the thermal stability of the devices. Our host-guest strategy provides a unique approach to developing high-efficiency and stable all-PHSCs processed from green solvents, paving the way for the industrial development of all-PHSCs.
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