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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 3. |
- Ding, Yijie, et al.
(author)
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Fuzzy Neural Tangent Kernel Model for Identifying DNA N4-methylcytosine Sites
- 2024
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In: IEEE transactions on fuzzy systems. - Piscataway, NJ : IEEE. - 1063-6706 .- 1941-0034.
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Journal article (peer-reviewed)abstract
- DNA N4-methylcytosine (4mC) site identification is a crucial field in bioinformatics, where machine learning methods have been effectively utilized. Due to the presence of noise, the existing deep learning methods for detecting 4mC have consistently low recognition rates in positive samples. With fuzzy rules and membership functions, fuzzy systems can achieve good results in processing noisy signals. In contrast to traditional fuzzy systems that lack deep feature representation and sample measurement, we introduce novel techniques to enhance generalization and feature representation. By incorporating the neural tangent kernel (NTK) and kernel learning algorithm into the fuzzy system, we propose the fuzzy neural tangent kernel (FNTK) model and the radius-based FNTK (R-FNTK) model to predict DNA 4mC sites. To achieve better generalization performance than traditional kernel functions, we first train the NTK for feature representation learning and sample measurement. Based on the membership function and NTK matrix, different fuzzy kernel matrices are constructed for each fuzzy subset of the fuzzy system. Finally, we utilize two types of iterative kernel optimization algorithms to effectively fuse multiple NTK-based fuzzy kernels and obtain the final prediction model. Rigorous testing using 6 benchmark datasets demonstrates the superiority of our approach, yielding significant improvements in the experiment's performance. © IEEE
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| 4. |
- Lian, Ke-Yan, et al.
(author)
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Big Bandgap in Highly Reduced Graphene Oxides
- 2013
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:12, s. 6049-6054
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Journal article (peer-reviewed)abstract
- It is generally believed that the bandgap of the graphene oxide is proportional to the concentration of the oxygen atoms and a highly reduced graphene oxide (rGO) without vacancy defects should be gapless. We show here from first principles calculations that the bandgap can be effectively opened even in low oxidation level with the absorption of oxygen atoms either symmetrically or asymmetrically. The properly arranged absorption can induce a bandgap up to 1.19 eV for a C/O ratio of 16/1 in a symmetric system and a bandgap up to 1.58 eV for a C/O ratio of 32/3 in an asymmetric system, at generalized gradient approximation (GGA) level. The hybridization between the in-plane p(xy) orbitals of oxygen atoms and the out-of-plane p(z) frontier orbital of graphene is responsible for the opening of the bandgap. This finding sheds new light on the bandgap engineering of graphene.
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| 5. |
- Lian, Ke-yan, et al.
(author)
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Stable High-Energy Density Super-Atom Clusters of Aluminum Hydride
- 2012
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In: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 25:2, s. 147-152
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Journal article (peer-reviewed)abstract
- With the concept of super-atom, first principles calculations propose a new type of super stable cage clusters AlnH3n that are much more energetic stable than the well established clusters, AlnHn+2. In the new clusters, the aluminum core-frame acts as a super-atom with n vertexes and 2n Al-Al edges, which allow to adsorb n hydrogen atoms at the top-site and 2n at the bridge-site. Using Al12H36 as the basic unit, stable chain structures, (Al12H36)(m), have been constructed following the same connection mechanism as for (AlH3)(n) linear polymeric structures. Apart from high hydrogen percentage per molecule, calculations have shown that these new clusters possess large heat of formation values and their combustion heat is about 4.8 times of the methane, making them a promising high energy density material.
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| 6. |
- Olsen, Thale Kristin, et al.
(author)
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DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma
- 2022
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In: JCI Insight. - : AMER SOC CLINICAL INVESTIGATION INC. - 2379-3708. ; 7:17
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Journal article (peer-reviewed)abstract
- Despite intensive therapy, children with high-risk neuroblastoma are at risk of treatment failure. We applied a multiomic system approach to evaluate metabolic vulnerabilities in human neuroblastoma. We combined metabolomics, CRISPR screening, and transcriptomic data across more than 700 solid tumor cell lines and identified dihydroorotate dehydrogenase (DHODH), a critical enzyme in pyrimidine synthesis, as a potential treatment target. Of note, DHODH inhibition is currently under clinical investigation in patients with hematologic malignancies. In neuroblastoma, DHODH expression was identified as an independent risk factor for aggressive disease, and high DHODH levels correlated to worse overall and event-free survival. A subset of tumors with the highest DHODH expression was associated with a dismal prognosis, with a 5-year survival of less than 10%. In xenograft and transgenic neuroblastoma mouse models treated with the DHODH inhibitor brequinar, tumor growth was dramatically reduced, and survival was extended. Furthermore, brequinar treatment was shown to reduce the expression of MYC targets in 3 neuroblastoma models in vivo. A combination of brequinar and temozolomide was curative in the majority of transgenic TH-MYCN neuroblastoma mice, indicating a highly active clinical combination therapy. Overall, DHODH inhibition combined with temozolomide has therapeutic potential in neuroblastoma, and we propose this combination for clinical testing.
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| 7. |
- Tian, Jingyi, et al.
(author)
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Active control of anapole states by structuring the phase-change alloy Ge2Sb2Te5
- 2019
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In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Journal article (peer-reviewed)abstract
- High-index dielectric nanoparticles supporting a distinct series of Mie resonances have enabled a new class of optical antennas with unprecedented functionalities. The great wealth of multipolar responses has not only brought in new physical insight but also spurred practical applications. However, how to make such a colorful resonance palette actively tunable is still elusive. Here, we demonstrate that the structured phase-change alloy Ge2Sb2Te5 (GST) can support a diverse set of multipolar Mie resonances with active tunability. By harnessing the dramatic optical contrast of GST, we realize broadband (del lambda/lambda similar to 15%) mode shifting between an electric dipole resonance and an anapole state. Active control of higher-order anapoles and multimodal tuning are also investigated, which make the structured GST serve as a multispectral optical switch with high extinction contrasts (>6 dB). With all these findings, our study provides a new direction for realizing active nanophotonic devices.
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| 8. |
- Wang, Fei, et al.
(author)
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Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level
- 2022
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-beta, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia.
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| 9. |
- Dai, Jin, et al.
(author)
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Ultrabroadband super-Planckian radiative heat transfer with artificial continuum cavity states in patterned hyperbolic metamaterials
- 2017
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 95:24
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Journal article (peer-reviewed)abstract
- Localized cavity resonances due to nanostructures at material surfaces can greatly enhance radiative heat transfer (RHT) between two closely placed bodies owing to stretching of cavity states in momentum space beyond the light line. Based on such understanding, we numerically demonstrate the possibility of ultrabroadband super-Planckian RHT between two plates patterned with trapezoidal-shaped hyperbolic metamaterial (HMM) arrays. The phenomenon is rooted not only in HMM's high effective index for creating subwavelength resonators but also its extremely anisotropic isofrequency contour. The two properties enable one to create photonic bands with a high spectral density to populate a desired thermal radiation window. At submicron gap sizes between such two plates, the artificial continuum states extend outside the light cone, tremendously increasing overall RHT. Our study reveals that structured HMM offers unprecedented potential in achieving a controllable super-Planckian radiative heat transfer for thermal management at nanoscale.
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| 10. |
- Dai, Jin, et al.
(author)
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Ultrabroadband super-Planckian radiative heat transfer with artificial continuum cavity states in patterned hyperbolic metamaterials
- 2017
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 95:24
-
Journal article (peer-reviewed)abstract
- Localized cavity resonances due to nanostructures at material surfaces can greatly enhance radiative heat transfer (RHT) between two closely placed bodies owing to stretching of cavity states in momentum space beyond the light line. Based on such understanding, we numerically demonstrate the possibility of ultrabroadband super-Planckian RHT between two plates patterned with trapezoidal-shaped hyperbolic metamaterial (HMM) arrays. The phenomenon is rooted not only in HMM's high effective index for creating subwavelength resonators but also its extremely anisotropic isofrequency contour. The two properties enable one to create photonic bands with a high spectral density to populate a desired thermal radiation window. At submicron gap sizes between such two plates, the artificial continuum states extend outside the light cone, tremendously increasing overall RHT. Our study reveals that structured HMM offers unprecedented potential in achieving a controllable super-Planckian radiative heat transfer for thermal management at nanoscale.
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