96 results on '"Jiamin Xiao"'
Search Results
2. DDHCN: Dual decoder Hyperformer convolutional network for Downstream-Adaptable user representation learning on app usage.
- Author
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Fanrui Zeng, Yizhou Li, Jiamin Xiao, and Denghui Yang
- Published
- 2024
- Full Text
- View/download PDF
Catalog
3. Regulating nitrogen vacancies within graphitic carbon nitride to boost photocatalytic hydrogen peroxide production
- Author
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Yanlin Zhu, Xuetao Liu, Heng Liu, Guangling He, Jiamin Xiao, Haijiao Xie, Yanyan Sun, and Lei Han
- Subjects
carbon nitride ,hydrogen peroxide ,nitrogen vacancies ,oxygen absorption ,Materials of engineering and construction. Mechanics of materials ,TA401-492 ,Environmental engineering ,TA170-171 - Abstract
Abstract Introducing nitrogen vacancies is an effective method to improve the catalytic performance of g‐C3N4‐based photocatalysts, whereas understanding how nitrogen vacancies types affect the catalytic performance remains unclear. Herein, two different types of nitrogen vacancies were successfully introduced into g‐C3N4 by pyrolysis of melamine under argon and ammonia atmosphere with subsequent HNO3 oxidation. The pyrolysis atmosphere is found to have a significant influence on the introduced nitrogen vacancies type, where tertiary nitrogen groups (N3C) and sp2‐hybridized nitrogen atoms (N2C) were the preferred sites for the formation of nitrogen vacancies under ammonia and argon pyrolysis, respectively. Moreover, nitrogen vacancies from N3C are experimentally and theoretically demonstrated to facilitate the narrowed band gap and the improved oxygen absorption capability. As expected, the optimal catalyst exhibits high H2O2 yield of 451.8 µM, which is 3.8 times higher than the pristine g‐C3N4 (119.0 µM) after 4 h and good stability after10 photocatalytic runs. more...
- Published
- 2022
- Full Text
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4. Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae)
- Author
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Jiamin Xiao, Rudan Lyu, Jian He, Mingyang Li, Jiaxin Ji, Jin Cheng, and Lei Xie
- Subjects
Clematis ,cyto-nuclear discordance ,genome partitioning ,genome skimming ,transcriptome ,phylogenomics ,Plant culture ,SB1-1110 - Abstract
Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa. more...
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- 2022
- Full Text
- View/download PDF
5. Preparation and Antibiosis Investigation of Kaolinite Nanotubes and Silver Nanowires Co-Doped Electrospinning-Silk Fibroin/Gelatin Porous Fiber Films
- Author
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Jiamin Xiao, Yanfang Li, Jianliang Wang, Yizhe Xu, Guoren Zhang, and Chongyan Leng
- Subjects
electrospinning ,kaolinite ,silver nanowires ,antibacterial activity ,Mining engineering. Metallurgy ,TN1-997 - Abstract
Skin wounds are one of the most common injuries for the human body; they can lead to an infection and cause tissue necrosis and even life-threatening injuries. Therefore, it is an urgent task to develop skin scaffold materials to meet the various needs of restoring skin’s structural integrity. In this research, kaolinite nanotubes and silver nanowires co-doped silk fibroin and gelatin composite porous fiber films were fabricated by an electrospinning method. The composition, micrograph, chemical states of elements included, biocompatibility, and antimicrobial properties of the samples produced were analyzed. After co-doping kaolinite nanotubes and silver nanowires, the fiber diameter of the porous fiber films became uniform, and the beads in the film were reduced significantly. The silk fibroin/gelatin/kaolinite nanotubes/silver nanowire (SF/GEL/KA-N/AgNWs) film shows antibacterial activity against S. aureus and E. coli, and the antibacterial rings were 7.42 mm and 5.76 mm, respectively. All the films were free of cytotoxicity and provided good biocompatibility, which is a great clinical application potential in skin. more...
- Published
- 2023
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6. Corrigendum: Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae
- Author
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Yike Luo, Jian He, Rudan Lyu, Jiamin Xiao, Wenhe Li, Min Yao, Linying Pei, Jin Cheng, Jinyu Li, and Lei Xie
- Subjects
chloroplast genome ,inversion ,Onagraceae ,phylogeny ,RNA editing ,biparental inheritance ,Genetics ,QH426-470 - Published
- 2022
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7. Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae
- Author
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Yike Luo, Jian He, Rudan Lyu, Jiamin Xiao, Wenhe Li, Min Yao, Linying Pei, Jin Cheng, Jinyu Li, and Lei Xie
- Subjects
chloroplast genome ,inversion ,Onagraceae ,phylogeny ,RNA editing ,biparental inheritance ,Genetics ,QH426-470 - Abstract
The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion. more...
- Published
- 2021
- Full Text
- View/download PDF
8. Direction- and polarization-tunable spontaneous emission beneficial from diffraction orders of a square R6G-nanopore array.
- Author
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Shijia He, Yi Wang, Tianyu Wang, Dongda Wu, Junqiao La, Jiang Hu, Jiamin Xiao, and Wenxin Wang
- Published
- 2023
- Full Text
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9. Revisiting the Role of Sulfur Functionality in Regulating the Electron Distribution of Single‐Atomic Fe Sites Toward Enhanced Oxygen Reduction
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Heng Liu, Luozhen Jiang, Yanyan Sun, Javid Khan, Bin Feng, Jiamin Xiao, Handong Zhang, Haijiao Xie, Lina Li, Shuangyin Wang, and Lei Han
- Subjects
Biomaterials ,Electrochemistry ,Condensed Matter Physics ,Electronic, Optical and Magnetic Materials - Published
- 2023
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10. Water-activated formation of porous graphitic carbon nitride with carbon vacancies to boost photocatalytic hydrogen peroxide production
- Author
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Yanlin Zhu, Handong Zhang, Heng Liu, Guangling He, Xuetao Liu, Jiamin Xiao, Yanyan Sun, and Lei Han
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Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,General Chemistry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
A facile water-activated method is developed for preparing porous graphitic carbon nitride with carbon vacancies by co-pyrolysis of melamine and water at a relatively low temperature under an Ar atmosphere, resulting in an increased specific surface area and the efficient separation of photo-generated electrons and holes. As expected, the optimal catalyst exhibited a high H more...
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- 2022
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11. Entanglement generation by strong coupling between surface lattice resonance and exciton in an Al nanoarray-coated WS2 quantum emitter
- Author
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Xiaoqi Shi, Zhihang Wang, Jiamin Xiao, Lingyao Li, Shibo Wei, Zhicheng Guo, Yi Wang, and Wenxin Wang
- Abstract
Strong light–matter interaction plays a central role in realizing quantum photonic technologies. The entanglement state, which results from the hybridization of excitons and cavity photons, forms the foundation of quantum information science. In this work, an entanglement state is achieved by manipulating the mode coupling between surface lattice resonance and quantum emitter into the strong coupling regime. At the same time, a Rabi splitting of 40 meV is observed. A full quantum model based on the Heisenberg picture is used to describe this unclassical phenomenon, and it perfectly explains the interaction and dissipation process. In addition, the observed concurrency degree of the entanglement state is 0.5, presenting the quantum nonlocality. This work effectively contributes to the understanding of nonclassical quantum effects arising from strong coupling and will intrigue more interesting potential applications in quantum optics. more...
- Published
- 2023
- Full Text
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12. Decorating Single‐Atomic Mn Sites with FeMn Clusters to Boost Oxygen Reduction Reaction
- Author
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Heng Liu, Luozhen Jiang, Javid Khan, Xinxin Wang, Jiamin Xiao, Handong Zhang, Haijiao Xie, Lina Li, Shuangyin Wang, and Lei Han
- Subjects
General Medicine ,General Chemistry ,Catalysis - Abstract
The regulation of electron distribution of single-atomic metal sites by atomic clusters is an effective strategy to boost their intrinsic activity of oxygen reduction reaction (ORR). Herein we report the construction of single-atomic Mn sites decorated with atomic clusters by an innovative combination of post-adsorption and secondary pyrolysis. The X-ray absorption spectroscopy confirms the formation of Mn sites via Mn-N4 coordination bonding to FeMn atomic clusters (FeMnac/Mn-N4C), which has been demonstrated theoretically to be conducive to the adsorption of molecular O2 and the break of O-O bond during the ORR process. Benefiting from the structural features above, the FeMnac/Mn-N4C catalyst exhibits excellent ORR activity with half-wave potential of 0.79 V in 0.5 M H2SO4 and 0.90 V in 0.1 M KOH as well as preeminent Zn-air battery performance. Such synthetic strategy may open up a route to construct highly active catalysts with tunable atomic structures for diverse applications. more...
- Published
- 2022
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13. Entanglement generation by strong coupling between surface lattice resonance and exciton in an Al nanoarray coated WS2 quantum emitter
- Author
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Xiaoqi Shi, Zhihang Wang, Jiamin Xiao, Lingyao Li, Shibo Wei, Zhicheng Guo, Yi Wang, and Wenxin Wang
- Abstract
Strong light-matter interaction plays a central role in realizing quantum photonic technologies. The entanglement state, which results from the hybridization of excitons and cavity photons, forms the foundation of quantum information science. In this work, an entanglement state is achieved by manipulating the mode coupling between surface lattice resonance and quantum emitter into the strong coupling regime. At the same time, a Rabi splitting of 40 meV is observed. A full quantum model based on the Heisenberg picture is used to describe this unclassical phenomenon, and it perfectly explains the interaction and dissipation process. In addition, the observed concurrency degree of the entanglement state is 0.5, presenting the quantum non-locality. This work effectively contributes to the understanding of non-classical quantum effects arising from strong coupling and will intrigue more interesting potential applications in quantum optics. more...
- Published
- 2022
- Full Text
- View/download PDF
14. Bound states in the continuum induced by the strong coupling within the plasmonic lattices
- Author
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Zhihang Wang, Lingyao Li, Xiaoqi Shi, Jiamin Xiao, Zhicheng Guo, and Wenxin Wang
- Subjects
General Physics and Astronomy - Abstract
Bound states in the continuum (BICs), manifesting themselves as the collapse of Fano resonance, are observed in many photonic and plasmonic systems. The BICs have been studied systematically through various methods such as the topological photonics analysis, temporal coupled mode theory, multipole decomposition method, and the cavity quantum electrodynamics (CQED) method. Since CQED can give a macroscopic and intrinsic description of light–matter interaction, it is expected to study BIC that participates in strong coupling. What is more, the relation between coupling strength, the Fano parameter, and the asymmetry property of BICs needs to be clarified. In this paper, we investigated the strong coupling between the cavity mode and Bloch-surface plasmon polariton (Bloch-SPP) mode induced by BICs within the plasmonic lattices of the metal-dielectric-metal (MDM) layer. The properties of strong coupling and BIC were revealed theoretically by the quantum model based on the CQED. The increase in the Fano parameters of BICs was proved to facilitate the coupling strength, which was indicated by the monotonically increasing relation between the Fano parameter and the coupling strength. This work may pave the way for flexible modulation and application of BIC in the fields of high-quality plasmonic nanocavity, low-threshold nano-lasers, and quantum information. more...
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- 2023
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15. Synthesis of heteroatom incorporated porous carbon encapsulated Fe-doped Co9S8 as an efficient bifunctional electrocatalyst for overall water splitting
- Author
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Javid Khan, Heng Liu, Jiamin Xiao, Yanlin Zhu, Asif Hayat, Hameed Ullah, Gulzar Ahmed, Handong Zhang, Yanyan Sun, and Lei Han
- Subjects
General Materials Science ,General Chemistry ,Condensed Matter Physics - Published
- 2023
- Full Text
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16. Feature importance analysis in guide strand identification of microRNAs.
- Author
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Daichuan Ma, Jiamin Xiao, Yizhou Li, Yuanbo Diao, Yanzhi Guo, and Menglong Li
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- 2011
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17. Atomic dynamics of stress-induced lattice misalignment structures in a KDP subsurface
- Author
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Hezhu Shao, Jun Zhuang, Ying Hu, Jiamin Xiao, Min Xu, Zhen Zhu, and Linlin Zhao
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010302 applied physics ,Materials science ,General Chemical Engineering ,Stress induced ,02 engineering and technology ,General Chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic units ,Crystal ,Ab initio molecular dynamics ,Chemical physics ,Lattice (order) ,0103 physical sciences ,Thermal stability ,Structural deformation ,0210 nano-technology - Abstract
We present an ab initio molecular dynamics study of the thermal stability and dynamics behaviors of lattice misalignment structures (LMSs) in the subsurface layers of KH2PO4 (KDP) crystals. The dehydration process at the atomic scale is observed in the LMS system, which is the same as that in a perfect KDP crystal. However, the paths entering the dehydration process are various. The interesting result is that compared with a perfect KDP crystal, many new paths appear in the LMS system, and even in the same paths, the dehydration is more likely to happen in the LMS system. This leads to a dramatic increase in the dehydration numbers in the LMS system, for which the reasons are given in terms of structural deformation and/or uneven distribution of protons. The results elucidate the underlying atomic mechanism of the effect of LMS defects on the thermal stability of KDP material. more...
- Published
- 2020
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18. Mid-long wavelength infrared absorptance of hyperdoped silicon via femtosecond laser microstructuring
- Author
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Haibin Sun, Xiaolong Liu, Li Zhao, Jianxin Jia, Changhui Jiang, Jiamin Xiao, Yuwei Chen, Long Xu, Zhiyong Duan, Peng Rao, Shengli Sun, Maanmittauslaitos, National Land Survey of Finland, Chinese Academy of Sciences, Department of Electronics and Nanoengineering, Fudan University, Finnish Geospatial Research Institute, Southwest University, Zhengzhou University, Aalto-yliopisto, and Aalto University more...
- Subjects
Solar cells ,Optical absorption ,Femtosecond lasers ,Laser irradiation ,Scanning electron microscopy ,Atomic and Molecular Physics, and Optics ,Laser beams - Abstract
Hyperdoped silicon (hSi) fabricated via femtosecond laser irradiation has emerged as a promising photoelectric material with strong broadband infrared (IR) absorption. In this work, we measured the optical absorptance of the hSi in the wavelength of 0.3–16.7 µm. Unlike the near to mid wavelength IR absorption, the mid-long wavelength IR (M–LWIR) absorption is heavily dependent on the surface morphology and the dopants. Furthermore, calculations based on coherent potential approximation (CPA) reveal the origin of free carrier absorption, which plays an important role in the M–LWIR absorption. As a result, a more comprehensive picture of the IR absorption mechanism is drawn for the optoelectronic applications of the hSi. more...
- Published
- 2022
19. Manipulating light–matter interaction into strong coupling regime for photon entanglement in plasmonic lattices
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Zhihang Wang, Lingyao Li, Shibo Wei, Xiaoqi Shi, Jiamin Xiao, Zhicheng Guo, Wei Wang, Yi Wang, and Wenxin Wang
- Subjects
General Physics and Astronomy - Abstract
Enhancing light–matter interaction into the strong coupling regime attracts tremendous attention in both theory and experiment, which presents essential significance in research from nano-optics to quantum information. In this work, the entanglement effect is observed in the photons emitted from a plasmonic lattice as the coherent light–matter interaction occurs into the strong coupling regime with a Rabi splitting of 93.4 meV. A full quantum mechanical treatment based on the number state representation is established to reveal the underlying physics of the strong coupling phenomenon, especially the femtosecond dynamics of energy exchange and damping. The entangled split states display oscillating concurrence and negative Wigner quasiprobability distribution function, which demonstrates that this designed plasmonic lattice system can serve as an on-demand entangled photon source for quantum information. more...
- Published
- 2023
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20. Directional amplified spontaneous emissions from Ag nanohole array with high diffraction orders
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Yujun Liu, Fanzhou Lv, Jiamin Xiao, Dongda Wu, Junqiao La, Xiaoli Yin, Yi Wang, and Wenxin Wang
- Subjects
Atomic and Molecular Physics, and Optics - Abstract
Surface plasmon excitations in metallic hole arrays have been extensively studied in the context of light–matter interaction, since the generated Bloch surface plasmon polariton (Bloch-SPP) exhibits unique properties of nanoscale light confinement, near-field enhancements, and long-range metal surface propagation. In this work, we experimentally demonstrate a plasmonic device that exhibits highly directional emission in visible light; using Ag film with a thickness of 100 nm deposited on a subwavelength porous alumina array as a plasmonic cavity, four-level rhodamine 6G (R6G) is selected as the gain material. It is suggested that a Bloch-SPP with high diffraction orders on a Ag nanohole array can generate a strong local electric field and a high Purcell factor at a nanohole edge. Moreover, directional five-fold enhanced amplified spontaneous emission (ASE) with polarization dependence is observed under a low threshold of 199.9 W/cm2 in the visible light region, which comes from the optical feedback provided by the 2D periodic nanohole array. This work opens up a wide range of applications for real-time tunable wavelength, controlled multimode laser, fluorescence detection, etc. more...
- Published
- 2023
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21. Urchin‐Like Structured MoO 2 /Mo 3 P/Mo 2 C Triple‐Interface Heterojunction Encapsulated within Nitrogen‐Doped Carbon for Enhanced Hydrogen Evolution Reaction
- Author
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Jiamin Xiao, Shishi Zhang, Yanyan Sun, Xuetao Liu, Guangling He, Heng Liu, Javid Khan, Yanlin Zhu, Yaqiong Su, Shuangyin Wang, and Lei Han
- Subjects
Biomaterials ,General Materials Science ,General Chemistry ,Biotechnology - Published
- 2023
- Full Text
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22. Boosting oxygen reduction with coexistence of single-atomic Fe and Cu sites decorated nitrogen-doped porous carbon
- Author
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Heng Liu, Luozhen Jiang, Yamin Wang, Xinxin Wang, Javid Khan, Yanlin Zhu, Jiamin Xiao, Lina Li, and Lei Han
- Subjects
General Chemical Engineering ,Environmental Chemistry ,General Chemistry ,Industrial and Manufacturing Engineering - Published
- 2023
- Full Text
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23. Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae
- Author
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Linying Pei, Jinyu Li, Jian He, Min Yao, Jiamin Xiao, Jin Cheng, Lei Xie, Yike Luo, Wenhe Li, and Rudan Lyu
- Subjects
RNA editing ,food.ingredient ,Oenothera ,Onagraceae ,QH426-470 ,theater ,phylogeny ,Genome ,inversion ,food ,Phylogenetics ,Epilobium ,Genetics ,Genetics (clinical) ,Circaea ,Original Research ,biology ,food and beverages ,IR expansion ,biology.organism_classification ,Evening primrose ,Chamaenerion ,biparental inheritance ,Evolutionary biology ,Molecular Medicine ,theater.play ,chloroplast genome - Abstract
The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion. more...
- Published
- 2021
24. A new method to characterize sludge stickiness during drying: Effects of sludge temperature and calcium oxide (CaO) on stickiness
- Author
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Zhicheng Lai, Jiamin Xiao, Wenyi Deng, and Yaxin Su
- Subjects
General Chemical Engineering ,04 agricultural and veterinary sciences ,02 engineering and technology ,Adhesion ,Pulp and paper industry ,040401 food science ,chemistry.chemical_compound ,0404 agricultural biotechnology ,020401 chemical engineering ,chemistry ,Cohesion (geology) ,0204 chemical engineering ,Physical and Theoretical Chemistry ,Calcium oxide ,Sludge - Abstract
Stickiness is a phenomenon widely observed in drying practices of sewage sludge. This work is aimed at demonstrating the effects of sludge temperature (30–70 °C) and calcium oxide (CaO) on the stic... more...
- Published
- 2019
- Full Text
- View/download PDF
25. Orthogonal experimental study on hydrothermal treatment of municipal sewage sludge for mechanical dewatering followed by thermal drying
- Author
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Wenyi Deng, Jiamin Xiao, Lei Wang, Yaxin Su, and Jinchen Ma
- Subjects
Renewable Energy, Sustainability and the Environment ,020209 energy ,Strategy and Management ,05 social sciences ,Chemical oxygen demand ,02 engineering and technology ,Pulp and paper industry ,Dewatering ,Industrial and Manufacturing Engineering ,Hydrothermal circulation ,chemistry.chemical_compound ,chemistry ,050501 criminology ,0202 electrical engineering, electronic engineering, information engineering ,Sewage treatment ,Particle size ,Calcium oxide ,Water content ,Sludge ,0505 law ,General Environmental Science - Abstract
This work is aimed at demonstrating the effect of hydrothermal treatment on the mechanical dewatering, thermal drying and stickiness of sewage sludge from two different wastewater treatment plants (SS1 and SS2). The analysis of particle size, microstructure and volatile matter content of sludge was conducted to explore the influencing mechanism of hydrothermal treatment. The impact and significance of three factors, i.e. hydrothermal temperature (130–220 °C), retention time (30–75 min) and calcium oxide content (0–5 wt.%), were studied by an orthogonal method. Range and variable analysis were carried out to investigate the significance of the factors. The results indicated that sludge particle size showed a 10–25% reduction after hydrothermal treatment, indicating a degradation of EPS and bacterial cells, which was also confirmed by microstructural analysis. Sludge dewatering performance was markedly promoted by increasing hydrothermal temperature, intention time or CaO content. But CaO showed 1.8–7.8 times higher significance than that of hydrothermal temperature and intention time. On the other hand, both hydrothermal temperature and retention time showed 2–5 times higher significance on chemical oxygen demand of filtrate and drying rate of dewatered sludge cakes than that of CaO. Increasing hydrothermal temperature or retention time led to the increase of the chemical oxygen demand and the decrease of the drying rate in general. Sludge decomposition was also manifested by the change of its volatile matter content which showed a strong positive correlation with the water content of dewatered sludge cakes and a negative correlation with the adhesive and cohesive stress of dewatered sludge cakes. Finally, the economic efficiency of hydrothermal treated sludge dewatering and thermal drying system was calculated and compared with that of conventional direct thermal drying. The total energy consumption of the system is about 25–40% lower than conventional drying for both of sludge, and the operation cost of the system is about 17–30% lower than that of the conventional drying. more...
- Published
- 2019
- Full Text
- View/download PDF
26. NaClO-induced sodium-doped cyano-rich graphitic carbon nitride nanosheets with nitrogen vacancies to boost photocatalytic hydrogen peroxide production
- Author
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Yanlin Zhu, Yanyan Sun, Javid Khan, Heng Liu, Guangling He, Xuetao Liu, Jiamin Xiao, Haijiao Xie, and Lei Han
- Subjects
General Chemical Engineering ,Environmental Chemistry ,General Chemistry ,Industrial and Manufacturing Engineering - Published
- 2022
- Full Text
- View/download PDF
27. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae
- Author
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Lei Xie, Jiamin Xiao, Jin Cheng, Yike Luo, Wenhe Li, Rudan Lyu, Jun Wen, Linying Pei, and Jian He
- Subjects
biology ,Introgression ,Silica Gel ,Ranunculaceae ,Phylogenetic network ,biology.organism_classification ,Coalescent theory ,Plant Leaves ,Evolutionary biology ,Phylogenetics ,Ranunculales ,GenBank ,Genetics ,RNA ,Clade ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using this data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms. more...
- Published
- 2022
- Full Text
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28. Application of boundary electro-osmotic pulse to reduce sludge-to-wall adhesion
- Author
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Yaxin Su, Wenyi Deng, Jiamin Xiao, Jie Zhou, Sirui Pan, Zhichen Lai, and Li Yu
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Environmental Engineering ,Materials science ,0208 environmental biotechnology ,02 engineering and technology ,010501 environmental sciences ,Wastewater ,01 natural sciences ,Waste Disposal, Fluid ,Cathodic protection ,law.invention ,law ,Composite material ,Waste Management and Disposal ,Water content ,Electrodes ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Sewage ,Ecological Modeling ,Water ,Pollution ,Cathode ,020801 environmental engineering ,Anode ,Adhesive ,Current density ,Sludge ,Intensity (heat transfer) - Abstract
Adhesion is one of the main features of sewage sludge. This paper aims at reducing sludge-to-wall adhesion through formation of a water layer induced by boundary electro-osmotic pulse (BEOP) which is characterized by distributing anodes and cathodes on one surface and exerting a pulsating current. The effects of the related parameters, including current intensity, exerting time, frequency, duty cycle (DTC), and the ratio of cathodic surface area to anodic surface area (C/A), on the adhesive stress of sewage sludge with different moisture content were thoroughly studied. The results indicated that, under the optimal conditions of BEOP, the adhesive stress of sludge with moisture content of 35%, 45%, 60% and 70% was reduced by 40.4%, 54.5%, 31%, and 24.4%, respectively. The migrations of water, ions and organic matters were also investigated to explore the functional mechanism of BEOP. The results showed that the water migrated from the anode side to the cathode side, whereas the organic matters migrated in the opposite direction. The increment of the sludge moisture content on the cathode surface was reduced with the increase of distance away from the anode. Based on theoretical modeling, the distributions of current density and temperature in sludge cake were obtained. The current flowed from anode to cathode and decayed quickly with the increase of the flowing distance, which well explained the moisture content distribution in sludge cake. more...
- Published
- 2020
29. Boron-doped cobalt-iron bimetal phosphides nanosheets for enhanced oxygen evolution
- Author
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Jiamin Xiao, Xuetao Liu, Yanlin Zhu, Lei Han, Guangling He, and Heng Liu
- Subjects
Tafel equation ,Materials science ,Mechanical Engineering ,Metals and Alloys ,Oxygen evolution ,chemistry.chemical_element ,Catalysis ,Bimetal ,Chemical engineering ,chemistry ,Mechanics of Materials ,Materials Chemistry ,Water splitting ,Bimetallic strip ,Cobalt ,Nanosheet - Abstract
Developing highly efficient earth-abundant catalysts for the electrochemical oxygen evolution reaction (OER) is essential to promote the commercial application of water splitting. Herein boron-doped cobalt-iron bimetal phosphides nanosheets as OER electrocatalysts have been successfully prepared by hydrothermal boronation of bimetallic metal-organic frameworks precursors with the subsequent low-temperature phosphidation. The synergistic effect between non-metal elements (B and P) and metals (Co and Fe) is found to play an important role on tuning the local electronic configuration surrounding the active metal centers. Moreover, the resultant nanosheet structures are beneficial for exposing the catalytically active sites and facilitating the mass/charge transport. As expected, the optimal catalyst exhibits superior catalytic performance toward the OER with long-term durability in 1.0 M KOH, affording a current density of 10 mA cm−2 at low over-potential of 294 mV and small Tafel slope of 49.5 mV dec−1. more...
- Published
- 2022
- Full Text
- View/download PDF
30. Novel feature for catalytic protein residues reflecting interactions with other residues.
- Author
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Yizhou Li, Gongbing Li, Zhining Wen, Hui Yin, Mei Hu, Jiamin Xiao, and Menglong Li
- Subjects
Medicine ,Science - Abstract
Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship. more...
- Published
- 2011
- Full Text
- View/download PDF
31. An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene
- Author
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Jin Cheng, Yike Luo, Rudan Lyu, Lei Xie, Shuangxi Yan, Lele Lin, Linying Pei, Jian He, Jin-Yu Li, Min Yao, Jun Wen, Jiamin Xiao, and Liang-Qian Li
- Subjects
Clematis ,Pleistocene ,Phylogenetic tree ,Range (biology) ,Bayes Theorem ,Biology ,Late Miocene ,biology.organism_classification ,DNA, Ribosomal ,Habits ,Evolutionary biology ,Phylogenetics ,Convergent evolution ,Genetics ,Taxonomy (biology) ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas. more...
- Published
- 2021
- Full Text
- View/download PDF
32. Cu-doped molybdenum carbide encapsulated within two-dimensional nanosheets assembled hierarchical tubular nitrogen-doped carbon for enhanced hydrogen evolution
- Author
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Heng Liu, Yanlin Zhu, Guangling He, Jiamin Xiao, Xuetao Liu, and Lei Han
- Subjects
Tafel equation ,Hydrogen bond ,Chemistry ,General Chemical Engineering ,chemistry.chemical_element ,Electrolyte ,Electrocatalyst ,Analytical Chemistry ,Catalysis ,Chemical engineering ,Electrochemistry ,Nanorod ,Carbon ,Hydrogen production - Abstract
The development of low cost and high efficiency electrocatalyst for hydrogen evolution reaction (HER) is a key step in the realization of hydrogen production from electrolytic water. In this study, we report a feasible strategy to fabricate Cu-doped molybdenum carbide encapsulated within two-dimensional nanosheets assembled hierarchical tubular nitrogen-doped carbon (Cu/Mo2C@HTNC) through the coordination reaction between MoO3 nanorod as template and dopamine in alkaline medium followed by two-step consecutive pyrolysis. The effective Cu doping into Mo2C crystal structure is found to increase the electron density around Mo and catalytic active sites density for optimizing the strength of Mo–H bond, thus facilitating the HER process. As expected, the optimal Cu/Mo2C@HTNC exhibits excellent HER performance with a low over-potential of 113 mV at a current density of 10 mA cm−2 and a small Tafel slope of 55 mV dec−1 as well as excellent stability in 1 M KOH. more...
- Published
- 2021
- Full Text
- View/download PDF
33. Borate Anion Dopant Inducing Oxygen Vacancies over Co3O4 Nanocages for Enhanced Oxygen Evolution
- Author
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Jiamin Xiao, Lei Han, Yanlin Zhu, Xuetao Liu, Heng Liu, and Guangling He
- Subjects
Materials science ,TP1-1185 ,02 engineering and technology ,Overpotential ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,Catalysis ,oxygen vacancies ,oxygen evolution ,chemistry.chemical_compound ,Nanocages ,Imidazolate ,Physical and Theoretical Chemistry ,QD1-999 ,borate anion dopant ,Tafel equation ,Dopant ,Chemical technology ,Oxygen evolution ,Co3O4 nanocages ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Chemistry ,Chemical engineering ,chemistry ,Water splitting ,0210 nano-technology - Abstract
The rational design of cost effective and highly efficient oxygen evolution reaction (OER) catalysts plays an extremely important role in promoting the commercial applications of electrochemical water splitting. Herein we reported a sacrificial template strategy for the preparation of borate anion doped Co3O4@ZIF-67 nanocages assembled with nanosheets (B-Co3O4@ZIF-67) by hydrothermal boronation of zeolitic imidazolate framework-67 (ZIF-67). During the preparation process, two different kinds of borate anion sources were found to regulate the morphological structures by tuning the etching rate between ZIF precursors and the borate anion. Moreover, borate anion doping was also found to induce oxygen vacancy defects, which is beneficial for modulating the electronic structure and accelerating electron transport. Meanwhile, the resultant B-Co3O4@ZIF-67 nanocages possess a large specific surface area, which is beneficial for the mass transfer of the electrolyte and exposing more catalytic active sites. Benefiting from the advantages above, the resultant B-Co3O4@ZIF-67 nanocages exhibit impressive OER performance with a small overpotential of 334 mV, a current density of 10 mA cm−2, a small Tafel slope of 73.88 mV dec−1, as well as long-term durability in an alkaline electrolyte. more...
- Published
- 2021
- Full Text
- View/download PDF
34. Predicting disease-associated substitution of a single amino acid by analyzing residue interactions.
- Author
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Yizhou Li, Zhining Wen, Jiamin Xiao, Hui Yin, Lezheng Yu, Li Yang, and Menglong Li
- Published
- 2011
- Full Text
- View/download PDF
35. Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure.
- Author
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Jiamin Xiao, Xiaojing Tang, Yizhou Li, Zheng Fang, Daichuan Ma, Yangzhige He, and Menglong Li
- Published
- 2011
- Full Text
- View/download PDF
36. In silico method for systematic analysis of feature importance in microRNA-mRNA interactions.
- Author
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Jiamin Xiao, Yizhou Li, Kelong Wang, Zhining Wen, Menglong Li, Lifang Zhang, and Xuanmin Guang
- Published
- 2009
- Full Text
- View/download PDF
37. Crystallinity and Sub-Band Gap Absorption of Femtosecond-Laser Hyperdoped Silicon Formed in Different N-Containing Gas Mixtures
- Author
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Haibin Sun, Jun Zhuang, Li Zhao, Yue Hu, Suwan Zhu, Jiamin Xiao, and Guojin Feng
- Subjects
hyperdoped ,Materials science ,Silicon ,Band gap ,Analytical chemistry ,chemistry.chemical_element ,02 engineering and technology ,01 natural sciences ,Article ,nitrogen ,Crystallinity ,femtosecond laser ,0103 physical sciences ,General Materials Science ,Surface layer ,Absorption (electromagnetic radiation) ,crystallinity ,sub-band gap absorption ,010302 applied physics ,Doping ,021001 nanoscience & nanotechnology ,Nitrogen ,chemistry ,Femtosecond ,0210 nano-technology - Abstract
Femtosecond (fs)-laser hyperdoped silicon has aroused great interest for applications in infrared photodetectors due to its special properties. Crystallinity and optical absorption influenced by co-hyperdoped nitrogen in surface microstructured silicon, prepared by fs-laser irradiation in gas mixture of SF6/NF3 and SF6/N2 were investigated. In both gas mixtures, nitrogen and sulfur were incorporated at average concentrations above 1019 atoms/cm3 in the 20–400 nm surface layer. Different crystallinity and optical absorption properties were observed for samples microstructured in the two gas mixtures. For samples prepared in SF6/N2, crystallinity and light absorption properties were similar to samples formed in SF6. Significant differences were observed amongst samples formed in SF6/NF3, which possess higher crystallinity and strong sub-band gap absorption. The differing crystallinity and light absorption rates between the two types of nitrogen co-hyperdoped silicon were attributed to different nitrogen configurations in the doped layer. This was induced by fs-laser irradiating silicon in the two N-containing gas mixtures. more...
- Published
- 2017
- Full Text
- View/download PDF
38. Systematic analysis revealed better performance of random forest algorithm coupled with complex network features in predicting microRNA precursors
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Jiamin Xiao, Zheng Fang, Zhining Wen, Xiaojing Tang, Menglong Li, and Yizhou Li
- Subjects
Basis (linear algebra) ,Computer science ,Process Chemistry and Technology ,Function (mathematics) ,Complex network ,Net (mathematics) ,computer.software_genre ,Computer Science Applications ,Analytical Chemistry ,Random forest ,Identification (information) ,Permutation ,Feature (machine learning) ,Data mining ,computer ,Spectroscopy ,Software - Abstract
The improvement of computational methods greatly benefits the investigation of miRNAs. Our study validates the features in miRNA identification with an independent dataset, and provides researchers with common practices of the development of predictive models. A total number of 84 representative features, which occurred in researches of miRNAs classification, have been extracted and divided into four feature sets, i.e. complex network feature set (NET), structural feature set (STRUC), thermodynamic feature set (THERMO), and hybrid feature set (TOTAL). Systematic analysis is carried out on network, structural, thermodynamic and hybrid features. The dominant features are discriminated from uninformative features in both single and hybrid sets, on the basis of permutation importance strategy. Random forest models are constructed using only informative network, structural, thermodynamic and hybrid variables, resulting in area under the receiver operating curve (AUC) values of 0.9611, 0.9563, 0.9351, and 0.9469, respectively, based on validated datasets. The result suggests that the best performance could be got by using features derived from complex network. These results would be invaluable in understanding biological mechanism and function of miRNAs. All the data and scripts used in this article are freely available for download at http://cic.scu.edu.cn/bioinformatics/Extended_miRNA.zip . more...
- Published
- 2012
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39. Composition-dependent band gaps and indirect-direct band gap transitions of group-IV semiconductor alloys
- Author
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Jun Zhuang, Yin Wang, Ronggen Cao, Haibin Sun, Zhen Zhu, Yue Hu, Jiamin Xiao, and Li Zhao
- Subjects
Materials science ,Condensed matter physics ,Bowing ,Band gap ,Alloy ,General Physics and Astronomy ,engineering.material ,Semimetal ,Transition point ,engineering ,Coherent potential approximation ,Direct and indirect band gaps ,Physical and Theoretical Chemistry ,Line (formation) - Abstract
We used the coherent potential approximation to investigate the band structures of group-IV semiconductor alloys, including Si(x)Ge(1-x), Ge(1-y)Sn(y) and Si(x)Ge(1-x-y)Sn(y). The calculations for Si(x)Ge(1-x) prove the reliability and accuracy of the method we used. For Ge(1-y)Sn(y), the direct band gap optical bowing parameter we obtained is 2.37 eV and the indirect-direct band gap transition point is at y = 0.067, both consistent with the existing experimental data. For Si(x)Ge(1-x-y)Sn(y), with the increase of the Si concentration, the compositional dependency of the band gap becomes complex. An indirect-direct band gap transition is found in Si(x)Ge(1-x-y)Sn(y) in the range of 0x≤ 0.20, and the indirect-direct crossover line in the compositional space has the quadratic form of y = 3.4x(2) + 1.11x + 0.07, not the linear form as suggested before. Furthermore, for the Ge lattice-matched alloy Ge(1-x()Si0.79Sn0.21)(X), our results show that those with 0.18X0.253 have band gaps larger than 0.8 eV at room temperature. more...
- Published
- 2015
40. Insight into Effects of Disordered Sulfur on the Electronic Band Structure of S-hyperdoped Silicon
- Author
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Jiamin Xiao, Zhen Zhu, and Jun Zhuang
- Subjects
Crystallography ,Solar cell efficiency ,Materials science ,chemistry ,Silicon ,Condensed matter physics ,Physics::Instrumentation and Detectors ,Impurity ,chemistry.chemical_element ,Electronic structure ,Thin film ,Electronic band structure ,Sulfur - Abstract
We employ supercells to investigate the electronic structure of hyperdoped silicon with periodic S and random distribution of S, respectively and reveal disordering of impurities on the band structure of hyperdoped silicon cannot be ignored. more...
- Published
- 2015
- Full Text
- View/download PDF
41. Using auto covariance method for functional discrimination of membrane proteins based on evolution information.
- Author
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Li Yang, Yizhou Li, Rongquan Xiao, Yuhong Zeng, Jiamin Xiao, Fuyuan Tan, and Menglong Li
- Subjects
BIOLOGICAL transport ,MEMBRANE proteins ,BIOLOGICAL membranes ,SUPPORT vector machines ,AMINO acid sequence - Abstract
Membrane transporters are critical in living cells. Therefore, the discrimination of the types of membrane proteins based on their functions is of great importance both for helping genome annotation and providing a supplementary role to experimental researchers to gain insight into membrane proteins’ function. There are a lot of computational methods to facilitate the identification of the functional types of membrane proteins. However, in these methods, the local sequence environment was not integrated into the constructed model. In this study, we described a new strategy to predict the functional types of membrane proteins using a model based on auto covariance and position-specific scoring matrix. The novelty of the presented approach is considering the distribution of different positions of functional conservation sites in protein sequences. Thereby, this model adequately takes into account the long-range correlation between such sites during sequential evolution. Fivefold cross-validation test shows that this method greatly improves the prediction accuracy and achieves an acceptable prediction accuracy of 87.51%. The result indicates that the current approach might be an effective tool for predicting the functional types of membrane proteins only using the primary sequences. The code and dataset used in this article are freely available at . [ABSTRACT FROM AUTHOR] more...
- Published
- 2010
- Full Text
- View/download PDF
42. Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure
- Author
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Zheng Fang, Jiamin Xiao, Xiaojing Tang, Daichuan Ma, Menglong Li, Yizhou Li, and Yangzhige He
- Subjects
Feature extraction ,Stability (learning theory) ,Biology ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Artificial Intelligence ,Structural Biology ,RNA Precursors ,Feature (machine learning) ,Animals ,Humans ,RNA, Messenger ,Representation (mathematics) ,lcsh:QH301-705.5 ,Molecular Biology ,Complement (set theory) ,Genetics ,Models, Statistical ,business.industry ,Applied Mathematics ,Pattern recognition ,Stem-loop ,Computer Science Applications ,Random forest ,MicroRNAs ,Identification (information) ,lcsh:Biology (General) ,lcsh:R858-859.7 ,Nucleic Acid Conformation ,Artificial intelligence ,business ,Algorithms ,Research Article - Abstract
Background MicroRNAs (miRNAs) play a key role in regulating various biological processes such as participating in the post-transcriptional pathway and affecting the stability and/or the translation of mRNA. Current methods have extracted feature information at different levels, among which the characteristic stem-loop structure makes the greatest contribution to the prediction of putative miRNA precursor (pre-miRNA). We find that none of these features alone is capable of identifying new pre-miRNA accurately. Results In the present work, a pre-miRNA stem-loop secondary structure is translated to a network, which provides a novel perspective for its structural analysis. Network parameters are used to construct prediction model, achieving an area under the receiver operating curves (AUC) value of 0.956. Moreover, by repeating the same method on two independent datasets, accuracies of 0.976 and 0.913 are achieved, respectively. Conclusions Network parameters effectively characterize pre-miRNA secondary structure, which improves our prediction model in both prediction ability and computation efficiency. Additionally, as a complement to feature extraction methods in previous studies, these multifaceted features can reflect natural properties of miRNAs and be used for comprehensive and systematic analysis on miRNA. more...
- Published
- 2011
- Full Text
- View/download PDF
43. Feature importance analysis in guide strand identification of microRNAs
- Author
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Jiamin Xiao, Yuanbo Diao, Menglong Li, Daichuan Ma, Yanzhi Guo, and Yizhou Li
- Subjects
Guanine ,Base pair ,Computational biology ,Biochemistry ,Negative regulator ,Cytosine ,Mice ,Schmidtea mediterranea ,Structural Biology ,RNA interference ,microRNA ,Gene expression ,Databases, Genetic ,Animals ,Platypus ,Base Pairing ,Genetics ,biology ,Organic Chemistry ,Computational Biology ,Planarians ,biology.organism_classification ,Random forest ,Computational Mathematics ,MicroRNAs ,ROC Curve ,Homo sapiens ,RNA Interference ,Algorithms - Abstract
Graphical abstractDisplay Omitted Highlights? In this study, we constructed random forest models based on local sequence-structure feature to identify miRNA in four species. ? We achieved the accuracies of 86.51% for Homo sapiens, 81.66% for Ornithorhynchus anatinus, 82.33% for Mus musculus and 85.71% for Schmidtea mediterranea, respectively. ? We implemented the importance analysis of all feature elements by using the conditional feature importance strategy. ? We concluded that the GC base pair is crucial to the selection of guide strand. MicroRNA (miRNA) is the negative regulator of gene expression, also known as guide strand of transient miRNA:miRNA* duplex. It is critical in maintaining the normal physiological processes such as development, differentiation, and apoptosis in many organisms. With increasing miRNA data, it is desirable to design methods to identify guide strand based on machine learning algorithms. In this study, the random forest models based on local sequence-structure features were proposed to identify miRNA in four species. The accuracies achieved were 86.51% for Homo sapiens, 81.66% for Ornithorhynchus anatinus, 82.33% for Mus musculus and 85.71% for Schmidtea mediterranea, respectively. Furthermore, the important analysis of feature elements was carried out by using the conditional feature importance strategy. The analysis results revealed that most of the significant elements were related to guanine-cytosine (GC) base pair. We believed that our method could be beneficial to annotate the function of miRNA and help the further understanding of the RNA interference mechanism. more...
- Published
- 2011
44. Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
- Author
-
Li Yang, Lezheng Yu, Hui Yin, Menglong Li, Jiamin Xiao, Zhining Wen, and Yizhou Li
- Subjects
DNA Mutational Analysis ,Single-nucleotide polymorphism ,Biology ,lcsh:Computer applications to medicine. Medical informatics ,Biochemistry ,Polymorphism, Single Nucleotide ,Structural Biology ,Sequence Analysis, Protein ,Humans ,Cluster coefficient ,Single amino acid ,Databases, Protein ,Molecular Biology ,lcsh:QH301-705.5 ,Genetic Association Studies ,Genetics ,chemistry.chemical_classification ,Residue (complex analysis) ,Models, Statistical ,Applied Mathematics ,Computational Biology ,Proteins ,Amino acid substitution ,Amino acid ,Computer Science Applications ,chemistry ,Amino Acid Substitution ,lcsh:Biology (General) ,Mutation ,lcsh:R858-859.7 ,DNA microarray ,Algorithms ,Research Article - Abstract
Background The rapid accumulation of data on non-synonymous single nucleotide polymorphisms (nsSNPs, also called SAPs) should allow us to further our understanding of the underlying disease-associated mechanisms. Here, we use complex networks to study the role of an amino acid in both local and global structures and determine the extent to which disease-associated and polymorphic SAPs differ in terms of their interactions to other residues. Results We found that SAPs can be well characterized by network topological features. Mutations are probably disease-associated when they occur at a site with a high centrality value and/or high degree value in a protein structure network. We also discovered that study of the neighboring residues around a mutation site can help to determine whether the mutation is disease-related or not. We compiled a dataset from the Swiss-Prot variant pages and constructed a model to predict disease-associated SAPs based on the random forest algorithm. The values of total accuracy and MCC were 83.0% and 0.64, respectively, as determined by 5-fold cross-validation. With an independent dataset, our model achieved a total accuracy of 80.8% and MCC of 0.59, respectively. Conclusions The satisfactory performance suggests that network topological features can be used as quantification measures to determine the importance of a site on a protein, and this approach can complement existing methods for prediction of disease-associated SAPs. Moreover, the use of this method in SAP studies would help to determine the underlying linkage between SAPs and diseases through extensive investigation of mutual interactions between residues. more...
- Published
- 2011
45. Novel feature for catalytic protein residues reflecting interactions with other residues
- Author
-
Zhining Wen, Jiamin Xiao, Mei Hu, Hui Yin, Menglong Li, Gongbing Li, and Yizhou Li
- Subjects
Proteomics ,Protein Structure ,Protein Conformation ,Structure Prediction ,lcsh:Medicine ,Biochemistry ,Catalysis ,Protein structure ,Macromolecular Structure Analysis ,lcsh:Science ,Mutual dependence ,Biology ,Multidisciplinary ,Chemistry ,lcsh:R ,A protein ,Proteins ,Computational Biology ,Genomics ,Enzyme structure ,Enzymes ,Protein Interaction Networks ,Enzyme Structure ,Protein folding ,lcsh:Q ,Biological system ,Sequence Analysis ,Research Article - Abstract
Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship. more...
- Published
- 2010
46. Identification of RNA-binding sites in proteins by integrating various sequence information
- Author
-
Menglong Li, Jiamin Xiao, Cui-cui Wang, and Yaping Fang
- Subjects
chemistry.chemical_classification ,Binding Sites ,Protein Conformation ,Organic Chemistry ,Clinical Biochemistry ,Computational Biology ,RNA-Binding Proteins ,Computational biology ,Biology ,Proteomics ,Biochemistry ,Ribosome ,Amino acid ,Data set ,chemistry ,Sequence Analysis, Protein ,Sliding window protocol ,Protein biosynthesis ,Position-Specific Scoring Matrices ,RNA ,Databases, Protein ,Peptide sequence ,Smoothing ,Protein Binding - Abstract
RNA-protein interactions play a pivotal role in various biological processes, such as mRNA processing, protein synthesis, assembly, and function of ribosome. In this work, we have introduced a computational method for predicting RNA-binding sites in proteins based on support vector machines by using a variety of features from amino acid sequence information including position-specific scoring matrix (PSSM) profiles, physicochemical properties and predicted solvent accessibility. Considering the influence of the surrounding residues of an amino acid and the dependency effect from the neighboring amino acids, a sliding window and a smoothing window are used to encode the PSSM profiles. The outer fivefold cross-validation method is evaluated on the data set of 77 RNA-binding proteins (RBP77). It achieves an overall accuracy of 88.66% with the Matthew's correlation coefficient (MCC) of 0.69. Furthermore, an independent data set of 39 RNA-binding proteins (RBP39) is employed to further evaluate the performance and achieves an overall accuracy of 82.36% with the MCC of 0.44. The result shows that our method has good generalization abilities in predicting RNA-binding sites for novel proteins. Compared with other previous methods, our method performs well on the same data set. The prediction results suggest that the used features are effective in predicting RNA-binding sites in proteins. The code and all data sets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/Predict_RBP.rar . more...
- Published
- 2009
47. Using auto covariance method for functional discrimination of membrane proteins based on evolution information
- Author
-
Jiamin Xiao, Li Yang, Fuyuan Tan, Yizhou Li, Rong-quan Xiao, Menglong Li, and Yuhong Zeng
- Subjects
Analysis of Variance ,Current (mathematics) ,Organic Chemistry ,Clinical Biochemistry ,Membrane Proteins ,Computational biology ,Genome project ,Function (mathematics) ,Biology ,Proteomics ,Bioinformatics ,Biochemistry ,Biological Evolution ,Support vector machine ,Identification (information) ,Autocovariance ,Membrane protein - Abstract
Membrane transporters are critical in living cells. Therefore, the discrimination of the types of membrane proteins based on their functions is of great importance both for helping genome annotation and providing a supplementary role to experimental researchers to gain insight into membrane proteins' function. There are a lot of computational methods to facilitate the identification of the functional types of membrane proteins. However, in these methods, the local sequence environment was not integrated into the constructed model. In this study, we described a new strategy to predict the functional types of membrane proteins using a model based on auto covariance and position-specific scoring matrix. The novelty of the presented approach is considering the distribution of different positions of functional conservation sites in protein sequences. Thereby, this model adequately takes into account the long-range correlation between such sites during sequential evolution. Fivefold cross-validation test shows that this method greatly improves the prediction accuracy and achieves an acceptable prediction accuracy of 87.51%. The result indicates that the current approach might be an effective tool for predicting the functional types of membrane proteins only using the primary sequences. The code and dataset used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/predict_membrane.zip. more...
- Published
- 2009
48. Bound states in the continuum induced by the strong coupling within the plasmonic lattices.
- Author
-
Wang, Zhihang, Li, Lingyao, Shi, Xiaoqi, Xiao, Jiamin, Guo, Zhicheng, and Wang, Wenxin
- Subjects
POLARITONS ,BOUND states ,PLASMONICS ,FANO resonance ,QUANTUM electrodynamics ,DECOMPOSITION method - Abstract
Bound states in the continuum (BICs), manifesting themselves as the collapse of Fano resonance, are observed in many photonic and plasmonic systems. The BICs have been studied systematically through various methods such as the topological photonics analysis, temporal coupled mode theory, multipole decomposition method, and the cavity quantum electrodynamics (CQED) method. Since CQED can give a macroscopic and intrinsic description of light–matter interaction, it is expected to study BIC that participates in strong coupling. What is more, the relation between coupling strength, the Fano parameter, and the asymmetry property of BICs needs to be clarified. In this paper, we investigated the strong coupling between the cavity mode and Bloch-surface plasmon polariton (Bloch-SPP) mode induced by BICs within the plasmonic lattices of the metal-dielectric-metal (MDM) layer. The properties of strong coupling and BIC were revealed theoretically by the quantum model based on the CQED. The increase in the Fano parameters of BICs was proved to facilitate the coupling strength, which was indicated by the monotonically increasing relation between the Fano parameter and the coupling strength. This work may pave the way for flexible modulation and application of BIC in the fields of high-quality plasmonic nanocavity, low-threshold nano-lasers, and quantum information. [ABSTRACT FROM AUTHOR] more...
- Published
- 2023
- Full Text
- View/download PDF
49. Manipulating light–matter interaction into strong coupling regime for photon entanglement in plasmonic lattices.
- Author
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Wang, Zhihang, Li, Lingyao, Wei, Shibo, Shi, Xiaoqi, Xiao, Jiamin, Guo, Zhicheng, Wang, Wei, Wang, Yi, and Wang, Wenxin
- Subjects
DISTRIBUTION (Probability theory) ,PLASMONICS ,WIGNER distribution ,PHOTONS ,PHOTON pairs ,INFORMATION resources ,POLARITONS - Abstract
Enhancing light–matter interaction into the strong coupling regime attracts tremendous attention in both theory and experiment, which presents essential significance in research from nano-optics to quantum information. In this work, the entanglement effect is observed in the photons emitted from a plasmonic lattice as the coherent light–matter interaction occurs into the strong coupling regime with a Rabi splitting of 93.4 meV. A full quantum mechanical treatment based on the number state representation is established to reveal the underlying physics of the strong coupling phenomenon, especially the femtosecond dynamics of energy exchange and damping. The entangled split states display oscillating concurrence and negative Wigner quasiprobability distribution function, which demonstrates that this designed plasmonic lattice system can serve as an on-demand entangled photon source for quantum information. [ABSTRACT FROM AUTHOR] more...
- Published
- 2023
- Full Text
- View/download PDF
50. Complete Plastid Genomes of Nine Species of Ranunculeae (Ranunculaceae) and Their Phylogenetic Inferences.
- Author
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Ji, Jiaxin, Luo, Yike, Pei, Linying, Li, Mingyang, Xiao, Jiamin, Li, Wenhe, Wu, Huanyu, Luo, Yuexin, He, Jian, Cheng, Jin, and Xie, Lei
- Subjects
GENOMES ,MICROSATELLITE repeats ,RNA editing ,RANUNCULACEAE ,SPECIES ,TRANSFER RNA ,GENETIC code ,RIBOSOMAL DNA - Abstract
The tribe Ranunculeae, Ranunculaceae, comprising 19 genera widely distributed all over the world. Although a large number of Sanger sequencing-based molecular phylogenetic studies have been published, very few studies have been performed on using genomic data to infer phylogenetic relationships within Ranunculeae. In this study, the complete plastid genomes of nine species (eleven samples) from Ceratocephala, Halerpestes, and Ranunculus were de novo assembled using a next-generation sequencing method. Previously published plastomes of Oxygraphis and other related genera of the family were downloaded from GenBank for comparative analysis. The complete plastome of each Ranunculeae species has 112 genes in total, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The plastome structure of Ranunculeae samples is conserved in gene order and arrangement. There are no inverted repeat (IR) region expansions and only one IR contraction was found in the tested samples. This study also compared plastome sequences across all the samples in gene collinearity, codon usage, RNA editing sites, nucleotide variability, simple sequence repeats, and positive selection sites. Phylogeny of the available Ranunculeae species was inferred by the plastome data using maximum-likelihood and Bayesian inference methods, and data partitioning strategies were tested. The phylogenetic relationships were better resolved compared to previous studies based on Sanger sequencing methods, showing the potential value of the plastome data in inferring the phylogeny of the tribe. [ABSTRACT FROM AUTHOR] more...
- Published
- 2023
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