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Advances in computational ChlA-PET data analysis

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Frontiers of Electrical and Electronic Engineering in China 2016年第3期4卷 217-225页

作者： Chao He guipeng Li Diekidel M. Nadhir Yang chen Xiaowo Wang Michael Q. Zhang MOE Key Laboratory of Bioinformatics and Bioinformatics Division TNLIST Center for Synthetic and Systems Biology/ Department of Automation Tsinghua University Beijing 100084 China Departmeni of Biological sciences Cenier for SystemsBio/ogy ihe University of Texas at Dallas Richardson TX 75080-3021 USA

Genome-wide chromatin interaction analysis has become important for understanding 3D topological structure of a genome as well as for linking distal cis-regulatory elements to their target genes. Compared to the Hi-C method, chromatin interaction analysis by paired-end tag sequencing （ChlA-PET） is unique, in that one can interrogate thousands of chromatin interactions （in a genome） mediated by a specific protein of interest at high resolution and reasonable cost. However, because of the noisy nature of the data, efficient analytical tools have become necessary. Here, we review some new computational methods recently developed by us and compare them with other existing methods. Our intention is to help readers to better understand ChlA-PET results and to guide the users on selection of the most appropriate tools for their own projects.

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Temporally Separated CO_(2) Photoreduction and H_(2)O Photooxidation over Redox-Active Conjugated Organic Polymer Films

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CCS Chemistry 2023年第8期5卷 1854-1865页

作者： guipeng Ji Yuepeng Wang Wenqiang Ye Meifang chen Fengtao Zhang Yanfei Zhao Shengrui Tong Buxing Han Zhimin Liu Beijing National Laboratory for Molecular Sciences Key Laboratory of ColloidInterfaceand ThermodynamicsCAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of Sciences(CAS)100190 Beijing University of Chinese Academy of Sciences 100049 Beijing School of Science China University of Geosciences100083 Beijing

Photocatalytic CO_(2) reduction with H_(2)O of chemicals without H2 generation is interesting but ***,we report temporally separated CO_(2) photoreduction and H_(2)O photooxidation that are achieved over redox-active o-hydroxyazo-based conjugated organic polymer films(HAzo-COPFs),affording CO with high efficiency as the sole reduction ***-COPFs are prepared via interfacial diazo-coupling reactions of aromatic diamines and diphenols,and HAzo-COPF-1 from 4,4′-biphenol and benzidine shows the best performance with a CO generation rate of 53.6μmol g−1 h−1 under visible-light irradiation(>420 nm).Interestingly,we discovered that diphenol(DP-OH)moieties in HAzo-COPFs,serving as electron and proton donors to participate in CO_(2) photoreduction,are oxidized into quinone(DP=O)moieties,which are subsequently photoreduced to regenerate DP-OH in H_(2)O ***,CO_(2) photoreduction and H_(2)O photooxidation are temporally separated and perfectly coupled via redox transformation between DP-OH and DP=O that form in situ,affording enhanced charge carrier separation and inhibiting the hydrogen evolution *** work provides new insights for the design of COP photocatalysts and artificial photosynthesis.

关键词： CO_(2)photoreduction conjugated organic polymers carbon monoxide redox transformation artificial photosynthesis

PHOTOCATALYTIC HYDROGEN EVOLUTION FROM WATER SPLITTING UNDER VISIBLE LIGHT IRRADIATION ON NOVEL PHOTOCATALYST FULLENES-PVP-ZN0.999NI0.001S

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Chinese Journal of Reactive Polymers 2006年第1期15卷 35-39页

作者： XUE Zhixin YANG guipeng chen Dianbao MA Xiaomei ZHANG Xiqin QUAN Zhenlan College of Chemical Engineering and Environment Qingdao University Qingdao 266071 China Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education Ocean University of China Qingdao 266003 P.R. China Fullerenes Materials Group Qingdao University of Science and Technology Qingdao 266071 China

Fullerenes （C60/C70） linked up to Ni-doped ZnS through the medium of an amphalic polymer polyvinyl pyrrolidone （PVP） to form a new kind of photocatalyst for hydrogen evolution from aqueous Na2S/Na2SO3 solution under visible light irradiation, the photocatalytic activities of this novel photocatalyst C60/C70-PVP- Zn0.999Ni0.001S are 3-5 fold higher compared with that of precurse catalyst Zn0.999Ni0.001S. This result could be attributed to Schottky barrier layer built between C60/C70 and Zn0.999Ni0.001S due to the electro-negativity of C60 and characteristic of being used as a multiple electron acceptor. C60 or C60/C70 its moiety, with its low energy first excited singlet state, is a good energy acceptor and in addition readily accepts multiple electrons, making it a potential electron accumulate as we know, which could protect the separation between electrons and holes against combination. This is an important reason for the marked increase of amount of H2 evolution during the photocatalytic process for the composite system C60/C70-PVP- Zn0.999Ni0.001S.

关键词： Fullerenes (C60/C70) Photocatalyst Hydrogen Water splitting Visible light.

层状结构富Mg的Mg_(2)Sn薄膜相组成与热电性能

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稀有金属材料与工程 2022年第5期51卷 1780-1788页

作者：刘莹宋贵宏李贵鹏陈雨胡方沈阳工业大学材料科学与工程学院辽宁沈阳110870

利用高真空磁控溅射设备,通过顺序沉积制备富Mg的Mg_(2)Sn热电薄膜。使用X射线衍射仪(XRD)、扫描电子显微镜(SEM)以及能谱仪(EDS)研究了沉积薄膜的物相组成、表面和截面形貌、元素含量及分布。使用塞贝克(Seebeck)系数/电阻分析系统LSR-... 详细信息

利用高真空磁控溅射设备,通过顺序沉积制备富Mg的Mg_(2)Sn热电薄膜。使用X射线衍射仪(XRD)、扫描电子显微镜(SEM)以及能谱仪(EDS)研究了沉积薄膜的物相组成、表面和截面形貌、元素含量及分布。使用塞贝克(Seebeck)系数/电阻分析系统LSR-3测量了沉积薄膜的电阻率和Seebeck系数,进而研究不同Mg含量的Mg_(2)Sn薄膜的功率因子。结果表明,采用磁控溅射法可以制备出立方反萤石结构的Mg_(2)Sn相薄膜,XRD显示,沉积薄膜是由立方结构的Mg_(2)Sn相和少量的纳米尺寸的金属Mg相组成。随着Mg靶溅射时间的增加,纳米金属Mg相的含量增加,电阻率和Seebeck系数均表现为先升高后降低,这归因于少量纳米金属Mg相与基体相之间存在相界面。适量的金属Mg相存在于Mg_(2)Sn薄膜中,有利于提高Seebeck系数。含有适量纳米尺寸金属Mg相的Mg_(2)Sn沉积膜,因其Seebeck系数较高,电阻率适当,可获得较高的功率因子。层状结构的Mg_(2)Sn薄膜可显著提高Seebeck系数,尽管电阻率也增加,但最终使薄膜的功率因子显著提高。

关键词：热电材料 Mg_(2)Sn薄膜 Seebeck系数层状结构电阻率

医学学报类F5000论文特征的文献计量学分析

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中国科技期刊研究 2019年第1期30卷 88-94页

作者：陈汐敏丁贵鹏南京医科大学学报编辑部南京医科大学病理学系

【目的】利用文献计量学研究医学学报类F5000论文特征,为相关期刊争取稿源、提高期刊质量提供参考。【方法】利用F5000论文平台得到2017年"中国精品科技期刊"中的医科大学学报,收集相关学报2012—2016年所有入选的F5000论文,并分析相关... 详细信息

【目的】利用文献计量学研究医学学报类F5000论文特征,为相关期刊争取稿源、提高期刊质量提供参考。【方法】利用F5000论文平台得到2017年"中国精品科技期刊"中的医科大学学报,收集相关学报2012—2016年所有入选的F5000论文,并分析相关论文特征。【结果】2017年F5000精品期刊共收录医科大学学报7种,F5000论文283篇,2011—2013年入选的文献数量最多。临床研究类论文数量最多;综述的篇均被引频次和篇均下载频次最高,其次是流行病学研究;基础研究论文的篇均被引频次最低;基金资助论文的数量和篇均下载频次略高于无基金资助论文。F5000论文集中在某些研究方向和研究专题。部分院校作者发表的F5000论文数量较多。【结论】我国医学学报的办刊质量需要进一步提高,应注意期刊栏目设置,留意关注度高的研究方向和研究主题,根据各自地理优势有的放矢地组约重点科研机构的优质稿件,以促进期刊质量和影响力的提升。此外,应采取措施进一步完善F5000展示平台,最大程度发挥平台功能。

关键词：医学学报 F5000 论文特征被引频次下载频次

我国医学期刊视频出版存在问题及JOVE的经验

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编辑学报 2017年第3期29卷 278-281页

作者：陈汐敏丁贵鹏南京医科大学学报编辑部南京医科大学病理学系南京211166

对95种中华医学会系列期刊和36种医学综合类中文核心期刊的视频出版情况进行了初步调查,认为国内医学期刊视频出版尚存在一些问题:期刊自身宣传不够,观看体验不佳,在第三方数据库中的显示度不强,相关规范急需建立。对此,可结合JOVE期刊... 详细信息

对95种中华医学会系列期刊和36种医学综合类中文核心期刊的视频出版情况进行了初步调查,认为国内医学期刊视频出版尚存在一些问题:期刊自身宣传不够,观看体验不佳,在第三方数据库中的显示度不强,相关规范急需建立。对此,可结合JOVE期刊的经验制订详细规范、注意细节设计、增强观看体验、注重读者服务和互动。做强自己,多方面联合,利用好我国的医学视频出版资源,提高期刊的竞争力和影响力。

关键词：视频出版全媒体出版 JOVE 医学期刊

Machine learning predictive model for severe COVID-19

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Machine learning predictive model for severe COVID-19

2021海峡两岸暨港澳精准医学青年博士论坛

作者： Jianhong Kang Ting chen Honghe Luo Yifeng Luo guipeng Du Mia Jiming-Yang Department of Thoracic Surgery First Affiliated Hospital Sun-Yat-sen University chengdu Medical College Department of Respiratory and Critical Care Medicine First Affiliated Hospital Sun-Yat-sen University Department of Respiratory and Critical Care Medicine The Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital) Medicine Campus Oberfranken University of Bayreuth

To develop a modified predictive model for severe COVID-19 in people infected with Sars-Cov-2. We developed the predictive model for severe patients of COVID-19 based on the clinical date from the Tumor Center of Union Hospital affiliated with Tongji Medical College, China. A total of 151 cases from Jan. 26 to Mar. 20, 2020, were included. Then we followed 5 steps to predict and evaluate the model: data preprocessing, data splitting, feature selection, model building, prevention of overfitting, and Evaluation, and combined with artificial neural network algorithms. We processed the results in the 5 steps. In feature selection, ALB showed a strong negative correlation(r = 0.771, P < 0.001) whereas GLB(r = 0.661, P < 0.001) and BUN(r = 0.714, P < 0.001) showed a strong positive correlation with severity of COVID-19. TensorFlow was subsequently applied to develop a neural network model. The model achieved good prediction performance, with an area under the curve value of 0.953(0.889–0.982). Our results showed its outstanding performance in prediction. GLB and BUN may be two risk factors for severe COVID-19. Our findings could be of great benefit in the future treatment of patients with COVID-19 and will help to improve the quality of care in the long term. This model has great significance to rationalize early clinical interventions and improve the cure rate.

关键词： Severe COVID-19 Machine learning Predictive model

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中国肿瘤学稿件外流现象与对策分析

中国科技期刊研究 2018年第6期29卷 568-573页

作者：陈汐敏丁贵鹏南京医科大学学报编辑部南京医科大学病理学系

【目的】分析中国肿瘤学论文的发表现状,探讨中国肿瘤学稿件外流现象与相关对策。【方法】利用Web of Science数据库,对2013—2017年中国作者发表的肿瘤学论文及发表期刊进行分析。【结果】我国肿瘤学英文论文发表平台有限,大部分论文... 详细信息

【目的】分析中国肿瘤学论文的发表现状,探讨中国肿瘤学稿件外流现象与相关对策。【方法】利用Web of Science数据库,对2013—2017年中国作者发表的肿瘤学论文及发表期刊进行分析。【结果】我国肿瘤学英文论文发表平台有限,大部分论文发表于国外期刊。中国作者倾向于选择发文量大、中国作者论文占比高、影响因子≤3的期刊,论文影响力有限。发表于国外SCI收录期刊的中国肿瘤学研究论文数量逐年提高,而中国科学引文数据库收录期刊发表的我国肿瘤学研究论文总量却逐年降低。【结论】中国高质量肿瘤学稿件外流现象较严重。我国肿瘤学期刊尚有较大发展空间,应在采取各种有效措施提高自身办刊效率基础上,扩大宣传范围,出台配套政策,以鼓励中国作者向本国期刊投稿。

关键词： SCI Web of Science 肿瘤学论文肿瘤学期刊中国作者

冬季和夏季长江口及其邻近海域一氧化碳的分布、海-气通量和微生物消耗的研究

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海洋环境科学 2023年第6期42卷 813-824页

作者：杨晨张婧杨桂朋中国海洋大学化学化工学院山东青岛266100 青岛海洋科学与技术试点国家实验室海洋生态与环境科学功能实验室山东青岛266237 中国海洋大学海洋化学研究所山东青岛266100

海洋是大气中一氧化碳(CO)的重要来源,河口区域在调节气候活性气体收支方面发挥着重要作用。本文旨在研究长江口作为典型河口在全球海洋CO生物地球化学循环中的地位,并进一步了解河口区域海水和大气中CO浓度的变化情况。本文基于2021年... 详细信息

海洋是大气中一氧化碳(CO)的重要来源,河口区域在调节气候活性气体收支方面发挥着重要作用。本文旨在研究长江口作为典型河口在全球海洋CO生物地球化学循环中的地位,并进一步了解河口区域海水和大气中CO浓度的变化情况。本文基于2021年冬季和夏季在长江口及其邻近海域的现场调查,对该海域CO分布、海-气通量和微生物消耗速率进行了研究。结果表明,冬季和夏季调查海域大气中CO的体积分数平均值分别为(530.39±120.40)×10^(-9)和(416.91±102.01)×10^(-9),大气中CO含量受人类活动影响较大;受光照强度和陆源输入有机物的影响,夏季表层海水中CO的浓度平均值[(4.52±2.13)nmol/L]显著高于冬季[(1.30±0.79)nmol/L];相应地,夏季海—气通量平均值[0.95μmol/(m^(2)·d)]亦显著高于冬季[0.10μmol/(m^(2)·d)]。冬季的微生物消耗速率常数(kbio)的平均值[(0.46±0.31)/h]明显高于夏季[(0.26±0.07)/h],其空间分布差异不大。本文的研究结果有助于深入认识河口区域在全球海洋CO生物地球化学循环中的地位。

关键词：一氧化碳浓度分布海—气通量微生物消耗长江口及其邻近海域