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GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

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Journal of Genetics and Genomics 2021年第12期48卷 1122-1129页

作者： Yi-Bo Tong Meng-Wei Shi Sheng Hu Qian yu-jie chen Zhi-Hui Luo Yi-Xuan Tu yu-Li Xiong Ying-jie Geng Chunyan chen Zhen-Xia chen Hubei Hongshan Laboratory College of Biomedicine and HealthHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China Interdisciplinary Sciences Institute Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityShenzhen 518000China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here,we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into Gen Origin(http://***/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In Gen Origin, the information such as gene age estimates,annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.

关键词： Gene age Gene family Comparative analysis

An indirect approach for quantum-mechanical eigenproblems: duality transforms

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Communications in Theoretical Physics 2022年第5期74卷 24-44页

作者： yu-jie chen Shi-Lin Li Wen-Du Li Wu-Sheng Dai Department of Physics Tianjin UniversityTianjin300350 China College of Physics and Materials Science Tianjin Normal UniversityTianjin 300387China

We suggest an indirect approach for solving eigenproblems in quantum *** the usual method,this method is not a technique for solving differential *** exists a duality among potentials in quantum *** first example is the Newton–Hooke duality revealed by Newton in *** that are dual to each other form a duality family consisting of infinite numbers of family *** one potential in a duality family is solved,the solutions of all other potentials in the family can be obtained by duality *** of directly solving the eigenequation of a given potential,we turn to solve one of its dual potentials which is easier to *** solution of the given potential can then be obtained from the solution of this dual potential by a duality *** approach is as follows:first to construct the duality family of the given potential,then to find a dual potential which is easier to solve in the family and solve it,and finally to obtain the solution of the given potential by the duality *** this paper,as examples,we solve exact solutions for general polynomial potentials.

关键词： duality family general polynomial potential exact solution

Cyclophilin D-induced mitochondrial impairment confers axonal injury after intracerebral hemorrhage in mice

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Neural Regeneration Research 2023年第4期18卷 849-855页

作者： Yang Yang Kai-yuan Zhang Xue-Zhu chen Chuan-Yan Yang Ju Wang Xue-Jiao Lei yu-Lian Quan Wei-Xiang chen Heng-Li Zhao Li-Kun Yang yu-Hai Wang yu-jie chen Hua Feng Department of Neurosurgery The 904th Hospital of PLAAnhui Medical UniversityWuxiJiangsu ProvinceChina Department of Neurosurgery and State Key Laboratory of Trauma Burn and Combined InjurySouthwest HospitalThird Military Medical University(Army Medical University)ChongqingChina Chongqing Key Laboratory of Precision Neuromedicine and Neuroregenaration Third Military Medical University(Army Medical University)ChongqingChina Wuxi Translational Medicine Center WuxiJiangsu ProvinceChina Department of Neurosurgery General Hospital of Xinjiang Military Command of PLAUrumqiXinjiang Uygur Autonomous RegionChina Department of Neurology The Second Medical Center&National Clinical Research Center for Geriatric DiseasesChinese PLA General HospitalBeijingChina

The mitochondrial permeability transition pore is a nonspecific transmembrane *** of mitochondrial permeability transition pore opening has been shown to alleviate mitochondrial swelling,calcium overload,and axonal *** D is an important component of the mitochondrial permeability transition *** cyclophilin D participates in mitochondrial impairment and axonal injury after intracerebral hemorrhage is not *** this study,we established mouse models of intracerebral hemorrhage in vivo by injection of autologous blood and oxyhemoglobin into the striatum in Thy1-YFP mice,in which pyramidal neurons and axons express yellow fluorescent *** also simulated intracerebral hemorrhage in vitro in PC12 cells using *** found that axonal degeneration in the early stage of intracerebral hemorrhage depended on mitochondrial swelling induced by cyclophilin D activation and mitochondrial permeability transition pore *** further investigated the mechanism underlying the role of cyclophilin D in mouse models and PC12 cell models of intracerebral *** found that both cyclosporin A inhibition and short hairpin RNA interference of cyclophilin D reduced mitochondrial permeability transition pore opening and mitochondrial *** addition,inhibition of cyclophilin D and mitochondrial permeability transition pore opening protected corticospinal tract integrity and alleviated motor dysfunction caused by intracerebral *** findings suggest that cyclophilin D is used as a key mediator of axonal degeneration after intracerebral hemorrhage;inhibition of cyclophilin D expression can protect mitochondrial structure and function and further alleviate corticospinal tract injury and motor dysfunction after intracerebral *** findings provide a therapeutic target for preventing axonal degeneration of white matter injury and subsequent functional impairment in central nervous diseases.

关键词： axonal injury corticospinal tract cyclophilin D cyclosporin A intracerebral hemorrhage mitochondrial impairment mitochondrial permeability transition pore motor dysfunction retraction bulb white matter

Lead-free Nb-based dielectric film capacitors for energy storage applications

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Tungsten 2022年第4期4卷 296-315页

作者： jie-yu chen yun-Peng Zhou Fei Guo Zhe-Hong Tang Shi-Feng Zhao College of Science Inner Mongolia University of TechnologyHohhot010051China Inner Mongolia Key Lab of Nanoscience and Nanotechnology School of Physical Science and TechnologyInner Mongolia UniversityHohhot010021China

Dielectric capacitors are the ideal energy storage devices because they have excellent power density,high working voltages,and a long *** its lower size and better energy storage density,film capacitors make them simpler to incorporate into circuits than traditional dielectric capacitor ***-free Nb-based perovskite ferroelectric/antiferroelectric films have strong orbital hybridization with O 2p orbitals due to unfilled d orbitals of Nb elements,forming a series of energy storage film materials with potential application ***,we provide an overview of the state-of-the-art lead-free Nb-based films for energy storage applications,which include K_(0.5)Na_(0.5)NbO_(3)-based,K_(0.5)Na_(0.5)Bi_(4)NbTi_(3)O_(15)-based,AgNbO_(3)-based and NaNbO_(3)-based *** overview of the benefits and drawbacks of each kind of Nb-based perovskite ferroelectric/antiferroelectric films is provided,along with a description of the design tactics used to achieve high energy storage performances.

关键词： Energy storage Nb-based films Relaxor Ferroelectric films Lead free materials

Slow Down Dewetting in Polymer Films by Isocyanate-treated Graphite Oxide

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Chinese Journal of Polymer Science 2018年第9期36卷 1070-1076页

作者： Yong Zhou Pei Bai Miao Huo yu-jie chen Hua Li Hong-Mei Kang He-Zhou Liu yun-Long Guo The State Key Lab of Metal Matrix Composites Shanghai Jiao Tong University School of Materials Science and Engineering Shanghai Jiao Tong University University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong University

Isocyanate-treated graphite oxides （iGOs） were well-dispersed into the polystyrene （PS） thin films and formed a novel network structure. With control in fabrication, an iGOs-web layer was horizontally embedded near the surface of the films and thus formed a composite slightly doped by iGOs. This work demonstrated that the iGOs network can remarkably depress the dewetting process in the polymer matrix of the composite, while dewetting often leads to rupture of polymer films and is considered as a major practical limit in using polymeric materials above their glass transition temperatures （Tg）. Via annealing the 50-120 nm thick composite and associated neat PS films at temperatures ranging from 35℃ to 70 ℃ above Tg, surface morphology evolution of the films was monitored by atomic force microscopy （AFM）. The iGOs-doped PS exhibited excellent thermal stability, i.e., the number of dewetting holes was greatly reduced and the long-term hole growth was fairly restricted. In contrast, the neat PS film showed serious surface fluctuation and a final rupture induced by ordinary dewetting. The method developed in this work may pave a road to reinforce thin polymer films and enhance their thermal stability, in order to meet requirements by technological advances.

关键词： Dewetting Thin polymer films Thermal instability iGOs network

Changes of Oxidative Stress and Soluble Sugar in Anthers Involve in Rice Pollen Abortion Under Drought Stress

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Agricultural Sciences in China 2011年第7期10卷 1016-1025页

作者： FU Guan-fu SONG Jian XIONG jie LI yu-rong chen Hui-zhe LE Ming-kai TAO Long-xing State Key Laboratory of Rice Biology China National Rice Research Institute Hangzhou 310006 P.R.China

Two rice maintaining lines with different drought tolerances, viz., Jin 23B （tolerant） and Zhenshan 97B （sensitive）, were used to study the oxidative stress and soluble sugar in rice anthers and pollen viability under drought stress during flowering stage. Higher antioxidant enzyme activities and lower malonaldehyde （MDA） content in rice anthers were observed in Jin 23B than in Zhenshan 97B under drought stress. Further, a great increase in the content of soluble sugar in rice anthers of Jin 23B was observed across the whole drought exposure, while Zhenshan 97B showed significant decrease in soluble sugar during 9-12 d after drought stress （DADS）. Accordingly, a marked decline of pollen fertility and activity, pollen numbers in an anther and pollen numbers on a stigma was observed in Zhenshan 97B, whereas little difference was found in Jin 23B. Thus, we suggest that pollen abortion caused by drought stress may be related with the reciprocity between oxidative stress and soluble sugar content in rice anthers.

关键词： drought stress oxidative stress soluble sugar pollen abortion rice anthers flowering stage

Differences in HER2 over-expression between proximal and distal gastric cancers in the Chinese population

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World Journal of Gastroenterology 2013年第21期19卷 3316-3323页

作者： Xiang-Shan Fan jie-yu chen Chang-Feng Li Yi-Fen Zhang Fan-Qing Meng Hong-Yan Wu An-Ning Feng Qin Huang Department of Pathology the Affiliated Drum Tower HospitalNanjing University Medical School Department of Statistics Nanjing University of Finance and Economics Department of Pathology and Laboratory Medicine Veterans Affairs Boston Healthcare System and Harvard Medical School

AIM: To investigate HER2 expression and its correlation with clinicopathological variables between proximal and distal gastric cancers (GC) in the Chinese population. METHODS: Immunostaining of HER2 was performed and scored on a scale of 0-3 in 957 consecutive GC cases, according to the revised scoring criteria of HercepTest TM as used in the ToGA trial. Correlations between HER2 expression and clinicopathologic variables of proximal (n = 513) and distal (n = 444) GC were investigated. RESULTS: Our results showed that HER2 expression was significantly higher in the proximal than in distal GC (P < 0.05). Overall, HER2 expression was significantly higher in male patients (P < 0.01), the Lauren intestinal type (P < 0.001), low-grade (P < 0.001) and pM1 (P < 0.01) diseases, respectively. There was a significant difference in HER2 expression among some pTNM stages (P < 0.05). In contrast, HER2 expression in the distal GC was significantly higher in male patients (P < 0.001), low-grade histology (P < 0.001), the Lauren intestinal type(P < 0.001), and pM1 (P < 0.001). In the proximal GC, however, higher HER2 expression scores were observed only in tumors with low-grade histology (P < 0.001) and the Lauren intestinal type (P < 0.001). CONCLUSION: HER2 over-expression in GC of Chinese patients was significantly more common in proximal than in distal GC, and significantly correlated with the Lauren intestinal type and low-grade histology in both proximal and distal GC, and with pM1 disease and male gender in distal GC.

关键词： HER2 Gastric cancer Immunohistochemistry Clinicopathology

Isothermal reduction kinetics of zinc calcine under carbon monoxide

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Transactions of Nonferrous Metals Society of China 2020年第8期30卷 2274-2282页

作者： yu-jie chen yun-yan WANG Ning PENG Yan-jie LIANG Bing PENG Institute of Environmental Science and Engineering School of Metallurgy and EnvironmentCentral South UniversityChangsha 410083China Chinese National Engineering Research Center for Control&Treatment of Heavy Metal Pollution Changsha 410083China School of Materials Science and Engineering Central South UniversityChangsha 410083China

The reduction kinetics of zinc calcine under a CO atmosphere was evaluated by isothermal reductive roasting in a temperature range of 600-800℃.The extent of reaction of zinc calcine was measured using thermogravimetry(TG),and the decomposition mechanism of zinc ferrite in zinc calcine was analyzed based on variations in the soluble zinc and ferrous *** results indicate that the reaction was controlled by the nucleation of the products,with an apparent activation energy of 65.28 k J/*** partial pressure of CO affected the reaction rate more strongly than the CO intensity(defined as PCO/(PCO+PCO2)).The generation rate of zinc oxide was higher than that of ferrous oxide;therefore,the nucleation of ferrous oxide is the rate-determining step of the reaction.

关键词： reduction kinetics zinc calcine zinc ferrite carbon monoxide

Ultraviolet Induced Skin Inflammation

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International Journal of Dermatology and Venereology 2021年第4期4卷 229-235页

作者： Hai-Chao Zhao Ta Xiao yu-jie chen Hospital for Skin Diseases(Institute of Dermatology) Chinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingJiangsu 210042China

Ultraviolet(UV)induced skin inflammation(UISI)is associated with many skin ***,the mechanism by which UV causes skin inflammation remains *** evaluating UISIin vivo have mainly been conducted using mouse *** investigations indicate that the classic inflammatory pathways involving nuclear factor kappa B and Toll-like receptor contribute to the regulation of ***,more novel signaling factors have been identified as being involved in this process,including interleukin 22 receptor-α,cluster of differentiation 28 and cluster of differentiation 1d,serum amyloid A1,estrogen,melatonin,peroxisome proliferator activated receptorsβ/δ,isocitrate dehydrogenase 2,and transglutaminase *** addition,the gene mutation offermitin family member 1 and selenium deficiency are reported to affect the phenotype of *** the actual roles of UISI in UV-related skin diseases need to be clarified,recent studies have reported the potent contribution of UISI to *** clarify the process and modulation of UISI,the special profiles of cytokines and inflammatory mediators and the core regulatory pathways should be identified *** investigations would be promoted rapidly,accompanied by the conduction of high-quality clinical research on patients with UV-related skin disease and the construction of precise animal models of UISI.

关键词： inflammation skin ultraviolet