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| 2. |
- 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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| 3. |
- 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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| 4. |
- Gu, Jian, et al.
(författare)
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Visualizing Material Processing via Photoexcitation-Controlled Organic-Phase Aggregation-Induced Emission
- 2021
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Ingår i: RESEARCH. - : American Association for the Advancement of Science (AAAS). - 2639-5274. ; 2021
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Tidskriftsartikel (refereegranskat)abstract
- Aggregation-induced emission (AIE) has been much employed for visualizing material aggregation and self-assembly. However, water is generally required for the preparation of the AIE aggregates, the operation of which limits numerous material processing behaviors. Employing hexathiobenzene-based small molecules, monopolymers, and block copolymers as different material prototypes, we herein achieve AIE in pure organic phases by applying a nonequilibrium strategy, photoexcitation-controlled aggregation. This strategy enabled a dynamic change of molecular conformation rather than chemical structure upon irradiation, leading to a continuous aggregation-dependent luminescent enhancement (up to similar to 200-fold increase of the luminescent quantum yield) in organic solvents. Accompanied by the materialization of the nonequilibrium strategy, photoconvertible self-assemblies with a steady-state characteristic can be achieved upon organic solvent processing. The visual monitoring with the luminescence change covered the whole solution-to-film transition, as well as the in situ photoprocessing of the solid-state materials.
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| 5. |
- Yue, Bingbing, et al.
(författare)
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Photoexcitation-Based Supramolecular Access to Full-Scale Phase-Diagram Structures through in situ Phase-Volume Ratio Phototuning
- 2022
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Ingår i: Angewandte Chemie International Edition. - : John Wiley & Sons. - 1433-7851 .- 1521-3773. ; 61:43
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Tidskriftsartikel (refereegranskat)abstract
- Controlling phase separation and transition plays a core role in establishing and maintaining the function of diverse self-assembled systems. However, it remains challenging to achieve wide-range continuous phase transition for dynamically producing a variety of assembled structures. Here, we developed a far-from-equilibrium system, upon the integration of photoexcitation-induced aggregation molecules and block copolymers, to establish an in situ phase-volume ratio photocontrol strategy. Thus, full-scale phase-diagram structures, from lamellar structure to gyroidal, cylindrical, and finally to a spherical one, can be accessed under different irradiation periods. Moreover, the phase transition was accompanied by considerable aggregation-induced phosphorescence and hydrophilicity/hydrophobicity change for building a functional surface. This strategy allows for a conceptual advance of accessing a wide range of distinct self-assembled structures and functions in real time.
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| 6. |
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| 7. |
- Gan, Yong, et al.
(författare)
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Association between alcohol consumption and the risk of stroke in middle-aged and older adults in China
- 2021
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Ingår i: Drug And Alcohol Dependence. - : Elsevier BV. - 0376-8716 .- 1879-0046. ; 229
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Tidskriftsartikel (refereegranskat)abstract
- Objective: This study aimed to investigate the association between alcohol consumption and the prevalence of stroke in Chinese adults aged 40 years and over.Method: We conducted a cross-sectional analysis among 113,573 Chinese adults aged >= 40 years in the China National Stroke Prevention Project (2014-2015) to examine correlations of alcohol consumption with the prevalence of stroke. Logistic regression models were used to calculate odds ratios (ORs) and 95% confidence intervals (CIs), controlling for various confounders, e.g., gender, age, smoking, physical activity and other health conditions.Results: Within the study population, a total of 12,753 stroke survivors were identified. The prevalence of light to moderate and of heavy alcohol consumption was 10.1% and 5.7% respectively. The multivariate logistic regression results show that light to moderate alcohol consumption was associated with reduced risk of stroke of all types [0.91 (95%CI: 0.85-0.97)] and of ischemic stroke [0.90 (0.84-0.97)]. No association was found between alcohol consumption and hemorrhagic stroke. Compared with abstainers, the adjusted ORs of all stroke were 0.83 (0.75-0.92) for those who drank 11-20 years, and no association was found between 1 and 10 years or over 20 years of drinking and risk of stroke.Conclusions: These results indicate that light to moderate alcohol consumption may be protective against all and ischemic stroke, and heavy drinking was not significantly associated with risk of all stroke in China. No association between alcohol consumption and hemorrhagic stroke was found.
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| 8. |
- Ji, Cheng, et al.
(författare)
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Crystallography of low Z material at ultrahigh pressure : Case study on solid hydrogen
- 2020
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Ingår i: Matter and Radiation at Extremes. - : American Institute of Physics (AIP). - 2468-2047 .- 2468-080X. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Diamond anvil cell techniques have been improved to allow access to the multimegabar ultrahigh-pressure region for exploring novel phenomena in condensed matter. However, the only way to determine crystal structures of materials above 100 GPa, namely, X-ray diffraction (XRD), especially for low Z materials, remains nontrivial in the ultrahigh-pressure region, even with the availability of brilliant synchrotron X-ray sources. In this work, we perform a systematic study, choosing hydrogen (the lowest X-ray scatterer) as the subject, to understand how to better perform XRD measurements of low Z materials at multimegabar pressures. The techniques that we have developed have been proved to be effective in measuring the crystal structure of solid hydrogen up to 254 GPa at room temperature [C. Ji et al., Nature 573, 558–562 (2019)]. We present our discoveries and experiences with regard to several aspects of this work, namely, diamond anvil selection, sample configuration for ultrahigh-pressure XRD studies, XRD diagnostics for low Z materials, and related issues in data interpretation and pressure calibration. We believe that these methods can be readily extended to other low Z materials and can pave the way for studying the crystal structure of hydrogen at higher pressures, eventually testing structural models of metallic hydrogen.
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| 9. |
- Ji, Xinyu, et al.
(författare)
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Epigenetic–smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
- 2020
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Ingår i: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 14:11, s. 2759-2774
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Tidskriftsartikel (refereegranskat)abstract
- Tripartite motif containing 27 (TRIM27) is highly expressed in lung cancer, including non-small-cell lung cancer (NSCLC). Here, we profiled DNA methylation of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tumours from 613 early-stage NSCLC patients and evaluated associations between CpG methylation of TRIM27 and overall survival. Significant CpG probes were confirmed in 617 samples from The Cancer Genome Atlas. The methylation of the CpG probe cg05293407TRIM27 was significantly associated with overall survival in patients with LUSC (HR = 1.65, 95% CI: 1.30–2.09, P = 4.52 × 10−5), but not in patients with LUAD (HR = 1.08, 95% CI: 0.87–1.33, P = 0.493). As incidence of LUSC is associated with higher smoking intensity compared to LUAD, we investigated whether smoking intensity impacted on the prognostic effect of cg05293407TRIM27 methylation in NSCLC. LUSC patients had a higher average pack-year of smoking (37.49LUAD vs 54.79LUSC, P = 1.03 × 10−19) and included a higher proportion of current smokers than LUAD patients (28.24%LUAD vs 34.09%LUSC, P = 0.037). cg05293407TRIM27 was significantly associated with overall survival only in NSCLC patients with medium–high pack-year of smoking (HR = 1.58, 95% CI: 1.26–1.96, P = 5.25 × 10−5). We conclude that cg05293407TRIM27 methylation is a potential predictor of LUSC prognosis, and smoking intensity may impact on its prognostic value across the various types of NSCLC.
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| 10. |
- Li, Lili, et al.
(författare)
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UV-protection and fluorescence properties of the exoskeleton obtained from a living diatom modified by an Eu3+-complex
- 2021
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Ingår i: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 9:31, s. 10005-10012
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Tidskriftsartikel (refereegranskat)abstract
- In this article, a natural biological porous material, from living diatoms, is used to prepare new UV-protection hybrid materials with an Eu3+-complex. By removing the organic protoplasm of living diatoms, the exoskeleton with a regular pore structure arrangement was obtained. The Eu3+-complex was chemically bonded to the exoskeleton modified by the silane coupling agent (3-aminopropyl)trimethoxy silane (APTMS). Compared with pure Eu3+-complexes, the fluorescence intensity of this hybrid material was increased by approximately 10 times. For illustrating its applications in the field of UV-protection, we mixed the USDU with polyacrylonitrile to produce flexible and transparent polymer films. The hybrid composite film (USDU@PAN) achieved partial absorption of ultraviolet light between 200 and 400 nm. At the same time, it also emits visible fluorescence and the intensity of the fluorescence is greatly increased. Therefore, the USDU@PAN film has wide application prospects in areas such as photoelectric sensors and UV-protection devices. More importantly, we transform natural organisms into materials with excellent optical properties. Therefore, it can be used in the field of UV-protection.
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