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1. chinaXiv:201904.00073 [pdf]

Prevent culture-driven invasive species spread

Xiong Li; Supriyo Basak; Rui Zhou; Wei-zhe Zhang; Yao Fu; Xin-mao Zhou; Chao Shi; Hou-Cheng Xi; Yong-ping Yang
Subjects: Biology >> Ecology

地区文化(如宗教、饮食或旅游文化)有时会驱动入侵生物的扩散,我们必须采取措施来阻止入侵生物融入大众文化。

submitted time 2020-02-24 Hits3652Downloads365 Comment 0

2. chinaXiv:202002.00009 [pdf]

一种新型冠状病毒肺炎(COVID-19)药物与天然产物快速发现的计算药理学方法

全源; 梁峰吉; 熊江辉
Subjects: Biology >> Virology

新发传染病爆发流行期间,亟需提出候选药物功效与机制的科学假说。疫苗或新药研发均需要一定时间,因而药物重定位(老药新用)策略有其独特价值。但是新发疾病其病原体、宿主反应的临床数据不充分,制约了候选药物假设的提出。此阶段常根据病人临床特征进行广谱抗病毒药物的尝试。本文借鉴人工智能领域常见的启发式搜索思路,提出一种新方法(aCODE),基于前期有一定疗效提示的广谱抗病毒药,获得其宿主靶蛋白集合,在全基因组尺度上搜索与之相关性最高的基因模块组合,进而对候选化合物(如已批准上市药物、天然产物)进行模式匹配与统计检验排序。本方法可根据临床实践的进展更新输入药物,迭代输出更精准结果,输出的天然产物或中药、药食同源成分结合其它信息后可实施快速测试,形成敏捷研发测试闭环。本方法的第二版更新及其与文献证据的比对分析请参考:http://chinaxiv.org/abs/202002.00024。

submitted time 2020-02-21 Hits2408Downloads668 Comment 0

3. 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 Hits68497Downloads15606 Comment 0

4. chinaXiv:202002.00028 [pdf]

新型冠状病毒(2019-nCoV)时空数据集及其典型应用

林浩; 鲍君雅
Subjects: Survey & Drawing Science and Technology >> Photogrammetry and Remote Sensing
Subjects: Statistics >> Biomedical Statistics

目前,新型冠状病毒(2019-nCoV)疫情正受到全球各科研工作者的广泛关注。然而,当前尚没有一个官方的渠道对2019-nCoV疫情数据进行实时开源,为了促进本次疫情相关的科研工作,本研究旨在为广大科研工作者提供权威的、开放的和多尺度的新型冠状病毒(2019-nCoV)时空数据集,为疫情监测、防控、预测和预警提供重要的数据来源。此外,该数据集还能应用于2019-nCoV疫情的多尺度、多时相制图和可视化,为疫情的空间分布、演化、趋势分析和模拟预测提供指导。

submitted time 2020-02-19 Hits2379Downloads384 Comment 0

5. chinaXiv:202002.00021 [pdf]

关于新型冠状病毒感染人数的预测研究

吴宇宸
Subjects: Mathematics >> Mathematics (General)

2019年12月,新型冠状病毒肺炎(NCP,又称2019-nCoV)疫情从武汉开始爆发,几天内迅速传播到全国乃至海外,对我国的工农业生产和人民生活产生了重要影响。科学有效掌控疫情发展对疫情防控至关重要。本文基于中国卫健委及湖北省卫健委每日公布的累计确诊数,采用逻辑斯蒂模型对数据进行了拟合,以期给该疾病的防控治提供科学依据。通过公布的疫情数据,我们反演了模型的参数,进而有效地模拟了目前疫情的发展,并预测了疫情未来的趋势。我们预测,湖北省疫情还要持续至少2周,而在全国其他地区,疫情可望1周左右达到顶峰。

submitted time 2020-02-18 Hits2327Downloads980 Comment 0

6. chinaXiv:202002.00024 [pdf]

新冠肺炎(COVID-19)中药天然产物计算筛选与文献证据集成分析

高敏; 朱月星; 熊江辉
Subjects: Medicine, Pharmacy >> Other Disciplines of Medicine and Pharmacology

药物重定位(老药新用)策略在新发传染病中具有独特应用前景。我们前期提出了一种新的药物重定位系统——aCODE,可以基于疾病流行早期有限信息对潜在有效的天然产物进行预测。本文基于计算工具与文献证据,对可能在新冠病毒肺炎(COVID-19)防治中发挥作用的中药天然产物进行理论研究,发现:(1)文献调研共发现56种经过实验验证具有抗冠状病毒活性的天然产物成分,可靶向冠状病毒的结构蛋白和非结构蛋白;(2)将aCODE系统所预测的抗冠状病毒天然产物成分与文献证据对比,发现交集有大黄素、甘草酸、人参皂苷R1、利血平和杨梅素等。大黄素可破坏冠状病毒S蛋白与宿主ACE2相互作用,阻止病毒入侵宿主细胞;同时具有抑制3a蛋白离子通道、阻止病毒释放的作用。甘草酸或其衍生物也是国内相关团队在新冠病毒肺炎治疗研究中重点关注的候选药物,已进入临床试验。(3)针对中药预测结果中大量出现的芳香化合物,aCODE系统增加芳香植物提取物数据源,计算发现氨基肉桂酸、肉桂醛、茴香烯、紫苏醇、芳樟醇、柠檬烯具有潜在的抗病毒效应。提示“芳香避秽”的细胞分子学机理值得进一步深入研究。

submitted time 2020-02-17 Hits1003Downloads227 Comment 0

7. chinaXiv:202002.00015 [pdf]

人工智能在新型冠状病毒(2019-nCoV)肺炎的应用进展:需求和机遇

王永桂; 李强; 余晴; 杨水化; 徐子怡; 谢天奕; 胡珊
Subjects: Computer Science >> Computer Application Technology

[目的]探究人工智能在新型冠状病毒(2019-nCoV)的诊断、治疗和控制中的应用场景和进展,以利用人工智能为新型冠状病毒肺炎的防控提供助力。 [方法]剖析新型冠状病毒肺炎防控的技术需求,从人工智能基因测序、辅助诊断、远程专家系统、药物筛查与研制等方面,分析当前的应用进展,挖掘应用的机遇。 [结果]中国是新型冠状病毒疫情最严重的国家,存在诸多的技术短板有待科技助力,AI能在疫情防控中发挥出重要的作用,但目前处于初步阶段,缺乏经过验证的落地成果;AI辅助诊断领域重复性研发较多,其他方面研究较少。 [局限]当前应用的数据大部分来自网站报道,如有更多的学术性成果,进展的分析将更全面。 [结论]需要加大投入和调控,在数据、算法和算力共享的基础上,各方面全面展开研发。

submitted time 2020-02-15 Hits1871Downloads352 Comment 0

8. 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 Hits42212Downloads11809 Comment 0

9. chinaXiv:202001.00113 [pdf]

从不显著结果中提取信息的方法:原理及其实现

陆春雷; 王珺; 宋琼雅; 贾彬彬; 许岳培; 胡传鹏
Subjects: Psychology >> Statistics in Psychology

在实证研究中,研究者有时需要证实当前的数据支持零假设,即没有差异或者没有效应。在零假设显著性检验(Null hypothesis significance test, NHST)框架之下,p > .05的结果(即不显著结果,non-significant results)却无法区分以下两种情况:“有证据表明没有效应(evidence of absence)”和“没有证据表明有效应(absence of evidence)”。然而,研究者经常将p > .05错误地解读为“有证据表明没有效应”,即“支持零假设”。近年来,研究者开始使用等价性检验、贝叶斯估计和贝叶斯因子来从不显著结果中提取有意义的信息,区分以上两种情况。在频率统计框架下,等价性检验通过检验效应是否在最小感兴趣效应的范围内,提供支持零效应的证据;在贝叶斯统计框架下,贝叶斯估计通过对比后验分布的最高密度区间和实际等价区的重叠情况,提供支持或拒绝零效应的证据;而贝叶斯因子则是通过计算当前数据支持零效应和有效应的相对程度,得到贝叶斯因子,进而评估相对于备择假设,当前数据支持零假设的程度。其中,等价性检验和贝叶斯估计中的最小感兴趣效应区间和实际等价区一般通过理论或者以往研究的数据来确定。文章通过分析同一个实例,分别展示了等价性检验、贝叶斯估计和贝叶斯因子如何应用,以及如何确定最小感兴趣效应区间和实际等价区。正确解读不显著结果有利于充分地从数据中提取信息,促进实证研究中证据的累积。

submitted time 2020-01-15 Hits927Downloads274 Comment 0

10. chinaXiv:201910.00029 [pdf]

Stand up to Action: The Postural Effect on Deontological Responding and the Boundary Condition of Dual Process

刘传军; 廖江群
Subjects: Psychology >> Social Psychology

Present research aimed to uncover a postural effect on deontological responding and its boundary condition of dual process. Previous literatures demonstrated a possibility that people have a stronger controlled cognitive process propensity, thus being less deontological in standing than sitting postures, and that this postural effect can be moderated by dual process. We conducted two studies in which participant read dilemma scenarios and rated the morally acceptance and action intention of the utilitarian proposal after each scenario when sitting or standing. The hypothesized postural effect was verified in a field study (Study 1) and also replicated in an experimental study (Study 2). Compared with those in sitting postures, participants in standing postures approved more to the utilitarian proposal and became less deontological. Furthermore, the postural effect was dismissed when participants made moral decisions with a dual task to increase cognitive load and reversed when participants made moral decisions after deliberate consideration of the sacrificial proposal (Study 2). Thus, the postural effect was stable across field and experimental studies and moderated by dual process. The present research supports and extends the dual process morality theory by confirming that body posture can affect moral decision-making, and also offers a novel evidence confirming the moderating role of dual process on embodiment effects. It enriches our knowledge that morality is evolutionarily embodied in postures and dual process can moderate the embodiment effects.

submitted time 2020-01-14 Hits4026Downloads676 Comment 0

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