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Intracellular organelle networks： Understanding their organization and communication through systems-level modeling and analysis

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Frontiers in Biology 2017年第1期12卷 7-18页

作者： Qinle ba Ge Yang Department of Biomedical Engineering Carnegie Mellon University Pittsburgh PA 15213 USA Department of Computational Biology Carnegie Mellon University Pittsburgh PA 15213 USA

baCKGROUND： Membrane-bound intracellular organelles are biochemically distinct compartments used by eukaryotic cells for serving specialized physiological functions and organizing their internal environment. Recent studies revealed surprisingly extensive communication between these organelles and highlighted the network nature of their organization and communication. Since organization and communication of the organelles are carried out at the systems level through their networks, systems-level studies are essential for understanding the underlying mechanisms. METHODS： We reviewed recent studies that used systems-level quantitative modeling and analysis to understand organization and communication of intracellular organelle networks. RESULTS： We first review modeling and analysis studies on how fusion/fission and degradation/biogenesis, two essential and closely related classes of activities of individual organelles, collectively mediate the dynamic organization of their networks. We then turn to another important aspect of the dynamic organization of the organelle networks, namely how organelles are physically connected within their networks, a property referred to as the topology of the networks in mathematics, and summarize some of their distinct properties. Lastly, we briefly review modeling and analysis studies that aim to understand communication between different organelle networks, focusing on cellular calcium homeostasis as an example. We conclude with a brief discussion of future directions for research in this area. CONCLUSIONS： Together, the reviewed studies provide critical insights into how diverse activities of individual organelles collectively mediate the organization and communication of their networks. They demonstrate the essential role of systems- level modeling and analysis in understanding complex behavior of such networks.

关键词： intracellular organelle organelle network organelle communication network analysis systems modeling

Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology

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Frontiers of Electrical and Electronic Engineering in China 2018年第4期6卷 344-358页

作者： Xiaoqi Chai Qinle ba Ge Yang Department of Biomedical Engineering Carnegie Mellon UniversityPittsburghPA 15213USA Department of Computational Biology Carnegie Mellon UniversityPittsburghPA 15213USA

Quantitative analysis of mitochondrial morphology plays important roles in studies of mitochondrial biology. The analysis depends critically on segmentation of mitochondria, the image analysis process of extracting mitochondrial morphology from images. The main goal of this study is to characterize the performance of convolutional neural networks (CNNs) in segmentation of mitochondria from fluorescence microscopy images. Recently, CNNs have achieved remarkable success in challenging image segmentation tasks in several disciplines. So far, however, our knowledge of their performance in segmenting biological images remains limited. In particular, we know little about their robustness, which defines their capability of segmenting biological images of different conditions, and their sensitivity, which defines their capability of detecting subtle morphological changes of biological objects. We have developed a method that uses realistic synthetic images of different conditions to characterize the robustness and sensitivity of CNNs in segmentation of mitochondria. Using this method, we compared performance of two widely adopted CNNs: the fully convolutional network (FCN) and the U-Net. We further compared the two networks against the adaptive active-mask (AAM) algorithm, a representative of high-performance conventional segmentation algorithms. The FCN and the U-Net consistently outperformed the AAM in accuracy, robustness, and sensitivity, often by a significant margin. The U-Net provided overall the best performance. Our study demonstrates superior performance of the U-Net and the FCN in segmentation of mitochondria. It also provides quantitative measurements of the robustness and sensitivity of these networks that are essential to their applications in quantitative analysis of mitochondrial morphology.

关键词： convolutional neural network mitochondrial morphology image segmentation robustness sensitivity

基于GEE的白洋淀水体生态补水后时空格局变化分析

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中国农村水利水电 2024年第4期 122-131,140页

作者：阳星王世岩韩祯李步东王亮汪洁孙龙巴艺博流域水循环模拟与调控国家重点实验室北京100038 中国水利水电科学研究院水生态环境研究所北京100038

生态补水是白洋淀生态环境治理的一项重要举措,根据生态补水机制的变化过程,将白洋淀的生态补水过程分为临时补水阶段、应急补水阶段和稳定补水阶段。为进行各生态补水阶段下白洋淀水体的时空格局变化分析,通过GEE对白洋淀在1990-2022年... 详细信息

生态补水是白洋淀生态环境治理的一项重要举措,根据生态补水机制的变化过程,将白洋淀的生态补水过程分为临时补水阶段、应急补水阶段和稳定补水阶段。为进行各生态补水阶段下白洋淀水体的时空格局变化分析,通过GEE对白洋淀在1990-2022年的701幅遥感影像进行水体和冰体提取,分析不同阶段下水体时空变化格局,以及专门分析了冬季结冰期的冰体面积变化。主要得出以下结论:①在各个生态补水阶段,白洋淀水体面积均呈现在夏季最小,冬春季最大的特点,而随着生态补水机制的不断完善,白洋淀水体面积变化幅度逐渐减小,呈现“削峰补低”的变化规律,其中临时补水阶段的逐月平均水体面积介于0.63~186.03 km^(2),稳定补水阶段的逐月平均水体面积介于17.88~109.15 km^(2),变化幅度减小了50.77%;②生态补水机制的完善让白洋淀呈现永久性水体大幅增加,间歇性水体大幅减小的变化规律,其中临时补水阶段永久性水体面积为7.66 km^(2),而稳定补水阶段的永久性水体面积为23.62 km^(2),增加了208.16%,间歇性水体面积则从263.50 km^(2)减少到143.58 km^(2),减小了45.51%;③从冰体面积变化角度分析,随着生态补水机制的不断完善,白洋淀的冰体面积不断减小,其中一月份的平均冰体面积从72.77 km^(2)减小到12.60 km^(2),减小了82.69%。结果表明:生态补水机制的完善并没有导致白洋淀水体面积不断增加,而是使白洋淀的水体环境更加破碎化;在全球变暖以及其他因素的影响下,白洋淀的冰体面积大幅减小;这种趋于破碎化、板块化的水域特征可能不利于生物多样性的保护,但鉴于生态系统对于水文响应具有滞后性,今后需进一步加强生态水文响应过程监测和研究。

关键词：白洋淀 GEE 生态补水水体提取冰体提取时空变化

CorelKit:An Extensible CorelDraw Vba Program for Geoscience Drawing

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Journal of Earth Science 2023年第3期34卷 735-757页

作者： Junwu Zhang Xian Liang Fangyue Wang Huaikun Wang Yu Fan Te ba Xiangxi Meng School of Resources and Environmental Engineering Hefei University of TechnologyHefei 230009China Mongolia Zhengyuan Co. LtdJinan 250101China

CorelKit is developed with the built-in Vba environment of CorelDraw?,and is a new plug-in in CorelDraw for geological and geochemical *** can help users quickly and easily draw geological and geochemical graphs,such as scatterplot,triangular scatterplot,line chart,histogram,bar chart,box plot,pie graph,*** order to adapt to the geological application,the above functions are *** and triangular scatterplot provide nearly 150 common basemaps,covering rock classification,structural environment discrimination,mineral genesis,isotope geochemistry,etc.,for the convenience of the user ***,CorelKit further provides a structural joint rose diagram and sulfur isotopic composition *** software also has many practical functions such as Bézier line topology,Multiple Bézier lines close fill,Single inner fill,Correction basemap,Add a compass,Add a scale,which facilitates daily geological *** software has a friendly interface,in both Chinese and English versions,and is suitable for CorelDraw X4 and later *** introduced the Bézier line topology to CorelKit for the first time,which is similar to the GIS®topology for geological *** to the“GB/T 958-2015 Geological Legends Used for Regional Geological Map”,a two-color filling library of rock pattern pictures is established,which is convenient to realize the twocolor filling of sedimentary rocks,metamorphic rocks and magmatic rocks ***,CorelKit makes up for many shortcomings of CorelDraw in geosciences and is a very practical tool for geoscience researchers.

关键词： CorelKit geoscience geochemistry data drawing CorelDraw Vba topology

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西藏山南吉如寺藏写卷《大般若经》题记考证

攀登（藏文版） 2024年第1期 45-57页

作者：达娃次仁西藏大学文学院

西藏山南吉如寺保存的写卷是近年来在西藏境内发现的重要藏文古籍文献。一经发现被国内外藏学界高度重视,相关研究报告层出不穷。特别是题记中出现的编校者关于“喇嘛尚”的考证,就目前而言,国内外藏学界公认为“喇嘛尚”是蔡巴噶举派... 详细信息

西藏山南吉如寺保存的写卷是近年来在西藏境内发现的重要藏文古籍文献。一经发现被国内外藏学界高度重视,相关研究报告层出不穷。特别是题记中出现的编校者关于“喇嘛尚”的考证,就目前而言,国内外藏学界公认为“喇嘛尚”是蔡巴噶举派创始人“公堂喇嘛尚·尊珠扎巴”。此问题不仅关系到编校者的确切身份,而且也直接影响到该文献的成书年代。对此,作者基于前人研究和查阅大量相关文献资料及多次实地调研的基础上,提出吉如寺现存三部《大般若经》题记中出现的编校者“喇嘛尚”应系12世纪初出生于当地的著名“喇嘛尚·松托巴”大师,而非“公堂喇嘛尚·尊珠扎巴”,并对“喇嘛尚·松托巴”的生平作了简要介绍,以便抛砖引玉,推动这一问题的研究。

关键词：吉如寺大般若经题记喇嘛尚

高龄急性脑梗死患者机械取栓治疗近期预后列线图模型的构建与评价

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湖南师范大学学报（医学版） 2024年第1期21卷 103-109,114页

作者：刘培慧赵金艳姜扬曹晓攀巴一陈英沈迪申达光葫芦岛市中心医院神经介入科葫芦岛125000 沈阳市第一人民医院神经内科沈阳110041 本溪市中心医院神经内科本溪117099

目的:构建高龄急性脑梗死患者机械取栓治疗近期预后的列线图模型,并评价该模型的准确性以及临床适用性。方法:回顾性分析三个高级卒中中心行机械取栓治疗的高龄急性脑梗死患者的临床资料,根据90天后改良Rankin量表评分将其分为预后良好... 详细信息

目的:构建高龄急性脑梗死患者机械取栓治疗近期预后的列线图模型,并评价该模型的准确性以及临床适用性。方法:回顾性分析三个高级卒中中心行机械取栓治疗的高龄急性脑梗死患者的临床资料,根据90天后改良Rankin量表评分将其分为预后良好组以及预后不良组,采用Logistic分析导致高龄急性脑梗死患者机械取栓治疗后近期预后不良的独立危险因素,基于上述独立危险因素利用R语言构建列线图模型,利用ROC曲线、Bootstrap方法以及临床决策曲线验证该模型的准确性和临床决策的获益性。结果:导致高龄急性脑梗死患者机械取栓治疗后近期预后不良的独立危险因素为:入院时NIHSS评分,合并糖尿病,股动脉穿刺到血管再通时间(PTR),术后合并肺部感染,术后发生症状性脑出血,侧枝循环差。ROC曲线验证列线图模型显示:构建的列线图模型预测高龄急性脑梗死患者机械取栓治疗近期预后的预测能力较强(AUC=0.876,95%CI:0.71~0.94),Bootstrap方法显示校准曲线的平均绝对误差为0.015,说明校准曲线与理想曲线贴合良好。临床决策曲线显示,列线图模型预测高龄急性脑梗死患者机械取栓治疗近期预后的发生阈值为0.04~0.95之间时该模型图的适用性最佳。结论:构建的列线图模型预测准确性高,具有较广泛的临床适用性。

关键词：高龄急性脑梗死机械取栓列线图模型预后

Resilient Modulus of Compacted Lateritic Soils from Senegal at OPM Conditions

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Geomaterials 2013年第4期3卷 165-171页

作者： Fatou Samb Meissa Fall Yves Berthaud Makhaly ba Laboratoire d’ Alembert—Université Pierre et Marie Curie Paris France Laboratoire de Mécanique et Modélisation—UFR Sciences de l’ Ingénieur Université de Thiès Thiès Sénégal

Repeated load triaxial tests were performed on five compacted gravel lateritic soils collected from different locations in Senegal: Sébikotane, Dougar, pa Lo, Mont-Rolland and Ngoundiane. The study revealed that resilient modulus decreases with the increase of the bulk and deviatoric stress in constant confining pressure. In addition, resilient modulus increases with the percentage of cement for appreciably equal contents of moisture. This effect tends to stop for higher stress. Besides, correlations were made with some models of resilient modulus such as the Uzan-Witczack model (Witczack and Uzan, 1988 [1]) and the National Highway Research Program (NCHRP) model (2004 [2]). The study confirms that both models give very good results with the best correlations being obtained with the Uzan-Witczack model.

关键词： Gravel Lateritic Soils Resilient Modulus Mechanical Behaviour pavement Cyclic Triaxial Test Mechanistic Design

Geochemistry and mineralogy of platinum-group elements(PGE)in chromites from CentralnoyeⅠ,Polar Urals,Russia

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Geoscience Frontiers 2011年第1期2卷 81-85页

作者： Jan pa.a.a.Ilja Knésl Anna Vymazalová Ivan Vavrín Ludmila Ivanovna Gurskaya Leonid Ruslanovich Kolbantsev Czech Geological Survey Geologicka 6152 00 Praha 5Czech Republic All Russia Geological Research Institute(VSEGEI) 74 Srechy Pr.199 106 St.PetersburgRussia

The Polar Urals region of northern Russia is well known for large chromium （Cr）-bearing massifs with major chromite orebodies, including the Centralnoye I deposit in the Ray-Iz ultramafic massif of the Ural ophiolite belt. New data on platinum （Pt）-group elements （PGE）, geochemistry and mineralogy of the host dunite shows that the deposit has anomalous iridium （Ir） values. These values indicate the predominance of ruthenium--osmium--iridium （Ru--Os--Ir）-bearing phases among the platinum-group mineral （PGM） assemblage that is typical of mantle-hosted chromite ores. Low Pt values in chromites and increased Pt values in host dunites might reflect the presence of cumulus PGM grains. The most abundant PGM found in the chromite is erlichmanite （up to 15 μm）. Less common are cuproiridsite （up to 5 μm）, irarsite （up to 4--5 μm）, and laurite （up to 4 μm）. The predominant sulfide is heazlewoodite, in intergrowth with Ni--Fe alloys, sporadically with pentlandite, and rarely with pure nickel. based on the average PGE values and esti- mated Cr-ore resources, the Centralnoye I deposit can be considered as an important resource of PGE.

关键词： Platinum-group elements Platinum-group minerals Chromite Ophiolites Centralnoye I deposit Polar Urals

Inhaled unfractionated heparin improves abnormalities of alveolar coagulation, fibrinolysis and inflammation in endotoxemia-induced lung injury rats

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Chinese Medical Journal 2013年第2期126卷 318-324页

作者： WANG Zong-yu WU Sheng-nan ZHU Zhao-zhong YANG ba-xian ZHU Xi Department of Intensive Care Unit Peking University ThirdHospital Beijing 100191 China Department of Cardiac Surgery Peking University First HospitalBeijing 100034 China Department of Biomedical Engineering Case Western ReserveUniversity Cleveland OH44106-2675 USA Department of Anesthesiology Peking University People'sHospital Beijing 100044 China

background Acute lung injury/acute respiratory distress syndrome presents with not only local inflammation, but also pulmonary coagulopathy which is characterized by an alveolar procoagulant response, anticoagulant inhibition, fibrinolytic supression and fibrin deposition. We thus had hypothesized that if aerosolized unfractionated heparin was inhaled into alveolar spaces, it could block the procoagulant tendency, lessen depletion of coagulation factors, and even influence the inflammatory response. We also assessed the effects of different administration regimens of heparin. Methods Male Wistar rats were given inhaled heparin starting 30 minutes before （prophylactic heparin） or 2 hours after （therapeutic heparin） intravenous lipopolysaccharide （LPS） was administered at 6-hour intervals; control groups received inhaled normal saline with or without being exposed to LPS. Thrombin-antithrombin complexes, activated protein C, tissue type and urokinase type plasminogen activators （t-pa/u-pa）, plasminogen activator inhibitor-1 （pal-l）, tumor necrosis factor-a, interleukin-6 in bronchoalveolar lavage, and lung tissue myeloperoxidase activity, and histology score were measured at three time-points. paI-1/（t-pa ＋ u-pa） was calculated based on the before-mentioned parameters. Statistical analysis was made using one-way analysis of variance （ANOVA） with post hoc test or Student＇s t test in the case of heterogeneity of variance. Results An alveolar procoagulant reaction, depressed fibrinolysis, and inflammatory response occurred in endotoxemia-induced lung injury. Local prophylactic application of heparin attenuated coagulation and early inflammation, promoted fibrinolysis, and reduced the histology score. Therapeutic application of heparin had similar, but weaker effects. Conclusions Intrapulmonary application of unfractionated heparin by inhalation might inhibit alveolar procoagulant reaction and the early inflammatory response, promote fibrinolysis, and alleviate pulmonary

关键词： acute lung injury, endotoxemia heparin,administration by inhalation, coagulation