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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 Hits238178Downloads59659 Comment 0

2. 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 Hits70568Downloads14175 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 Hits67097Downloads8228 Comment 0

4. 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 Hits59562Downloads15640 Comment 0

5. 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 Hits55036Downloads6309 Comment 0

6. chinaXiv:201703.00895 [pdf]

Sharing deep generative representation for perceived image reconstruction from human brain activity

Du, Changde; Du, Changying; He, Huiguang
Subjects: Computer Science >> Computer Application Technology

Decoding human brain activities via functional magnetic resonance imaging (fMRI) has gained increasing attention in recent years. While encouraging results have been reported in brain states classification tasks, reconstructing the details of human visual experience still remains difficult. Two main challenges that hinder the development of effective models are the perplexing fMRI measurement noise and the high dimensionality of limited data instances. Existing methods generally suffer from one or both of these issues and yield dissatisfactory results. In this paper, we tackle this problem by casting the reconstruction of visual stimulus as the Bayesian inference of missing view in a multiview latent variable model. Sharing a common latent representation, our joint generative model of external stimulus and brain response is not only ``deep" in extracting nonlinear features from visual images, but also powerful in capturing correlations among voxel activities of fMRI recordings. The nonlinearity and deep structure endow our model with strong representation ability, while the correlations of voxel activities are critical for suppressing noise and improving prediction. We devise an efficient variational Bayesian method to infer the latent variables and the model parameters. To further improve the reconstruction accuracy, the latent representations of testing instances are enforced to be close to that of their neighbours from the training set via posterior regularization. Experiments on three fMRI recording datasets demonstrate that our approach can more accurately reconstruct visual stimuli.

submitted time 2017-05-20 Hits49051Downloads2532 Comment 1

7. chinaXiv:201606.00145 [pdf]

生物磁受体蛋白MagR/IscA研究进展

汪红霞; 向远彩; 张义国
Subjects: Biology >> Molecular Biology

铁硫簇蛋白是一类重要的线粒体功能蛋白,在细胞能量代谢、电子传递、底物结合与激活、铁/硫存储、酶促反应、基因表达调控等诸多过程中均发挥了关键作用. 一旦铁硫簇组装及转运过程发生障碍,必将严重影响细胞内铁的稳态及铁硫蛋白的功能. 其中,分子量约 11-kDa 的 IscA,是铁硫蛋白亚家族 hesB 之一的高保守性成员,能结合铁离子及[2Fe-2S]簇,从而参与铁硫簇蛋白的合成,因此在铁硫簇组装蛋白系统中具有重要的作用. 更值得关注的是,2015 年谢灿和张生家各自研究组分别发现了 IscA1 具有独特的磁感应(magnetic sensor,MagS)与磁受体(magnetic receptor,MagR)功能. 尤为重要的是,通过外磁场刺激相关磁基因表达,能够调控神经活动及行为定位. 鉴于磁受体的独特功能并结合相关技术,遂将其统称为磁遗传学(磁基因学). 本文简要介绍 IscA 蛋白的始初发现与鉴定历程、进化保守性及其独特的生理生物学功能,并凝练出磁遗传假说机制调控模型.

submitted time 2016-06-16 Hits43353Downloads3350 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 Hits37983Downloads6630 Comment 0

9. chinaXiv:201607.00065 [pdf]

Entropy-Decreasing Processes With Helium-4 Superflows

Yongle Yu
Subjects: Physics >> Condensed Matter: Structural, Mechanical and Thermal Properties

We argue microscopically that helium-4 superflows carry heat unavoidably. We then show that a heterogeneous helium-4 superflow loop can be used to realize an entropy-decreasing process, thus providing an exception to the second law of thermodynamics. This exception is a quantum effect for its essential dependence on the quantum phenomenon of superfluidity.

submitted time 2017-01-10 Hits37329Downloads3151 Comment 0

10. chinaXiv:201703.00485 [pdf]

快速沉积与侵蚀对地温场及天然气水合物成藏演化的影响:以南海北部陆坡为例 Impacts of fast sedimentation and erosion on the evolution of geothermal field and gas hydrate system: cases of Northern South China Sea

张毅, 何丽娟, 汪集旸
Subjects: Geosciences >> Space Physics

海洋沉积物中天然气水合物的存在与分布与地温条件紧密相关。南海北部陆坡大部分区域更、全新世沉积速率较高,同时局部地区(如神狐天然气水合物钻探区)发育有大量的海底冲蚀谷。这些快速沉积或侵蚀作用可以对地温场及天然气水合物的形成与赋存产生重要影响,然而目前注意到这些问题的研究相对较少。本文中我们结合南海北部陆坡的实际情况,建立了针对地温场发生动态变化时的水合物成藏数值模型。我们给出两个成藏模拟案例,其一是快速沉积的情形,其二是地形遭受侵蚀、产生冲蚀谷时的情形。结果表明,在这两种情形下地温场将发生不同的瞬态调整,并对天然气水合物在地层中聚集及分布产状产生重要影响。在快速沉积发生时,地温梯度将变小,天然气水合物稳定带(HSZ)将增厚;然而当其底界将随着热传递而上升,天然气水合物将不断在原稳定带底界分解,而后在新的稳定带底界处重新生成水合物。这样长时间的快速沉积作用可以造成水合物主要富集在稳定带底界处。而当快速侵蚀作用发生时,地温梯度将变大,天然气水合物稳定带的厚度将变薄,原来位于冲蚀谷处的水合物藏将被侵蚀作用破坏。而后,随着热平衡的发展,逐渐形成新的、类似于似海底反射层的稳定带底界。单纯考虑甲烷扩散作用下,高丰度水合物的形成需要较长的时间,相对而言脊下的水合物成藏较好,形成矿点的概率较大。 The occurrence and distribution of gas hydrate in marine sediments is closely related to the state of geothermal field. The sedimentation rate is relatively high during the Pleistocene and Holocene in the northern margin of the South China Sea. Moreover, there are many erosional canyons at the sea bottom in some local areas. Such fast sedimentation and erosion can greatly affect the geothermal regime and the formation and occurrence of gas hydrate deposits. However, there are few studies that consider such scenarios. In this study, considering the geological reality, we build a numerical reservoir model aimed to simulate the evaluation of the gas hydrate system upon two cases: the fast sedimentation and the development of erosional canyons. The results indicate the geothermal filed and the accumulation and distribution of gas hydrate can be adjusted dynamically when the fast sedimentation or erosion occurs. Under fast sedimentation, the geothermal gradient becomes smaller and the thickness of gas hydrate stability zone (HSZ) becomes larger. However, due to the role of heat transfer, the bottom of HSZ rises upward. This process leads to the hydrate near the previous bottom of HSZ being dissociated and depositing near the bottom of new HSZ. After a long duration, the fast sedimentation will result the formation of hydrate being mainly enriched near the bottom of HSZ. By contrast, when fast erosion occurs, the geothermal gradient increases and the HSZ turn thinner. The gas hydrate deposit system can be partially destroyed by the formation of canyons. A long time is necessary for the recovery of a gas hydrate deposit with significant abundance. Relatively, the deposits under the residual ridges are more possible to be potential “sweet spots”.

submitted time 2017-03-23 Hits36097Downloads2302 Comment 0

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