| 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. |
- Gong, Qingyuan, et al.
(författare)
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Exploring the power of social hub services
- 2019
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Ingår i: World wide web (Bussum). - : Springer Science and Business Media LLC. - 1386-145X .- 1573-1413. ; 22:6, s. 2825-2852
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Tidskriftsartikel (refereegranskat)abstract
- Given the diverse focuses of emerging online social networks (OSNs), it is common that a user has signed up on multiple OSNs. Social hub services, a.k.a., social directory services, help each user manage and exhibit her OSN accounts on one webpage. In this work, we conduct a data-driven study by crawling over one million user profiles from about.me, a representative online social hub service. Our study aims at gaining insights on cross-OSN social influence from the crawled data. We first analyze the composition of the social hub users. For each user, we collect her social accounts from her social hub webpage, and aggregate the content generated by these accounts on different OSNs to gain a comprehensive view of this user. According to our analysis, there is a high probability that a user would provide consistent information on different OSNs. We then explore the correlation between user activities on different OSNs, based on which we propose a cross-OSN social influence prediction model. With the model, we can accurately predict a user’s social influence on emerging OSNs, such as Instagram, Foursquare, and Flickr, based on her data published on well-established OSNs like Twitter.
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| 3. |
- Liu, Lei, et al.
(författare)
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Irreversible phase transitions of the multiferroic oxide Mn3TeO6 at high pressures
- 2022
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Ingår i: Applied Physics Letters. - : American Institute of Physics (AIP). - 0003-6951 .- 1077-3118. ; 121:4
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Tidskriftsartikel (refereegranskat)abstract
- Due to their large bandgaps, multiferroic oxides, the promising candidates for overcoming the disadvantages of metal-halide perovskites as light absorbers, have so far very limited use in solar cell applications. Previous investigations demonstrate that high pressure represents an efficient tool for tuning the bandgap of multiferroic Mn3TeO6 (MTO). However, the underlying mechanism of the giant bandgap reduction discovered in MTO remains unclear, which critically prevents the design of next-generation light absorbers. In this study, we performed in situ x-ray diffraction analyses on the structure evolution of MTO upon compression and decompression, discovering a sequence of irreversible phase transitions R(3)over bar -> C2/c -> P2(1)/n. The experimental results, supported by electronic structure calculations, show the shortening of Mn-O-Mn bonding, and, to a lower extent, the decrease in connectivity of octahedra across the phase transition, explain the giant bandgap reduction of MTO. These findings will facilitate the design and synthesis of next-generation light absorbers in solar cells.
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| 4. |
- Shen, Qian, et al.
(författare)
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The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis
- 2018
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Ingår i: Molecular Plant. - : Cell Press. - 1674-2052 .- 1752-9867. ; 11:6, s. 776-788
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Tidskriftsartikel (refereegranskat)abstract
- Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.
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| 5. |
- Zhang, Huai, et al.
(författare)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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Ingår i: Hepatology international. - 1936-0541.
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Tidskriftsartikel (refereegranskat)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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| 6. |
- Zhang, Juqing, et al.
(författare)
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Super-enhancers conserved within placental mammals maintain stem cell pluripotency
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:40
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Tidskriftsartikel (refereegranskat)abstract
- Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolu-tion in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in pla-cental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of plu-ripotency as well as species-specific modulation of the pluripotency-associated regula-tory networks in mammals.
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| 7. |
- Zhang, Wei, et al.
(författare)
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Balancing Adsorption, Catalysis, and Desorption in Cathode Catalyst For Li–S Batteries
- 2023
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Ingår i: Advanced Energy Materials. - 1614-6832 .- 1614-6840. ; 13:43
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Tidskriftsartikel (refereegranskat)abstract
- The complicated electrochemical catalytic conversion process of polysulfides in metal–sulfur batteries involves three steps: adsorption, catalysis, and desorption process. Even as huge efforts are made for the understanding of the separate steps (especially for the adsorption and catalysis process), research focusing on the entire process is still scarce. Herein, a series of cobalt phosphides (CoP, CoP2, and CoP3) is employed with identical hollow morphology as model electrocatalysts to investigate the significance of the desorption process and discuss the balancing among the adsorption, catalysis, and desorption of lithium polysulfides (LiPSs). The experimental data demonstrate that, compared to CoP and CoP3, CoP2 exhibits moderate adsorption of LiPSs, which enhances the reduction kinetics of S8 to Li2S and regulates the desorption of short-chain LiPSs. Theoretical calculations further confirm that CoP2 with moderate adsorption of LiPSs exhibits better redox kinetics of LiPSs compared to CoP and CoP3. Moderate adsorption enables the CoP2-based sulfur cathode to deliver excellent stability with 86% capacity retention (2.6 and 2.0 times higher than CoP and CoP3, respectively) over 1000 cycles at 1 C. All these results indicate that in the adsorption-catalysis-desorption chain for LiPSs, all steps need to be considered rather than just focusing on one step of the process.
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| 8. |
- Zhu, Zhenshuo, et al.
(författare)
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Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to define a pluripotency gene regulatory network
- 2021
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Ingår i: The FASEB Journal. - : John Wiley & Sons. - 0892-6638 .- 1530-6860. ; 35:6
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Tidskriftsartikel (refereegranskat)abstract
- The pluripotency gene regulatory network of porcine induced pluripotent stem cells(piPSCs), especially in epigenetics, remains elusive. To determine the biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder. By dissecting the dynamic change of H3K9 methylation during loss of pluripotency, we demonstrated that the H3K9 demethylases KDM3A and KDM3B regulated global H3K9me2/me3 level and that their co-depletion led to the collapse of the pluripotency gene regulatory network. Immunoprecipitation-mass spectrometry (IP-MS) provided evidence that KDM3A and KDM3B formed a complex to perform H3K9 demethylation. The genome-wide regulation analysis revealed that OCT4 (O) and SOX2 (S), the core pluripotency transcriptional activators, maintained the pluripotent state of piPSCs depending on the H3K9 hypomethylation. Further investigation revealed that O/S cooperating with histone demethylase complex containing KDM3A and KDM3B promoted pluripotency genes expression to maintain the pluripotent state of piPSCs. Together, these data offer a unique insight into the epigenetic pluripotency network of piPSCs.
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