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Application of deep learning in genomics

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Science China(Life Sciences) 2020年第12期63卷 1860-1878页

作者： Jianxiao Liu Jiying Li Hai Wang Jianbing Yan National Key laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China College of Informatics Huazhong Agricultural UniversityWuhan 430070China Microsoft Corporation Redmond 98052USA National Maize Improvement Center Key Laboratory of Crop Heterosis and UtilizationJoint Laboratory for International Cooperation in Crop Molecular BreedingChina Agricultural UniversityBeijing 100193China

In recent years, deep learning has been widely used in diverse fields of research, such as speech recognition, image classification,autonomous driving and natural language processing. Deep learning has showcased dramatically improved performance in complex classification and regression problems, where the intricate structure in the high-dimensional data is difficult to discover using conventional machine learning algorithms. In biology, applications of deep learning are gaining increasing popularity in predicting the structure and function of genomic elements, such as promoters, enhancers, or gene expression levels. In this review paper, we described the basic concepts in machine learning and artificial neural network, followed by elaboration on the workflow of using convolutional neural network in genomics. Then we provided a concise introduction of deep learning applications in genomics and synthetic biology at the levels of DNA, RNA and protein. Finally, we discussed the current challenges and future perspectives of deep learning in genomics.

关键词： deep learning genomics convolutional neural network

Zn/O ratio and oxygen chemical state ofnanocrystalline ZnO films grown atdifferent temperatures

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Chinese Physics B 2012年第3期21卷 475-479页

作者：范海波郑新亮吴思诚刘志刚姚合宝 Department of Physics National Key Laboratory of Photoelectric Technology and Functional Materials(Culture Base)National Photoelectric Technology and Functional Materials & Application of Science and Technology International Cooperation BaseNorthwest University

ZnO nanocrystalline films are prepared on Si substrates at different temperatures by using metal-organic chemical vapour deposition （MOCVD）. It is observed that when the growth temperature is low, the stoichiometric ratio between Zn and 0 atoms has a large deviation from the ideal ratio of 1：1. The ZnO grains in the film have small sizes and are not well crystallized, resulting in a poor photoluminescence （PL） property. When the temperature is increased to an appropriate value, the Zn/O ratio becomes optimized, and most of Zn and 0 atoms are combined into Zn-O bonds. Then the film has good crystal quality and good PL property. If the temperature is fairly high, the interracial mutual diffusion of atoms between the substrate and the epitaxial film appears, and the desorption process of the oxygen atoms is enhanced. However, it has no effect on the film property. The film still has the best crystal quality and PL property.

关键词： ZnO film metal-organic chemical vapour deposition growth temperature Zn/O ratio

Shear-responsive peptide/siRNA complexes as lung-targeting gene vectors

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Chinese Chemical Letters 2021年第5期32卷 1731-1736页

作者： Dongxiao Yin Mengjie Zhang Jiaxin Chen Yuanyu Huang Dehai Liang Beijing National laboratory for molecular Sciences and the Key laboratory of Polymer Chemistry and Physics of Ministry of Education College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China School of Life Science Advanced Research Institute of Multidisciplinary ScienceInstitute of Engineering MedicineKey Laboratory of Molecular Medicine and BiotherapyBeijing Institute of TechnologyBeijing 100081China

Particles administrated intravenously will pass through the pulmonary capillary network before being distributed to the ***,fabrication of vectors sensitive to blood shear and active with blood components should be a practical approach to develop lung-targe ting gene carriers self-regulated by circulatory *** this work,we designed a series of cationic peptides with the same charge density but varying hydrophobicity and capacity to form hydrogen bonds,and investigated their ability to form co mplexes with siRNA,the behaviours of peptide/siRNA complexes in the presence of serum under shear,and the lung-targeting efficacy of the complexes regulated by *** hydrophobic interaction co ntrols the complexation between peptide and siRNA,while the hydrogen bonds are responsible for the binding of peptides to the serum components in *** vivo tests show that all the peptide/siRNA complexes can accumulate in ***,only the complexes that exhibit weak interaction with serum components and can be broken down by shear avoid the inflammation and death caused by pulmonary ***,the peptide with strong hydrophobicity can retain siRNA in lung without early release of the *** study provides a step toward the development of adaptive gene carriers under the regulation of circulatory system.

关键词： Peptide Gene delivery Shear Polyelectrolyte complexes

CXCL12/SDF-1α Activates NF-κB and Promotes Oral Cancer Invasion through the Carma3/Bcl10/Malt1 Complex

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international Journal of Oral Science 2009年第3期1卷 105-118页

作者： Aasia O. Rehman Cun-yu Wang laboratory of molecular Signaling Division of Oral Biology and Medicine UCLA School of Dentistry Los Angeles USA

Aim To determine how SDF-1α/CXCR4 activates nuclear factor-kappa B （NF-κB） and promotes oral squamous cell carcinoma （OSCC） *** A lentivirus-based knockdown approach was utilized to deplete gene expression. NF-κB activation was evaluated by Western blot analysis and electrophoretic mobility shift （EMSA）. Results We show that the activation of NF-κB by CXCR4 occurs through the Carma3/Bcl10/Maltl （CBM） complex in OSCC. We found that loss of components of the CBM complex in HNSCC can inhibit SDF-1α induced phosphorylation and degradation of IκBα, while TNFα induced IKK activation remains unchanged. Further, we identified a role for novel and atypical, but not classical, PKCs in activating IKK through CXCR4. Importantly, inhibition of the CBM complex leads to a significant decrease in SDF-1α mediated invasion of OSCC. Conclusion The CBM complex plays a critical role in CXCR4-induced NF-κB activation in OSCC. Targeting molecular components of the NF-κB signaling pathway may provide an important therapeutic opportunity in controlling the progression and metastasis of OSCC mediated by SDF-1α.

关键词： CXCR4 NF-κB head and neck cancer invasion signal transduction

Highly-efficient CoRuO_(x)nanocatalysts for acidic oxygen evolution:The merit of optimum ordering degree of carbon nanotube support

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Particuology 2024年第7期90卷 470-477页

作者： Wenwen Li Yanni Wang Zhenzhen Zhao Meiqi Liu Qing Liang Yuhua Liu Fuxi Liu Zhou Jiang Xu Zou Bingsen Zhang Wei Zhang Key laboratory of Automobile Materials MOE School of Materials Science&EngineeringJilin Provincial International Cooperation Key Laboratory of High-Efficiency Clean Energy MaterialsElectron Microscopy CenterInternational Center of Future ScienceJilin UniversityChangchun 130012China Shenyang National laboratory for Materials Science Institute of Metal ResearchChinese Academy of Sciences110016ShenyangChina

Hydrogen production from proton exchange membrane water electrolysis is constrained by the sluggish kinetics of the anodic oxygen evolution ***_(2)has attracted considerable attention due to its low reaction overpotential,but its inferior stability remains a major ***,a strategy is proposed to enhance the catalytic activity and stability of CoRuOx nanoparticles by doping Co and regulating the ordering degree of carbon nanotubes(CNTs)by air *** was found that the CoRuOx@CNTs-300 catalyst exhibited the best catalytic activity and stability when the annealing temperature was 300°*** the current density of 10 mA cm−2,the overpotential of this catalyst was only 201 mV,which was nearly 100 mV lower than that of commercial RuO_(2)(300 mV).Surprisingly,there was no significant increase in the overpotential when tested at a current density of 10 mA cm−2 for 50 *** density functional theory calculations indicate that the high activity of the catalyst is due to the electronic coupling of CoRuOx nanoparticles and CNTs,and that the introduction of Co and CNTs improves the electronic structure and solvation energies of the Ru in the active site,dramatically increasing the structural stability.

关键词： Electrocatalysis RuO_(2) CNTs Oxygen evolution reaction

The gap report of global climate change mitigation, finance, and governance after the United States declared its withdrawal from the Paris Agreement

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Chinese Journal of Population,Resources and Environment 2017年第3期15卷 196-208页

作者： Qimin Chai Sha Fu Huaqing Xu Weiran Li Yan Zhong Department of international cooperation National Center for Climate Change Strategy and International Cooperation(NCSC) Research Center for Contemporary Management (RCCM) Tsinghua University

On 1 June 2017, the US President Donald Trump officially announced the withdrawal from the Paris Agreement, thus the study on the reasons of withdrawal, the potential impacts, and coping strategies has become a focus among policy circles and of the international community. Based on the self-developed US Policy Assessment Model, this paper systematically evaluates the three potential ＂major deficits＂ in terms of mitigation, climate finance, and global climate governance, as a result of the US withdrawal from the Paris Agreement and puts forward policy suggestions for coping with such transformations accordingly. The study shows that the United States ＇withdrawal from the Paris Agreement will affect the existence and implementation of successive climate policies and result in an additional 8.8-13.4% increase in the global emissions reduction deficit. The United States＇ withdrawal will also deteriorate the existing climate finance mechanism. The Green Climate Fund （GCF）＇s funding gap will increase by USS2 billion, while the gap of long-term climate finance will increase by about USS5 billion a year. Either the China-EU or the ＂BASIC plus＂ mechanism could fill the governance deficit caused by the United States and the lack of political momentum may continue for a while in the future.

关键词： Trump administration Paris Agreement mitigationdeficit finance deficit global climate governance deficit

HDAC6 inhibitor loaded bimetallene nanosheets with antagonizing thermoresistance for augmented mild photothermal therapy

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Chinese Chemical Letters 2023年第9期34卷 235-242页

作者： Lingyu Qiu Shan Lei Jing Zhang Ruhan Yan Wansi Chen Jing Lin Wei-Guo Zhu Peng Huang Guangdong Key laboratory of Genome Instability and Human Disease Prevention Department of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhen 518055China Base for international Science and Technology cooperation:Carson Cancer Stem Cell Vaccines R&D Center International Cancer CenterShenzhen University Medical SchoolShenzhen 518055China Marshall laboratory of Biomedical Engineering International Cancer CenterLaboratory of Evolutionary Theranostics(LET)School of Biomedical EngineeringShenzhen University Medical SchoolShenzhen 518060China

Photothermal therapy(PTT)induces thermoresistance through cellular heat shock response,which impairs the therapeutic efficacy of the *** resolve this problem,we developed a photothermal theranostics(denoted as PMH),which integrated the photothermal conversion agent of PdMo bimetallene with histone deacetylase 6(HDAC6)selected inhibitor(ACY-1215),showing the synergistic antitumor effect both in vitro and in ***,under the photoacoustic imaging(PA)navigation,the released ACY-1215 triggered by NIR laser irradiation decrease the heat shock proteins(HSPs)expression and weaken the HDAC6-regulated HSP90 deacetylation,thus hindering the degradation of PTT-induced misfolded or unfold proteins through proteasome dependent ***,mild photothermal therapy(mPTT)treatment compromised the autophagy,which induced by HDAC6 inhibition,leading to mPTTinduced misfolded or unfold proteins further *** that inhibition of HDAC6 plus m PTT contribute to tumor *** study develops a promising combination strategy based on m PTT for future cancer treatment.

关键词： Mild photothermal therapy Thermoresistance Histone deacetylase 6 Heat shock proteins Autophagy

To Include Dyslipidemia Management into National Basic Public Health Service: from Project Practice to Policy

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China CDC weekly 2022年第36期4卷 811-814页

作者： Yingjie Cao Zhuoqun Wang Yanfang Zhao Yuanli Liu international Health Exchange and cooperation Center National Health CommissionBeijingChina

As cardiovascular diseases have been increasingly endangering the health and quality of life of Chinese residents,all relevant parties have been actively looking for policies and measures to effectively control the risk factors of the *** and diabetes have been included in the National Basic Public Health Service Project since 2009;however,as one of the most crucial risk factors for cardio-cerebrovascular diseases,dyslipidemia has not yet been covered by the project due to various *** prevalence of dyslipidemia in China increased rapidly from 18.6%in 2002 to 40.4%in 2012(1),whereas the management of dyslipidemia has been lagging behind and become the“short board”in the prevention and control of cardiocerebrovascular diseases.

关键词： prevention Basic Service

Mixed-cation chiral perovskites displaying warm-white circularly polarized luminescence

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Science China Chemistry 2023年第5期66卷 1425-1434页

作者： Hua-Li Liu Hua-Yang Ru Meng-En Sun Zhao-Yang Wang Shuang-Quan Zang Henan Key laboratory of Crystalline molecular Functional Materials Henan International Joint Laboratory of Tumor Theranostical Cluster MaterialsGreen Catalysis Centerand College of ChemistryZhengzhou UniversityZhengzhou 450001China

Chiral perovskites with exceptional structural flexibility and optoelectrical properties are regarded as promising materials for optoelectronic and spintronic ***,the effects of achiral organic ligands on the chiroptical activity of chiral perovskites have been rarely ***,we present four one-dimensional lead bromide perovskites R-/S-(AMP)_(2)Pb_(3)Br_(10)(1-R and 1-S)with mono-cation and R-/S-AMP(DMA)Pb Br_(5)(2-R and 2-S)with mixed-cation templated by chiral R-/S-2-aminomethylpyrrolidine(R-/S-AMP)and achiral dimethylammonium(DMA).All four compounds demonstrate broadband emissions from self-trapped excitons(STEs).Derived from the stronger chirality transfer synergistically induced by achiral DMA,amplified bathochromically-shifted circular dichroism signals and strong warm-white circularly polarized emissions have been observed in 2-R and *** mixed-cation structural engineering provides a new route toward developing chiral perovskites for optoelectronic applications.

关键词： chiral perovskites achiral cations chirality transfer circular dichroism circularly polarized luminescence