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In Silico Ligand Docking Approaches to Characterise the Binding of Known Allosteric Modulators to the Glucagon-Like Peptide 1 Receptor and Prediction of ADME/Tox Properties 硅配体对接方法表征已知变构调节剂与胰高血糖素样肽1受体的结合和ADME/Tox特性的预测
Pub Date : 2022-08-02 DOI: 10.3390/applbiosci1020010
Chiemela S. Odoemelam, E. Hunter, J. Simms, Z. Ahmad, Ming‐Wei Chang, B. Percival, Ian H. Williams, M. Molinari, S. C. Kamerlin, P. Wilson
The glucagon-like peptide 1 receptor (GLP-1R) is a member of the family (or class) B G-protein-coupled receptor (GPCR). The receptor is a regulator of insulin and a key target in treating Type 2 diabetes mellitus. In this investigation, computational chemistry techniques such as molecular docking were combined with in silico ADME/Tox predictions to determine the position and structure of the allosteric binding site, as well as to examine how the allosteric modulators bind to the binding site. In silico evaluation was used to evaluate the ADME/Tox properties of the allosteric modulators. The findings of the ligand docking studies suggest that the allosteric binding site is situated around the transmembrane (TM) domain TM 6 of the receptor in the active state. ADME/Tox characterisation of the allosteric modulators demonstrate that compounds 1–3 (2,6,7-trichloro-3-(trifluoromethyl)quinoxaline, 1-(5-(4-(tert-butyl)phenyl)-1,3,4-oxadiazol-2-yl)-6,6-dimethyl-3-(methylsulfonyl)-6,7-dihydrobenzo[c]thiophen-4(5H)-one, 2-((4-chlorophenyl)thio)-3-(trifluoromethyl)quinoxaline, respectively) complied with the traditional method of evaluating drug-likeness; Lipinski’s rule of 5. The allosteric modulator compound 4 (3-(8-chloro-6-(trifluoromethyl)imidazo[1,2-a]pyridin-2-yl)phenyl cyclohexanecarboxylate) failed to comply with Lipinski’s rule of five as a result of having a logP value of over 5.6. Moreover, molecular docking studies provide insights into potential allosteric binding sites and possible interactions. Finally, the in silico ADME/Tox study results are described as relevant to developing a viable drug candidate.
胰高血糖素样肽1受体(GLP-1R)是B家族(或类)g蛋白偶联受体(GPCR)的一员。该受体是胰岛素的调节因子,是治疗2型糖尿病的关键靶点。在本研究中,计算化学技术(如分子对接)与计算机ADME/Tox预测相结合,以确定变构结合位点的位置和结构,并研究变构调节剂如何与结合位点结合。采用计算机评价方法对变构调制剂的ADME/Tox性能进行了评价。配体对接研究结果表明,变构结合位点位于活性状态下受体的跨膜结构域TM 6附近。ADME/Tox表征表明,化合物1- 3(2,6,7-三氯-3-(三氟甲基)喹啉、1-(5-(4-(叔丁基)苯基)-1,3,4-恶二唑-2-基)-6,6-二甲基-3-(甲基磺酰基)-6,7-二氢苯并[c]噻吩-4(5H)- 1,2 -((4-氯苯基)硫)-3-(三氟甲基)喹啉符合传统的药物相似性评价方法;利平斯基的5法则。变构调节剂化合物4(3-(8-氯-6-(三氟甲基)咪唑[1,2-a]吡啶-2-基)苯基环己anecarboxylate)由于logP值大于5.6而不符合Lipinski的五法则。此外,分子对接研究提供了潜在的变构结合位点和可能的相互作用的见解。最后,计算机ADME/Tox研究结果被描述为与开发可行的候选药物相关。
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引用次数: 3
Ruthenium Complexes, an Emerging Class of Leishmanicidal Drug Candidates 钌配合物,一类新兴的利什曼尼候选药物
Pub Date : 2022-07-05 DOI: 10.3390/applbiosci1020009
S. Braga
This review addresses the search for activity enhancement of leishmanicidal organic compounds through their coordination chemistry with ruthenium. In an introduction to leishmaniasis, its clinical manifestations, geographical distribution, available forms of treatment, and challenges to disease management are presented. Ruthenium complexes, owing to their physico-chemical and biological properties, are introduced as a suitable molecular library from which to find alternatives to current medicines. The main sections of the review describe complexes reported in the literature, organised into two main groups: organometallics and inorganic complexes. The activity of the ruthenium complexes is presented compared with that of the ligands for a critical assessment of their utility in future clinical application.
本文综述了利用利什曼尼类有机化合物与钌的配位化学来增强活性的研究进展。在介绍利什曼病,其临床表现,地理分布,现有的治疗形式,并对疾病管理的挑战提出。钌配合物,由于其物理化学和生物学特性,被介绍为一个合适的分子文库,从中寻找现有药物的替代品。综述的主要部分描述了文献中报道的配合物,分为两大类:有机金属配合物和无机配合物。钌配合物的活性与配体的活性进行了比较,以对其在未来临床应用中的效用进行关键评估。
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引用次数: 3
Progress in Plant Genome Sequencing 植物基因组测序研究进展
Pub Date : 2022-07-04 DOI: 10.3390/applbiosci1020008
R. Henry
The genome sequence of any organism is key to understanding the biology and utility of that organism. Plants have diverse, complex and sometimes very large nuclear genomes, mitochondrial genomes and much smaller and more highly conserved chloroplast genomes. Plant genome sequences underpin our understanding of plant biology and serve as a key platform for the genetic selection and improvement of crop plants to achieve food security. The development of technology that can capture large volumes of sequence data at low costs and with high accuracy has driven the acceleration of plant genome sequencing advancements. More recently, the development of long read sequencing technology has been a key advance for supporting the accurate sequencing and assembly of chromosome-level plant genomes. This review explored the progress in the sequencing and assembly of plant genomes and the outcomes of plant genome sequencing to date. The outcomes support the conservation of biodiversity, adaptations to climate change and improvements in the sustainability of agriculture, which support food and nutritional security.
任何生物体的基因组序列都是理解该生物体的生物学和实用性的关键。植物有多样、复杂、有时非常大的核基因组、线粒体基因组和小得多、高度保守的叶绿体基因组。植物基因组序列巩固了我们对植物生物学的理解,并为作物的遗传选择和改良提供了关键平台,以实现粮食安全。能够以低成本和高精度捕获大量序列数据的技术的发展推动了植物基因组测序技术的加速发展。近年来,长读段测序技术的发展已成为支持染色体水平植物基因组精确测序和组装的关键进展。本文综述了植物基因组测序和组装的进展以及迄今为止植物基因组测序的成果。成果支持保护生物多样性、适应气候变化和提高农业可持续性,从而支持粮食和营养安全。
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引用次数: 5
Multifilm Mass Transfer and Time Constants for Mass Transfer in Food Digestion: Application to Gut-on-Chip Models 多膜传质和食物消化传质的时间常数:应用于肠片模型
Pub Date : 2022-06-24 DOI: 10.3390/applbiosci1020007
T. Langrish
This review highlights the involvement of mass transfer in animal food-digestion processes. There may be several mass-transfer steps during the dissolution of food components, starting from the food itself, moving into the digestive juices, then moving through the walls of the gastrointestinal tract. These steps create a sequence of film resistances to mass transfer, where one film resistance often limits the overall mass-transfer process. Mass-transfer rates, mass-transfer coefficients, and the time scales and time constants for different parts of the food-digestion process are all interlinked, and the connections have been explained. In some parts of the food-digestion process, the time constants for the mass-transfer process are similar to the residence times for food digestion, emphasising the importance of mass transfer in these parts of food digestion, such as the duodenum. The mass-transfer and transport behaviour for in vivo human digestive systems and in vitro guts-on-a-chip may be very similar, suggesting that cells on the intestine walls, whether in vitro (guts-on-a-chip) or in vivo, may see similar transport behaviour for both nutrients towards the cells, and waste products away from them.
这篇综述强调了质量传递在动物食物消化过程中的作用。在食物成分的溶解过程中,可能会有几个传质步骤,从食物本身开始,进入消化液,然后通过胃肠道壁。这些步骤产生一系列传质膜阻力,其中一个膜阻力通常限制了整个传质过程。传质速率、传质系数以及食物消化过程中不同部分的时间尺度和时间常数都是相互联系的,并且这种联系已经得到了解释。在食物消化过程的某些部分,传质过程的时间常数与食物消化的停留时间相似,强调了传质在食物消化的这些部分(如十二指肠)的重要性。体内人类消化系统和体外肠道芯片的质量传递和运输行为可能非常相似,这表明,无论是体外(肠道芯片)还是体内,肠壁上的细胞都可能看到类似的营养物质向细胞的运输行为,以及废物从细胞中流出的运输行为。
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引用次数: 1
Does Intestine Morphology Still Have Secrets to Reveal? A Proposal about the “Ghost” Layer of the Bowel 肠形态还有秘密要揭示吗?关于肠“鬼”层的建议
Pub Date : 2022-06-07 DOI: 10.3390/applbiosci1010006
Francesco Cappello, D. Saguto, S. Burgio, L. Paladino, F. Bucchieri
In this brief Opinion paper, the term “muco-microbiotic layer” is introduced to describe the innermost layer of the intestinal wall. This layer may contribute not only to the overall health of the bowel, but also to that of extraintestinal organs. Its constituents, in terms of soluble molecules and nanovesicles, need to be studied further. Moreover, one can hypothesize the existence of an analogous layer in other organs, such as the airways or some parts of the genital tracts. Further studies on it are needed.
在这篇简短的观点文章中,引入了术语“粘膜微生物层”来描述肠壁的最内层。这一层不仅有助于肠道的整体健康,也有助于肠外器官的健康。从可溶性分子和纳米囊泡的角度来看,其成分需要进一步研究。此外,人们可以假设在其他器官中也存在类似的层,例如气道或生殖道的某些部分。需要对其进行进一步的研究。
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引用次数: 0
Anti-Tumour Activities from Secondary Metabolites and Their Derivatives in Bryophytes: A Brief Review 苔藓植物次生代谢物及其衍生物的抗肿瘤活性研究进展
Pub Date : 2022-06-02 DOI: 10.3390/applbiosci1010005
P. Cianciullo, F. Cimmino, V. Maresca, S. Sorbo, P. Bontempo, A. Basile
Bryophytes are a poorly studied group of land plants that have been used in traditional medicine as a multipurpose remedy for centuries. Due to their peculiar morphology and physiology, bryophytes synthesise a multitude of secondary metabolites with a wide range of nutraceutical and pharmaceutical activities. Research has highlighted that secondary metabolites in bryophytes can also act as antitumour agents. Several studies have shown that bryophyte extracts and pure metabolites are cytotoxic against many cancer cell lines. Interestingly, some of these molecules and their derivatives are capable of acting on a specific target in cancer cells. Some macrocyclic(bis)bibenzyls from bryophytes can inhibit P-glycoprotein, reverting multidrug resistant cancer cell phenotypes, induce depolymerization of tubulin, stimulate apoptotic pathways, and inhibit angiogenesis. This brief review aims to collect recent knowledge on secondary metabolites of bryophytes and their derivatives, which have demonstrated an interaction with different molecular processes in cancer cells.
苔藓植物是一种研究很少的陆地植物,几个世纪以来一直被用作传统医学的多用途药物。由于其独特的形态和生理,苔藓植物合成了大量具有广泛营养和药物活性的次生代谢物。研究强调,苔藓植物的次生代谢物也可以作为抗肿瘤药物。几项研究表明,苔藓植物提取物和纯代谢物对许多癌细胞系具有细胞毒性。有趣的是,其中一些分子及其衍生物能够作用于癌细胞中的特定目标。苔藓植物中的一些大环(bis)联苯能抑制p -糖蛋白,恢复多药耐药癌细胞表型,诱导微管蛋白解聚,刺激凋亡途径,抑制血管生成。本文综述了苔藓植物及其衍生物次生代谢产物与肿瘤细胞中不同分子过程相互作用的最新研究进展。
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引用次数: 0
Expedient Access to Type II Kinase Inhibitor Chemotypes by Microwave-Assisted Suzuki Coupling 利用微波辅助铃木偶联法获得II型激酶抑制剂的化学型
Pub Date : 2022-05-31 DOI: 10.3390/applbiosci1010004
Lorenza Destro, Ross Van Melsen, A. Gobbi, Andrea Terzi, Matteo Genitoni, A. Zambon
Functionalized pyrazole-urea scaffolds are a common type II chemotype for the inhibition of protein kinases (PKs), binding simultaneously into the ATP-binding pocket with an ATP bioisostere and into a vicinal allosteric pocket with a pyrazole group. Standard approaches to the scaffold require multi-step synthesis of the ATP bioisostere followed by phosgene or triphosgene-mediated coupling with the substituted pyrazole group. Here we report an expedient approach to the chemotype, characterized by an optimized MW-assisted Suzuki coupling on easily accessed bromo-phenyl pyrazole ureas. The new protocol allowed quick access a large library of target analogues covering a broad chemical space of putative protein kinases inhibitors (PKIs).
功能化吡唑-尿素支架是一种常见的II型化学型,用于抑制蛋白激酶(PKs),同时结合到ATP结合袋中,与ATP生物同位体结合,并与吡唑基团结合到附近的变构袋中。标准的支架方法需要多步合成ATP生物同位体,然后与取代的吡唑基团进行光气或三光气介导的偶联。在这里,我们报告了一种方便的化学型方法,其特点是在易于接近的溴苯基吡唑脲上优化的分子量辅助铃木偶联。新方案允许快速访问覆盖广泛的假定蛋白激酶抑制剂(PKIs)化学空间的大型靶类似物库。
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引用次数: 1
Early Detection of Phototrophic Biofilms in the Polychrome Panel, El Castillo Cave, Spain 西班牙El Castillo洞穴彩色面板中光合生物膜的早期检测
Pub Date : 2022-04-19 DOI: 10.3390/applbiosci1010003
V. Jurado, J. Gonzalez-Pimentel, Á. Fernández-Cortés, Tamara Martin-Pozas, R. Ontañón, E. Palacio, B. Hermosin, S. Sánchez-Moral, C. Saiz-Jimenez
European caves contain some of the world’s greatest Paleolithic paintings, and their conservation is at risk due to the use of artificial lighting. Both lighting and high CO2 promotes the growth of phototrophic organisms on walls, speleothems and ground sediments. In addition, the combined effect of increases in CO2, vapor concentration and temperature variations induced by visitors can directly affect the development of corrosion processes on the cave rock surfaces. An early detection of the occurrence of phototrophic biofilms on Paleolithic paintings is of the utmost importance, as well as knowing the microorganisms involved in the colonization of rocks and walls. Knowledge of the colonizing species and their ecology will allow the adoption of control measures. However, this is not always possible due to the limited amount of biomass available for molecular analyses. Here, we present an alternative approach to study faint green biofilms of Chlorophyta in the initial stage of colonization on the Polychrome Panel in El Castillo Cave, Cantabria, Spain. The study of the biofilms collected on the rock art panel and in the ground sediments revealed that the lighting of the cave promoted the development of the green algae Jenufa and Coccomyxa, as well as of complex prokaryotic and eukaryotic communities, including amoebae, their endoparasites and associated bacteria and fungi. The enrichment method used is proposed as a tool to overcome technical constraints in characterizing biofilms in the early stages, allowing a preliminary characterization before deciding for direct or indirect interventions in the cave.
欧洲的洞穴藏有一些世界上最伟大的旧石器时代的绘画,由于人工照明的使用,它们的保护面临风险。光照和高二氧化碳都能促进墙壁、洞穴和地面沉积物上光养生物的生长。此外,游客引起的CO2、蒸汽浓度增加和温度变化的综合作用可以直接影响洞穴岩石表面腐蚀过程的发展。早期发现旧石器时代绘画上的光合生物膜是至关重要的,同时也要知道微生物在岩石和墙壁上的定植。了解定殖物种及其生态将有助于采取控制措施。然而,由于可用于分子分析的生物量有限,这并不总是可能的。在这里,我们提出了另一种方法来研究在西班牙坎塔布里亚El Castillo洞穴的彩色面板上定殖初期的淡绿色绿藻生物膜。对岩石壁画面板和地面沉积物中收集的生物膜的研究表明,洞穴的照明促进了绿藻Jenufa和Coccomyxa的发展,以及复杂的原核和真核生物群落,包括变形虫、它们的内寄生虫和相关的细菌和真菌。所使用的富集方法被认为是一种工具,可以克服早期阶段表征生物膜的技术限制,在决定对洞穴进行直接或间接干预之前进行初步表征。
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引用次数: 7
Physico-chemical characteristics of the biochars of Acacia sp, Bambusa sp, Eichchornia crassipes and Hymenocardia acida. 金合欢、竹、石竹和酸膜心草生物炭的理化特性。
Pub Date : 2022-02-28 DOI: 10.35759/jabs.170.2
Alasca Lombolu Ekuya, Jeancy Ntuka Luta, Irene Kibal Mande, Paul Mafuka Mbe-Mpie
ABSTRACT Objective: In order to promote the rational use of the various biochars in the sandy soils of Kinshasa, a study was carried out to evaluate some physicochemical parameters of four types of biochars (Acacia sp, Bambusa sp, Eichchornia crassipes and Hymenocardia acida). Methodology and results: four species of trees were used to make the biochars. These were analysed and the following parameters determined: cation exchange capacity, pH-water, nitrogen and total carbon, assimilable phosphorus, potassium, calcium and water retention capacity. With regard to the physico-chemical parameters analysed, the following conclusions were formulated; regarding pH, biochars from hardwoods (Acacia sp and Hymenocardia acida) showed an alkaline pH and those from less softwoods (Bambusa sp and Eichchornia crassipes) had neutral pH; the same results were found with the cation exchange capacity. All biochars used are generally rich in carbon and potassium content. On the other hand, nitrogen and exchangeable cation contents are low, except for the biochars of Acacias sp. The water retention capacity is very high on hardwood biochars than on those made from softer woods. Conclusion and application of the results: To amend sandy and acidic tropical soils with biochars require the following recommendations. - The use of biochars from hardwoods because they contain high concentrations of plants nutriments and have a good pH (8.1) that could play the essential role in neutralizing soil acidity. - Biochar should be ground to obtain a particle size of less than 2 mm for good retention of water and mineral elements. The smallest particles induce faster effects; however, their impact is often short-lived. Keywords: biochars, Acacia sp, Bambusa sp, Eichchornia crassipes and Hymenocardia acida. RÉSUMÉ Objectif : Dans le but de promouvoir l’utilisation rationnelle des différents biochars dans les sols sableux de Kinshasa, une étude a été menée pour évaluer certains paramètres physico-chimiques de quatre types des biochars (fabriqués à partir d’Acacia sp, Bambusa sp, Eichchornia crassipes et Hymenocardia acida) afin de préconiser ceux qui présentent les meilleurs caractéristiques. Méthodologie et résultats : quatre espèces d’arbres ont été utilisées pour fabriquer les biochars ; ces derniers ont été analysés et les paramètres suivants ont été déterminés : la capacité d’échange cationique, le pH-eau, les teneurs en azote et carbone total, phosphore assimilable, potassium, 17680 Ekuya et al., J. Appl. Biosci. Vol: 170, 2022 Physico-chemical characteristics of the biochars of Acacia sp, Bambusa sp, Eichchornia crassipes and Hymenocardia acida. calcium et la capacité de rétention d’eau. Au regard des paramètres physico-chimiques analysés, les conclusions ci-après ont été formulées ; concernant le pH, les biochars issus des bois durs (Acacia sp et Hymenocardia acida) ont présenté un pH alcalin et ceux de bois moins durs (Bambusa sp et Eichchornia crassipes) ont le pH presque
摘要目的:为了促进合理使用的各种生物炭在金沙萨的沙土,一项研究进行了评估的一些物理化学参数四种生物炭(金合欢sp、Bambusa sp Eichchornia凤眼莲和Hymenocardia acida)。方法与结果:采用四种树种制备生物炭。对这些进行了分析,并确定了以下参数:阳离子交换量、ph -水、氮和总碳、可同化磷、钾、钙和保水能力。通过对理化参数的分析,得出以下结论:在pH值方面,硬木(金合欢属和酸膜心)的生物炭呈碱性,较少软木(竹属和石竹属)的生物炭呈中性;阳离子交换容量也有相同的结果。所有使用的生物炭通常都富含碳和钾。另一方面,除金合欢生物炭外,其他生物炭的氮和交换阳离子含量均较低。硬木生物炭的保水能力比软木生物炭高。结论及应用:利用生物炭对热带砂质和酸性土壤进行改良,需要以下建议。-使用来自硬木的生物炭,因为它们含有高浓度的植物营养物质,并且具有良好的pH值(8.1),可以在中和土壤酸度方面发挥重要作用。-生物炭应研磨成粒径小于2毫米的颗粒,以保持水分和矿物元素。最小的粒子产生更快的效应;然而,它们的影响往往是短暂的。关键词:生物炭,金合欢,竹,石竹,酸膜心草RÉSUMÉ目的:研究不同类型的生物炭在金沙萨的应用、不同类型的生物炭在金沙萨的应用、不同类型的生物炭在金沙萨的应用、不同类型的生物炭在金沙萨的应用、不同类型的生物炭在金沙萨的应用、不同类型的生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用、不同类型生物炭在金沙萨的应用等方面的应用。msamthodologie et rs - sultats: quatespires d 'arbres ont ,和,利用,,和,生物炭;[3]陈志强等,陈志强等,陈志强等,陈志强等,陈志强等,陈志强等,陈志强等。Biosci。金合欢、黄竹、青竹和酸膜心草生物炭的理化特性。钙离子和离子交换电容。关于物理-化学-化学分析的参数,没有结论-化学-化学-化学-化学-化学-化学-化学-化学-化学;与酸碱度有关的生物炭(金合欢和酸膜心)和酸碱度有关的生物炭(金合欢和酸膜心)和酸碱度有关的生物炭(金合欢和酸膜心)和酸碱度有关的生物炭(金合欢和酸膜心)和酸碱度有关的生物炭(金合欢和酸膜心)和酸碱度有关的生物炭(金合欢)和酸碱度有关;等里面的模因结果用挺行了那儿capacite d 'echange cationique。在营养方面,我们有大量的生物炭,它们含有丰富的碳和钾。在生物炭和acacias sp的例外情况下,在生物炭和acacias sp的例外情况下,在生物炭和acacias sp的例外情况下,在生物炭和acacias的例外情况下,在生物炭和acacias的例外情况下,在生物炭和acacias的例外情况下,生物炭和acacias的例外情况。结论:该技术的应用结果表明:可减少生物炭的使用,减少热带生物炭的使用,方便推荐使用;使用莱斯生物炭issu des木香大调的车盲降contiennent mineraux et des浓度与en元素possede联合国bon pH值(8,1)可以以周素卿le角色资本倒缓冲器de儿子酸性岩。我将为你提供一个便利的条件,那就是你的兄弟,你的兄弟,你的兄弟,你的姊姊,你的姊姊,你的姊姊,你的姊姊,你的姊姊,你的姊姊,你的姊姊,你的姊姊。颗粒小,颗粒细,工业效应大,速度快;因此,我们认为这是一种对社会影响最大的变革。主要分类:生物炭、金合欢属、竹属、石竹属、酸膜心属
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引用次数: 1
Applied Biosciences: Application of Biological Science and Technology 应用生物科学:生物科学与技术应用
Pub Date : 2022-02-23 DOI: 10.3390/applbiosci1010002
R. Henry
The 21st century has been defined as the age of biology [...]
21世纪被定义为生物学的时代[…]
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引用次数: 1
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