| 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. |
- Bhat, Goutam, et al.
(författare)
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NTIRE 2022 Burst Super-Resolution Challenge
- 2022
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Ingår i: 2022 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW 2022). - : IEEE. - 9781665487399 - 9781665487405 ; , s. 1040-1060
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Konferensbidrag (refereegranskat)abstract
- Burst super-resolution has received increased attention in recent years due to its applications in mobile photography. By merging information from multiple shifted images of a scene, burst super-resolution aims to recover details which otherwise cannot be obtained using a simple input image. This paper reviews the NTIRE 2022 challenge on burst super-resolution. In the challenge, the participants were tasked with generating a clean RGB image with 4x higher resolution, given a RAW noisy burst as input. That is, the methods need to perform joint denoising, demosaicking, and super-resolution. The challenge consisted of 2 tracks. Track 1 employed synthetic data, where pixel-accurate high-resolution ground truths are available. Track 2 on the other hand used real-world bursts captured from a handheld camera, along with approximately aligned reference images captured using a DSLR. 14 teams participated in the final testing phase. The top performing methods establish a new state-of-the-art on the burst super-resolution task.
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| 3. |
- 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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| 4. |
- Guo, Hui-Hui, et al.
(författare)
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Alleviation of allergic asthma by rosmarinic acid via gut-lung axis
- 2024
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Ingår i: Phytomedicine. - : Elsevier. - 0944-7113 .- 1618-095X. ; 126
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Tidskriftsartikel (refereegranskat)abstract
- Background: Asthma affects 3% of the global population, leading to over 0.25 million deaths. Due to its complexity, asthma is difficult to cure or prevent, and current therapies have limitations. This has led to a growing demand for alternative asthma treatments. We found rosmarinic acid (RosA) as a potential new drug candidate from natural medicine. However, RosA has poor bioavailability and remains mainly in the gastrointestinal tract after oral administration, suggesting the involvement of gut microbiota in its bioactivity. Purpose: To investigate the mechanism of RosA in alleviating allergic asthma by gut-lung axis. Methods: We used 16S rRNA gene sequencing and metabolites analysis to investigate RosA's modulation of gut microbiota. Techniques of molecular biology and metabolomics were employed to study the pharmacological mechanism of RosA. Cohousing was used to confirm the involvement of gut microbiota in RosA-induced improvement of allergic asthma. Results: RosA decreased cholate levels from spore-forming bacteria, leading to reduced 5-hydroxytryptamine (5HT) synthesis, bronchoconstriction, vasodilation, and inflammatory cell infiltration. It also increased short-chain fatty acids (SCFAs) levels, facilitating the expression of intestinal tight junction proteins to promote intestinal integrity. SCFAs upregulated intestinal monocarboxylate transporters (MCTs), thereby improving their systemic delivery to reduce Th2/ILC2 mediated inflammatory response and suppress eosinophil influx and mucus production in lung. Additionally, RosA inhibited lipopolysaccharide (LPS) production and translocation, leading to reduced TLR4-NF kappa B mediated pulmonary inflammation and oxidative stress. Conclusions: The anti-asthmatic mechanism of oral RosA is primarily driven by modulation of gut microbiotaderived 5-HT, SCFAs, and LPS, achieving a combined synergistic effect. RosA is a safe, effective, and reliable drug candidate that could potentially replace glucocorticoids for asthma treatment.
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| 5. |
- Shen, Shen, et al.
(författare)
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Edible Long-Afterglow Photoluminescent Materials for Bioimaging
- 2024
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Ingår i: Advanced Materials. - : WILEY-V C H VERLAG GMBH. - 0935-9648 .- 1521-4095.
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Tidskriftsartikel (refereegranskat)abstract
- Confining luminophores into modified hydrophilic matrices or polymers is a straightforward and widely used approach for afterglow bioimaging. However, the afterglow quantum yield and lifetime of the related material remain unsatisfactory, severely limiting the using effect especially for deep-tissue time-resolved imaging. This fact largely stems from the dilemma between material biocompatibility and the quenching effect of water environment. Herein an in situ metathesis promoted doping strategy is presented, namely, mixing approximate to 10-3 weight ratio of organic-emitter multicarboxylates with inorganic salt reactants, followed by metathesis reactions to prepare a series of hydrophilic but water-insoluble organic-inorganic doping afterglow materials. This strategy leads to the formation of edible long-afterglow photoluminescent materials with superior biocompatibility and excellent bioimaging effect. The phosphorescence quantum yield of the materials can reach dozens of percent (the highest case: 66.24%), together with the photoluminescent lifetime lasting for coupes of seconds. Specifically, a long-afterglow barium meal formed by coronene salt emitter and BaSO4 matrix is applied into animal experiments by gavage, and bright stomach afterglow imaging is observed by instruments or mobile phone after ceasing the photoexcitation with deep tissue penetration. This strategy allows a flexible dosage of the materials during bioimaging, facilitating the development of real-time probing and theranostic technology. A universal strategy is proposed to construct edible photoluminescent long-afterglow materials by embedding luminophore multicarboxylates into a series of inorganic salt lattices. Particularly, edible afterglow barium meal formed by coronene salt doped BaSO4 can be applied into gastrointestinal afterglow imaging captured by instruments or mobile phone. image
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| 6. |
- Byun, Jinyoung, et al.
(författare)
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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer
- 2022
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Ingår i: Nature Genetics. - : Nature Research. - 1061-4036 .- 1546-1718. ; 54:8, s. 1167-1177
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Tidskriftsartikel (refereegranskat)abstract
- To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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| 7. |
- Chen, Feiyang, et al.
(författare)
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Cambrian ecological complexities: Perspectives from the earliest brachiopod – supported benthic communities in the early Cambrian Guanshan Lagerstätte
- 2022
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Ingår i: Gondwana Research. - Amsterdam : Elsevier. - 1342-937X .- 1878-0571. ; 107, s. 30-41
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Tidskriftsartikel (refereegranskat)abstract
- The Cambrian radiation is characterized by the emergence of diverse bilaterian animal phyla and theestablishment of complex marine ecosystems. The Guanshan Biota records an unusual ecological transition from trilobite- to brachiopod-dominated communities during Cambrian Stage 4. This community transition is accompanied by direct evidence of in situ biological interactions such as durophagous pre-dation and kleptoparasitism. Here we describe new material from the Guanshan biota, focusing on an association of palaeoscolecidomorphs and brachiopods with parasitic tube worms that occur on micro-bedding planes. The bedding plane assemblages are dominated by the organophosphatic brachiopod Neobolus wulongqingensis encrusted with kleptoparasitic tube-dwelling worms, along with infaunal palaeoscolecidans. Taphonomic and sedimentological evidence indicates that these specimens are com-monly preserved in life position, and thus the association between individuals represent potential biological interactions. This case study reveals that ecosystems during the early Cambrian exhibited a well-developed system of tiering and a complex trophic network, easily distinguished from the simple communities typical of precursor deposits in the Ediacaran. Brachiopods forming extremely dense concentrations on the sea floor are effectively acting as ecosystem engineers, not only to stabilize the soft-substrate seafloor, but also act as an alternative substrate for the oldest empirically demonstrated kleptoparasites.The in situ biological interactions preserved in the Guanshan Biota are critical for filling gaps in ourknowledge of ecosystem complexity in the Cambrian.
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| 8. |
- Cheng, Chao, et al.
(författare)
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Mosaic chromosomal alterations are associated with increased lung cancer risk : insight from the INTEGRAL-ILCCO cohort analysis
- 2023
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Ingår i: Journal of Thoracic Oncology. - : Elsevier. - 1556-0864 .- 1556-1380.
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. Methods: In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. Results: We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. Conclusions: Our study established a link between mCAs in white blood cells and increased risk of lung cancer.
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| 9. |
- Chuan, Ting, et al.
(författare)
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Asynchronous changes in terrestrial near-surface wind speed among regions across China from 1973 to 2017
- 2024
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Ingår i: Atmospheric Research. - 0169-8095. ; 300
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the characteristics and causes of asynchronous changes in near-surface wind speed (NSWS) improves the ability of climate projection, but yet to be comprehended are the asynchronous features in NSWS and possible causes over China. In this study, the asynchronous variations in NSWS among regions are considerable across China. The non-synchronization of variations in intra-annual NSWS was manifested in the amplitudes and periods of NSWS. The amplitudes and periods of intra-annual NSWS among regions were in the ranges of 0.08–0.20 m s−1 and 0.24–0.32 years, respectively. The intra-annual changes in NSWS in different regions were influenced by different large–scale ocean–atmosphere circulations (LOACs). The non-synchronization of variations in interannual NSWS was also manifested in the amplitudes and periods of NSWS, and the strongest and weakest interannual variations in NSWS occurred over northeast and northwest China. The interannual variations in NSWS could be induced by El Niño–Southern Oscillation (ENSO). At intra-annual and interannual scales, LOACs mainly controlled the changes in the phase of NSWS, which could not be responsible for the amplitudes of NSWS. The interdecadal NSWS also showed regional differences, and it mainly exhibited an increase after the 1990s in all regions except for South China. The interdecadal changes in NSWS among regions were also dominated by LOACs, which contributed reached 50.0% to the NSWS changes. Furthermore, the LOACs dominated not only the changes in the phase of interdecadal NSWS but also the changes in amplitudes of interdecadal NSWS.
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| 10. |
- Du, Mulong, et al.
(författare)
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Cyp2a6 activity and cigarette consumption interact in smoking-related lung cancer susceptibility
- 2024
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Ingår i: Cancer Research. - : American Association For Cancer Research (AACR). - 0008-5472 .- 1538-7445. ; 84:4, s. 616-625
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Tidskriftsartikel (refereegranskat)abstract
- Cigarette smoke, containing both nicotine and carcinogens, causes lung cancer. However, not all smokers develop lung cancer, highlighting the importance of the interaction between host susceptibility and environmental exposure in tumorigenesis. Here, we aimed to delineate the interaction between metabolizing ability of tobacco carcinogens and smoking intensity in mediating genetic susceptibility to smoking-related lung tumorigenesis. Single-variant and gene-based associations of 43 tobacco carcinogen–metabolizing genes with lung cancer were analyzed using summary statistics and individual-level genetic data, followed by causal inference of Mendelian randomization, mediation analysis, and structural equation modeling. Cigarette smoke–exposed cell models were used to detect gene expression patterns in relation to specific alleles. Data from the International Lung Cancer Consortium (29,266 cases and 56,450 controls) and UK Biobank (2,155 cases and 376,329 controls) indicated that the genetic variant rs56113850 C>T located in intron 4 of CYP2A6 was significantly associated with decreased lung cancer risk among smokers (OR = 0.88, 95% confidence interval = 0.85–0.91, P = 2.18 X 10-16), which might interact (Pinteraction = 0.028) with and partially be mediated (ORindirect = 0.987) by smoking status. Smoking intensity accounted for 82.3% of the effect of CYP2A6 activity on lung cancer risk but entirely mediated the genetic effect of rs56113850. Mechanistically, the rs56113850 T allele rescued the downregulation of CYP2A6 caused by cigarette smoke exposure, potentially through preferential recruitment of transcription factor helicase-like transcription factor. Together, this study provides additional insights into the interplay between host susceptibility and carcinogen exposure in smoking-related lung tumorigenesis.
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