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Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer 基于 MOF 的循环核酸提取方法揭示了肝癌中的无细胞 RNA 特征
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-12 DOI: 10.1093/nsr/nwae022
Yuqing Sun, Haixin Yu, Shaoqing Han, Ruoxi Ran, Ying Yang, Yongling Tang, Yuhao Wang, Wenhao Zhang, Heng Tang, Boqiao Fu, Boshi Fu, Xiaocheng Weng, Song-Mei Liu, Hexiang Deng, Shuang Peng, Xiang Zhou
Cell-free RNA (cfRNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cfRNA isolation technologies due to the low abundance and instability of cfRNA. Here, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids (containing cfRNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework (MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cfRNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The Whole transcriptome mapping characteristics of cfRNA in serum from patients with liver cancer was described and a cfRNA signature with 6 cfRNAs was identified to diagnose liver cancer with high diagnostic efficiency (AUC = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.
无细胞 RNA(cfRNA)可用于评估各种人体器官的健康状况、状态和表型,是一种潜在的生物标志物,可用于无创诊断多种疾病。然而,由于 cfRNA 丰度低且不稳定,目前还缺乏高效、无偏差的 cfRNA 分离技术。在此,我们开发了一种基于金属有机框架(MOF)材料包合核酸的可重复、高效的血清/血浆中不同类型无细胞核酸(含 cfRNA 和病毒 RNA)的分离技术,与最广泛使用的研究试剂盒方法相比,该技术大大提高了分离效率,并能保持 RNA 的完整性。重要的是,用 MOF 方法提取的 cfRNA 质量约为试剂盒方法的 10 倍,而且 MOF 方法分离出的不同类型 RNA 是试剂盒方法的三倍多。研究人员描述了肝癌患者血清中 cfRNA 的全转录组图谱特征,并利用这种 MOF 方法鉴定出了包含 6 个 cfRNA 的 cfRNA 特征,诊断肝癌的效率很高(独立验证队列中的 AUC = 0.905)。因此,这种新的 MOF 分离技术将推动液体活检领域的发展,并有可能诊断肝癌。
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引用次数: 0
Deciphering the controlling factors for phase transitions in zeolitic imidazolate frameworks 破译沸石咪唑酸盐框架中相变的控制因素
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-12 DOI: 10.1093/nsr/nwae023
Tao Du, Shanwu Li, Sudheer Ganisetti, Mathieu Bauchy, Yuanzheng Yue, Morten M Smedskjaer
Zeolitic imidazolate frameworks (ZIFs) feature complex phase transitions, including polymorphism, melting, vitrification, and polyamorphism. Experimentally probing their structural evolution during transitions involving amorphous phases is a significant challenge, especially at the medium-range length scale. To overcome this challenge, here we first train a deep learning-based force field to identify the structural characteristics of both crystalline and non-crystalline ZIF phases. This allows us to reproduce the structural evolution trend during the melting of crystals and formation of ZIF glasses at various length scales with an accuracy comparable to that of ab initio molecular dynamics, yet at a much lower computational cost. Based on this, we propose a new structural descriptor, namely, the ring orientation index, to capture the propensity for crystallization of ZIF-4 (Zn(Im)2, Im = C3H3N2−) glasses, as well as for the formation of ZIF-zni (Zn(Im)2) out of the high-density amorphous phase. This crystal formation process is a result of the reorientation of imidazole rings by sacrificing the order of the structure around the zinc-centered tetrahedra. The outcomes of this work are applicable to studying phase transitions in other metal-organic frameworks (MOFs) and may thus guide the design of MOF glasses.
沸石咪唑啉框架(ZIF)具有复杂的相变特征,包括多晶、熔化、玻璃化和多晶。在涉及非晶相的转变过程中,实验探测其结构演变是一项重大挑战,尤其是在中程长度尺度上。为了克服这一挑战,我们首先训练了一个基于深度学习的力场,以识别结晶和非晶 ZIF 相的结构特征。这样,我们就能在各种长度尺度上重现晶体熔化和 ZIF 玻璃形成过程中的结构演变趋势,其精确度可与原子分子动力学相媲美,但计算成本却低得多。在此基础上,我们提出了一种新的结构描述符,即环取向指数,用于捕捉 ZIF-4 (Zn(Im)2, Im = C3H3N2-) 玻璃的结晶倾向,以及从高密度无定形相中形成 ZIF-zni (Zn(Im)2) 的倾向。这一晶体形成过程是咪唑环通过牺牲锌中心四面体周围结构的有序性而重新定向的结果。这项研究成果适用于研究其他金属有机框架(MOFs)中的相变,从而为 MOF 玻璃的设计提供指导。
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引用次数: 0
In-situ synthesis of quantum dots in the nucleus of live cells 在活细胞核内原位合成量子点
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-11 DOI: 10.1093/nsr/nwae021
Yusi Hu, Zhi-Gang Wang, Haohao Fu, Chuanzheng Zhou, Wensheng Cai, Xueguang Shao, Shu-Lin Liu, Dai-Wen Pang
Cell nucleus is the main site for the storage and replication of genetic material, and the synthesis of substances in the nucleus is rhythmic, regular, and strictly regulated with physiological processes. However, whether exogenous substances, such as nanoparticles, can be synthesized in situ in the nucleus of live cells has not been reported. Here, we have achieved in-situ synthesis of CdSxSe1−x quantum dots (QDs) in the nucleus by regulation of the glutathione (GSH) metabolic pathway. High enrichment of GSH in the nucleus can be accomplished by the addition of GSH with the help of the Bcl-2 protein. Then, high-valence Se is reduced to low-valence Se by glutathione reductase (GR)-catalyzed GSH, and interacts with Cd precursor formed through Cd and thiol-rich proteins, eventually generating QDs in the nucleus. Our work contributes to a new understanding of the syntheses of substances in cell nucleus and will pave the way to the development of advanced ‘supercells’.
细胞核是储存和复制遗传物质的主要场所,细胞核内物质的合成具有节律性、规律性,并受到生理过程的严格调控。然而,外源物质(如纳米粒子)能否在活细胞核内原位合成尚未见报道。在这里,我们通过调控谷胱甘肽(GSH)代谢途径,在细胞核中实现了 CdSxSe1-x 量子点(QDs)的原位合成。在Bcl-2蛋白的帮助下,通过添加GSH可以实现细胞核中GSH的高度富集。然后,高价硒被谷胱甘肽还原酶(GR)催化的GSH还原成低价硒,并与通过镉和富硫醇蛋白形成的镉前体相互作用,最终在细胞核中生成QDs。我们的工作有助于对细胞核内物质合成的新认识,并将为开发先进的 "超级细胞 "铺平道路。
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引用次数: 0
Conductive catalysis by subsurface transition metals 次表层过渡金属的导电催化作用
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-10 DOI: 10.1093/nsr/nwae015
Xin Deng, Caiyan Zheng, Yangsheng Li, Zeyu Zhou, Jiamin Wang, Yihua Ran, Zhenpeng Hu, Fan Yang, Landong Li
The nature of catalysis is being hotly pursued for over a century, and current research is focused on understanding active centers and their electronic structures. Herein, the concept of conductive catalysis is proposed and verified by theoretical simulations and experimental observations. Metallic systems containing buried catalytically active transitional metals and exposed catalytically inert main group metals are constructed, and the electronic interaction between them via metallic bonding is disclosed. Through the electronic interaction, the catalytic properties of subsurface transitional metals (Pd or Rh) can be transferred to outermost main group metals (Al or Mg) for several important transformations like semi-hydrogenation, Suzuki-coupling and hydroformylation. The catalytic force is conductive, in analogy with the magnetic force and electrostatic force. The traditional definition of active centers is challenged by the concept of conductive catalysis and the electronic nature of catalysis is more easily understood. It might provide new opportunities for shielding traditional active centers against poisoning or leaching and allow for precise regulation of their catalytic properties by the conductive layer.
一个多世纪以来,催化的本质一直受到人们的热烈追捧,目前的研究重点是了解活性中心及其电子结构。本文提出了导电催化的概念,并通过理论模拟和实验观察进行了验证。构建了含有埋藏的催化活性过渡金属和暴露的催化惰性主族金属的金属体系,并揭示了它们之间通过金属键产生的电子相互作用。通过电子相互作用,地下过渡金属(钯或铑)的催化特性可以转移到最外层的主族金属(铝或镁)上,用于半加氢、铃木偶联和加氢甲酰化等几种重要的转化。催化力与磁力和静电力类似,具有传导性。导电催化的概念对活性中心的传统定义提出了挑战,催化的电子性质也更容易理解。它可能为保护传统活性中心免受毒害或浸蚀提供了新的机会,并允许导电层对其催化特性进行精确调节。
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引用次数: 0
Universal insertion of molecules in ionic compounds under pressure 离子化合物中分子在压力下的普遍插入
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-10 DOI: 10.1093/nsr/nwae016
Feng Peng, Yanming Ma, Chris J Pickard, Hanyu Liu, Maosheng Miao
Using first-principles calculations and crystal structure search methods, we found that many covalently bonded molecules such as H2, H2O, NH3, CH4, and C2H6 may react with NaCl, a prototype ionic solid, and form stable compounds under pressure while retaining their molecular structure. These molecules, despite whether they are homonuclear or heteronuclear, polar or non-polar, small or large, do not show strong chemical interactions with surrounding Na and Cl ions. In contrast, the most stable molecule among all examples, N2, is found to transform into cyclo-N5− anions while reacting with NaCl under high pressures. It provides a new route to synthesize pentazolates, which are promising green energy materials with high energy density. Our work demonstrates a unique and universal hybridization propensity of covalently bonded molecules and solid compounds under pressure. This surprising miscibility suggests possible mixing regions between the molecular and rock layers in the interiors of large planets.
利用第一原理计算和晶体结构搜索方法,我们发现许多共价键分子(如 H2、H2O、NH3、CH4 和 C2H6)都可能与离子固体原型 NaCl 发生反应,并在压力下形成稳定的化合物,同时保留其分子结构。这些分子,无论同核或异核、极性或非极性、小或大,都不会与周围的 Na 离子和 Cl 离子发生强烈的化学作用。相反,在所有例子中,最稳定的分子 N2 在高压下与 NaCl 反应时会转化为环-N5-阴离子。这为合成具有高能量密度的绿色能源材料--五氮唑提供了一条新途径。我们的工作证明了共价键分子和固体化合物在压力下独特而普遍的杂化倾向。这种令人惊讶的混溶性表明,大行星内部的分子层和岩石层之间可能存在混合区域。
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引用次数: 0
Polaron interfacial entropy as a route to high thermoelectric performance in DAE-doped PEDOT:PSS films 将极化界面熵作为掺杂 DAE 的 PEDOT:PSS 薄膜实现高热电性能的途径
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-09 DOI: 10.1093/nsr/nwae009
Jiajia Zhang, Caichao Ye, Genwang Wei, Liang Guo, Yuhang Cai, Zhi Li, Xin-Kun Wu, Fangyi Sun, Qikai Li, Yupeng Wang, Huan Li, Yuchen Li, Shuaihua Wang, Wei Xu, Xuefeng Guo, Wenqing Zhang, Weishu Liu
Enhancing the thermoelectric (TE) transport properties of conductive polymer materials has been a long-term challenge, in spite of the success seen with molecular doping strategies [1–8]. However, the strong coupling between the thermopower and the electrical conductivity limits the thermoelectric performance. Here, we use polaron interfacial occupied entropy engineering to break through this intercoupling for a PEDOT:PSS (poly(3,4-ethylenedioxythiophene-poly(4-styrenesulfonate)) thin film by using photochromic diarylethene (DAE) dopants coupled with UV-light modulation. With a 10-fold enhancement of the thermopower from 13.5 μV K−1 to 135.4 μV K−1 and almost unchanged electrical conductivity, the DAE-doped PEDOT: PSS thin film achieved an extremely high power factor of 521.28 μW m−1 K−2 from an original value of 6.78 μW m−1 K−2. The thermopower was positively correlated with the UV light intensity but decreased with increasing temperature, indicating resonant coupling between the planar closed DAE molecule and PEDOT. Both the experiments and theoretical calculations consistently confirmed the formation of an interface state due to this resonant coupling Interfacial entropy engineering of polarons could play a critical role in enhancing the thermoelectric performance of the organic film.
尽管分子掺杂策略取得了成功[1-8],但增强导电聚合物材料的热电(TE)传输特性一直是一项长期挑战。然而,热功率与电导率之间的强耦合限制了热电性能。在这里,我们利用极子界面占熵工程,通过光致变色二元噻吩(DAE)掺杂剂和紫外光调制,突破了 PEDOT:PSS(聚(3,4-亚乙二氧基噻吩-聚(4-苯乙烯磺酸))薄膜的这种相互耦合。掺杂 DAE 的 PEDOT.PSS 薄膜的热功率从 13.5 μV K-1 提高到 135.4 μV K-1,提高了 10 倍,而导电率几乎保持不变:PSS 薄膜的功率因数从原来的 6.78 μW m-1 K-2 提高到 521.28 μW m-1 K-2。热功率与紫外光强度呈正相关,但随着温度的升高而降低,这表明平面封闭 DAE 分子与 PEDOT 之间存在共振耦合。实验和理论计算一致证实,这种共振耦合形成了一种界面态 极子的界面熵工程在提高有机薄膜的热电性能方面可能起到关键作用。
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引用次数: 0
Hot versus cold subduction initiation 热俯冲启动与冷俯冲启动
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-09 DOI: 10.1093/nsr/nwae012
Zhong-Hai Li
Initiation of a new subduction zone could act in two different ways, forming either a hot or cold incipient subduction channel with contrasting geological records.
新俯冲带的形成可能有两种不同的方式,要么形成热俯冲通道,要么形成冷俯冲通道,其地质记录截然不同。
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引用次数: 0
Uncovering the dominant contribution of intermediate volatility compounds in secondary organic aerosol formation from biomass-burning emissions 揭示中间挥发性化合物在生物质燃烧排放形成的二次有机气溶胶中的主要作用
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-09 DOI: 10.1093/nsr/nwae014
Kun Li, Jun Zhang, David M Bell, Tiantian Wang, Houssni Lamkaddam, Tianqu Cui, Lu Qi, Mihnea Surdu, Dongyu Wang, Lin Du, I. Haddad, J. Slowik, A. Prévôt
Organic vapors from biomass burning are a large source of secondary organic aerosol (SOA). Previous smog chamber studies found that the SOA contributors in biomass-burning emissions are mainly volatile organic compounds (VOCs). While intermediate volatility organic compounds (IVOCs) are efficient SOA precursors and a considerable fraction of biomass-burning emissions, their contribution to SOA formation has not been directly observed. Here, by deploying a newly-developed oxidation flow reactor to study SOA formation from wood burning, we find that IVOCs can contribute ∼70% of the formed SOA, i.e., >2 times more than VOCs. This previously missing SOA fraction is interpreted to be due to the high wall losses of semi-volatile oxidation products of IVOCs in smog chambers. The finding in this study reveals that SOA production from biomass burning is much higher than previously thought, and highlights the urgent need for more research on the IVOCs from biomass burning and potentially other emission sources.
生物质燃烧产生的有机蒸汽是二次有机气溶胶(SOA)的一大来源。以前的烟雾室研究发现,生物质燃烧排放的 SOA 主要是挥发性有机化合物(VOC)。虽然中间挥发性有机化合物(IVOCs)是有效的 SOA 前体,并且在生物质燃烧排放物中占相当大的比例,但它们对 SOA 形成的贡献尚未被直接观测到。在这里,通过部署一个新开发的氧化流动反应器来研究木材燃烧产生的 SOA,我们发现 IVOC 在形成的 SOA 中的贡献率可达 70%,即比 VOC 高出 2 倍以上。我们认为,之所以会出现之前所缺失的 SOA 部分,是因为烟雾室中 IVOCs 的半挥发性氧化产物的壁面损失较高。这项研究的发现揭示了生物质燃烧产生的 SOA 比以前认为的要高得多,并强调了对生物质燃烧产生的 IVOC 以及其他潜在排放源进行更多研究的迫切性。
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引用次数: 0
Preface: paving the road for AI in molecular sciences 序言:为分子科学中的人工智能铺平道路
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-09 DOI: 10.1093/nsr/nwae010
Yi Qin Gao
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引用次数: 0
Magnetic Methods in Studies of New Superconducting Hydrides in a Diamond Anvil Cell 在金刚石砧室中研究新型超导氢化物的磁学方法
IF 20.6 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Pub Date : 2024-01-05 DOI: 10.1093/nsr/nwae005
V. Struzhkin, Ho-kwang Mao
In recent years, we witnessed a great success in discoveries of the high-Tc hydrides in high pressure experiments. This was achieved by creating metallic hydrogen ‘alloys’ with other elements across the periodic table. Although the original idea suggested by Neil Aschcroft [1] was to use alloying to reduce the pressure required for producing pure metallic hydrogen, the pressures required to stabilize these hydrides are still so high that in-situ measurements of the complete expulsion of the magnetic field (the Meissner state), a defining character of superconductivity, is difficult to obtain. Such deficit of the Meissner effect studies has provoked multiple critiques on claims of superconductivity in these new hydride materials, and stimulated new technical developments to meet these challenges. In this perspective article, we will provide a short summary of the results obtained with four alternative techniques which were used to probe the magnetic field expulsion and the Meissner state in a diamond-avnvil cell (DAC), which is the only high-pressure vessel capable of studying the high Tc superconducting hydrides at very high pressures.
近年来,我们在高压实验中成功发现了高锝氢化物。这是通过与元素周期表中的其他元素制造金属氢 "合金 "实现的。虽然 Neil Aschcroft [1] 最初提出的想法是利用合金来降低生产纯金属氢所需的压力,但稳定这些氢化物所需的压力仍然很高,以至于很难在原位测量到磁场的完全释放(迈斯纳状态),而这正是超导性的一个决定性特征。迈斯纳效应研究的这种不足引发了对这些新型氢化物材料超导性说法的多种批评,并刺激了新的技术发展以应对这些挑战。在这篇视角文章中,我们将简要总结利用四种替代技术探测磁场驱逐和金刚石砧室(DAC)中的迈斯纳状态所取得的结果,DAC 是唯一能够在极高压下研究高 Tc 超导氢化物的高压容器。
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引用次数: 0
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