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Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses. 从全基因组水平研究甜菜膨胀素基因家族及其在非生物胁迫下的表达反应。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-09-01 Epub Date: 2023-08-29 DOI: 10.1007/s42977-023-00176-1
Dima Faris Abdulkhadum Al-Mamoorı, Yasemin Celik Altunoglu, Erdoğan Horuz, Büşra Özkan Kök

Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.

甜菜主要用于世界各地的食糖生产。膨胀蛋白是一个有效调节细胞壁结构的细胞壁蛋白基因家族。它们还参与发育阶段,包括细胞和叶片生长、根系发育和果实成熟。本研究全面表征了在甜菜基因组中发现的膨胀蛋白基因家族成员。此外,本研究还通过qRT-PCR方法对不同非生物胁迫条件下甜菜膨胀素基因的计算机表达分析和干旱和高温联合胁迫下膨胀素基因表达谱进行了评估。共鉴定出31个甜菜膨胀素基因。BvuEXLA-02和BvuEXLB-02基因除了在正常发育中发挥作用外,还可以发挥非生物胁迫耐受作用。家庭成员测定甜菜膨胀素的性质可以帮助实现纤维素水解机制并提高植物生物量。阐明甜菜膨胀素基因在可变胁迫条件下的表达谱可以支持提高植物生产力。目前的研究结果也可能有助于未来深入了解甜菜膨胀素基因。
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引用次数: 0
Biofilm-forming plant growth-promoting rhizobacterial consortia isolated from mines and dumpsites assist green remediation of toxic metal (Ni and Pb) using Brassica juncea. 从矿山和垃圾场分离出的形成生物膜的促进植物生长的根际细菌群落有助于使用芥菜对有毒金属(Ni和Pb)进行绿色修复。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-09-01 Epub Date: 2023-09-21 DOI: 10.1007/s42977-023-00179-y
Sarita Sharma, Meenu Saraf

To study how biofilm-forming rhizobacteria isolated from mines and dumpsites improved the phytoremediation efficacy of B. juncea in metal-contaminated soil. Out of 91 isolates, six were chosen for research based on their tolerance to metals, and their efficient PGPR properties, and subjected to the design of a consortium. A compatibility study revealed no antagonistic interaction between rhizobacterial-consortiums. The results of the biofilm formation and FEG-SEM studies revealed that a consortium-BC8 formed a strong biofilm on the root surface of B. juncea seedlings. Based on results obtained with the phytoextraction efficiency of B. juncea in consortium-BC8 (SMHMZ46 and SMHMP23), they were identified as Klebsiella variicola and Pseudomonas otitidis, respectively, and submitted to NCBI GenBank with accession numbers MZ145092 and OK560623. This rhizobacteria is the first to be reported as assisting Ni and Pb phytoremediation by employing B. juncea. Soil inoculation with consortium-BC8 increased the amount of soluble Ni and Pb by 13.25-fold and 10.69-fold, respectively, when compared to the control. These consortiums-BC8 significantly increased vegetative growth and metal accumulation in root and shoot with a translocation-factor of 1.58 for Ni and soil to root with a bioconcentration-factor of 1.3 for Pb in B. juncea grown in individual soil contamination with 96.05 mg/kg NiCl2 and 89.63 mg/kg Pb(NO3)2, which are significantly higher than other consortium treatments and the non-inoculated control. B. juncea amendments with a biofilm-forming consortium-BC8 having TF, BCF, and BAC > 1 for Ni, whereas BCF > 1, TF, and BAC < 1 for Pb, are appropriate for green remediation of Ni and phytostabilization of Pb.

研究从矿山和垃圾场分离出的形成生物膜的根际细菌如何提高芥子菜在金属污染土壤中的植物修复效果。在91个分离株中,根据其对金属的耐受性和有效的PGPR特性,选择了6个进行研究,并接受了联合体的设计。一项兼容性研究显示,根际细菌群落之间没有拮抗相互作用。生物膜的形成和FEG-SEM研究结果表明,BC8在芥菜幼苗的根表面形成了强大的生物膜。根据对芥菜B.juncea在联合体BC8(SMHMZ46和SMHMP23)中的植物提取效率的研究结果,它们分别被鉴定为变异克雷伯菌和奥蒂假单胞菌,并以登录号MZ145092和OK560623提交给NCBI GenBank。该根际细菌是第一个被报道通过使用芥菜芽孢杆菌来辅助Ni和Pb植物修复的根际细菌。与对照相比,接种BC8联合体的土壤中可溶性Ni和Pb的含量分别增加了13.25倍和10.69倍。这些群落-BC8显著增加了在96.05 mg/kg NiCl2和89.63 mg/kg Pb(NO3)2的单独土壤污染中生长的芥菜中的营养生长和根和地上部的金属积累,其中Ni的迁移因子为1.58,其显著高于其他联合体处理和未接种的对照。B.具有形成生物膜的复合体的酒渣鼻改良剂-BC8,具有TF、BCF和BAC > Ni为1,而BCF > 1、TF和BAC
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引用次数: 0
How much (evil) intelligence can be encoded by 30 kb? 30 kb可以编码多少(邪恶的)情报?
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00153-8
Ernő Duda

Genomes of most RNA viruses are rarely larger than the size of an average human gene (10-15 kb) and still code for a number of biologically active polypeptides that modify the immune system and metabolism of the host organism in an amazingly complex way. Prolonged coevolution developed tricks by which viruses can dodge many protective mechanisms of the host and lead to the formation of molecular mimicry patterns. Some viruses inhibit the interferon response, interfere with the membrane destroying effects of the activated complement cascade. They can replicate in cellular compartments formed by inner membranes of the cell hiding their characteristic features from diverse pattern recognition receptors. In many cases-and in this respect, the new coronavirus is a champion-they can exploit our own defensive mechanisms to cause serious harm, severe symptoms and frequently deadly disease.

大多数RNA病毒的基因组很少大于人类平均基因的大小(10-15 kb),并且仍然编码许多生物活性多肽,这些多肽以一种令人惊讶的复杂方式改变宿主生物的免疫系统和代谢。长期的共同进化发展出病毒可以避开宿主的许多保护机制并导致分子模仿模式的形成的技巧。一些病毒抑制干扰素反应,干扰激活补体级联的膜破坏作用。它们可以在细胞内膜形成的细胞区室中复制,这些细胞区室隐藏了它们的特征,不受各种模式识别受体的影响。在许多情况下——在这方面,新型冠状病毒是一个冠军——它们可以利用我们自身的防御机制,造成严重伤害、严重症状和经常致命的疾病。
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引用次数: 0
Biologia Futura: does the aging process contribute to the relativity of time? 《未来生物学》:衰老过程对时间的相对性有贡献吗?
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00167-2
Vladimir Z Ajdžanović, Branka T Šošić-Jurjević, Jovan T Ranin, Branko R Filipović

In his Theory of relativity, Einstein determined that the time is relative to the reference frame of the observer. Under specific conditions, there is a difference in the elapsed time between two clocks, known as time dilation. A similar relativistic effect could be attributed to the brain operating at different frequencies, e.g., while it is slow and during the thought process. Time flow and the aging process are causally linked. Herein, we introduce physical relativity into the mind/thought context and elaborate changed perception of the time flow (the impression of the time acceleration) with aging. The phenomenology of time is observed in the context of physical and biological clock, as well as by introducing the category of 'mind time.' Mental processing impairment is crucial for the "aging-caused relativity of time," while adjusting of its' perception seems to be a matter of body/mind rest, mental hygiene and physical activity of the aging subject. We also provide a brief overview of the perception of time flow in some disease states that coincide with aging. Our main idea has a perspective for future development in the interdisciplinary synergy of philosophy, physical-mathematical elaboration, experimental biology and clinical investigations.

在他的相对论中,爱因斯坦确定时间是相对于观察者的参考系的。在特定条件下,两个时钟之间的运行时间存在差异,称为时间膨胀。类似的相对论效应可以归因于大脑以不同的频率运行,例如,当它缓慢且在思考过程中。时间流动和老化过程是有因果关系的。在此,我们将物理相对论引入思维语境,并详细阐述了随着年龄增长对时间流(时间加速的印象)的变化。时间现象学是在生理时钟和生物钟的背景下观察到的,同时也引入了“心灵时间”的范畴。心理处理障碍对“衰老导致的时间相对性”至关重要,而调整其“感知”似乎是衰老主体身心休息、心理卫生和身体活动的问题。我们还简要概述了在一些与衰老相吻合的疾病状态中对时间流的感知。我们的主要思想是对哲学、物理数学阐述、实验生物学和临床研究的跨学科协同的未来发展的展望。
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引用次数: 0
Learning from cancer to address COVID-19. 从癌症中学习应对COVID-19。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00156-5
Edit Oláh

Patients with cancer have been disproportionately affected by the novel coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Knowledge collected during the last three decades of cancer research has helped the medical research community worldwide to respond to many of the challenges raised by COVID-19, during the pandemic. The review, briefly summarizes the underlying biology and risk factors of COVID-19 and cancer, and aims to present recent evidence on cellular and molecular relationship between the two diseases, with a focus on those that are related to the hallmarks of cancer and uncovered in the first less than three years of the pandemic (2020-2022). This may not only help answer the question "Why cancer patients are considered to be at a particularly high risk of developing severe COVID-19 illness?", but also helped treatments of patients during the COVID-19 pandemic. The last session highlights the pioneering mRNA studies and the breakthrough discovery on nucleoside-modifications of mRNA by Katalin Karikó, which led to the innovation and development of the mRNA-based SARSCoV-2 vaccines saving lives of millions and also opened the door for a new era of vaccines and a new class of therapeutics.

由严重急性呼吸系统综合征冠状病毒2型(SARS-CoV-2)引起的2019年新型冠状病毒病(COVID-19)大流行对癌症患者的影响尤为严重。在过去三十年的癌症研究中收集的知识帮助世界各地的医学研究界在大流行期间应对了COVID-19带来的许多挑战。该综述简要总结了2019冠状病毒病和癌症的潜在生物学和危险因素,旨在介绍两种疾病之间细胞和分子关系的最新证据,重点关注那些与癌症特征相关并在大流行的头三年(2020-2022年)内发现的证据。这不仅有助于回答“为什么癌症患者被认为是患COVID-19严重疾病的特别高风险?”这个问题,而且有助于在COVID-19大流行期间对患者的治疗。最后一节重点介绍了开创性的mRNA研究和Katalin Karikó在mRNA核苷修饰方面的突破性发现,这导致了基于mRNA的SARSCoV-2疫苗的创新和发展,挽救了数百万人的生命,也为疫苗的新时代和新一类治疗方法打开了大门。
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引用次数: 0
Cryptogamic communities on flatroofs in the city of Debrecen (East Hungary). 德布勒森市(东匈牙利)屋顶上的神秘社区。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00166-3
Rebeka Aszalósné Balogh, Gábor Matus, László Lőkös, Balázs Adorján, Csongor Freytag, Ilona Mészáros, Viktor Oláh, Péter Szűcs, Peter Erzberger, Edit Farkas

Cryptogams of ten urban flatroofs, contrasting in their age and size, were studied between 2016 and 2018. Siliceous (bituminous felt, gravel, brick) and calcareous (concrete) substrata occurred at each site. Microclimate (T, RH) at two sites of contrasting shading was monitored from September 2016 to January 2017. Biomass of two differently aged, exposed flatroofs was sampled in October 2018. Taxa of Cladonia and Xanthoparmelia have been identified by spot tests and HPTLC. A total of 61 taxa (25 bryophytes, 36 lichens), mostly widespread synanthropic species, have been detected with an explicit difference of species composition between shaded and exposed sites. Floristically interesting species included acidophilous bryophytes (Hedwigia ciliata, Racomitrium canescens) and lichens (Xanthoparmelia conspersa, Stereocaulon tomentosum) of montane character. The most widespread lichen is Cladonia rei which accounted for a significant part of the biomass at selected sites. Species-area curves for bryophytes at exposed sites have become saturated at 100-150 m2. In contrast, saturation of lichen diversity has not been reached even at the largest sites. Flatroofs with traditional roofing techniques can harbour relatively diverse microhabitats and species-rich synanthropic vegetation. It is urgent to study these sites before renovation with modern roofing techniques eliminates them. Diversification of urban surroundings is possible in the future via application of various substrats in renovated and newly constructed roofs.

在2016年至2018年期间,研究人员对10个城市屋顶的密码进行了研究,对比了它们的年龄和大小。硅质(沥青毡、砾石、砖)和钙质(混凝土)基底都出现在每个地点。2016年9月至2017年1月对两个对比遮阳点的小气候(T、RH)进行了监测。2018年10月,对两个不同年龄的暴露平顶的生物量进行了采样。通过斑点试验和HPTLC鉴定了Cladonia和Xanthoparmelia的分类群。共检测到61个类群(苔藓类25个,地衣类36个),主要是广泛分布的合生种,在遮荫地和暴露地物种组成上存在明显差异。植物区系上有趣的物种包括喜酸苔藓植物(Hedwigia ciliata, Racomitrium canescens)和山地特征的地衣(Xanthoparmelia conspersa, Stereocaulon tomentosum)。分布最广的地衣是绿枝藓属(Cladonia rei),占所选样地生物量的很大一部分。暴露地点苔藓植物的种面积曲线在100-150 m2范围内趋于饱和。相比之下,即使在最大的地点,地衣多样性也没有达到饱和。采用传统屋面技术的平顶可以容纳相对多样化的微生境和物种丰富的共生植被。在用现代屋面技术进行改造之前,对这些遗址进行研究是迫在眉睫的。通过在翻新和新建的屋顶中应用各种基材,未来城市环境的多样化成为可能。
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引用次数: 1
Lipoamide dehydrogenase (LADH) deficiency: medical perspectives of the structural and functional characterization of LADH and its pathogenic variants. 脂酰胺脱氢酶(LADH)缺乏:LADH及其致病变异的结构和功能特征的医学观点
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00155-6
Eszter Szabó, Attila Ambrus

(Dihydro)lipoamide dehydrogenase (LADH) deficiency is an autosomal recessive genetic metabolic disorder. It generally presents with an onset in the neonatal age and premature death. The clinical picture usually involves metabolic decompensation and lactic acidosis that lead to neurological, cardiological, and/or hepatological outcomes. Severity of the disease is due to the fact that LADH is a common E3 subunit to the pyruvate, alpha-ketoglutarate, alpha-ketoadipate, and branched-chain alpha-keto acid dehydrogenase complexes and is also part of the glycine cleavage system; hence, a loss in LADH activity adversely affects several central metabolic pathways simultaneously. The severe clinical manifestations, however, often do not parallel the LADH activity loss, which implies the existence of auxiliary pathological pathways; stimulated reactive oxygen species (ROS) production as well as dissociation from the relevant multienzyme complexes proved to be auxiliary exacerbating pathomechanisms for selected disease-causing LADH mutations. This review provides an overview on the therapeutic challenges of inherited metabolic diseases, structural and functional characteristics of the mitochondrial alpha-keto acid dehydrogenase complexes, molecular pathogenesis and structural basis of LADH deficiency, and relevant potential future medical perspectives.

二氢脂酰胺脱氢酶(LADH)缺乏症是一种常染色体隐性遗传代谢疾病。它通常表现为在新生儿年龄发病和过早死亡。临床表现通常包括代谢性失代偿和乳酸性酸中毒,可导致神经学、心脏病学和/或肝病预后。疾病的严重性是由于LADH是丙酮酸、α -酮戊二酸、α -酮己二酸和支链α -酮酸脱氢酶复合物的共同E3亚基,也是甘氨酸裂解系统的一部分;因此,LADH活性的丧失同时对几种中枢代谢途径产生不利影响。但严重的临床表现往往与LADH活性丧失不一致,提示存在辅助病理通路;受刺激的活性氧(ROS)产生以及相关多酶复合物的解离被证明是辅助加剧了某些致病LADH突变的病理机制。本文综述了遗传性代谢性疾病的治疗挑战、线粒体α -酮酸脱氢酶复合物的结构和功能特征、LADH缺乏的分子发病机制和结构基础以及相关的潜在医学前景。
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引用次数: 1
Genes regulating oxidative-inflammatory response in circulating monocytes and neutrophils in septic syndrome. 脓毒症综合征循环单核细胞和中性粒细胞中调节氧化-炎症反应的基因。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 Epub Date: 2023-06-08 DOI: 10.1007/s42977-023-00168-1
Nesrine Elloumi, Mabrouk Bahloul, Emna Benabdallah, Sana Kharrat, Raouia Fakhfakh, Karama Bouchaala, Olfa Abida, Kamilia Chtara, Hatem Masmoudi, Mounir Bouaziz

Despite significant progress in the past decades, sepsis still lacks a specific treatment. Under normal conditions, leucocytes play a critical role in controlling infection and it is suggested that their activity is impaired during sepsis which contribute to the dysregulation of immune reactions. Indeed, in response to infection, several intracellular pathways are affected mainly those regulating the oxidative- inflammatory axis. Herein, we focused on the contribution of NF-kB, iNOS, Nrf2, HO-1 and MPO genes in the pathophysiology of septic syndrome, by analyzing the differential expression of their transcripts in circulating monocytes and neutrophils, and monitoring the nitrosative/oxidative status in septic syndrome patients. Circulating neutrophils of septic patients displayed a significant overexpression of NF-kB compared to other groups. In monocytes, patients with septic shock expressed the highest levels of iNOS and NF-kB mRNA. However, genes involved in cytoprotective response had increased expression in patients with sepsis, in particular, the Nrf2 and its target gene HO-1. Moreover, patient monitoring indicates that the iNOS enzyme expression and NO plasma levels may play a role in assessing the severity of septic conditions. Overall, in either monocytes or neutrophils, we pointed out the major role of NF-κB and Nrf2 in the pathophysiological process. Therefore, therapies targeted to redox abnormalities may be useful for better management of septic patients.

尽管在过去几十年中取得了重大进展,但败血症仍然缺乏特定的治疗方法。在正常情况下,白细胞在控制感染方面发挥着关键作用,而在败血症期间,白细胞的活动会受到影响,从而导致免疫反应失调。事实上,在应对感染时,一些细胞内通路会受到影响,主要是那些调节氧化-炎症轴的通路。在此,我们通过分析 NF-kB、iNOS、Nrf2、HO-1 和 MPO 基因在循环单核细胞和中性粒细胞中的转录本表达差异,并监测脓毒症患者的亚硝酸盐/氧化状态,重点研究了这些基因在脓毒症病理生理学中的作用。与其他组别相比,脓毒症患者循环中性粒细胞的 NF-kB 表达明显过高。在单核细胞中,脓毒性休克患者的 iNOS 和 NF-kB mRNA 表达水平最高。然而,参与细胞保护反应的基因,特别是 Nrf2 及其靶基因 HO-1 在脓毒症患者中的表达增加。此外,对患者的监测表明,iNOS 酶的表达和 NO 血浆水平可在评估脓毒症严重程度方面发挥作用。总之,在单核细胞或中性粒细胞中,我们指出了 NF-κB 和 Nrf2 在病理生理过程中的主要作用。因此,针对氧化还原异常的疗法可能有助于更好地治疗脓毒症患者。
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引用次数: 0
The importance of equally accessible genomic surveillance in the age of pandemics. 在大流行病时代平等地进行基因组监测的重要性。
IF 1.8 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 Epub Date: 2023-05-18 DOI: 10.1007/s42977-023-00164-5
Safia Zeghbib, Gábor Kemenesi, Ferenc Jakab

Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.

目前,基因组流行病学已成为调查疾病爆发期间的传播情况以及未来应对新出现的人畜共患病的准备工作的核心组成部分。在过去几十年中,出现了几种病毒性疾病,强调了分子流行病学在追踪传播途径、支持适当的缓解措施和开发适当疫苗方面的重要性。在这篇透视文章中,我们总结了迄今为止在基因组流行病学领域所做的工作以及未来应考虑的问题。我们追溯了长期以来应对人畜共患病的方法和方案。无论是小规模疫情,如 2002 年在中国广东首次发现的严重急性呼吸系统综合征(SARS)疫情,还是全球性大流行,如 2019 年以来我们正在经历的大流行,当时严重急性呼吸系统综合征 2(SARS-CoV-2)病毒在中国武汉继几例肺炎病例之后出现,随后在全球范围内传播。我们探讨了依靠基因组流行病学所带来的益处和遇到的不足,并明确提出了世界各地,尤其是经济欠发达国家在获取这些工具方面存在的不公平弊端。为了有效应对未来的流行病,在全球范围内努力实现更好的测序公平至关重要。
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引用次数: 0
The fire of research: Katalin Karikó's legacy. 研究之火:Katalin Karikó的遗产。
IF 2.1 4区 生物学 Q3 BIOLOGY Pub Date : 2023-06-01 DOI: 10.1007/s42977-023-00160-9
Norbert Pardi, Ádám Miklósi
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引用次数: 0
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