Fundamental Research最新文献_第5页

Geobacter-associated prophages confer beneficial effect on dissimilatory reduction of Fe(III) oxides 地杆菌相关的噬菌体对Fe(III)氧化物的异化还原具有有益的作用

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-11-01 DOI: 10.1016/j.fmre.2022.10.013

Guiqin Yang, Annian Lin, Xian Wu, Canfen Lin, Siyue Zhu, Li Zhuang

The dissimilatory reduction of Fe(III) oxides driven by Fe(III)-reducing bacteria (FRB) is an important biogeochemical process that influences not only iron cycling but also the biogeochemical cycles of carbon, trace metals, nutrients and contaminants. Phages have central roles in modulating the population and activity of FRB, but the mechanism for phage-involved Fe(III) oxide reduction is still unclear. This work used a common FRB, Geobacter soli, to explore the roles and underlying mechanisms of FRB-harboring prophages in the dissimilatory reduction of Fe(III) oxides. Bioinformatic analysis predicted 185 phage-related genes in the G. soli genome, comprising functional prophages that were verified to be induced to form tailed phage particles. Ferrihydrite reduction was facilitated as prophage induction was stimulated and declined as prophage induction was inhibited, which indicated a positive role of G. soli-harboring prophages in Fe(III) oxide reduction. A comparison of gene expression and released phage particles in the cells grown with Fe(III)-citrate and ferrihydrite suggested that microbial ferrihydrite reduction would activate the SOS response and consequently induce the prophages to enter lytic cycles. The prophage-mediated lysis of the subpopulation resulted in an increased release of extracellular DNA and membrane vesicles that were conducive to Fe(III) oxide reduction, which might explain the positive role of prophages in ferrihydrite reduction. In summary, our results revealed the functional roles and underlying mechanisms of FRB-associated prophages in facilitating the dissimilatory reduction of Fe(III) oxides, which will advance our understanding of iron cycling in natural ecosystems.

铁（III）还原菌（FRB）驱动铁（III）氧化物的异化还原是一个重要的生物地球化学过程，不仅影响铁的循环，而且影响碳、微量金属、营养物质和污染物的生物地球化学循环。噬菌体在调节FRB的数量和活性方面发挥着核心作用，但噬菌体参与铁（III）氧化物还原的机制尚不清楚。本研究使用了一种常见的FRB，土杆菌，来探索FRB在Fe（III）氧化物的异化还原中的作用和潜在机制。生物信息学分析预测了185个与噬菌体相关的基因，包括功能性噬菌体，这些噬菌体被证实可以诱导形成尾状噬菌体颗粒。刺激原噬菌体诱导有利于水合铁还原，抑制原噬菌体诱导有利于水合铁还原，说明G. soli- containing原噬菌体对Fe（III）氧化物还原具有积极作用。用铁(III)-柠檬酸盐和水铁酸盐培养的细胞中基因表达和释放的噬菌体颗粒的比较表明，微生物水铁酸盐还原会激活SOS反应，从而诱导噬菌体进入裂解循环。原噬菌体介导的亚群裂解导致细胞外DNA和膜囊泡的释放增加，有利于Fe（III）氧化物的还原，这可能解释了原噬菌体在还原水合铁中的积极作用。总之，我们的研究结果揭示了frb相关噬菌体在促进Fe（III）氧化物异化还原中的功能作用和潜在机制，这将有助于我们对自然生态系统中铁循环的理解。

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引用次数: 0

The retinal pigment epithelium: Functions and roles in ocular diseases 视网膜色素上皮：在眼部疾病中的功能和作用

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-11-01 DOI: 10.1016/j.fmre.2023.08.011

Shasha Wang , Wanhong Li , Min Chen , Yihai Cao , Weisi Lu , Xuri Li

The retinal pigment epithelium (RPE) between retinal photoreceptors and choroidal capillaries is a single layer of cells that are of critical importance to the eye. RPE cells are derived from the anterior neural plate of neuroectodermal origin. Instructed by specific molecules and signaling pathways, the RPE undergoes formation and maturation to form a functional unit together with photoreceptors. The RPE plays crucial roles in maintaining normal retinal structure and functions, such as phagocytosis; barrier function; transportation of nutrients, ions, and water; resistance to oxidative damage; maintenance of visual cycle; and production of various important factors. RPE cells have an efficient metabolic machinery to provide sufficient energy to the retina. RPE dysfunction or atrophy can lead to many retinopathies, such as age-related macular degeneration and proliferative vitreoretinopathy. Here, we discuss RPE development, functions, and roles in various ocular diseases, and the mechanisms involved. A better understanding of the functions of the RPE and related regulatory pathways may help identify novel or better therapies for the treatment of many blinding diseases.

视网膜色素上皮（RPE）介于视网膜光感受器和脉络膜毛细血管之间，是对眼睛至关重要的单层细胞。RPE细胞来源于神经外胚层起源的前神经板。在特定分子和信号通路的指导下，RPE与光感受器一起形成和成熟，形成一个功能单元。RPE在维持正常的视网膜结构和功能（如吞噬）中起着至关重要的作用；屏障功能;输送营养物质、离子和水分；抗氧化损伤；视觉周期的维持；和生产的各种重要因素。RPE细胞具有高效的代谢机制，为视网膜提供足够的能量。RPE功能障碍或萎缩可导致许多视网膜病变，如年龄相关性黄斑变性和增殖性玻璃体视网膜病变。在这里，我们讨论RPE的发展，功能，在各种眼病中的作用，以及涉及的机制。更好地了解RPE的功能和相关的调控途径可能有助于确定新的或更好的治疗许多致盲疾病的方法。

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引用次数: 0

Intelligent vehicles and Smart transportation 智能车辆和智能交通

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2024.08.004

Jin Huang , Samuel Labi , Balázs Adam Kulcsár , Yue Gao , Cristina Olaverri Monreal , Fei Wu , Zhicheng He , Xiaobo Qu

引用次数: 0

Bi-level ramp merging coordination for dense mixed traffic conditions 密集混合交通条件下的双层匝道合流协调

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2023.03.015

Connected and Autonomous Vehicles (CAVs) hold great potential to improve traffic efficiency, emissions and safety in freeway on-ramp bottlenecks through coordination between mainstream and on-ramp vehicles. This study proposes a bi-level coordination strategy for freeway on-ramp merging of mixed traffic consisting of CAVs and human-driven vehicles (HDVs) to optimize the overall traffic efficiency and safety in congested traffic scenarios at the traffic flow level instead of platoon levels. The macro level employs an optimization model based on fundamental diagrams and shock wave theories to make optimal coordination decisions, including optimal minimum merging platoon size to trigger merging coordination and optimal coordination speed, based on macroscopic traffic state in mainline and ramp (i.e., traffic volume and penetration rates of CAVs). Furthermore, the micro level determines the real platoon size in each merging cycle as per random arrival patterns and designs the coordinated trajectories of the mainline facilitating vehicle and ramp platoon. A receding horizon scheme is implemented to accommodate human drivers’ stochastics as well. The developed bi-level strategy is tested in terms of improving efficiency and safety in a simulation-based case study under various traffic volumes and CAV penetration rates. The results show the proposed coordination addresses the uncertainties in mixed traffic as expected and substantially improves ramp merging operation in terms of merging efficiency and traffic robustness, and reducing collision risk and emissions, especially under high traffic volume conditions.

车联网和自动驾驶汽车（CAV）通过协调主流车辆和匝道车辆，在提高高速公路匝道瓶颈的交通效率、排放和安全性方面具有巨大潜力。本研究针对高速公路匝道上由 CAV 和人类驾驶车辆（HDV）组成的混合交通提出了一种双层协调策略，以便在交通流层面而非排层面优化拥堵交通场景下的整体交通效率和安全性。宏观层面采用基于基本图和冲击波理论的优化模型，根据主线和匝道的宏观交通状态（即交通流量和 CAV 的渗透率）做出最优协调决策，包括触发并线协调的最优最小并线排数和最优协调速度。此外，微观层面根据随机到达模式确定每个合流周期的实际排量，并设计主线促进车辆和匝道排量的协调轨迹。此外，还实施了一个后退视平线方案，以适应人类驾驶员的随机性。在不同交通流量和 CAV 渗透率的情况下，通过基于仿真的案例研究，测试了所开发的双层策略在提高效率和安全性方面的效果。结果表明，所提出的协调方法如预期般解决了混合交通中的不确定性问题，并在合并效率和交通稳健性方面大大改善了匝道合并操作，降低了碰撞风险和排放，尤其是在高交通流量条件下。

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引用次数: 0

Recent progress on mechanisms that allocate cellular space to plastids 细胞空间分配给质体机制的最新进展

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2022.09.004

Mechanisms that allocate cellular space to organelles are of fundamental importance to biology but remain poorly understood. A detailed understanding of mechanisms that allocate cellular space to plastids, such as chloroplasts, will lead to high-yielding crops with enhanced nutritional value. The HIGH PIGMENT (HP) genes in tomato contribute to regulated proteolysis and abscisic acid metabolism. The HP1 gene was the first gene reported to influence the amount of cellular space occupied by chloroplasts and chromoplasts almost 20 years ago. Recently, our knowledge of mechanisms that allocate cellular space to plastids was enhanced by new information on the influence of cell type on the amount of cellular space occupied by plastids and the identification of new genes that help to allocate cellular space to plastids. These genes encode proteins with unknown and diverse biochemical functions. Several transcription factors were recently reported to regulate the numbers and sizes of chloroplasts in fleshy fruit. If these transcription factors do not induce compensating effects on cell size, they should affect the amount of cellular space occupied by plastids. Although we can now propose more detailed models for the network that allocates cellular space to plastids, many gaps remain in our knowledge of this network and the genes targeted by this network. Nonetheless, these recent breakthroughs provide optimism for future progress in this field.

为细胞器分配细胞空间的机制对生物学至关重要，但人们对这一机制仍然知之甚少。详细了解为叶绿体等质体分配细胞空间的机制将有助于培育出营养价值更高的高产作物。番茄中的高色素（HP）基因有助于调节蛋白分解和脱落酸代谢。近 20 年前，HP1 基因是第一个被报道影响叶绿体和染色质所占细胞空间大小的基因。最近，关于细胞类型对质体所占细胞空间大小的影响的新信息，以及有助于为质体分配细胞空间的新基因的发现，增进了我们对质体细胞空间分配机制的了解。这些基因编码的蛋白质具有未知的多种生化功能。最近有报道称，有几种转录因子可以调节肉质果实中叶绿体的数量和大小。如果这些转录因子不会对细胞大小产生补偿作用，那么它们应该会影响质体占据的细胞空间。虽然我们现在可以为质体分配细胞空间的网络提出更详细的模型，但我们对这一网络以及这一网络所针对的基因的了解仍有许多空白。不过，这些最新的突破为这一领域未来的进展提供了乐观的前景。

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引用次数: 0

Structural rejuvenation of a well-aged metallic glass 老化金属玻璃的结构返老还老

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2022.12.004

Rejuvenation of glassy structures in general is characterized by the exothermic enthalpy prior to the glass transition. In the present work, we find that this situation is not applicable to a heavily-aged Zr-based metallic glass that rejuvenates by anelastic deformation before yield. Instead, its rejuvenation can be precisely captured by the low-temperature boson heat capacity peak as well as the effective enthalpy change with the glass-to-liquid transition. These results demonstrate that a structurally stable glass could rejuvenate by decreasing mechanical stability of its basin of potential energy landscape, but without changing the basin's energy level. The underlying mechanism points toward the redistribution of the atomic free volume with a constant system-averaged value. We further find that the rejuvenation limit of this glass is its steady-flow state with self-similar inherent structures at both short- and long-time scales. Our findings refresh the understanding of glass rejuvenation and suggest that the boson peak is a better probe for the structural rejuvenation of glasses.

玻璃结构的返老还童一般以玻璃转变前的放热焓为特征。在本研究中，我们发现这种情况并不适用于一种严重老化的锆基金属玻璃，这种玻璃在屈服前会通过非弹性形变恢复活力。相反，低温玻色子热容量峰以及玻璃到液体转变过程中的有效焓变可以精确捕捉到它的年轻化过程。这些结果表明，结构稳定的玻璃可以通过降低其势能景观盆地的机械稳定性而恢复活力，但盆地的能级不会发生变化。其基本机制是以恒定的系统平均值重新分配原子自由体积。我们进一步发现，这种玻璃的年轻化极限是其在短期和长期尺度上具有自相似固有结构的稳定流动状态。我们的发现刷新了人们对玻璃年轻化的认识，并表明玻色子峰是玻璃结构年轻化的更好探针。

引用次数: 0

Unsupervised learning of interacting topological phases from experimental observables 基于实验观测的相互作用拓扑相位的无监督学习

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2022.12.016

Classifying topological phases of matter with strong interactions is a notoriously challenging task and has attracted considerable attention in recent years. In this paper, we propose an unsupervised machine learning approach that can classify a wide range of symmetry-protected interacting topological phases directly from the experimental observables and without a priori knowledge. We analytically show that Green’s functions, which can be derived from spectral functions that can be measured directly in an experiment, are suitable for serving as the input data for our learning proposal based on the diffusion map. As a concrete example, we consider a one-dimensional interacting topological insulators model and show that, through extensive numerical simulations, our diffusion map approach works as desired. In addition, we put forward a generic scheme to measure the spectral functions in ultracold atomic systems through momentum-resolved Raman spectroscopy. Our work circumvents the costly diagonalization of the system Hamiltonian, and provides a versatile protocol for the straightforward and autonomous identification of interacting topological phases from experimental observables in an unsupervised manner.

对具有强相互作用的物质拓扑相进行分类是一项极具挑战性的任务，近年来引起了广泛关注。在本文中，我们提出了一种无监督机器学习方法，它可以直接从实验观测数据中对各种对称保护的相互作用拓扑相进行分类，而无需先验知识。我们通过分析表明，格林函数可以从实验中直接测量的光谱函数中导出，适合作为我们基于扩散图的学习建议的输入数据。作为一个具体的例子，我们考虑了一维相互作用拓扑绝缘体模型，并通过大量的数值模拟表明，我们的扩散图方法可以达到预期的效果。此外，我们还提出了一种通过动量分辨拉曼光谱测量超冷原子系统光谱函数的通用方案。我们的工作规避了代价高昂的系统汉密尔顿对角化，并提供了一种通用方案，可在无监督的情况下从实验观测数据中直接、自主地识别相互作用拓扑相。

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引用次数: 0

Large-scale heterogeneous synthesis of monodisperse high performance colloidal CsPbBr3 nanocrystals 单分散高性能胶体CsPbBr3纳米晶的大规模非均相合成

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2022.05.030

Colloidal lead halide perovskite nanocrystals (LHP NCs) are promising semiconductor materials for optoelectronic devices, but the high ionicity of LHP NCs makes their crystallization control and post-treatment difficult. Here, phosphonic acids (PAs) are employed as ligands to design a solid-liquid heterogeneous reaction system to regulate the LHP NC crystallization and achieve the desired focusing growth. During the heterogeneous synthesis, the precursors in the liquid phase are responsible for the burst nucleation and initial growth of NCs. Afterwards, the focusing growth of NCs is supported by the precursors released from the solid phase. In addition, the strong binding ability of PAs enables effective passivation of LHP NCs. Without post-treatment, gram-scale monodisperse CsPbBr₃ NCs having photoluminescence with a full width at half-maximum of 18 nm and a quantum yield of near-unity are obtained. The CsPbBr₃ NCs covered by a compact ligand layer keep initial quantum yield even after 18 cycles of purification, exhibiting excellent stability against polar solvents, ultraviolet irradiation and heat treatment. As scintillators, the prepared CsPbBr₃ NCs show strong radioluminescence emission and high-resolution X-ray imaging.

胶体卤化铅过氧化物纳米晶体（LHP NCs）是一种很有前途的光电器件半导体材料，但 LHP NCs 的高离子性使其结晶控制和后处理变得困难。本文采用膦酸 (PA) 作为配体，设计了一种固液异构反应体系来调节 LHP NC 结晶并实现理想的聚焦生长。在异相合成过程中，液相中的前驱体负责 NC 的迸发成核和初始生长。随后，固相中释放的前驱体为 NC 的聚焦生长提供了支持。此外，PAs 的强结合能力可有效钝化 LHP NCs。无需后处理，就能获得克级单分散 CsPbBr3 NCs，其光致发光的半最大全宽为 18 nm，量子产率接近单位。由紧密配体层覆盖的 CsPbBr3 NCs 在经过 18 次纯化后仍能保持初始量子产率，对极性溶剂、紫外线照射和热处理具有极佳的稳定性。作为闪烁体，所制备的 CsPbBr3 NCs 具有很强的放射性发射和高分辨率 X 射线成像能力。

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引用次数: 0

Machine learning methods to predict cadmium (Cd) concentration in rice grain and support soil management at a regional scale 用机器学习方法预测稻谷中的镉（Cd）浓度并支持区域范围内的土壤管理

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2023.02.016

Rice is a major dietary source of the toxic metal cadmium (Cd). Concentration of Cd in rice grain varies widely at the regional scale, and it is challenging to predict grain Cd concentration using soil properties. The lack of reliable predictive models hampers management of contaminated soils. Here, we conducted a three-year survey of 601 pairs of soil and rice samples at a regional scale. Approximately 78.3% of the soil samples exceeded the soil screening values for Cd in China, and 53.9% of rice grain samples exceeded the Chinese maximum permissible limit for Cd. Predictive models were developed using multiple linear regression and machine learning methods. The correlations between rice grain Cd and soil total Cd concentrations were poor (R² < 0.17). Both linear regression and machine learning methods identified four key factors that significantly affect grain Cd concentrations, including Fe-Mn oxide bound Cd, soil pH, field soil moisture content, and the concentration of soil reducible Mn. The machine learning-based support vector machine model showed the best performance (R² = 0.87) in predicting grain Cd concentrations at a regional scale, followed by machine learning-based random forest model (R² = 0.67), and back propagation neural network model (R² = 0.64). Scenario simulations revealed that liming soil to a target pH of 6.5 could be one of the most cost-effective approaches to reduce the exceedance of Cd in rice grain. Taken together, these results show that machine learning methods can be used to predict Cd concentration in rice grain reliably at a regional scale and to support soil management and safe rice production.

水稻是有毒金属镉（Cd）的主要膳食来源。水稻谷粒中的镉浓度在区域范围内差异很大，利用土壤特性预测谷粒中的镉浓度具有挑战性。缺乏可靠的预测模型阻碍了对受污染土壤的管理。在此，我们在区域范围内对 601 对土壤和水稻样本进行了为期三年的调查。约 78.3% 的土壤样本超过了中国土壤镉筛选值，53.9% 的稻谷样本超过了中国镉最高允许限值。利用多元线性回归和机器学习方法建立了预测模型。米粒镉和土壤总镉浓度之间的相关性较差（R2 < 0.17）。线性回归和机器学习方法确定了对谷粒镉浓度有显著影响的四个关键因素，包括氧化铁-氧化锰结合镉、土壤 pH 值、田间土壤含水量和土壤可还原锰的浓度。基于机器学习的支持向量机模型在预测区域范围内谷物镉浓度方面表现最佳（R2 = 0.87），其次是基于机器学习的随机森林模型（R2 = 0.67）和反向传播神经网络模型（R2 = 0.64）。情景模拟显示，将土壤酸碱度限制在 6.5 的目标值是降低稻谷镉超标最经济有效的方法之一。综上所述，这些结果表明，机器学习方法可用于在区域范围内可靠地预测稻谷中的镉浓度，并为土壤管理和水稻安全生产提供支持。

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引用次数: 0

Towards in vivo photoacoustic human imaging: Shining a new light on clinical diagnostics 走向体内光声人体成像：为临床诊断提供新的视角

IF 6.2 3区综合性期刊 Q1 Multidisciplinary

Fundamental Research

Pub Date : 2024-09-01 DOI: 10.1016/j.fmre.2023.01.008

Multiscale visualization of human anatomical structures is revolutionizing clinical diagnosis and treatment. As one of the most promising clinical diagnostic techniques, photoacoustic imaging (PAI), or optoacoustic imaging, bridges the spatial-resolution gap between pure optical and ultrasonic imaging techniques, by the modes of optical illumination and acoustic detection. PAI can non-invasively capture multiple optical contrasts from the endogenous agents such as oxygenated/deoxygenated hemoglobin, lipid and melanin or a variety of exogenous specific biomarkers to reveal anatomy, function, and molecular for biological tissues in vivo, showing significant potential in clinical diagnostics. In 2001, the worldwide first clinical prototype of the photoacoustic system was used to screen breast cancer in vivo, which opened the prelude to photoacoustic clinical diagnostics. Over the past two decades, PAI has achieved monumental discoveries and applications in human imaging. Progress towards preclinical/clinical applications includes breast, skin, lymphatics, bowel, thyroid, ovarian, prostate, and brain imaging, etc., and there is no doubt that PAI is opening new avenues to realize early diagnosis and precise treatment of human diseases. In this review, the breakthrough researches and key applications of photoacoustic human imaging in vivo are emphatically summarized, which demonstrates the technical superiorities and emerging applications of photoacoustic human imaging in clinical diagnostics, providing clinical translational orientations for the photoacoustic community and clinicians. The perspectives on potential improvements of photoacoustic human imaging are finally highlighted.

人体解剖结构的多尺度可视化正在彻底改变临床诊断和治疗。作为最有前途的临床诊断技术之一，光声成像（PAI）或光声成像通过光学照明和声学检测模式，弥补了纯光学和超声成像技术之间的空间分辨率差距。PAI 可以无创捕捉内源性物质（如含氧/脱氧血红蛋白、脂质和黑色素）或各种外源性特异性生物标记物的多种光学对比，从而揭示体内生物组织的解剖、功能和分子，在临床诊断方面显示出巨大的潜力。2001 年，全球首个光声系统临床原型被用于体内乳腺癌筛查，拉开了光声临床诊断的序幕。在过去的二十年里，PAI 在人体成像领域取得了不朽的发现和应用。临床前/临床应用的进展包括乳腺、皮肤、淋巴、肠道、甲状腺、卵巢、前列腺和脑成像等，毫无疑问，PAI 正在为实现人类疾病的早期诊断和精确治疗开辟新的途径。本综述重点总结了体内光声人体成像的突破性研究和关键应用，展示了光声人体成像在临床诊断中的技术优势和新兴应用，为光声学界和临床医生提供了临床转化方向。最后还强调了光声人体成像的潜在改进前景。

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引用次数: 0