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Jurassic amber in Lebanon

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Acta Geologica Sinica(English Edition) 2010年第4期84卷 977-983页

作者： Dany AZAR Raymond GEZE Antoine EL-SAMRANI Jacaueline MAALOULY André NEL Department of Natural Sciences Faculty of Sciences ⅡLebanese UniversityFanarLebanon Museum National d'Histoire Naturelle ParisFrance

Reports of amber predating the Lower Cretaceous are unusual and scarce; they mostly refer to amber pieces of millimetric dimension. In the present study, we report the discovery of 10 new outcrops of Jurassic amber in Lebanon. Some of these had large centimetric-sized pieces of amber. The new localities are described, amber is characterized, and its infrared spectra given. Although the new Jurassic amber yielded to date no more than fungal inclusions, this material is significant and promising. The discovery, of several Jurassic outcrops provides crucial information on the prevailing paleoenvironment of that time.

关键词： amber Lebanon Late Jurassic Kimmeridgian infrared spectrum

Room-Temperature Phosphorescence and Lifetime of Fossil Resins (amber) from Dominican Republic, Mexico, Baltic Sea, Myanmar, and Fushun, China

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宝石和宝石学杂志（中英文） 2023年第4期25卷 111-119页

作者： Zhiqing Zhang Yamei Wang Andy H.Shen College of Natural Resources and Geographic Information HuBei Land Resources Vocational CollegeWuhan 430090China Gemmological Institute China University of GeosciencesWuhan 430074China

amber can emit room temperature phosphorescence(RTP)under the well-known 365 nm fluorescence ultraviolet *** paper is devoted to the phosphorescence study of 20 pieces of amber materials from the Dominican Republic,Mexico,Baltic sea,Myanmar,and Fushun,*** results show that amber from the same geographic origin has similar shape in phosphorescence ***,the shape of the amber phosphorescence spectra varies depending on their different ***(amber from Myanmar)and Fushun amber have a bright yellow phosphorescence with a long lifetime,while the Dominican and Mexican ones are weaker and last *** irradiation of Baltic amber becomes faint or even *** spectral Gaussian fitting results suggest an emission maximum near 550 nm in most amber *** phosphorescence lifetime,analyzed through the exponential function fitting,is up to 1 second in Burmite and Fushun samples,shorter in the Dominican and Mexican ones,about 0.230 s,and the shortest in Baltic amber,close to 0.151 *** variations of phosphorescence lifetime and intensity are related to the relative geological ages of these *** indicated that the phosphorescence agent was probably formed during the long geological *** the anomaly occurred in Baltic amber,the only one found in a sea secondary deposit form,it demonstrated that the terrestrial geological environment these amber preserved has prevented the phosphorescence agent to be deactivated.

关键词： ossil resin amber room-temperature phosphorescence(RTP) phosphorescence lifetime

Day-to-Day Variability of H Component of Geomagnetic Field in Central African Sector Provided by Yaoundé-Cameroon amber Station

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International Journal of Geosciences 2014年第10期5卷 1190-1205页

作者： Messanga Etoundi Honore Kosh Djaka Comelo Mbane Biouele Cesar Laboratory of Earth’s Atmosphere Physics Department of Physics University of Yaoundé I Yaoundé Cameroun

The geomagnetic data obtained from amber Network station in Cameroon have been used for this study. The variability of H component of geomagnetic field has been examined by using geomagnetic field data of X and Y components recorded at amber magnetometer station hosted by the Department of Physics of University of Yaoundé (3.87°N, 11.52°E). The day-to-day variability of the horizontal intensity of the geomagnetic field was examined and shows that the scattering of H component of magnetic field variation is more on disturbed than that on quiet condition. The signatures H of geomagnetic Sq and Sd variations in intensities in the geomagnetic element, has been studied. This study shows that the daytime variations in intensities of geomagnetic elements H, Sq(H) and Sd(H) respectively are generally greater than night-time ones. This paper interests answering the two questions: 1) how can geomagnetic variations be used to study the equatorial ionosphere electrodynamics and electrojet equatorial over Africa in general and Cameroon in particular? 2) How can geomagnetic variations be used to monitor and predict space weather events in Cameroon? This paper presents and interprets the results of H component of geomagnetic field variations during magnetic storms and on quiet days.

关键词： Geomagnetic Field amber Magnetometer Station Magnetic Storms Equatorial Electrojet

Diversification of Eupolypods in Mid-Cretaceous—Evidenced by Myanmar amber Forest

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Open Journal of Geology 2019年第10期9卷 726-730页

作者： Cunxiang Li Libing Zhang State Key Laboratory of Palaeobiology and Stratigraphy Center for Excellence in Life and Palaeoenvironment Nanjing Institute of Geology and Palaeontology Nanjing China Missouri Botanical Garden St. Louis Missouri USA Chengdu Institute of Biology Chinese Academy of Sciences Chengdu China

The evolutionary history of Eupolypods still remains unclear, especially on its diversification scenarios. In recent years, it has been found that approximately 100 million-year-old Myanmar amber provides a unique source of polypod fossils. Different families and numerous sporangia, spores, and scales have been found in Myanmar amber. These discoveries are nevertheless important because they provided the first unequivocal fossil evidence that the diversity of eupolypod ferns was present already in the mid-Cretaceous Myanmar amber forest. This clearly shows that Eupolypods originated before mid-Cretaceous, probably as early as the Early Jurassic, which is consistent with the recent divergence time estimate based on molecular dating.

关键词： Mid-Cretaceous Myanmar amber Eupolypods Divergence Time

Lesion presenting with a “blue amber” pattern

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World Journal of Clinical Cases 2016年第10期4卷 333-335页

作者： Calogero Pagliarello Francesca Peccerillo Alfredo Zucchi Rocco Giuseppe Tortorella Roberto Ricci Ignazio Stanganelli Claudio Feliciani Sergio Di Nuzzo Section of Dermatology Department of Clinical and Experimental MedicineUniversity of Parma Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori(IRST)IRCCS

Atypical fibroxanthoma(AFX) is a spindle cell neoplasm with low metastatic potential but high tendency to recur after surgery. Because of the rarity of this lesion and its aspecific clinical features, AFX could be easily misdiagnosed and undertreated by many clinicians who encounter them. Dermoscopy represents a valuable tool for easily assessing skin lesions, even though histological examination is required for final diagnosis. We report a case of a cheek lesion with dermoscopic "blue amber pattern", easily recognisable and not observed in others skin tumours, which could represent an additional feature useful in differentiating this tumour from other skin neoplasms.

关键词： Atypical fibroxanthoma Dermoscopy Blue amber pattern Vascular structures

天河2号上一种分子动力学模拟软件amber的并行化加速技术研究

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天河2号上一种分子动力学模拟软件AMBER的并行化加速技术研究

作者：刘欣国防科学技术大学

学位级别：硕士

分子动力学模拟是一种对原子和分子的物理运动进行计算机模拟的方法,随着分子动力学模拟方法的不断改进和完善,其功能越来越丰富,模拟的分子体系规模和时间长度也一直在增长。然而,大规模原子体系进行微秒级的分子动力学模拟需要耗费大... 详细信息

分子动力学模拟是一种对原子和分子的物理运动进行计算机模拟的方法,随着分子动力学模拟方法的不断改进和完善,其功能越来越丰富,模拟的分子体系规模和时间长度也一直在增长。然而,大规模原子体系进行微秒级的分子动力学模拟需要耗费大量的计算资源和时间,当前现有的服务器和分子动力学模拟算法已经无法及时有效的处理如此大规模的动力学模拟任务。本课题就是针对上述问题,根据天河2号超算系统上的大规模CPU-MIC微异构体系结构,对最常用的分子动力学模拟软件Assisted Model Building with Energy Refinement(amber)进行并行算法设计和优化加速研究。在保证结果正确的前提下,在不同层次上和规模上对amber进行深度并行优化,主要研究工作如下:首先,针对amber软件包的sander程序,在CPU上对其进行细粒度的并行优化。sander作为amber软件包的模拟器程序,是分子动力学模拟的核心。针对sander程序热点部分,提出了去除循环依赖、改进数据结构等手段,基于OpenMP编程技术,实现了对分子动力学模拟程序amber-sander细粒度并行优化加速。我们还利用MIC(Many Integrated Cores)协处理器Intel Xeon Phi超强的并行计算能力,将amber-sander的核心计算任务移植到MIC上,首次实现了基于MIC的分子动力学模拟程序amber-sander的并行加速。相比原来的amber-sander程序,基于MIC的sander-mic获得了3-4倍的加速。其次,为了充分利用CPU与MIC的计算资源,我们设计和实现了面向天河2号的CPU与MIC微异构协同的分子动力学模拟并行优化算法。提出了内存管理优化、数据传输优化、通信延迟隐藏、向量化以及负载均横等多种并行优化方法,在单节点上,对分子动力学模拟软件amber-sander实现了5-6倍的加速,把单CPU单MIC协同并行加速扩展到面向天河2号的单节点多CPU多MIC卡的协同并行。最后,通过对amber-sander的可扩展性进行分析,在多节点层面对其进行并行加速。对于分子动力学模拟算法本身而言,由于迭代次数多,每次迭代都需要进行数据规约和数据分发,通信开销成为多节点并行加速的一个主要问题和瓶颈。我们在保证计算结果的误差在一定范围内,对算法进行了跨节点并行优化,由原来的每一次迭代都要进行数据规约操作,变成每隔固定次迭代再进行数据规约操作,使得通信开销大大减少,程序可以在天河2号多个节点上高效地运行,全面提高了程序的并行可扩展性。总之,本文基于天河2号,通过在以上3个层面上对分子动力学模拟软件amber-sander进行并行优化加速,从单CPU上的细粒度OpenMP并行、单节点CPU与MIC协同的并行优以及多节点多MIC卡的协同并行,相比原来的程序都有不同程度的加速,最高的加速比达到5-6倍。

关键词：分子动力学模拟 amber sander MIC 天河2号并行

改进的amber力场研究Trp-cage的折叠机理

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改进的AMBER力场研究Trp-cage的折叠机理

作者：牟丽蓉华东师范大学

学位级别：硕士

探索蛋白质折叠的机理对于治疗因蛋白质错误折叠导致的疾病以及蛋白质工程都有着非常重要的意义。这个领域在过去的几十年间取得了很大的进展。作为实验的补充,分子动力学在广泛的时间范围内给出了蛋白质在原子层面上的动力学性质和热... 详细信息

探索蛋白质折叠的机理对于治疗因蛋白质错误折叠导致的疾病以及蛋白质工程都有着非常重要的意义。这个领域在过去的几十年间取得了很大的进展。作为实验的补充,分子动力学在广泛的时间范围内给出了蛋白质在原子层面上的动力学性质和热力学性质描述,而这些通常是无法通过实验观察到的。分子动力学模拟已经研究了一些多肽和小蛋白,这得益于它们的体积小和折叠速率快。其中,一个由20个残基组成的小蛋白Trp-cage(氨基酸序列号：NLYIQ WLKDG GPSSG RPPPS)是研究的理想体系,它在实验和理论方面都己被广泛研究。Trp-cage由一段α螺旋(残基2-8)、一段短的310螺旋(残基11-14)和一段多脯氨酸Ⅱ螺旋结构组成。酪氨酸-3和四个脯氨酸(脯氨酸-12,17,18和19)的侧链形成疏水核,而色氨酸-6的吲哚环位于疏水核的中心。另外,天冬氨酸-9的羧基与精氨酸-16的胍基可以形成盐桥。有人认为盐桥有助于稳定蛋白质结构,但一些实验和理论研究表明当盐桥消除后,Trp-cage仍然能保持折叠状态。随着力场的不断改进,折叠这类小蛋白已经没什么困难,但要重现实验观测量,比如熔解温度,依然是一项挑战。关于Trp-cage的折叠机理,还有很多问题有待解决：(1)折叠过程中的决速步是哪一步?(2)Trp-cage的折叠是简单的两态模型还是更复杂的模型?(3)环境约束是如何影响折叠过程的?(4)二级结构和疏水核哪个先形成?人们做了大量的研究来探索这些问题的答案。NMR和CD实验表明Trp-cage的折叠机理是两态机理,而一些别的实验则倾向于一种更为复杂的折叠机理,且在折叠发生前会先出现中间体。Duan等人在分析了77个Trp-cage的分子动力学模拟后,提出折叠过程的决速步是色氨酸-6侧链的正确定位。Tian等人认为边界的大小、极性以及溶剂相互作用的影响决定了折叠路径。Zhou等人认为α螺旋在折叠的最后阶段形成。与之相反的是,一些实验结果显示在Trp-cage的非折叠态有螺旋结构的迹象,这表明α螺旋形成于折叠早期。所有的争论都是由实验和理论的局限性导致的。蛋白质折叠路径的理论预测依赖于相空间的遍历性和所使用力场的可靠性。近年来,由于计算技术的迅猛发展,对力场精确性的要求就显得越来越迫切。人们致力于力场的不断改进。Best等人优化了amber和CHARMM全原子力场。Li等人使用下坡单向最小值法优化了二面角扭转势,使其与NMR实验值更为符合。与力场amber99SB相比,新的力场amber99SBnmr结果更好。Lindorff-Larsen等人优化了某些残基的侧链二面角参数,使其与高阶量子力学计算相匹配。然而,我们认为当前力场的主要缺点在于主链二面角的函数形式过于简单。由于主链二面角(φ和Ψ)是不可分离的,所以对主链二面角采用耦合项是必须的,尤其是用来描述对大的构型变化至关重要的势能能垒时。针对这个问题,我们采用耦合的二维主链二面角项发展了一组新的主链二面角参数。蛋白质模拟的初试表明,与原始的amber力场相比,新力场能得到更加平衡的二级结构分布。本文中,我们利用新力场amber032D模拟研究Trp-cage的折叠。amber032D力场是在amber力场的基础上加入优化二维主链二面角项得到的,其它的项都是直接从amber03力场中提取的。amber032D模拟得到的天然态构型与NMR构型符合得很好,且预测的熔解温度与实验值也比较接近。同时,我们得到了Trp-cage的一个可能的折叠机理。

关键词：力场 amber 蛋白质折叠 Trp-cage 二面角参数

A new species of Chresmodidae from Mid-Cretaceous amber discovered in Myanmar

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Zoological Systematics 2017年第2期42卷 243-247页

作者： Weiwei Zhang Wanzhi Cai Wenzhu Li Xingke Yang Siqin Ge Key Laboratory of Zoological Systematies and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101 China P.O. Box 4680 Chongqing 400015 China Department of Entomology China Agricultural University Beijing 100193 China

The extinct new species, Chresmoda chikuni Zhang ＆ Ge, sp. nov. is described from the Mid-Cretaceous amber from northern Myanmar. This amber insect exhibits a very peculiar combination of derived characters like strongly elongated, free coxa, non-clawed pretarsus. The type specimens are deposited in the Three Gorges Entomological Museum, Chongqing, China.

关键词： amber new species Chresmodidae Myanmar Cretaceous

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amber软件介绍

辐射防护通讯 2006年第1期26卷 24-26页

作者：刘建琴孙庆红中国辐射防护研究院太原030006

介绍了用于放射性废物处置系统安全评价的amber软件的应用范围、特点、使用限制和步骤,及其所包含的几个应用实例。

关键词：放射性废物处置安全评价 amber 库室模型