| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Guo, Xingyi, et al.
(author)
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Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects
- 2020
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In: Gastroenterology. - : Elsevier. - 0016-5085 .- 1528-0012. ; 160:4, s. 1164-1178
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Journal article (peer-reviewed)abstract
- Background and Aims: Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes.Methods: Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted.Results: We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis.Conclusions: Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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| 3. |
- Zhang, Huai, et al.
(author)
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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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In: Hepatology international. - 1936-0541.
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Journal article (peer-reviewed)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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| 4. |
- Zhang, Juqing, et al.
(author)
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Super-enhancers conserved within placental mammals maintain stem cell pluripotency
- 2022
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In: 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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Journal article (peer-reviewed)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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| 5. |
- Lin, Qing-Fang, et al.
(author)
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A stable aluminosilicate zeolite with intersecting three-dimensional extra-large pores
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6575, s. 1605-1608
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Journal article (peer-reviewed)abstract
- Zeolites are crystalline porous materials with important industrial applications, including uses in catalytic and adsorption-separation processes. Access into and out of their inner confined space, where adsorption and reactions occur, is limited by their pore apertures. Stable multidimensional zeolites with larger pores able to process larger molecules are in demand in the fine chemical industry and for the oil processing on which the world still relies for fuels. Currently known extra-large-pore zeolites display poor stability and/or lack pore multidimensionality, limiting their usefulness. We report ZEO-1, a robust, fully connected aluminosilicate zeolite with mutually intersecting three-dimensional extra-large plus three-dimensional large pores. ZEO-1 is stable up to 1000 degrees C, has an extraordinary specific surface area (1000 square meters per gram), and shows potential as a catalytic cracking catalyst.
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| 6. |
- Liu, Daosheng, et al.
(author)
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Investigation on heating aging mechanism of cellulose paper for oil-immersed transformer main insulation
- 2019
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In: Proceedings - IEEE International Conference on Dielectric Liquids. - 2153-3733 .- 2153-3725. ; 2019-June:June
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Conference paper (peer-reviewed)abstract
- Power transformer plays a vital role in maintaining reliable and efficient electricity supply. However, in service is increasing and growing older, much and much attention has been paid on their aging condition and life assessment than ever. The aging and degradation of transformer insulation will determine the life-time of its operation. The intensities of these depend on mechanical, thermal and environmental stresses that act on the insulations. Due to the temperature rise, the lifetime of insulation material will be shortened. The accelerated thermal aging method is often adopted to do some evaluation on the oil-paper insulation materials under different temperature for the thermal lifetime model. According to existing aging test, both insulation paper and mineral oil were aged at the same temperature. In this paper, the thermal aging experiments were implemented on the transformer main insulation model made with modified and unmodified insulation paper. The accelerated thermal aging tests were finished, and the superior electric characteristics of the nano-TiO2 and cellulose composition insulation were validated.
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| 7. |
- Liu, Daosheng, et al.
(author)
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Suppression Mechanism of TiO 2 for the Partial Discharge of Oil-paper Insulation in Intensive Electric Field
- 2019
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In: Proceedings - IEEE International Conference on Dielectric Liquids. - 2153-3733 .- 2153-3725. ; 2019-June
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Conference paper (peer-reviewed)abstract
- With the rapid development of modern HVDC transmission technology, higher insulation properties are put forward on the oil-paper insulation system of the transformer, which determine the transformer service life to a certain extent. Traditional transformer oil-paper insulation is becoming increasingly difficult to meet the demands of insulation system with large capacity and miniaturization at ultra-high voltage level. In order to improve the insulation strength of oil-paper system, the insulation cellulose paper modified by TiO2 nanoparticles of different diameters (5 nm, 10 nm, 20 nm, 30 nm) were prepared, in addition, each of modified cellulose paper has different mass fraction of TiO2 nanoparticles (1%, 3%, 5%, 7% wt.). The partial discharge (PD) detection platform was established, and the partial discharge inception voltage (PDIV) values of the oil-paper insulation system with and without nanoparticles were measured. To investigate the PD characteristics, the PD waveforms and PD frequency spectrums of modified cellulose paper and the unmodified were obtained. The suppression mechanism of TiO2 nanoparticles on PD was explored through scanning electron microscope (SEM) observation. All the experiment results indicate that adding nano-TiO2 is beneficial to enhance the insulation properties of oil-paper insulation, and the optimum diameter and mass fraction of TiO2 nanoparticles to suppress oil-paper PD were obtained.
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| 8. |
- Liu, Lei, et al.
(author)
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Irreversible phase transitions of the multiferroic oxide Mn3TeO6 at high pressures
- 2022
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In: Applied Physics Letters. - : American Institute of Physics (AIP). - 0003-6951 .- 1077-3118. ; 121:4
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Journal article (peer-reviewed)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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| 9. |
- Long, Chang, et al.
(author)
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Regulating reconstruction of oxide-derived Cu for electrochemical CO2 reduction toward n-propanol
- 2023
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In: Science Advances. - 2375-2548. ; 9:43
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Journal article (peer-reviewed)abstract
- Oxide-derived copper (OD-Cu) is the most efficient and likely practical electrocatalyst for CO2 reduction toward multicarbon products. However, the inevitable but poorly understood reconstruction from the pristine state to the working state of OD-Cu under strong reduction conditions largely hinders the rational construction of catalysts toward multicarbon products, especially C-3 products like n-propanol. Here, we simulate the reconstruction of CuO and Cu2O into their derived Cu by molecular dynamics, revealing that CuO-derived Cu (CuOD-Cu) intrinsically has a richer population of undercoordinated Cu sites and higher surficial Cu atom density than the counterpart Cu2O-derived Cu (Cu2OD-Cu) because of the vigorous oxygen removal. In situ spectroscopes disclose that the coordination number of CuOD-Cu is considerably lower than that of Cu2OD-Cu, enabling the fast kinetics of CO2 reaction and strengthened binding of *C-2 intermediate(s). Benefiting from the rich undercoordinated Cu sites, CuOD-Cu achieves remarkable n-propanol faradaic efficiency up to similar to 17.9%, whereas the Cu2OD-Cu dominantly generates formate.
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| 10. |
- Sun, Xiaoyu, et al.
(author)
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Revealing microstructural degradation mechanism induced by interdiffusion between Amdry365 coating and IN792 superalloy
- 2024
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In: Materials and Design. - : ELSEVIER SCI LTD. - 1873-4197 .- 0264-1275. ; 241
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Journal article (peer-reviewed)abstract
- Metallic coatings are widely employed to improve the oxidation resistance of superalloys. However, the interdiffusion between the metallic coatings and the superalloys leads to microstructural degradation in both. Some of the underlying degradation mechanisms are still elusive, e.g., the γ′ (Ni3Al) phase depletion in superalloys, where a large amount of γ′ precipitates are dissolved in the γ matrix even though the incoming Al from coatings indeed increases the Al content. Here, we investigated the interdiffusion behavior between the Amdry365 coating and the IN792 superalloy at 1100 °C, using multiple microscopic techniques and thermodynamics calculations. Our results showed an excellent agreement between experiments and thermodynamics simulations, indicating the dominant role of Al on the initial diffusion-induced phase transitions. We proposed the Al-Cr interference effect to account for the pile-up behavior of Cr and the reduced Al content near the coating/superalloy interface. The local phase equilibrium calculations revealed that the γ′ depletion in the superalloy is primarily attributed to the loss of γ′-forming elements, such as Ta and Ti. Our findings opened up an avenue for studies on the superalloy/coating interdiffusion, contributing to reducing this damaging impact.
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