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Review of the article "Statistical analysis of numerical preclinical radiobiological data", J.H. Pitt and H.Z.Hill, D, Scienceopen, 2016 “临床前放射生物学数值数据的统计分析”,J.H. Pitt和H.Z.Hill, D, Scienceopen, 2016
Pub Date : 2016-01-01 DOI: 10.14293/S2199-1006.1.SOR-STAT.AFHTWC.v1.RBGXSM
C.H.J. Hartgerink
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引用次数: 0
Açık erişim ve yayıncılık değerlendirme kriterleri
Pub Date : 2015-11-16 DOI: 10.14293/S2199-1006.1.SOR-EDU.AMHUHV.V1
Tom Olijhoek, Dominic Mitchell, Lars Bjørnshauge
Olijhoek, T., Bjornshauge, L. ve Mitchell, D. (2015). Criteria for open access and publishing. ScienceOpen Research, (8s.) makalesinin cevirisidir.
Olijhoek, T., Bjornshauge, L. ve Mitchell, D.(2015)。开放获取和出版标准。科学与开放研究,(8):制菌素。
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引用次数: 21
Lipids contribute to epigenetic control via chromatin structure and functions 脂质通过染色质结构和功能参与表观遗传控制
Pub Date : 2015-10-06 DOI: 10.14293/S2199-1006.1.SOR-LIFE.AUXYTR.V2
R. Zhdanov, E. C. Schirmer, A. Venkatasubramani, Alastair R W Kerr, Elena Mandrou, G. R. Blanco, A. Kagansky
AbstractIsolated cases of experimental evidence over the last few decades have shown that, where specifically tested, both prokaryotes and eukaryotes have specific lipid species bound to nucleoproteins of the genome. In vitro, some of these lipid species exhibit stoichiometric association with DNA polynucleotides with differential affinities toward certain secondary and tertiary structures. Hydrophobic interactions with inner nuclear membrane could provide attractive anchor points for lipid-modified nucleoproteins in organizing the dynamic genome and accordingly there are precedents for covalent bonds between lipids and core histones and, under certain conditions, even DNA. Advances in biophysics, functional genomics, and proteomics in recent years brought about the first sparks of light that promises to uncover some coherent new level of the epigenetic code governed by certain types of lipid–lipid, DNA–lipid, and DNA-protein–lipid interactions among other biochemical lipid transactions in the nucleus. Here, we review some of the older and more recent findings and speculate on how critical nuclear lipid transactions are for individual cells, tissues, and organisms.
在过去的几十年里,实验证据的孤立案例表明,在特定的测试中,原核生物和真核生物都有特定的脂质物种与基因组的核蛋白结合。在体外实验中,这些脂类中的一些表现出与DNA多核苷酸的化学计量关联,对某些二级和三级结构具有不同的亲和力。与核膜的疏水相互作用可以为脂质修饰的核蛋白在组织动态基因组时提供有吸引力的锚点,因此在脂质和核心组蛋白之间,甚至在某些条件下,DNA之间存在共价键的先例。近年来,生物物理学、功能基因组学和蛋白质组学的进步带来了第一道曙光,有望揭示表观遗传密码的一些连贯的新水平,这些密码由某些类型的脂质-脂质、dna -脂质和dna -蛋白-脂质相互作用以及细胞核中其他生化脂质交易所控制。在这里,我们回顾了一些较早的和最近的发现,并推测核脂质交易对单个细胞、组织和生物体是多么重要。
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引用次数: 11
Time-dependent Dirichlet Conditions in Finite Element Discretizations 有限元离散中的时变狄利克雷条件
Pub Date : 2015-10-06 DOI: 10.14293/S2199-1006.1.SOR-MATH.AV2JW3.V1
P. Benner, J. Heiland
For the modelling and the numerical approximation of problems with timedependent Dirichlet boundary conditions one can call on several consistent and inconsistent approaches. We show that spatially discretized boundary control problems can be brought into a standard state space form accessible for standard optimization and model reduction techniques. We discuss several methods that base on standard finite-element discretizations, propose a newly developed problem formulation, and investigate their performance in numerical examples. We illustrate that penalty schemes require a wise choice of the penalization parameters in particular for iterative solves of the algebraic equations. Incidentally we confirm that standard finite element discretizations of higher order may not achieve the optimal order of convergence in the treatment of boundary forcing problems and that convergence estimates by the common method of manufactured solutions can be misleading.
对于时变狄利克雷边界条件问题的建模和数值逼近,可以采用几种一致和不一致的方法。我们证明了空间离散的边界控制问题可以转化为标准的状态空间形式,从而适用于标准的优化和模型约简技术。我们讨论了几种基于标准有限元离散化的方法,提出了一种新的问题表述,并通过数值算例研究了它们的性能。我们说明了惩罚方案需要明智地选择惩罚参数,特别是对代数方程的迭代解。顺便提一下,我们确认,在处理边界强迫问题时,高阶的标准有限元离散化可能无法达到最优收敛阶,并且用常见的制造解方法进行收敛估计可能会产生误导。
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引用次数: 12
Lipids contribute to epigenetic control via chromatin structure and functions: Epigenetics is Getting Fat: How lipids may be involved in the structure of the genome and it's regulation 脂质通过染色质结构和功能参与表观遗传控制:表观遗传正在变胖:脂质如何参与基因组结构及其调控
Pub Date : 2015-10-06 DOI: 10.14293/S2199-1006.1.SOR-LIFE.AUXYTR.V1
R. Zhdanov, E. C. Schirmer, A. Venkatasubramani, Alastair R W Kerr, Elena Mandrou, G. R. Blanco, A. Kagansky
Isolated cases of experimental evidence over the last few decades have shown that, where specifically tested, both prokaryotes and eukaryotes have specific lipid species bound to nucleoproteins of the genome. In vitro, some of these lipid species exhibit stoichiometric association with DNA polynucleotides with differential affinities toward certain secondary and tertiary structures. Hydrophobic interactions with inner nuclear membrane could provide attractive anchor points for lipid-modified nucleoproteins in organizing the dynamic genome and accordingly there are precedents for covalent bonds between lipids and core histones and, under certain conditions, even DNA. Advances in biophysics, functional genomics, and proteomics in recent years brought about the first sparks of light that promises to uncover some coherent new level of the epigenetic code governed by certain types of lipid–lipid, DNA–lipid, and DNA-protein–lipid interactions among other biochemical lipid transactions in the nucleus. Here, we review some of the older and more recent findings and speculate on how critical nuclear lipid transactions are for individual cells, tissues, and organisms. INTRODUCTION The importance of many lipid classes in biology is without question as they act as secondary messengers and signaling molecules that are added post-translationally to proteins to regulate their function and targeting. Species of a variety of lipid classes (e.g., phospholipids, sphingolipids, neutral lipids, cholesterol, fatty acids) are also responsible for the formation of membrane barriers between cellular compartments. Membrane lipids hold a unique place among cellular biomolecules for their dual nature: they have both hydrophobic long carbon side chains (up to 28 carbon atoms chain length, presumably of trans-configuration and rarely hydroxylated) and hydrophilic polar head groups (conjugated to hydrophobic part by esterand/or ether bond) that enable them to interact with both organic and aqueous environments. To form lipid bilayer membranes, the hydrophobic regions interact with one another while their polar side chains on the outside interact with the aqueous cellular environment. At the same time, a variety of lipid classes at the edge of the cellular compartment provide a stably organized hydrophobic environment to support functions SOR-LIFE
在过去的几十年里,实验证据的孤立案例表明,在特定的测试中,原核生物和真核生物都有特定的脂质物种与基因组的核蛋白结合。在体外实验中,这些脂类中的一些表现出与DNA多核苷酸的化学计量关联,对某些二级和三级结构具有不同的亲和力。与核膜的疏水相互作用可以为脂质修饰的核蛋白在组织动态基因组时提供有吸引力的锚点,因此在脂质和核心组蛋白之间,甚至在某些条件下,DNA之间存在共价键的先例。近年来,生物物理学、功能基因组学和蛋白质组学的进步带来了第一道曙光,有望揭示表观遗传密码的一些连贯的新水平,这些密码由某些类型的脂质-脂质、dna -脂质和dna -蛋白-脂质相互作用以及细胞核中其他生化脂质交易所控制。在这里,我们回顾了一些较早的和最近的发现,并推测核脂质交易对单个细胞、组织和生物体是多么重要。许多脂类在生物学中的重要性是毋庸置疑的,因为它们作为次级信使和信号分子,在翻译后添加到蛋白质中以调节其功能和靶向性。各种脂类(如磷脂、鞘脂、中性脂、胆固醇、脂肪酸)也负责细胞间膜屏障的形成。膜脂在细胞生物分子中占有独特的地位,因为它们具有双重性质:它们具有疏水的长碳侧链(长达28个碳原子链长,可能是反式构型,很少羟基化)和亲水的极性头基(通过酯或醚键共轭到疏水部分),使它们能够与有机和水环境相互作用。为了形成脂质双层膜,疏水区域彼此相互作用,而它们在外部的极性侧链与水细胞环境相互作用。同时,细胞隔室边缘的各种脂类提供了一个稳定组织的疏水环境,以支持SOR-LIFE功能
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引用次数: 2
Peer review – issues, limitations, and future development 同行评议——问题、限制和未来发展
Pub Date : 2015-09-29 DOI: 10.14293/S2199-1006.1.SOR-EDU.AYXIPS.V1
Jan Velterop
AbstractPeer review is almost universally seen as the crux of scientific journal publishing. The role of peer reviewers is (1) to help avoid unnecessary errors in the published article, and (2) to judge publication-worthiness (in the journal that arranges for the review). This happens. Sometimes. But the notion of peer review is rather vague, and since most of it is anonymous, it is very difficult – arguably impossible – for researchers to know if the articles they read have been reliably peer reviewed and which criteria have been used to come to the decision to accept for publication. On top of that, peer review is very expensive. Not the peer review itself, as it is mostly done by researchers without being paid for it, but the process as arranged by publishers. This has several underlying causes, but it is clear that the actual cost of technically publishing an article is but a fraction of the average APC (Article Processing Charge) income or per-article subscription revenues publishers routinely realize. Some (e.g. Richard Smith, ex-Editor of the British Medical Journal) advocate abolishing peer review altogether. This is certainly not without merit, but even without abolishing it, there are ways to make peer review more reliable and transparent, and much cheaper to the scientific community.
摘要同行评议几乎被普遍认为是科学期刊出版的关键。同行审稿人的作用是(1)帮助避免发表文章中出现不必要的错误,(2)判断发表价值(在安排审稿的期刊上)。发生这种情况。有时。但是同行评议的概念相当模糊,而且由于大多数都是匿名的,研究人员很难——可以说是不可能——知道他们读过的文章是否经过了可靠的同行评议,以及在决定接受发表时采用了哪些标准。最重要的是,同行评议非常昂贵。不是同行评议本身,因为它大多是由研究人员无偿完成的,而是由出版商安排的过程。这有几个潜在的原因,但很明显,从技术上讲,发表一篇文章的实际成本只是出版商通常实现的平均APC(文章处理费用)收入或每篇文章订阅收入的一小部分。一些人(如《英国医学杂志》前编辑理查德·史密斯)主张完全废除同行评议。这当然不是没有价值的,但即使不废除它,也有办法使同行评议更加可靠和透明,对科学界来说也便宜得多。
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引用次数: 3
Publishing in transition – do we still need scientific journals? 转型中的出版——我们还需要科学期刊吗?
Pub Date : 2015-09-04 DOI: 10.14293/S2199-1006.1.SOR-SOCSCI.ACKE0Y.V1
A. Grossmann
AbstractFor decades, scientific journals were the only way to communicate new research findings. Up until today, very little has changed in that respect. The overwhelming majority of all scientific journals still functions as they did in the times when there was no Internet, no social networks, or crowd-based knowledge platforms. Is this form of dissemination of research findings still suitable in the 21st century? The author says: no.
摘要几十年来,科学期刊是传播新研究成果的唯一途径。直到今天,这方面几乎没有什么变化。绝大多数科学期刊仍然像没有互联网、没有社交网络或基于人群的知识平台的时代一样运作。这种传播研究成果的方式在21世纪还适用吗?作者说:不。
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引用次数: 4
The evolution of head structures in lower Diptera 下双翅目昆虫头部结构的进化
Pub Date : 2015-09-01 DOI: 10.14293/S2199-1006.1.SOR-LIFE.ALTCE1.V2
R. Beutel, K. Schneeberg
The head of adult dipterans is mainly characterized by modifications and more or less far reaching reductions of the mouthparts (e.g., mandibles, maxillae), linked with the specialization on liquid food and the reduced necessity to process substrates mechanically. In contrast, the compound eyes and the antennae, sense organs used for orientation and for finding a suitable mating partner and oviposition site, are well developed. Some evolutionary novelties are specific adaptations to feeding on less liquefied substrates, such as labellae with furrows or pseudotracheae on their surface, and the strongly developed pre- and postcerebral pumping apparatuses. In some dipteran groups specialized on blood the mandibles are still present as piercing stylets. They are completely reduced in the vast majority of families. Within the group far-reaching modifications of the antennae take place, with a strongly reduced number of segments and a specific configuration in Brachycera. The feeding habits and mouthparts of dipteran larvae are much more diverse than in the adults. The larval head is prognathous and fully exposed in the dipteran groundplan and most groups of lower Diptera. In Tipuloidea and Brachycera the head is partly or largely retracted and the sclerotized elements of the external head capsule are partly or fully reduced. The head of Cyclorrhapha is largely reduced. A complex and unique feature of this group is the cephaloskeleton. The movability of the larvae is limited due to the lack of thoracic legs. This can be partly compensated by the mouthparts, which are involved in locomotion in different groups. The mouth hooks associated with the cyclorrhaphan cephaloskeleton provide anchorage in the substrate.
双翅目成虫头部的主要特征是口器的变化和或多或少的大幅度减少(例如,下颌骨,上颌骨),这与专门食用液体食物和减少机械加工基质的必要性有关。相比之下,复眼和触角,用于定位和寻找合适的交配对象和产卵地点的感觉器官,是很发达的。一些进化上的新奇之处是对以液化程度较低的基质为食的特殊适应,如唇瓣表面有沟槽或假气管,以及发达的脑前和脑后泵送装置。在一些以血液为专长的双翅目动物群体中,下颌骨仍然像穿刺的针一样存在。它们在绝大多数家庭中是完全减少的。在这个群体中,触角发生了深远的变化,在短尾目中,触角的片段数量大大减少,并且具有特定的结构。双翅目幼虫的食性和口器比成虫多样化得多。在双翅目陆生昆虫和大多数低双翅目昆虫群中,幼虫头是有头的,并且是完全暴露的。在短尾目和短尾目中,头部部分或大部分缩回,外头囊的硬化成分部分或全部缩小。环裂头大大减小。这个群体的一个复杂而独特的特征是头骨骼。由于缺乏胸腿,幼虫的活动能力受到限制。这可以由口器部分补偿,口器参与不同群体的运动。与环形头骨架相关联的口钩在底物中提供锚定。
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引用次数: 13
Science and the media 科学与媒体
Pub Date : 2015-08-05 DOI: 10.14293/S2199-1006.1.SOR-SOCSCI.AO0K8X.V1
T. Naumann
Science seeks and needs the attention of the public and the media, and the media are eager for news from the world of research. This sometimes seduces scientists to communicate their results in early stages of their work and may bring them into the situation of the sorcerer’s apprentice – they can’t get rid of the ghosts they called. We give some recent examples of early or doubtful communication in physics and ask for a responsible cooperation of science and the media which takes care of the peculiarities of the scientific process. Times of uncertainty are a normal part of the research process. It took from 1974 to 1978 till a handful of peculiar events in the MARK I experiment at the electron–positron storage ring Stanford Positron Electron Asymmetric Ring of the Stanford Linear Accelerator Centre (SLAC) in California could be interpreted reliably as being due to the first member of a new third family of elementary particles. For this discovery of the tau lepton Martin Perl received the Physics Nobel Prize in 1995. Perl first mentioned his observations in 1975 at a summer school in Canada. A reliable interpretation of the results he dared only in 1977 at the International Lepton-Photon conference in Hamburg. Perl himself describes this process of clarification of all uncertainties in his memoirs [1] “Is it a Lepton: From Uncertainty and Controversy to Confirmation: 1976-1978.” THE HIGGS – DISCOVERED TWICE? An example of early communication is the discovery of the Higgs boson at the Large Hadron Collider (LHC) at the European Centre of Nuclear Physics CERN in Geneva. There are two important differences between the discovery of the tau lepton and the Higgs boson: first, Perl‘s team in 1977 consisted of 36 physicists, while in the discovery of the Higgs boson in 2012 more than 5,000 researchers in two experiments were involved. Second, in 1977 there was not the hype and pressure from the media present in 2012 during the hunt for the Higgs. Already the start-up of the LHC was accompanied by slogans such as “The Hunt for the God Particle” (National Geographic), etc. And third, internal details on the state of the search could not go around the world via new media such as Facebook, Twitter, blogs, etc. within seconds. High pressure and exaggerated expectations on more than 5,000 physicists and a major international laboratory create an atmosphere that makes an undisturbed completion of the research difficult. The LHC start-up was accompanied by more than 2,500 television broadcasts and 5,800 press articles worldwide, and there were over 100 million hits on the website of CERN. The day before the CERN Colloquium on July 4, 2012, the “Higgsteria” reached an unprecedented level. The auditorium at CERN was literally besieged. The day before, the German “Spiegel” had already promised a “hot trail to the God particle” [2]. On July 4, 2012, the experiments ATLAS and CMS announced the discovery of a “Higgs-like” particle [3]: “CERN experiments observe partic
科学寻求并需要公众和媒体的关注,而媒体渴望从研究界获得新闻。这有时会诱使科学家们在工作的早期阶段就把他们的结果告诉别人,这可能会使他们陷入巫师学徒的境地——他们无法摆脱自己所召唤的鬼魂。我们举出一些最近的例子,说明物理学中早期或可疑的交流,并要求科学和媒体之间负责任的合作,以照顾科学过程的特点。不确定的时候是研究过程中正常的一部分。从1974年到1978年,在加利福尼亚州斯坦福直线加速器中心(SLAC)的正电子-电子存储环(Stanford Positron - Electron Asymmetric ring)进行的MARK I实验中,出现了一些特殊事件,这些事件可以可靠地解释为是由于新的第三种基本粒子族的第一个成员引起的。由于发现了tau轻子,马丁·珀尔获得了1995年的诺贝尔物理学奖。Perl第一次提到他的观察是在1975年加拿大的一所暑期学校。直到1977年在汉堡举行的国际轻子光子会议上,他才敢对结果做出可靠的解释。Perl自己在他的回忆录[1]“它是一个轻子吗:从不确定和争议到确认:1976-1978”中描述了这个澄清所有不确定性的过程。希格斯粒子——被发现两次?早期交流的一个例子是在日内瓦欧洲核子研究中心(CERN)的大型强子对撞机(LHC)上发现希格斯玻色子。发现tau轻子和发现希格斯玻色子之间有两个重要的区别:首先,1977年Perl的团队由36名物理学家组成,而2012年发现希格斯玻色子时,有5000多名研究人员参与了两个实验。其次,1977年没有2012年寻找希格斯粒子时媒体的大肆宣传和压力。大型强子对撞机的启动已经伴随着诸如“寻找上帝粒子”(国家地理杂志)等口号。第三,搜索状态的内部细节无法在几秒钟内通过Facebook、Twitter、博客等新媒体传遍全球。对5000多名物理学家和一个主要国际实验室的高压和过高的期望造成了一种气氛,使研究难以不受干扰地完成。大型强子对撞机的启动在全球范围内获得了2500多场电视转播和5800多篇新闻报道,欧洲核子研究中心网站的点击量超过1亿次。2012年7月4日,在CERN学术会议的前一天,“Higgsteria”达到了前所未有的水平。欧洲核子研究中心的礼堂几乎被包围了。前一天,德国《明镜周刊》已经承诺要找到“上帝粒子的热迹”[2]。2012年7月4日,实验ATLAS和CMS宣布发现了一种“类希格斯”粒子[3]:“CERN实验观察到与长期寻找的希格斯玻色子一致的粒子”,CERN总干事Rolf Heuer在历史性的学术会议上说[4]:“作为一个外行人,我想说:我认为我们找到了……我们有一个发现。我们已经观察到一种与希格斯玻色子一致的新粒子。”鉴于存在的不确定性,Heuer向公众建议从测量中得出的结论。他的行为有点像彼拉多面前的耶稣,当彼拉多问他是否是犹太人的王时,他回答说:“你说的。”这个诡计的微妙之处当然被大多数媒体所忽视,他们得意洋洋地宣布:在欧洲核子研究中心发现了上帝粒子(“美国广播公司新闻”)[5],物理学家发现了难以捉摸的粒子,被视为宇宙的关键(“纽约时报”)[6],轰动!上帝粒子被发现了!研究人员破译了宇宙的起源吗?(《图片报》)[7],欧洲核子研究中心科学家发现希格斯玻色子。神秘的“上帝粒子”到底是什么意思(“FOCUS Online”)[8]等等。SOR-SOCSCI
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引用次数: 0
Active and stable platinum/ionic liquid/carbon nanotube electrocatalysts for oxidation of methanol 活性稳定的铂/离子液体/碳纳米管甲醇氧化电催化剂
Pub Date : 2015-07-29 DOI: 10.14293/S2199-1006.1.SOR-CHEM.AYZQJS.V2
Huan‐Tsung Chang, Z. Shih, A. Periasamy, Guan-Lin Lin
Abstract Platinum (Pt) nanoparticles (NPs) on carbon nanotubes (CNTs) have been prepared from PtCl62− ions through a facile ionic liquid (IL)-assisted method and used for methanol oxidation. 1-Butyl-3-methylimidazolium (BMIM) with four different counter ions (PF6−, Cl−, Br−, and I−) has been tested for the preparation of Pt/IL/CNT nanohybrids, showing the counter ions of ILs play an important role in the formation of small sizes of Pt NPs. Only [BMIM][PF6] and [BMIM][Cl] allow reproducible preparation of Pt/IL/CNT nanohybrids. The electroactive surface areas of Pt/[BMIM][PF6]/CNT, Pt/[BMIM][Cl]/CNT, Pt/CNT, and commercial Pt/C electrodes are 62.8, 101.5, 78.3, and 87.4 m2 g−1, respectively. The Pt/[BMIM][Cl]/CNT nanohybrid-modified electrodes provide higher catalytic activity (251.0 A g−1) at a negative onset potential of −0.60 V than commercial Pt/C-modified ones do (133.5 A g−1) at −0.46 V. The Pt/[BMIM][Cl]/CNT electrode provides the highest ratio (4.52) of forward/reverse oxidation current peak, revealing a little accumulation of carbonaceous residues.
摘要采用易溶离子液体(IL)辅助法制备了碳纳米管(CNTs)上的铂(Pt)纳米粒子(NPs),并用于甲醇氧化。用四种不同的反离子(PF6−、Cl−、Br−和I−)对1-丁基-3-甲基咪唑(BMIM)进行了制备Pt/IL/CNT纳米杂化物的实验,结果表明,IL的反离子在小尺寸Pt NPs的形成中起着重要作用。只有[BMIM][PF6]和[BMIM][Cl]可以重复制备Pt/IL/CNT纳米杂化物。Pt/[BMIM][PF6]/CNT、Pt/[BMIM][Cl]/CNT、Pt/CNT和商用Pt/C电极的电活性表面积分别为62.8、101.5、78.3和87.4 m2 g−1。Pt/[BMIM][Cl]/CNT纳米杂化修饰电极在−0.60 V负电位下的催化活性(251.0 A g−1)高于商业Pt/ c修饰电极在−0.46 V的催化活性(133.5 A g−1)。Pt/[BMIM][Cl]/CNT电极提供了最高的正向/反向氧化电流峰值比(4.52),显示出少量碳质残留物的积累。
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引用次数: 1
期刊
ScienceOpen research
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