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1. chinaXiv:202002.00033 [pdf]

Decoding evolution and transmissions of novel pneumonia coronavirus using the whole genomic data

Yu, Wen-Bin; Tang, Guang-Da; Zhang, Li; Corlett, Richard T.
Subjects: Biology >> Virology
Subjects: Biology >> Genetics

Background. The outbreak of COVID-19 started in mid-December 2019 in Wuhan, Central China. Up to February 18, 2020, SARS-CoV-2 has infected more than 70,000 people in China, and another 25 countries across five continents. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to decode the evolution and human-to-human transmissions of SARS-CoV-2 in the recent two months. Methods. Alignment of coding-regions was conducted haplotype analyses using DnaSP. Substitution sites were analyzed in codon. Evolutionary analysis of haplotypes used NETWORK. Population size changes were estimated using both DnaSP and Arlequin. Expansion date of population size was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. Findings. Eight coding-regions have 120 substitution sites, including 79 non-synonymous and 40 synonymous substitutions. Forty-two non-synonymous substitutions changed the biochemical property of amino acids. No evident combination was found. Fifty-eight haplotypes were classified as five groups, and 31 haplotypes were found in samples from both China and other countries, respectively. The rooted network suggested H13 and H35 to be ancestral haplotypes, and H1 (and its descendent haplotypes including all samples from the Hua Nan market) was derived H3 haplotype. Population size of SARS-CoV-2 were estimated to have a recent expansion on 6 January 2020, and an early expansion on 8 December 2019. Interpretation. Genomic variations of SARS-CoV-2 are still low in comparisons with published genomes of SARS-CoV and MERS-CoV. Phyloepidemiologic analyses indicated the SARS-CoV-2 source at the Hua Nan market should be imported from other places. The crowded market boosted SARS-CoV-2 rapid circulations in the market and spread it to the whole city in early December 2019. Furthermore, phyloepidemiologic approaches have recovered specific direction of human-to-human transmissions, and the import sources of international infectious cases.

submitted time 2020-02-21 Hits284387Downloads72145 Comment 0

2. chinaXiv:202003.00026 [pdf]

Effective Treatment of Severe COVID-19 Patients with Tocilizumab

Xu, Xiaoling; Han, Mingfeng; Li, Tiantian; Sun, Wei; Wang, Dongsheng; Fu, Binqing; Zhou, Yonggang; Zheng, Xiaohu; Yang, Yun; Li, Xiuyong; Zhang, Xiaohua; Pan, Aijun; Wei, Haiming
Subjects: Medicine, Pharmacy >> Clinical Medicine

Background: In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in Wuhan, China, which spread rapidly and has become a world-wide public health challenge. We aimed to assess the efficacy of tocilizumab in severe patients with Corona Virus Disease-19 (COVID-19) and seek a new therapeutic strategy. Methods: The patients diagnosed as severe or critical COVID-19 in The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital) and Anhui Fuyang Second People’s Hospital were given tocilizumab in addition to routine therapy between February 5 and February 14, 2020. The changes of clinical manifestations, CT scan image, and laboratory examinations were retrospectively analyzed. Findings: Within a few days, the fever returned to normal and all other symptoms improved remarkably. Fifteen of the 20 patients (75.0%) had lowered their oxygen intake and one patient need no oxygen therapy. CT scans manifested that the lung lesion opacity absorbed in 19 patients (90.5%). The percentage of lymphocytes in peripheral blood, which decreased in 85.0% patients (17/20) before treatment (mean, 15.52 ± 8.89%), returned to normal in 52.6% patients (10/19) on the fifth day after treatment. Abnormally elevated C-reactive protein decreased significantly in 84.2% patients (16/19). No obvious adverse reactions were observed. Nineteen patients (90.5%) have been discharged on average 13.5 days after the treatment with tocilizumab and the rest are recovering well. Interpretation: Tocilizumab is an effective treatment in severe patients of COVID-19, which provided a new therapeutic strategy for this fatal infectious disease.

submitted time 2020-03-05 Hits137716Downloads45585 Comment 0

3. chinaXiv:202002.00062 [pdf]

Furin, a potential therapeutic target for COVID-19

Hua Li; Canrong Wu; Yueying Yang; Yang Liu; Peng Zhang; Yali Wang; Qiqi Wang; Yang Xu; Mingxue Li; Mengzhu Zheng; Lixia Chen
Subjects: Medicine, Pharmacy >> Pharmacology

A novel coronavirus (SARS-CoV-2) infectious disease has broken out in Wuhan, Hubei Province since December 2019, and spread rapidly from Wuhan to other areas, which has been listed as an international concerning public health emergency. We compared the Spike proteins from four sources, SARS-CoV-2, SARS-CoV, MERS-CoV and Bat-CoVRaTG13, and found that the SARS-CoV-2 virus sequence had redundant PRRA sequences. Through a series of analyses, we propose the reason why SARS-CoV-2is more infectious than other coronaviruses. And through structure based virtual ligand screening, we foundpotentialfurin inhibitors, which might be used in the treatment of new coronary pneumonia.

submitted time 2020-02-23 Hits125698Downloads17212 Comment 0

4. chinaXiv:202002.00004 [pdf]

武汉2019冠状病毒S蛋白可能存在Furin蛋白酶切位点

李鑫; 段广有; 张伟; 施劲松; 陈嘉源; 陈舜梅; 高山; 阮吉寿
Subjects: Biology >> Virology

摘要:2019年12月,中国武汉报道了2019新型冠状病毒(2019 novel Coronavirus,2019-nCoV)引起的肺炎。基于基因组信息,我们前期研究结果显示2019-nCoV与SARS冠状病毒虽然同属于Beta冠状病毒B亚群(BB冠状病毒),但两种病毒差异很大,这一结果与两者临床症状差异一致。前期研究还发现了BB冠状病毒存在大量的可变翻译,并从分子水平揭示了BB冠状病毒变异快、多样性高的特点。本研究在国际上首次报道BB冠状病毒S蛋白上的一个重要突变,这个突变使2019-nCoV具有了一个可供Furin蛋白酶切的位点,是除鼠肝炎冠状病毒外所有的其它BB冠状病毒(包括SARS和SARS样(SARS-like)冠状病毒)所不具有的。这个突变有可能增强了2019-nCoV侵染细胞的效率,进而使其传播力显著大于SARS冠状病毒。由于这个突变,2019冠状病毒的包装机制也会不同于SARS等其它大部分Beta冠状病毒,而有可能与鼠肝炎冠状病毒、HIV、埃博拉病毒和一些禽流感病毒的包装机制相同。作为一个意外发现,一些禽流感病毒也可以通过突变获得Furin蛋白酶切位点。对这个重要突变的后续研究将为揭示2019-nCoV传播力强的原因,以及为药物、抗体和疫苗的开发等工作奠定基础。

submitted time 2020-02-14 Hits84984Downloads16069 Comment 0

5. chinaXiv:201605.00569 [pdf]

迁移学习研究进展

庄福振; 何清
Subjects: Computer Science >> Computer Application Technology

近年来,迁移学习已经引起了广泛的关注。迁移学习是运用已存有的知识对不同但相关领域问题进行求解的新的一种机器学习方法。传统机器学习基于两个基本假设:(1) 用于学习的训练样本与新的测试样本满足独立同分布的条件;(2) 必须有足够可利用的训练样本才能学习得到一个好的分类模型。迁移学习降低了要求,目的是迁移已有的知识来解决目标领域中仅有少量或没有有标签样本数据时的学习问题。本文对迁移学习算法以及相关理论研究进展进行了综述,并介绍了我们在该领域所做的研究工作,特别是利用生成模型在概念层面建立迁移学习模型。最后指出了迁移学习下一步可能的研究方向。

submitted time 2016-05-03 Hits42110Downloads9785 Comment 0

7. chinaXiv:201709.00120 [pdf]

贝叶斯因子及其在JASP中的实现

胡传鹏; 孔祥祯; Eric-Jan Wagenmakers; Alexander Ly; 彭凯平
Subjects: Psychology >> Statistics in Psychology

统计推断在科学研究中起到关键作用,然而当前科研中最常用的经典统计方法——零假设检验(Null hypothesis significance test, NHST)却因难以理解而被部分研究者误用或滥用。有研究者提出使用贝叶斯因子(Bayes factor)作为一种替代和(或)补充的统计方法。贝叶斯因子是贝叶斯统计中用来进行模型比较和假设检验的重要方法,其可以解读为对零假设H0或者备择假设H1的支持程度。其与NHST相比有如下优势:同时考虑H0和H1并可以用来支持H0、不“严重”地倾向于反对H0、可以监控证据强度的变化以及不受抽样计划的影响。目前,贝叶斯因子能够很便捷地通过开放的统计软件JASP实现,本文以贝叶斯t检验进行示范。贝叶斯因子的使用对心理学研究者来说具有重要的意义,但使用时需要注意先验分布选择的合理性以及保持数据分析过程的透明与公开。

submitted time 2018-05-08 Hits67965Downloads8188 Comment 0

8. chinaXiv:201603.00031 [pdf]

我国科研人员对arXiv认知和使用的现状调查与分析

张智雄; 张闪闪; 顾立平; 李麟
Subjects: Library Science,Information Science >> Library Science

【目的】了解中国用户对 arXiv预印本平台的认知、使用情况以及对 arXiv发展的意见建议。【方法】基于国内 9家高校及科研机构的教师、研究人员和研究生群体的问卷调查,作者获得 510份调查数据,并运用 SPSS等分析工具对调查数据进行分析。【结果】结果表明,我国科研人员对 arXiv的认知程度还不是很高,但熟悉 arXiv的国内科研人员已认识到在 arXiv上发布论文是占据成果首发权和征求同行意见的重要手段。【局限】在调查取样上仅限于中国 arXiv服务工作组的成员单位,非成员单位的 arXiv用户没有纳入。【结论】为了让 arXiv能够更多地惠及我国科研,中国 arXiv服务工作组需要采取更为积极的行动,加快推动 arXiv在国内更广泛深入的应用。

submitted time 2016-03-14 Hits45592Downloads7885 Comment 0

9. chinaXiv:201605.00570 [pdf]

深度学习概述

常虹; 山世光
Subjects: Computer Science >> Computer Application Technology

深度学习是机器学习领域的一个新的研究方向,其核心思想在于模拟人脑的层级抽象结构,通过无监 督的方式从大规模数据(例如图像、声音和文本)中学习特征。近年来,深度学习在计算机视觉、语音识 别等研究领域取得的巨大成功使得研究者们对其寄予更多的关注。本文从深度学习的概念、发展历程、模 型、训练方法以及应用等几个方面对其进行概述,并对深度学习的未来发展做出展望。

submitted time 2016-05-03 Hits42220Downloads7817 Comment 1

10. chinaXiv:202002.00084 [pdf]

Clinical remission of a critically ill COVID-19 patient treated by human umbilical cord mesenchymal stem cells

Bing Liang; Junhui Chen; Tao Li; Haiying Wu; Wenjie Yang; Yanjiao Li; Jianchun Li; Congtao Yu; Fangang Nie; Zhaoxia Ma; Mingxi Yang; Panrong Nie; Yanfeng Gao; Chuanyun Qian; Min Hu
Subjects: Medicine, Pharmacy >> Clinical Medicine

Background The COVID-19 cases increased very fast in the last two months. The mortality among critically ill patients, especially the elder ones, was relatively high. Considering that most of the dead patients were caused by severe inflammation response, it is very urgent to develop effective therapeutic agents and strategies for these patients. The human umbilical cord mesenchymal stem cells (hUCMSCs) have shown very good capability to modulate immune response and repair the injured tissue with good safety. Case Presentation Here, we reported the treatment process and clinical outcome of a 65-year-old female critically ill COVID-19 patient infected with 2019-nCoV (now called SARS-CoV-2). The significant clinical outcome and well tolerance was observed by the adoptive transfer of allogenic hUCMSCs. Conclusions Our results suggested that the adoptive transfer therapy of hUCMSCs might be an ideal choice to be used or combined with other immune modulating agents to treat the critically ill COVID-19 patients.

submitted time 2020-02-27 Hits28453Downloads5366 Comment 0

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