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Insights from metagenomic, metatranscriptomic, and molecular ecological network analyses into the effects

Quan Zheng, Minglu Zhang, Tingting Zhang, Xinhui Li, Minghan Zhu, Xiaohui Wang

《环境科学与工程前沿（英文）》 2020年 第14卷 第4期 doi: 10.1007/s11783-020-1239-8

摘要： Abstract • Cr NPs significantly promoted the denitrifying process and phosphorus removal. • The quantities of denitrifying and phosphorus genes greatly increased. • The transcription of denitrifying and phosphorus genes greatly increased. • The networks associated with nitrogen and phosphorus removal became complicated. • Cr NPs decreased some genera related to GAOs. The objectives of this study were to investigate the influence of chromium nanoparticles (Cr NPs) on the nitrogen and phosphorus removal performance and the bacterial structures of an activated sludge (AS) system. Also, we through molecular ecological networks (MENs) discussed the bacterial interactions. At last we researched the change of the functional genes and their expression patterns related to nitrogen and phosphorus removal in an AS system. The results showed that long-term exposure to 1 mg/L Cr NPs significantly promoted the denitrifying process and phosphorus removal in the AS system. The relative abundance of denitrifying and phosphorus removal microorganisms, such as Denitratisoma, Thauera, Dechloromonas, and Defluviicoccus, increased significantly. Candidatus Accumulibacter, well-known as polyphosphate-accumulating organisms (PAOs), increased significantly; the relative abundance of Candidatus Competibacter, known as glycogen-accumulating organisms (GAOs), decreased significantly. Furthermore, metagenomic and metatranscriptomic analysis revealed that most of the genera related to denitrifying and phosphorus removal had greatly increased, according to the quantities of denitrifying and phosphorus genes, and the corresponding transcription likewise greatly increased. Lastly, MENs analysis showed that although the overall network became smaller and looser in the presence of Cr NPs, the microbial connections among members related to nitrogen and phosphorus removal were enhanced. The abundance increases of denitrifiers and PAOs, and their increased transcription of functional genes, together with the enhanced interactions may be associated with the promotion of the denitrifying process and phosphorus removal.

关键词： Chromium nanoparticles (Cr NPs)     Metagenomic analysis     Metatranscriptomic analysis     Molecular ecological networks (MENs)     Nitrogen and phosphorus removal    

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Wheat research and breeding in the new era of a high-quality reference genome

Rudi APPELS

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 225-232 doi: 10.15302/J-FASE-2019265

摘要：

The publications of the International Wheat Genome Sequencing Consortium (IWGSC) released in August 2018 are reviewed and placed into the context of developments arising from the availability of the high-quality wheat genome assembly.

关键词： assembly technology     molecular markers     polyploidy     transcript networks     wheat genome    

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 1-3 doi: 10.1007/s11705-021-2134-y

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Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿（英文）》 2022年 第16卷 第2期   页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要： Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词： computer-aided molecular design     bio-oil additives     molecular signature descriptor    

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Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要：

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词： malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

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Molecular classification and molecular targeted therapy of cancer

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 147-149 doi: 10.1007/s11684-013-0274-2

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CONCENTRATIONS AND FLUXES OF DISSOLVED NUTRIENTS IN THE YANGTZE RIVER: LONG-TERM TRENDS AND ECOLOGICAL

《农业科学与工程前沿（英文）》 2021年 第8卷 第4期   页码 559-567 doi: 10.15302/J-FASE -2020344

摘要：

Intensifying human activity in the Yangtze River basin has substantially increased nutrient concentrations in the Yangtze River Estuary, leading to degradation of the coastal environment. Analysis of nutrient determinations published over the past 50 years reveals a gradual decreasing trend in the concentrations and fluxes of dissolved silicate (DSi). However, both dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphate (DIP) concentrations have increased significantly since the 1970s. The frequency of and area covered by red tide outbreaks have increased greatly during this period, mainly due to changes in nutrient supply ratios [i.e., N/P (DIN/DIP), N/Si (DIN/DSi), P/Si (DIP/DSi)]. A strong correlation was found between the riverine DIN fluxes and the estimated DIN inputs from the major N sources, particularly fertilizers and atmospheric deposition. The data provide a comprehensive assessment of nutrients in the Yangtze River basin and their ecological impacts and indicate a potentially significant influence of atmospheric deposition on DIN loadings and fluxes.

 

关键词： atmospheric deposition / ecological impacts / nitrogen sources / nutrients / Yangtze delta    

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Ecological conservation, remediation and construction for building an ecological civilization in China: concepts for ecological activity

Guofang SHEN

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 376-379 doi: 10.15302/J-FASE-2017186

摘要： This paper explains and discusses the concepts of ecological conservation and construction in China in three parts. The first part provides a brief description of the historical background of ecological activities in China and their major achievements in the past. The second part is a comprehensive review of various types of ecological control activity aimed at the improvement of natural and artificially established ecosystems at the landscape, regional (watershed) and higher levels. The scope of and differences between some ecological terms used in China such as ecological protection, conservation, remediation (rehabilitation), restoration as well as the reestablishment of new ecosystems are elaborated. The review suggests that the term “ecological conservation and construction” should be used to embrace all types of ecological control activity in China. Finally, five guidelines are proposed for promoting the implementation of ecological conservation and construction in China based on the two important governmental documents related to the development of ecological civilization in China.

关键词： ecological conservation     development     construction ”     description     important governmental    

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分子电子学的发展 Review

Paven Thomas Mathew, 房丰洲

《工程（英文）》 2018年 第4卷 第6期   页码 760-771 doi: 10.1016/j.eng.2018.11.001

摘要：

分子电子学（moletronics）是用分子作为单元对分子电子学器件进行装配。这是一个包含物理、化学、材料科学及工程等学科的多学科交叉领域。分子电子学致力于使硅元件尺寸进一步减小。科学家已经在等效分子器件方面进行了诸多探索性研究。分子电子学在电子以及光子应用中逐渐产生影响，如导电聚合物、光色材料、有机超导体、电致变色材料等。为了满足减小硅片尺寸的需求，研究人员有必要将这种新型技术引入到分子层面。虽然分子层面仪器的实验验证和建模分析是一项艰巨的任务，但分子电子学领域依然出现了突破性进展。本文将对不同分子器件和潜在的适用于不同器件的分子应用结合起来进行讨论，如分子晶体管、分子二极管、分子电容、分子导线和分子绝缘体等。本文简要讨论未来的发展趋势以及介绍各种基于石墨烯已取得一定研究成果的分子仪器。

关键词： 分子电子学     分子晶体管     分子二极管     分子电容器     分子导线     石墨烯    

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A green eco-environment for sustainable development: framework and action

Xuejun LIU, Wen XU, Zhipeng SHA, Yangyang ZHANG, Zhang WEN, Jingxia WANG, Fusuo ZHANG, Keith GOULDING

《农业科学与工程前沿（英文）》 2020年 第7卷 第1期   页码 67-74 doi: 10.15302/J-FASE-2019297

摘要：

Following its 40-year reform and ‘Open Door’ policy, China has recently proposed a new approach to green development and rural revitalization—the idea of Agriculture Green Development (AGD), with the key feature of creating a green eco-environment. In this mini-review we introduce the definition, theory, framework and major components of a green eco-environment as a key part of the AGD. We define a green eco-environment as including four key elements or measures: (1) a green eco-environmental indicator system; (2) environmental monitoring and warning networks; (3) emission standards and environmental thresholds for key pollutants; (4) emission controls and pollution remediation technologies. We have used Quzhou County (a typical county in the center of the North China Plain) as an example to show how detailed air, water and soil monitoring networks, as well as improved farmer practices and pollution control measures (especially ammonia emission mitigation and PM pollution reduction), can begin to create a green eco-environment in China and that AGD is possible. We conclude by stressing the need to improve the framework and practice for a green eco-environment, especially the importance of linking proposals and practices for a green eco-environment with the United Nations high priority Sustainable Development Goals.

关键词： monitoring networks     environmental thresholds     ammonia emission mitigation     green ecological environment     Quzhou County    

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Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 250-256 doi: 10.1007/s11705-009-0281-7

摘要： Two kinds of heavy oils were fractionated into eight fractions by Liquid-Solid Adsorption Chromatography, respectively, and samples were collected to measure properties. According to the elemental analysis, molecular weight and H-NMR data, average molecular structures of polycyclic aromatic and heavy resin were constructed with improved Brown-Ladner (B-L) method and several corrections. And then, the most stable conformations of polycyclic aromatic and heavy resin in vacuum and toluene solution were obtained by molecular dynamic simulation, and the molecular size was gotten via the radius of gyration analysis. The results showed that the radius of gyration of polycyclic aromatic and heavy resin was 0.55–0.70 nm in vacuum and 0.60–0.90 nm in toluene solution. With molecular weight increasing, the molecular size in vacuum and toluene solution also increased. Due to the swelling behavior of solvent, the alkyl side chains of heavy oil molecule in solution were more stretched. Thus, the molecular size in toluene solution was larger than that in vacuum.

关键词： dynamic simulation     molecular dynamic     behavior     molecule     Adsorption Chromatography    

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Research on port ecological suitability evaluation index system and evaluation model

Yaofeng XIE,Xia LV,Ru LIU,Liuyan MAO,Xiaoxi LIU

《结构与土木工程前沿（英文）》 2015年 第9卷 第1期   页码 65-70 doi: 10.1007/s11709-014-0258-6

摘要： Along with the rapid development of port building, the negative impacts of port’s construction and operation on the coastline ecosystem are also increasingly strong. Therefore, it’s urgent to establish a scientific and complete system of port ecological suitability evaluation. This paper pointed out the characteristics of port ecological effects and the principles of selecting evaluation index, and used the “pressure-state-response (PSR)” model to analysis the various pressures on the environment caused by port construction and operation, and the system’s response. On this basis, we constructed the port ecological suitability evaluation index. This model used the combination of qualitative and quantitative analytic hierarchy process, to meet the multi-level, multi-objective characteristics of evaluation index system. The evaluation index system and evaluation model can be used to analysis the ecological suitability of port projects comprehensively and have some guiding significance to the port ecological suitability evaluation.

关键词： port     ecological suitability     press-state-response (PSR) model     evaluation index system    

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HIGH QUALITY DEVELOPMENTAL APPROACH FOR SOIL AND WATER CONSERVATION AND ECOLOGICAL PROTECTION ON THE

《农业科学与工程前沿（英文）》 2021年 第8卷 第4期   页码 501-511 doi: 10.15302/J-FASE-2021425

摘要：

The Loess Plateau is the core area in the Yellow River basin for implementing environmental protection and high-quality development strategies. A series of ecological projects has implemented aimed at soil and water conservation and ecological management on the Loess Plateau over the past 70 years. The effects of the ecological projects are apparent mainly through a marked increase in vegetation cover, controlled soil erosion and reduced flow of sediment into the Yellow River, continual optimization of the industrial structure and increased production from arable land, poverty alleviation and greater prosperity, and optimal allocation of space for biological organisms. Major problems have also been analyzed in ecological management including the fragile ecosystem of the region, maintaining the stability of vegetation, lower agricultural productivity and continued risk from natural disasters. Some suitable schemes and models have been developed for the coordinated development of the region through research and demonstration, striking the optimum balance between rural industry and ecology, and increased regional capacity to supply high-quality ecological products. Countermeasures to address the problems are suggested to guide ecological management and high-quality development in the future.

 

关键词： ecological management     high quality development     industrial structure     soil erosion     soil and water conservation     Loess Plateau    

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Effect of / molecular structures on pyrolysis performance and heat sink of decalin isomers

《化学科学与工程前沿（英文）》 2023年 第18卷 第1期 doi: 10.1007/s11705-023-2375-z

摘要： Decalin is considered as an important compound of high-energy-density endothermic fuel, which is an ideal on-board coolant for thermal management of advanced aircraft. However, decalin contains two isomers with a tunable composition, and their effects on the pyrolysis performance, such as the heat sink and coking tendency have not been demonstrated. Herein, we investigated the pyrolysis of decalin isomers, i.e., cis-decalin, trans-decalin and their mixtures (denoted as mix-decalin), in order to clarify the effects of the cis-/trans-structures on the pyrolysis performance of decalin fuels. The pyrolysis results confirmed that conversion of the tested fuels (600–725 °C, 4 MPa) decreased in the order cis-decalin > mix-decalin > trans-decalin. Detailed analyses of the pyrolysis products were used to compare the product distributions from cis-decalin, mix-decalin and trans-decalin, and the yields of some typical components (such as cyclohexene, 1-methylcyclohexene, benzene and toluene) showed significant differences, which could be ascribed to deeper cracking of cis-decalin. Additionally, the heat sinks and coking tendencies of the decalins decreased in the order cis-decalin > mix-decalin > trans-decalin. This work demonstrates the relationship between the cis/trans structures and the pyrolysis performance of decalin, which provides a better understanding of the structure-activity relationships of endothermic hydrocarbon fuels.

关键词： endothermic fuel     decalin     pyrolysis     heat sink     molecular structure    

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CONCENTRATIONS AND FLUXES OF DISSOLVED NUTRIENTS IN THE YANGTZE RIVER: LONG-TERM TRENDS AND ECOLOGICAL

Yandan FU, Jiahui KANG, Ziyue LI, Xuejun LIU, Wen XU

《农业科学与工程前沿（英文）》 2021年 第8卷 第4期   页码 559-567 doi: 10.15302/J-FASE-2020344

摘要： Intensifying human activity in the Yangtze River Basin (YRB) has substantially increased nutrient concentrations in the Yangtze River Estuary, leading to degradation of the coastal environment. Analysis of nutrient determinations published over the past 50 years reveals a gradual decreasing trend in the concentrations and fluxes of dissolved silicate (DSi). However, both dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphate (DIP) concentrations have increased significantly since the 1970s. The frequency and area covered by red tide outbreaks have increased greatly during this period, mainly due to changes in nutrient supply ratios [i.e., N/P (DIN/DIP), N/Si (DIN/DSi), P/Si (DIP/DSi)]. A strong correlation was found between the riverine DIN fluxes and the estimated DIN inputs from the major N sources, particularly fertilizers and atmospheric deposition. The data provide a comprehensive assessment of nutrients in the YRB and their ecological impacts and indicate a potentially significant influence of atmospheric deposition on DIN loadings and fluxes.

关键词： atmospheric deposition     ecological impacts     nitrogen sources     nutrients     Yangtze River Delta    

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标题 作者 时间 类型 操作

Insights from metagenomic, metatranscriptomic, and molecular ecological network analyses into the effects

Quan Zheng, Minglu Zhang, Tingting Zhang, Xinhui Li, Minghan Zhu, Xiaohui Wang

期刊论文

Wheat research and breeding in the new era of a high-quality reference genome

Rudi APPELS

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

期刊论文

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文

CONCENTRATIONS AND FLUXES OF DISSOLVED NUTRIENTS IN THE YANGTZE RIVER: LONG-TERM TRENDS AND ECOLOGICAL

期刊论文

Ecological conservation, remediation and construction for building an ecological civilization in China: concepts for ecological activity

Guofang SHEN

期刊论文

分子电子学的发展

Paven Thomas Mathew, 房丰洲

期刊论文

A green eco-environment for sustainable development: framework and action

Xuejun LIU, Wen XU, Zhipeng SHA, Yangyang ZHANG, Zhang WEN, Jingxia WANG, Fusuo ZHANG, Keith GOULDING

期刊论文

Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

期刊论文

Research on port ecological suitability evaluation index system and evaluation model

Yaofeng XIE,Xia LV,Ru LIU,Liuyan MAO,Xiaoxi LIU

期刊论文

HIGH QUALITY DEVELOPMENTAL APPROACH FOR SOIL AND WATER CONSERVATION AND ECOLOGICAL PROTECTION ON THE

期刊论文

Effect of / molecular structures on pyrolysis performance and heat sink of decalin isomers

期刊论文

CONCENTRATIONS AND FLUXES OF DISSOLVED NUTRIENTS IN THE YANGTZE RIVER: LONG-TERM TRENDS AND ECOLOGICAL

Yandan FU, Jiahui KANG, Ziyue LI, Xuejun LIU, Wen XU

期刊论文