| 1. |
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| 2. |
- 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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| 3. |
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| 4. |
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| 5. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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| 6. |
- Kanoni, Stavroula, et al.
(author)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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In: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Journal article (peer-reviewed)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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| 7. |
- Chen, DS, et al.
(author)
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Single cell atlas for 11 non-model mammals, reptiles and birds
- 2021
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 7083-
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Journal article (peer-reviewed)abstract
- The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
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| 8. |
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| 9. |
- Luo, Yifei, et al.
(author)
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Technology Roadmap for Flexible Sensors
- 2023
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In: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Research review (peer-reviewed)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 10. |
- You, Xiaohu, et al.
(author)
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Towards 6G wireless communication networks: vision, enabling technologies, and new paradigm shifts
- 2021
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In: Science China Information Sciences. - : Science Press. - 1674-733X .- 1869-1919. ; 64:1
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Research review (peer-reviewed)abstract
- The fifth generation (5G) wireless communication networks are being deployed worldwide from 2020 and more capabilities are in the process of being standardized, such as mass connectivity, ultra-reliability, and guaranteed low latency. However, 5G will not meet all requirements of the future in 2030 and beyond, and sixth generation (6G) wireless communication networks are expected to provide global coverage, enhanced spectral/energy/cost efficiency, better intelligence level and security, etc. To meet these requirements, 6G networks will rely on new enabling technologies, i.e., air interface and transmission technologies and novel network architecture, such as waveform design, multiple access, channel coding schemes, multi-antenna technologies, network slicing, cell-free architecture, and cloud/fog/edge computing. Our vision on 6G is that it will have four new paradigm shifts. First, to satisfy the requirement of global coverage, 6G will not be limited to terrestrial communication networks, which will need to be complemented with non-terrestrial networks such as satellite and unmanned aerial vehicle (UAV) communication networks, thus achieving a space-air-ground-sea integrated communication network. Second, all spectra will be fully explored to further increase data rates and connection density, including the sub-6 GHz, millimeter wave (mmWave), terahertz (THz), and optical frequency bands. Third, facing the big datasets generated by the use of extremely heterogeneous networks, diverse communication scenarios, large numbers of antennas, wide bandwidths, and new service requirements, 6G networks will enable a new range of smart applications with the aid of artificial intelligence (AI) and big data technologies. Fourth, network security will have to be strengthened when developing 6G networks. This article provides a comprehensive survey of recent advances and future trends in these four aspects. Clearly, 6G with additional technical requirements beyond those of 5G will enable faster and further communications to the extent that the boundary between physical and cyber worlds disappears.
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| 11. |
- Xie, Jiaying, et al.
(author)
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STING activation in TET2-mutated hematopoietic stem/progenitor cells contributes to the increased self-renewal and neoplastic transformation
- 2023
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In: Leukemia. - : Springer Nature. - 0887-6924 .- 1476-5551. ; 37:12, s. 2457-2467
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Journal article (peer-reviewed)abstract
- Somatic loss-of-function mutations of the dioxygenase Ten-eleven translocation-2 (TET2) occur frequently in individuals with clonal hematopoiesis (CH) and acute myeloid leukemia (AML). These common hematopoietic disorders can be recapitulated in mouse models. However, the underlying mechanisms by which the deficiency in TET2 promotes these disorders remain unclear. Here we show that the cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) pathway is activated to mediate the effect of TET2 deficiency in dysregulated hematopoiesis in mouse models. DNA damage arising in Tet2-deficient hematopoietic stem/progenitor cells (HSPCs) leads to activation of the cGAS-STING pathway which in turn promotes the enhanced self-renewal and development of CH. Notably, both pharmacological inhibition and genetic deletion of STING suppresses Tet2 mutation-induced aberrant hematopoiesis. In patient-derived xenograft (PDX) models, STING inhibition specifically attenuates the proliferation of leukemia cells from TET2-mutated individuals. These observations suggest that the development of CH associated with TET2 mutations is powered through chronic inflammation dependent on the activated cGAS-STING pathway and that STING may represent a potential target for intervention of relevant hematopoietic diseases.
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| 12. |
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| 13. |
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| 14. |
- Wang, Haibin, et al.
(author)
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Strain in Copper/Ceria Heterostructure Promotes Electrosynthesis of Multicarbon Products
- 2023
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In: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:1, s. 346-354
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Journal article (peer-reviewed)abstract
- Elastic strains in metallic catalysts induce enhanced selectivity for carbon dioxide reduction (CO2R) toward valuable multicarbon (C2+) products. However, under working conditions, the structure of catalysts inevitably undergoes reconstruction, hardly retaining the initial strain. Herein, we present a metal/metal oxide synthetic strategy to introduce and maintain the tensile strain in a copper/ceria heterostructure, enabled by the presence of a thin interface layer of Cu2O/CeO2. The tensile strain in the copper domain and deficient electron environment around interfacial Cu sites resulted in strengthened adsorption of carbonaceous intermediates and promoted*CO dimerization. The strain effect in the copper/ceria heterostructure leads to an improved C2+ selectivity with a maximum Faradaic efficiency of 76.4% and a half-cell power conversion efficiency of 49.1%. The fundamental insights gained from this system can facilitate the rational design of heterostructure catalysts for CO2R.
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| 15. |
- Wang, Shi Zhi, et al.
(author)
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Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds
- 2024
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In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 41:7
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Journal article (peer-reviewed)abstract
- The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3′UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.
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| 16. |
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| 17. |
- Xing, Yi, et al.
(author)
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Integrated opposite charge grafting induced ionic-junction fiber
- 2023
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In: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- The emergence of ionic-junction devices has attracted growing interests due to the potential of serving as signal transmission and translation media between electronic devices and biological systems using ions. Among them, fiber-shaped iontronics possesses a great advantage in implantable applications owing to the unique one-dimensional geometry. However, fabricating stable ionic-junction on curved surfaces remains a challenge. Here, we developed a polyelectrolyte based ionic-junction fiber via an integrated opposite charge grafting method capable of large-scale continuous fabrication. The ionic-junction fibers can be integrated into functions such as ionic diodes and ionic bipolar junction transistors, where rectification and switching of input signals are implemented. Moreover, synaptic functionality has also been demonstrated by utilizing the fiber memory capacitance. The connection between the ionic-junction fiber and sciatic nerves of the mouse simulating end-to-side anastomosis is further performed to realize effective nerve signal conduction, verifying the capability for next-generation artificial neural pathways in implantable bioelectronics. Ionic-junction devices are difficult to integrate with fiber-shaped tissues like nerves and muscles for applications in implantable bioelectronics due to their large size and bulk structure. Authors realize here easy to implant fiber-shaped iontronics through an integrated opposite charge grafting process, enabling the construction of ionic logic gates and artificial neural pathways.
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| 18. |
- Cao, Huiming, et al.
(author)
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Effect of Enterohepatic Circulation on the Accumulation of Per- and Polyfluoroalkyl Substances : Evidence from Experimental and Computational Studies
- 2022
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 56:5, s. 3214-3224
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Journal article (peer-reviewed)abstract
- The pharmacokinetic characteristics of per- and polyfluoroalkyl substances (PFAS) affect their distribution and bioaccumulation in biological systems. The enterohepatic circulation leads to reabsorption of certain chemicals from bile back into blood and the liver and thus influences their elimination, yet its influence on PFAS bioaccumulation remains unclear. We explored the role of enterohepatic circulation in PFAS bioaccumulation by examining tissue distribution of various PFAS in wild fish and a rat model. Computational models were used to determine the reabsorbed fractions of PFAS by calculating binding affinities of PFAS for key transporter proteins of enterohepatic circulation. The results indicated that higher concentrations were observed in blood, the liver, and bile compared to other tissues for some PFAS in fish. Furthermore, exposure to a PFAS mixture on the rat model showed that the reabsorption phenomenon appeared during 8-12 h for most long-chain PFAS. Molecular docking calculations suggest that PFAS can bind to key transporter proteins via electrostatic and hydrophobic interactions. Further regression analysis adds support to the hypothesis that binding affinity of the apical sodium-dependent bile acid transporter is the most important variable to predict the human half-lives of PFAS. This study demonstrated the critical role of enterohepatic circulation in reabsorption, distribution, and accumulation of PFAS.
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| 19. |
- Cheng, Yingzhe, et al.
(author)
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Genetic Effects of NDUFAF6 rs6982393 and APOE on Alzheimer’s Disease in Chinese Rural Elderly : A Cross-Sectional Population-Based Study
- 2022
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In: Clinical Interventions in Aging. - 1176-9092 .- 1178-1998. ; 17, s. 185-194
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Journal article (peer-reviewed)abstract
- Purpose: To investigate the associations of genotypes of NDUFAF6 rs6982393 and APOE and their combined genotypes with the risk of Alzheimer’s disease (AD) and mild cognitive impairment (MCI) in Chinese rural elderly.Methods: This cross-sectional population-based study included 5096 older adults (age ≥ 60 years, 57.1% female). Genotypes of NDUFAF6 rs6982393 and APOE were detected using the multiple-polymerase chain reaction amplification. We diagnosed AD following the criteria of Diagnostic and Statistical Manual of Mental Disorders, the fourth edition and diagnosed MCI following the Petersen’s criteria MCI. Data were analyzed using the logistic regression model.Results: The overall prevalence of AD and MCI was 3.57% (95% confidence interval [CI]: 0.040, 0.053) and 22.65% (95% CI: 0.223, 0.247), separately. The TT versus CC/CT genotype of NDUFAF6 rs6982393 was related to a higher risk of AD with the multi-adjusted odds ratio (95% CI) being 1.61 (1.02, 2.54) in the total sample, 3.36 (1.48, 7.60) in those aged 60– 69, and 1.24 (0.71, 2.17) in those aged 70 years and above. The interaction between genotype of NDUFAF6 rs6982393 with age groups (60– 69 versus ≥ 70 years) was significant on the risk of AD. The presence of APOE ϵ4 was not significantly associated with the risk of AD. Carrying both NDUFAF6 TT and APOE ϵ4 was related to a higher risk of AD with the multi-adjusted odds ratio (95% CI) being 2.69 (1.10, 2.56). In addition, there was no significant association between the above genotypes and MCI.Conclusion: In Chinese rural elderly, the TT versus CT/CC genotype of NDUFAF6 rs6982393 was associated with an increased likelihood of AD; such an association only existed among young-old adults. Carrying both NDUFAF6 rs6982393-TT and APOE ϵ4 was related to a higher risk of AD. This finding highlights the importance of considering age and combined genotype in studying the genetic profiles of AD.
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| 20. |
- Delios, A., et al.
(author)
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Examining the generalizability of research findings from archival data
- 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. - 0027-8424 .- 1091-6490. ; 119:30
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Journal article (peer-reviewed)abstract
- This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability-for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples.
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| 21. |
- Dong, Yu, et al.
(author)
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Observation of a Ubiquitous (π, π)-Type Nematic Superconducting Order in the Whole Superconducting Dome of Ultra-Thin BaFe2–xNixAs2 Single Crystals
- 2021
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In: Chinese Physics Letters. - : Institute of Physics Publishing (IOPP). - 0256-307X .- 1741-3540. ; 38:9
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Journal article (peer-reviewed)abstract
- In iron-based superconductors, the (0, pi) or (pi, 0) nematicity, which describes an electronic anisotropy with a four-fold symmetry breaking, is well established and believed to be important for understanding the superconducting mechanism. However, how exactly such a nematic order observed in the normal state can be related to the superconducting pairing is still elusive. Here, by performing angular-dependent in-plane magnetoresistivity using ultra-thin flakes in the steep superconducting transition region, we unveil a nematic superconducting order along the (pi, pi) direction in electron-doped BaFe2 - x Ni x As2 from under-doped to heavily overdoped regimes with x = 0.065-0.18. It shows superconducting gap maxima along the (pi, pi) direction rotated by 45 degrees from the nematicity along (0, pi) or (pi, 0) direction observed in the normal state. A similar (pi, pi)-type nematicity is also observed in the under-doped and optimally doped hole-type Ba1 - y K y Fe2As2, with y = 0.2-0.5. These results suggest that the (pi, pi) nematic superconducting order is a universal feature that needs to be taken into account in the superconducting pairing mechanism in iron-based superconductors.
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| 22. |
- Du, Hao, et al.
(author)
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Side reactions/changes in lithium-ion batteries : mechanisms and strategies for creating safer and better batteries
- 2024
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In: Advanced Materials. - : John Wiley & Sons. - 0935-9648 .- 1521-4095.
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Research review (peer-reviewed)abstract
- Abstract Lithium-ion batteries (LIBs), in which lithium ions function as charge carriers, are considered the most competitive energy storage devices due to their high energy and power density. However, battery materials, especially with high capacity undergo side reactions and changes that result in capacity decay and safety issues. A deep understanding of the reactions that cause changes in the battery's internal components and the mechanisms of those reactions is needed to build safer and better batteries. This review focuses on the processes of battery failures, with voltage and temperature as the underlying factors. Voltage-induced failures result from anode interfacial reactions, current collector corrosion, cathode interfacial reactions, overcharge, and overdischarge, while temperature-induced failure mechanisms include SEI decomposition, separator damage, and interfacial reactions between electrodes and electrolytes. The review also presents protective strategies for controlling these reactions. As a result, the reader is offered a comprehensive overview of the safety features and failure mechanisms of various LIB components.
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| 23. |
- Guan, Tianfu, et al.
(author)
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Decoding the Self-Assembly Plasmonic Interface Structure in a PbS Colloidal Quantum Dot Solid for a Photodetector
- 2023
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In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 17:22, s. 23010-23019
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Journal article (peer-reviewed)abstract
- Hybrid plasmonic nanostructures have gained enormous attention in a variety of optoelectronic devices due to their surface plasmon resonance properties. Self-assembled hybrid metal/quantum dot (QD) architectures offer a means of coupling the properties of plasmonics and QDs to photodetectors, thereby modifying their functionality. The arrangement and localization of hybrid nanostructures have an impact on exciton trapping and light harvesting. Here, we present a hybrid structure consisting of self-assembled gold nanospheres (Au NSs) embedded in a solid matrix of PbS QDs for mapping the interface structures and the motion of charge carriers. Grazing-incidence small-angle X-ray scattering is utilized to analyze the localization and spacing of the Au NSs within the hybrid structure. Furthermore, by correlating the morphology of the Au NSs in the hybrid structure with the corresponding differences observed in the performance of photodetectors, we are able to determine the impact of interface charge carrier dynamics in the coupling structure. From the perspective of architecture, our study provides insights into the performance improvement of optoelectronic devices.
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| 24. |
- Han, Xiaolei, et al.
(author)
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KIBRA regulates amyloid β metabolism by controlling extracellular vesicles secretion
- 2022
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In: EBioMedicine. - : Elsevier BV. - 2352-3964. ; 78
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Journal article (peer-reviewed)abstract
- Background Previous research has revealed that KIBRA controls secretion of extracellular vesicles (EVs) by inhibiting the proteasomal degradation of Rab27a and EVs play an important role in amyloid β (Aβ) metabolism and transmission during Alzheimer's disease (AD) pathogenesis. Here, we further test the hypothesis that KIBRA regulates Aβ metabolism via the endosomal-lysosomal system.Methods We generated KIBRA knockout mice on a 5XFAD background and KIBRA knockdown cells in murine HT22 cells with stably overexpressing APP. Various forms of Aβ and quantification of EVs were analyzed by biochemical methods and nanoparticle tracking analysis, respectively. Multivesicular bodies (MVBs) were visualized by electron microscopy and confocal fluorescent microscopy. In a population-based cohort (n = 1419), KIBRA genotypes and plasma Aβ levels were analyzed using multiple-PCR amplification and Simoa, respectively.Findings Multiple forms of Aβ were dramatically attenuated in KIBRA knockout mouse brain, including monomers, oligomers, and extracellular deposition, but KIBRA knockout had no effect on intraneuronal APP C-terminal fragment β (APP-CTFβ)/Aβ levels. KIBRA depletion also decreased APP-CTFβ/Aβ-associated EVs secretion and subsequently enhanced MVBs number. Furthermore, we found that excessive accumulation of MVBs harboring APP-CTFβ/Aβ promoted the MVBs-lysosome fusion for degradation and inhibition of lysosomal function rescued secretion of APP-CTFβ/Aβ-associated EVs. More importantly, whole exon sequencing of KIBRA in a large population-based cohort identified the association of KIBRA rs28421695 polymorphism with plasma Aβ levels.Interpretation These results demonstrate that KIBRA regulates Aβ metabolism via controlling the secretion of APP-CTFβ/Aβ-associated EVs.
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| 25. |
- Janko, Matthew R., et al.
(author)
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In-situ bypass is associated with superior infection-free survival compared with extra-anatomic bypass for the management of secondary aortic graft infections without enteric involvement
- 2022
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In: Journal of Vascular Surgery. - : Elsevier. - 0741-5214 .- 1097-6809. ; 76:2, s. 546-
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Journal article (peer-reviewed)abstract
- Objective: The optimal revascularization modality following complete resection of aortic graft infection (AGI) without enteric involvement remains unclear. The purpose of this investigation is to determine the revascularization approach associated with the lowest morbidity and mortality using real-world data in patients undergoing complete excision of AGI. Methods: A retrospective, multi-institutional study of AGI from 2002 to 2014 was performed using a standardized database. Baseline demographics, comorbidities, and perioperative variables were recorded. The primary outcome was infection-free survival. Descriptive statistics, Kaplan-Meier survival analysis, and univariate and multivariable analyses were performed. Results: A total of 241 patients at 34 institutions from seven countries presented with AGI during the study period (median age, 68 years; 75% male). The initial aortic procedures that resulted in AGI were 172 surgical grafts (71%), 66 endografts (27%), and three unknown (2%). Of the patients, 172 (71%) underwent complete excision of infected aortic graft material followed by in situ (in-line) bypass (ISB), including antibiotic-treated prosthetic graft (35%), autogenous femoral vein (neo-aortoiliac surgery) (24%), and cryopreserved allograft (41%). Sixty-nine patients (29%) underwent extra-anatomic bypass (EAB). Overall median Kaplan-Meier estimated survival was 5.8 years. Perioperative mortality was 16%. When stratified by ISB vs EAB, there was a significant difference in Kaplan-Meier estimated infection-free survival (2910 days; interquartile range, 391-3771 days vs 180 days; interquartile range, 27-3750 days; P <.001). There were otherwise no significant differences in presentation, comorbidities, or perioperative variables. Multivariable Cox regression showed lower infection-free survival among patients with EAB (hazard ratio [HR], 2.4; 95% confidence interval [CI], 1.6-3.6; P <.001), polymicrobial infection (HR, 2.2; 95% CI, 1.4-3.5; P = .001), methicillin-resistant Staphylococcus aureus infection (HR, 1.7; 95% CI, 1.1-2.7; P = .02), as well as the protective effect of omental/muscle flap coverage (HR, 0.59; 95% CI, 0.37-0.92; P = .02). Conclusions: After complete resection of AGI, perioperative mortality is 16% and median overall survival is 5.8 years. EAB is associated with nearly a two and one-half-fold higher reinfection/mortality compared with ISB. Omental and/or muscle flap coverage of the repair appear protective.
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| 26. |
- Li, Zheng, et al.
(author)
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A Review of Spatter in Laser Powder Bed Fusion Additive Manufacturing: In Situ Detection, Generation, Effects, and Countermeasures
- 2022
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In: Micromachines. - : MDPI AG. - 2072-666X. ; 13:8
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Research review (peer-reviewed)abstract
- Spatter is an inherent, unpreventable, and undesired phenomenon in laser powder bed fusion (L-PBF) additive manufacturing. Spatter behavior has an intrinsic correlation with the forming quality in L-PBF because it leads to metallurgical defects and the degradation of mechanical properties. This impact becomes more severe in the fabrication of large-sized parts during the multi-laser L-PBF process. Therefore, investigations of spatter generation and countermeasures have become more urgent. Although much research has provided insights into the melt pool, microstructure, and mechanical property, reviews of spatter in L-PBF are still limited. This work reviews the literature on the in situ detection, generation, effects, and countermeasures of spatter in L-PBF. It is expected to pave the way towards a novel generation of highly efficient and intelligent L-PBF systems.
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| 27. |
- Liang, Lin, et al.
(author)
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Non-Interpenetrated Single-Crystal Covalent Organic Frameworks
- 2020
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In: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 59:41, s. 17991-17995
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Journal article (peer-reviewed)abstract
- Growth of covalent organic frameworks (COFs) as single crystals is extremely challenging. Inaccessibility of open-structured single-crystal COFs prevents the exploration of structure-oriented applications. Herein we report for the first time a non-interpenetrated single-crystal COF, LZU-306, which possesses the open structure constructed exclusively via covalent assembly. With a high void volume of 80 %, LZU-306 was applied to investigate the intrinsic dynamics of reticulated tetraphenylethylene (TPE) as the individual aggregation-induced-emission moiety. Solid-state(2)H NMR investigation has determined that the rotation of benzene rings in TPE, being the freest among the reported cases, is as fast as 1.0x10(4) Hz at 203 K to 1.5x10(7) Hz at 293 K. This research not only explores a new paradigm for single-crystal growth of open frameworks, but also provides a unique matrix-isolation platform to reticulate functional moieties into a well-defined and isolated state.
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| 28. |
- Liang, Wang, et al.
(author)
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Life cycle assessment of blast furnace ironmaking processes : A comparison of fossil fuels and biomass hydrochar applications
- 2023
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In: Fuel. - : Elsevier BV. - 0016-2361 .- 1873-7153. ; 345
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Journal article (peer-reviewed)abstract
- The impact of the iron and steel production process on the ecological environment cannot be ignored. This study aims to assess the impact of life cycle assessment on the traditional fossil fuel blast furnace ironmaking process and the biomass hydrochar blast furnace ironmaking process. The Simapro v9.0 software is used to comprehensively evaluate the life cycle impacts of biomass hydrochar in the blast furnace ironmaking process. The results show that the life cycle impact categories of the blast furnace ironmaking process mainly include global warming, non-renewable energy and respiratory inorganics. The global warming impact of the ironmaking process using hydrochar is 2054.00 kg CO2 eq, which is 420.61 kg CO2 eq less than that of traditional blast furnace ironmaking process. The global warming impact is mainly reflected in the emission of CO2 gas, and the main source is the generation of blast furnace gas and the use of sinter. The respiratory inorganics impact is mainly manifested in the emission of nitrogen oxides, sulfur oxides and particulates, which mainly comes from the mining of iron ore and the production of sinter. The non-renewable energy impact mainly comes from the coal resources, and the use of other renewable energy such as biomass energy is an important way to reduce the impact. Therefore, biomass hydrochar used in the metallurgical process is more suitable for sustainable devel-opment of the ecological environment.
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| 29. |
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| 30. |
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| 31. |
- Wang, Guangwei, et al.
(author)
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Hydrothermal carbonization mechanism of agricultural waste under different conditions : An experimental and ReaxFF molecular dynamics study
- 2023
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In: Journal of the Energy Institute. - : Elsevier BV. - 1743-9671 .- 1746-0220. ; 110
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Journal article (peer-reviewed)abstract
- Different hydrothermal carbonization (HTC) conditions will affect the yield, physicochemical properties and application of agricultural waste hydrochar. The hydrochar prepared under different HTC conditions was systematically studied through various experimental methods, and the experimental results were further verified and explained by ReaxFF molecular dynamics method. The results show that the higher HTC temperature, higher liquid-solid ratio and longer reaction time can reduce the yield of solid product. The volatile content of rice straw (RS) hydrochar decreased with the progresses of HTC, but the fixed carbon content increased. The HTC process is accompanied by the breakage of C-H bonds, C-O bonds, C-C bonds and O-H bonds, with C-O bond breaks comprising the most. The HTC process is also accompanied by the C-C bonds regeneration, indicating that decomposition and polymerization reactions coexist in the HTC process. At higher HTC temperature and longer reaction time, RS hydrochar showed lower specific surface area and porosity. The effect of the HTC temperature is the largest, while the effect of holding time is the smallest. Therefore, to expand the potential use of RS hydrochar, it is important to thoroughly investigate the influence of HTC conditions on the physicochemical properties of RS.
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| 32. |
- Wang, Ling, et al.
(author)
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Perfluorooctanesulfonate Induces Hepatomegaly and Lipoatrophy in Mice through Phosphoenolpyruvate Carboxykinase-Mediated Glyceroneogenesis Inhibition
- 2020
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In: Environmental Science and Technology Letters. - : American Chemical Society (ACS). - 2328-8930. ; 7:3, s. 185-190
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Journal article (peer-reviewed)abstract
- Perfluorooctansulfonate (PFOS) is a persistent organic pollutant that has attracted a great deal of attention due to toxic effects such as its lipid metabolism-disrupting potential. Exposure to PFOS can cause hepatomegaly and lipoatrophy in mice, but the underlying mechanisms are still unknown. Considering that glyceroneogenesis is the essential pathway for balancing the triglyceride (TG) cycle between liver and white adipose tissue (WAT), we speculate that PFOS acts via glyceroneogenesis inhibition to alter TG metabolism in the two tissues. Combining gene expression, protein expression, an enzyme activity assay, and molecular docking analysis, we report here that PFOS can interact with cytosolic phosphoenolpyruvate carboxykinase (PEPCK), the rate-limiting enzyme of glyceroneogenesis. Specifically, by repression of PEPCK, PFOS can inhibit the glyceroneogenesis process and thus decrease the glyceroneogenesis-derived glycerol level, leading to a reduced re-esterified TG level and causing atrophy in WAT. Moreover, in PFOS-exposed liver tissue, despite the fact that free glycerol and fatty acids released from WAT were being used for TG synthesis, the export of TG slowed. This eventually resulted in the continuous lipolysis of WAT and accumulation of lipid in the liver. PEPCK can be used as a key biomarker to assess the lipid metabolism disorders induced by other conventional and emerging per- and polyfluoroalkyl substances.
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| 33. |
- Wang, Mei jun, et al.
(author)
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SIRT1-dependent deacetylation of Txnip H3K9ac is critical for exenatide-improved diabetic kidney disease
- 2023
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In: Biomedicine and Pharmacotherapy. - 0753-3322. ; 167
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Journal article (peer-reviewed)abstract
- Glucagon-like peptide 1 receptor agonist exenatide (exendin-4) has potential protective capabilities against diabetic kidney disease (DKD). However, the underlying mechanism has not been fully elucidated. The expression of thioredoxin-interacting protein (Txnip) is upregulated during DKD progression by histone acetylation. Sirtuin 1 (SIRT1) is a deacetylase and is decreased in DKD, which indicates that it may regulate Txnip in this disease. Here, we used whole-body heterozygous Sirt1 knockout (Sirt1+/-) and kidney-specific Sirt1 knockout (KSK) mice to investigate whether SIRT1 regulates Txnip via histone deacetylation in DKD and exenatide-alleviated DKD. Exenatide substantially improved renal pathological damage, decreased the albumin-to-creatinine ratio (ACR), upregulated SIRT1 expression, and downregulated Txnip expression in kidneys of high-fat diet-treated C57BL/6J mice. However, these effects diminished in Sirt1+/- and KSK mice under exenatide treatment. The downregulation of Txnip expression by exendin-4 in high-glucose-treated SV40 MES13 cells was hampered during Sirt1 knockdown. These results demonstrate that kidney SIRT1 is indispensable in exenatide-improved DKD and downregulation of Txnip expression. Exendin-4 mechanistically downregulated Txnip histone 3 lysine 9 acetylation (H3K9ac) in a SIRT1-dependent manner and decreased spliced X-box binding protein 1 (XBP1s) recruitment to the Txnip promoter. These findings provide epigenetic evidence elucidating the specific mechanism for exenatide-mediated DKD alleviation and highlight the importance of Txnip as a promising therapeutic target for DKD.
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| 34. |
- Wang, Yu-Cheng, et al.
(author)
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Porous Carbon Membrane-Supported Atomically Dispersed Pyrrole-Type Fe-N-4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction
- 2020
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In: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 16:31
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Journal article (peer-reviewed)abstract
- The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-N-x sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-N-x single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type Fe-N-4 structure is identified as the real catalytic site in HzOR.
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| 35. |
- Wu, ZC, et al.
(author)
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Tumor suppressor ZHX2 inhibits NAFLD-HCC progression via blocking LPL-mediated lipid uptake
- 2020
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In: Cell death and differentiation. - : Springer Science and Business Media LLC. - 1476-5403 .- 1350-9047. ; 27:5, s. 1693-1708
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Journal article (peer-reviewed)abstract
- Non-alcoholic fatty liver disease (NAFLD) leads to hepatocellular carcinoma (HCC). However, the underlying mechanism remains largely unclear. Here, we investigated the role of the tumor suppressor Zinc fingers and homeoboxes 2 (ZHX2) in the progression of NAFLD to HCC. ZHX2 expression was significantly decreased in fatty liver tissues, especially in the liver with NAFLD–HCC. ZHX2 overexpression disturbed lipid homeostasis of cultured HCC cells, and inhibited lipid deposition in hepatocytes both in vitro and in vivo. Moreover, ZHX2 inhibited uptake of exogenous lipids through transcriptional suppression of lipid lipase (LPL), leading to retarded proliferation of HCC cells. Importantly, LPL overexpression significantly reversed ZHX2-mediated inhibition of HCC cell proliferation, xenograft tumor growth, lipid deposition, and spontaneous liver tumor formation. Consistently, IHC staining demonstrated a negative correlation of ZHX2 with LPL in an HCC cohort. Collectively, ZHX2 protects hepatocytes from abnormal lipid deposition in NAFLD through transcriptional repression of LPL, which subsequently retards cell growth and NAFLD–HCC progression. These findings illustrate a novel mechanism of NAFLD progression into HCC.
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| 36. |
- Xiao, Wenming, et al.
(author)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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In: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Journal article (peer-reviewed)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 37. |
- Yang, Bao, et al.
(author)
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Long-term decrease in Asian monsoon rainfall and abrupt climate change events over the past 6,700 years
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - Washington : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:30
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Journal article (peer-reviewed)abstract
- Asian summer monsoon (ASM) variability and its long-term ecological and societal impacts extending back to Neolithic times are poorly understood due to a lack of high-resolution climate proxy data. Here, we present a precisely dated and well-calibrated treering stable isotope chronology from the Tibetan Plateau with 1- to 5-y resolution that reflects high- to low-frequency ASM variability from 4680 BCE to 2011 CE. Superimposed on a persistent drying trend since the mid-Holocene, a rapid decrease in moisture availability between similar to 2000 and similar to 1500 BCE caused a dry hydroclimatic regime from similar to 1675 to similar to 1185 BCE, with mean precipitation estimated at 42 +/- 4% and 5 +/- 2% lower than during themid-Holocene and the instrumental period, respectively. This second-millennium-BCE megadrought marks the mid-to late Holocene transition, during which regional forests declined and enhanced aeolian activity affected northern Chinese ecosystems. We argue that this abrupt aridification starting similar to 2000 BCE contributed to the shift of Neolithic cultures in northern China and likely triggered human migration and societal transformation.
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| 38. |
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| 39. |
- Yang, Fan, et al.
(author)
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Uncovering a Distinct Gene Signature in Endothelial Cells Associated With Contrast Enhancement in Glioblastoma
- 2021
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In: Frontiers in Oncology. - : Frontiers Media S.A.. - 2234-943X. ; 11
-
Journal article (peer-reviewed)abstract
- Purpose Glioblastoma (GBM) is the most aggressive and lethal type of brain tumors. Magnetic resonance imaging (MRI) has been commonly used for GBM diagnosis. Contrast enhancement (CE) on T1-weighted sequences are presented in nearly all GBM as a result of high vascular permeability in glioblastomas. Although several radiomics studies indicated that CE is associated with distinct molecular signatures in tumors, the effects of vascular endothelial cells, the key component of blood brain barrier (BBB) controlling vascular permeability, on CE have not been thoroughly analyzed. Methods Endothelial cell enriched genes have been identified using transcriptome data from 128 patients by a systematic method based on correlation analysis. Distinct endothelial cell enriched genes associated with CE were identified by analyzing difference of correlation score between CE-high and CE-low GBM cases. Immunohistochemical staining was performed on in-house patient cohort to validate the selected genes associated with CE. Moreover, a survival analysis was conducted to uncover the relation between CE and patient survival. Results We illustrated that CE is associated with distinct vascular molecular imprints characterized by up-regulation of pro-inflammatory genes and deregulation of BBB related genes. Among them, PLVAP is up-regulated, whereas TJP1 and ABCG2 are down-regulated in the vasculature of GBM with high CE. In addition, we found that the high CE is associated with poor prognosis and GBM mesenchymal subtype. Conclusion We provide an additional insight to reveal the molecular trait for CE in MRI images with special focus on vascular endothelial cells, linking CE with BBB disruption in the molecular level. This study provides a potential new direction that may be applied for the treatment optimization based on MRI features.
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| 40. |
- Zhang, Shao-jie, et al.
(author)
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Genomic regions under selection in the feralization of the dingoes
- 2020
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In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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| 41. |
- Zhang, Xiao-Jie, et al.
(author)
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Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation
- 2024
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In: Nature Structural & Molecular Biology. - : NATURE PORTFOLIO. - 1545-9993 .- 1545-9985. ; 31:1
-
Journal article (peer-reviewed)abstract
- DNA cytosine methylation plays a vital role in repressing retrotransposons, and such derepression is linked with developmental failure, tumorigenesis and aging. DNA methylation patterns are formed by precisely regulated actions of DNA methylation writers (DNA methyltransferases) and erasers (TET, ten-eleven translocation dioxygenases). However, the mechanisms underlying target-specific oxidation of 5mC by TET dioxygenases remain largely unexplored. Here we show that a large low-complexity domain (LCD), located in the catalytic part of Tet enzymes, negatively regulates the dioxygenase activity. Recombinant Tet3 lacking LCD is shown to be hyperactive in converting 5mC into oxidized species in vitro. Endogenous expression of the hyperactive Tet3 mutant in mouse oocytes results in genome-wide 5mC oxidation. Notably, the occurrence of aberrant 5mC oxidation correlates with a consequent loss of the repressive histone mark H3K9me3 at ERVK retrotransposons. The erosion of both 5mC and H3K9me3 causes ERVK derepression along with upregulation of their neighboring genes, potentially leading to the impairment of oocyte development. These findings suggest that Tet dioxygenases use an intrinsic auto-regulatory mechanism to tightly regulate their enzymatic activity, thus achieving spatiotemporal specificity of methylome reprogramming, and highlight the importance of methylome integrity for development. Here the authors show that TET dioxygenases, the erasers of DNA methylation, use a self-limiting mechanism via their LCD domain to ensure adaptable methylome status and protect the genome from excessive oxidative methylation.
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| 42. |
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| 43. |
- Zhao, Yun, et al.
(author)
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Rational design of functional binder systems for high-energy lithium-based rechargeable batteries
- 2021
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In: Energy Storage Materials. - : Elsevier. - 2405-8289 .- 2405-8297. ; 35, s. 353-377
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Journal article (peer-reviewed)abstract
- Binders, which maintain the structural integrity of electrodes, are critical components of lithium-based rechargeable batteries (LBRBs) that significantly affect battery performances, despite accounting for 2 to 5 wt% (up to 5 wt% but usually 2 wt%) of the entire electrode. Traditional polyvinylidene fluoride (PVDF) binders that interact with electrode components via weak van der Waals forces are effective in conventional LBRB systems (graphite/LiCoO2, etc.). However, its stable fluorinated structures limit the potential for further functionalization and inhibit strong interactions towards external substances. Consequently, they are unsuitable for next-generation battery systems with high energy density. There is thus a need for new functional binders with facile features compatible with novel electrode materials and chemistries. Here in this review we consider the strategies for rationally designing these functional binders. On the basis of fundamental understandings of the issues for high-energy electrode materials, we have summarized seven desired functions that binders should possess depending on the target electrodes where the binders will be applied. Then a variety of leading-edge functional binders are reviewed to show how their chemical structures realize these above functions and how the employment of these binders affects the cell's electrochemical performances. Finally the corresponding design strategies are therefore proposed, and future research opportunities as well as challenges relating to LBRB binders are outlined.
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| 44. |
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| 45. |
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| 46. |
- Bai, JW, et al.
(author)
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Isolation and Characterization of vB_kpnM_17-11, a Novel Phage Efficient Against Carbapenem-Resistant Klebsiella pneumoniae
- 2022
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In: Frontiers in cellular and infection microbiology. - : Frontiers Media SA. - 2235-2988. ; 12, s. 897531-
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Journal article (peer-reviewed)abstract
- Phages and phage-encoded proteins exhibit promising prospects in the treatment of Carbapenem-Resistant Klebsiella pneumoniae (CRKP) infections. In this study, a novel Klebsiella pneumoniae phage vB_kpnM_17-11 was isolated and identified by using a CRKP host. vB_kpnM_17-11 has an icosahedral head and a retractable tail. The latent and exponential phases were 30 and 60 minutes, respectively; the burst size was 31.7 PFU/cell and the optimal MOI was 0.001. vB_kpnM_17-11 remained stable in a wide range of pH (4-8) and temperature (4-40°C). The genome of vB_kpnM_17-11 is 165,894 bp, double-stranded DNA (dsDNA), containing 275 Open Reading Frames (ORFs). It belongs to the family of Myoviridae, order Caudovirales, and has a close evolutionary relationship with Klebsiella phage PKO111. Sequence analysis showed that the 4530 bp orf022 of vB_kpnM_17-11 encodes a putative depolymerase. In vitro testing demonstrated that vB_kpnM_17-11 can decrease the number of K. pneumoniae by 105-fold. In a mouse model of infection, phage administration improved survival and reduced the number of K. pneumoniae in the abdominal cavity by 104-fold. In conclusion, vB_kpnM_17-11 showed excellent in vitro and in vivo performance against K. pneumoniae infection and constitutes a promising candidate for the development of phage therapy against CRKP.
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| 47. |
- Bailey, Matthew H., et al.
(author)
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.
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| 48. |
- Bao, Zijia, et al.
(author)
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A helical polypyrrole nanotube interwoven zeolitic imidazolate framework and its derivative as an oxygen electrocatalyst
- 2022
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In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 58:80, s. 11288-11291
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Journal article (peer-reviewed)abstract
- A helical polypyrrole nanotube interwoven zeolitic imidazolate framework (ZIF) has been prepared for the first time. After pyrolysis, the helical carbon could act as highly active sites, while the 3D-connected nanoarchitecture contributed to fast charge transfer. The derived carbon material exhibits high activity for the ORR and good performance for a Zn–air battery.
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| 49. |
- Bartocci, Pietro, et al.
(author)
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Bioenergy with Carbon Capture and Storage (BECCS) developed by coupling a Pressurised Chemical Looping combustor with a turbo expander: How to optimize plant efficiency
- 2022
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In: Renewable and Sustainable Energy Reviews. - : Elsevier BV. - 1879-0690 .- 1364-0321. ; 169
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Research review (peer-reviewed)abstract
- Carbon Capture and Storage is a technology of paramount importance for the fulfillment of the Sustainable Development Goal 7 (Affordable and Clean Energy) and the Sustainable Development Goal 5 (Climate Action). The European Union is moving rapidly towards low carbon technologies, for instance via the Energy Union Strategy. Coupling biofuels and carbon capture and storage to decarbonize the power and the industrial sector can be done through the development of BECCS (Bioenergy with Carbon Capture and Storage). Chemical Looping combustion is one of the cheapest way to capture CO2. A Chemical Looping Combustion (CLC) plant can be coupled with a turbo expander to convert energy to power, but it has to work in pressurised conditions. The effect of pressure on the chemical reactions and on fluidised bed hydrodynamics, at the moment, is not completely clear. The aim of this review is to summarize the most important highlights in this field and also provide an original method to optimize power plant efficiency. The main objective of our research is that to design a pressurised Chemical Looping Combustion plant which can be coupled to a turbo expander. To achieve this we need to start from the characteristics of the turbo expander itself (eg. the Turbine Inlet Temperature and the compression ratio) and then design the chemical looping combustor with a top down approach. Once the air and the fuel reactor have been dimensioned and the oxygen carrier inventory and circulation rate have been identified, the paper proposes a final optimization procedure based on two energy balances applied to the two reactors. The results of this work propose an optimization methodology and guidelines to be used for the design of pressurised chemical looping reactors to be coupled with turbo expanders for the production of power with carbon negative emissions.
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| 50. |
- Blokland, G. A. M., et al.
(author)
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Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders
- 2022
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In: Biological Psychiatry. - : Elsevier BV. - 0006-3223 .- 1873-2402. ; 91:1, s. 102-117
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Journal article (peer-reviewed)abstract
- Background: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. Methods: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. Results: Across disorders, genome-wide significant single nucleotide polymorphism–by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10−8), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10−6) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10−7; rs73033497, p = 8.8 × 10−7; rs7914279, p = 6.4 × 10−7), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10−7) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10−7), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10−7) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). Conclusions: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels. © 2021 Society of Biological Psychiatry
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