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Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

《环境科学与工程前沿（英文）》 2012年 第6卷 第1期   页码 82-97 doi: 10.1007/s11783-011-0306-6

摘要： Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant (WWTP). For the past 30 years, molecular biologic techniques explored for environmental microbial community (EMC) have spanned a broad range of approaches to facilitate the researches with the assistance of computer science: faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.

关键词： molecular biological technique     microbial community     denaturing gradient gel electrophoresis (DGGE)     terminal restriction fragment length polymorphism (T-RFLP)     environmental applications    

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Seasonal microbial community shift in a saline sewage treatment plant

Qingmei YAN, Xuxiang ZHANG, Tong ZHANG, Herbert H P FANG

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 40-47 doi: 10.1007/s11783-011-0304-8

摘要： Activated sludge was monthly sampled from a saline sewage treatment plant of Hong Kong (China) during June 2007 to May 2008 to analyze the microbial community shift along with environmental variations using denaturing gradient gel electrophoresis of polymerase chain reaction amplified 16S rDNA fragments. Environmental changes resulted into a seasonal microbial community shift characterized by alterations in species number and abundance in the sewage treatment plant. Correspondence analysis and cluster analysis on community structure profile showed that the 12 monthly samples fell into four groups, which is in accordance with season changing in Hong Kong. Canonical correspondence analysis revealed that and posed more significant effects on community structure than total phosphorus and total nitrogen, respectively. Compared with sludge retention time, influent total phosphorus had an inverse effect on the community structure shift, and chemical oxygen demand and showed a similar effects. Results of this study may contribute to the development of new knowledge involving the microbial community shift in sewage treatment plants.

关键词： sewage treatment plants     polymerase chain reaction (PCR)     denaturing gradient gel electrophoresis (DGGE)     canonical correspondence analysis     correspondence analysis    

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Interaction and independence on methane oxidation of landfill cover soil among three impact factors: water, oxygen and ammonium

Pinjing HE, Na YANG, Wenjuan FANG, Fan Lü, Liming SHAO

《环境科学与工程前沿（英文）》 2011年 第5卷 第2期   页码 175-185 doi: 10.1007/s11783-011-0320-8

摘要： To understand the influence patterns and interactions of three important environmental factors, i.e. soil water content, oxygen concentration, and ammonium addition, on methane oxidation, the soils from landfill cover layers were incubated under full factorial parameter settings. In addition to the methane oxidation rate, the quantities and community structures of methanotrophs were analyzed to determine the methane oxidation capacity of the soils. Canonical correspondence analysis was utilized to distinguish the important impact factors. Water content was found to be the most important factor influencing the methane oxidation rate and Type II methanotrophs, and the optimum value was 15% (w/w), which induced methane oxidation rates 10- and 6- times greater than those observed at 5% (w/w) and 20% (w/w), respectively. Ambient oxygen conditions were more suitable for methane oxidation than 3% oxygen. The addition of of ammonium induced different effects on methane oxidation capacity when conducted at low or high water content. With regard to the methanotrophs, Type II was sensitive to the changes of water content, while Type I was influenced by oxygen content. Furthermore, the methanotrophic acidophile, , was detected in soils with a pH of 4.9, which extended their known living environments.

关键词： quantitative polymerase chain reaction (PCR)     denaturing gradient gel electrophoresis (DGGE)     principal component analysis (PCA)     canonical correspondence analysis (CCA)    

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Cultivation of aerobic granular sludge in a conventional, continuous flow, completely mixed activated sludge system

Xi CHEN,Linjiang YUAN,Wenjuan LU,Yuyou LI,Pei LIU,Kun NIE

《环境科学与工程前沿（英文）》 2015年 第9卷 第2期   页码 324-333 doi: 10.1007/s11783-014-0627-3

摘要： Aerobic granules were formed in a conventional, continuous flow, completely mixed activated sludge system (CMAS). The reactor was inoculated with seed sludge containing few filaments and fed with synthetic municipal wastewater. The settling time of the sludge and the average dissolved oxygen (DO) of the reactor were 2 h and 4.2 mg·L , respectively. The reactor was agitated by a stirrer, with a speed of 250 r·min , to ensure good mixing．The granular sludge had good settleability, and the sludge volume index (SVI) was between 50 and 90 mL·g . The laser particle analyzer showed the diameter of the granules to be between 0.18 and 1.25 mm. A scanning electron microscope (SEM) investigation revealed the predominance of sphere-like and rod-like bacteria, and only few filaments grew in the granules. The microbial community structure of the granules was also analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Sequencing analysis indicated the dominant species were α, β, and γ- , , and . The data from the study suggested that aerobic granules could form, if provided with sufficient number of filaments and high shear force. It was also observed that a high height-to-diameter ratio of the reactor and short settling time were not essential for the formation of aerobic granular sludge.

关键词： aerobic granular sludge     completely mixed activated sludge system (CMAS)     continuous flow     shear force     filamentous bacteria     polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)    

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Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

《环境科学与工程前沿（英文）》 2009年 第3卷 第4期   页码 393-403 doi: 10.1007/s11783-009-0145-x

摘要： Proteomics involves the separation of proteins, identification of the amino acid sequence of the interested or target proteins, study of the function of the proteins, modification, structure and ultimate assignments to functional pathways in the cell. The proteomic investigations have contributed greatly to human diseases studies, new drugs discovery researches, and environmental science in recent years. This article provides a review on the development of the main proteomic technologies, including both the gel based and non-gel based technologies, and their applications in environmental science. Proteomic technologies have been utilized in the environmental stresses studies to analyze the induction or reduction of proteins at expression level and identify the target proteins to investigate their function in response to environmental stresses, such as high or low pH, oxidation stress, and toxic chemicals. Such protein responses are also helpful to understand the mechanisms of some cellular activities and the functions of some proteins.

关键词： proteomics     environmental stress     two dimensional (2D) gel electrophoresis     mass spectrometry    

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PulseNet China, a model for future laboratory-based bacterial infectious disease surveillance in China

null

《医学前沿（英文）》 2012年 第6卷 第4期   页码 366-375 doi: 10.1007/s11684-012-0214-6

摘要：

Surveillance is critical for the prevention and control of infectious disease. China’s real-time web-based infectious disease reporting system is a distinguished achievement. However, many aspects of the current China Infectious Disease Surveillance System do not yet meet the demand for timely outbreak detection and identification of emerging infectious disease. PulseNet, the national molecular typing network for foodborne disease surveillance was first established by the Centers for Disease Control and Prevention of the United States in 1995 and has proven valuable in the early detection of outbreaks and tracing the pathogen source. Since 2001, the China CDC laboratory for bacterial pathogen analysis has been a member of the PulseNet International family; and has been adapting the idea and methodology of PulseNet to develop a model for a future national laboratory-based surveillance system for all bacterial infectious disease. We summarized the development progress for the PulseNet China system and discussed it as a model for the future of China’s national laboratory-based surveillance system.

关键词： infectious disease     laboratory-based infectious disease surveillance     pulse field gel electrophoresis     multilocus sequencing typing     PulseNet China    

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Removable Dyes—The Missing Link for In-Depth N-glycan Analysis via Multi-Method Approaches

Samanta Cajic,René Hennig,Valerian Grote,Udo Reichl,Erdmann Rapp,

《工程（英文）》 doi: 10.1016/j.eng.2023.02.016

摘要： As the roles of glycans in health and disease continue to be unraveled, it is becoming apparent that glycans’ immense complexity cannot be ignored. To fully delineate glycan structures, we developed an integrative approach combining a set of cost-effective, widespread, and easy-to-handle analytical methods. The key feature of our workflow is the exploitation of a removable fluorescent label—exemplified by 9-fluorenylmethyl chloroformate (Fmoc)—to bridge the gap between diverse glycoanalytical methods, especially multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Through the detailed structural analysis of selected, dauntingly complex N-glycans from chicken ovalbumin, horse serum, and bovine transferrin, we illustrate the capabilities of the presented strategy. Moreover, this approach “visualizes” N-glycans that have been difficult to identify thus far—such as the sulfated glycans on human immunoglobulin A—including minute changes in glycan structures, potentially providing useful new targets for biomarker discovery.

关键词： Glycoproteins     N-glycans     Reversible labeling     Hydrophilic interaction liquid chromatography     Capillary gel electrophoresis     Mass spectrometry    

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可去除染料——N-聚糖多方法深入分析中的缺失环节 Article

Samanta Cajic, René Hennig, Valerian Grote, Udo Reichl, Erdmann Rapp

《工程（英文）》 2023年 第26卷 第7期   页码 132-150 doi: https://doi.org/10.1016/j.eng.2023.02.016

摘要：

As the roles of glycans in health and disease continue to be unraveled, it is becoming apparent that glycans'  immense complexity cannot be ignored. To fully delineate glycan structures, we developed an integrative approach combining a set of cost-effective, widespread, and easy-to-handle analytical methods. The key feature of our workflow is the exploitation of a removable fluorescent label—exemplified by 9-fluorenylmethyl chloroformate (Fmoc)—to bridge the gap between diverse glycoanalytical methods, especially multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Through the detailed structural analysis of selected, dauntingly complex N-glycans from chicken ovalbumin, horse serum, and bovine transferrin, we illustrate the capabilities of the presented strategy. Moreover, this approach "visualizes" N-glycans that have been difficult to identify thus far—such as the sulfated glycans on human immunoglobulin A—including minute changes in glycan structures, potentially providing useful new targets for biomarker discovery.

关键词： 糖蛋白     N-聚糖     可逆标签     亲水相互作用液相色谱法     毛细管凝胶电泳     质谱法    

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prediction and optimization design of sustainable concrete based on squirrel search algorithm-extreme gradient

《结构与土木工程前沿（英文）》   页码 1310-1325 doi: 10.1007/s11709-023-0997-3

摘要： Concrete is the most commonly used construction material. However, its production leads to high carbon dioxide (CO2) emissions and energy consumption. Therefore, developing waste-substitutable concrete components is necessary. Improving the sustainability and greenness of concrete is the focus of this research. In this regard, 899 data points were collected from existing studies where cement, slag, fly ash, superplasticizer, coarse aggregate, and fine aggregate were considered potential influential factors. The complex relationship between influential factors and concrete compressive strength makes the prediction and estimation of compressive strength difficult. Instead of the traditional compressive strength test, this study combines five novel metaheuristic algorithms with extreme gradient boosting (XGB) to predict the compressive strength of green concrete based on fly ash and blast furnace slag. The intelligent prediction models were assessed using the root mean square error (RMSE), coefficient of determination (R2), mean absolute error (MAE), and variance accounted for (VAF). The results indicated that the squirrel search algorithm-extreme gradient boosting (SSA-XGB) yielded the best overall prediction performance with R2 values of 0.9930 and 0.9576, VAF values of 99.30 and 95.79, MAE values of 0.52 and 2.50, RMSE of 1.34 and 3.31 for the training and testing sets, respectively. The remaining five prediction methods yield promising results. Therefore, the developed hybrid XGB model can be introduced as an accurate and fast technique for the performance prediction of green concrete. Finally, the developed SSA-XGB considered the effects of all the input factors on the compressive strength. The ability of the model to predict the performance of concrete with unknown proportions can play a significant role in accelerating the development and application of sustainable concrete and furthering a sustainable economy.

关键词： sustainable concrete     fly ash     slay     extreme gradient boosting technique     squirrel search algorithm     parametric analysis    

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Vibration analysis of nano-structure multilayered graphene sheets using modified strain gradient theory

Amir ALLAHBAKHSHI,Masih ALLAHBAKHSHI

《机械工程前沿（英文）》 2015年 第10卷 第2期   页码 187-197 doi: 10.1007/s11465-015-0339-9

摘要：

In this paper, for the first time, the modified strain gradient theory is used as a new size-dependent Kirchhoff micro-plate model to study the effect of interlayer van der Waals (vdW) force for the vibration analysis of multilayered graphene sheets (MLGSs). The model contains three material length scale parameters, which may effectively capture the size effect. The model can also degenerate into the modified couple stress plate model or the classical plate model, if two or all of the material length scale parameters are taken to be zero. After obtaining the governing equations based on modified strain gradient theory via principle of minimum potential energy, as only infinitesimal vibration is considered, the net pressure due to the vdW interaction is assumed to be linearly proportional to the deflection between two layers. To solve the governing equation subjected to the boundary conditions, the Fourier series is assumed for w=w(x, y). To show the accuracy of the formulations, present results in specific cases are compared with available results in literature and a good agreement can be seen. The results indicate that the present model can predict prominent natural frequency with the reduction of structural size, especially when the plate thickness is on the same order of the material length scale parameter.

关键词： graphene     van der Waals (vdW) force     modi- fied strain gradient elasticity theory     size effect parameter    

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Visual chiral recognition of 1,1′-binaphthol through enantioselective collapse of gel based on an amphiphilic

Xuhong Zhang, Haimiao Li, Xin Zhang, Meng An, Weiwei Fang, Haitao Yu

《化学科学与工程前沿（英文）》 2017年 第11卷 第2期   页码 231-237 doi: 10.1007/s11705-017-1633-3

摘要： A novel gelator that contained both Schiff base and L-lysine moieties was synthesized and its gelation behavior was tested. This gelator can form gels in various organic solvents. The resulting gel can be applied as a fascinating platform for visual recognition of enantiomeric 1-(2-hydroxynaphthalen-1-yl)naphthalen-2-ol (BINOL) through selective gel collapse. In addition, the mechanism for the reaction of the gel with chiral BINOL was investigated by scanning electron microscope and H nuclear magnetic resonance.

关键词： gelator     Schiff base     chiral recognition     gel formation     gel collapse    

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Microstructural and photocatalytic characterization of cement-paste sol-gel synthesized titanium dioxide

Elena CERRO-PRADA,Miguel MANSO,Vicente TORRES,Jesús SORIANO

《结构与土木工程前沿（英文）》 2016年 第10卷 第2期   页码 189-197 doi: 10.1007/s11709-015-0326-6

摘要： A route for the in paste synthesis of TiO loaded cement is described. TiO sols are blended with fresh cement paste as an alternative process to add photocatalytic functionality to cement. The modification of cement paste structure after the addition of TiO sols is analyzed by XRD, SEM and TGA. As a particular microstructural feature, TiO containing calcium silicate hydrate (C-H-S) particles are identified as networking centers of a C-S-H gel fiber matrix. The increase of the TiO sol concentration induces a decrease of pore size and an increase in the specific surface area in the cement composites. The photocatalytic activity of the TiO /cement system is evaluated from the degradation of Methylene Blue (MB) under UV irradiation, monitored through the absorbance at 665 nm. The results show that, although TiO phases reveal no long range order structure, the cement paste exothermal treatment in presence of hydrate products and alkaline conditions leads to a photocatalytic composite. Such new cement matrix may be twofold advantageous since it additionally promotes the formation of C-S-H gel, main determinant of cement mechanical properties.

关键词： cement composites     photocatalytic TiO2     sol-gel     C-S-H gel     microstructure    

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Velocity gradient elasticity for nonlinear vibration of carbon nanotube resonators

Hamid M. SEDIGHI, Hassen M. OUAKAD

《结构与土木工程前沿（英文）》 2020年 第14卷 第6期   页码 1520-1530 doi: 10.1007/s11709-020-0672-x

摘要： In this study, for the first time, we investigate the nonlocality superimposed to the size effects on the nonlinear dynamics of an electrically actuated single-walled carbon-nanotube-based resonator. We undertake two models to capture the nanostructure nonlocal size effects: the strain and the velocity gradient theories. We use a reduced-order model based on the differential quadrature method (DQM) to discretize the governing nonlinear equation of motion and acquire a discretized-parameter nonlinear model of the system. The structural nonlinear behavior of the system assuming both strain and velocity gradient theories is investigated using the discretized model. The results suggest that nonlocal and size effects should not be neglected because they improve the prediction of corresponding dynamic amplitudes and, most importantly, the critical resonant frequencies of such nanoresonators. Neglecting these effects may impose a considerable source of error, which can be amended using more accurate modeling techniques.

关键词： velocity gradient elasticity theory     nanotube resonators     differential-quadrature method     nonlinear vibration    

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Predicting shear strength of slender beams without reinforcement using hybrid gradient boosting trees

Thuy-Anh NGUYEN; Hai-Bang LY; Van Quan TRAN

《结构与土木工程前沿（英文）》 2022年 第16卷 第10期   页码 1267-1286 doi: 10.1007/s11709-022-0842-0

摘要： Shear failure of slender reinforced concrete beams without stirrups has surely been a complicated occurrence that has proven challenging to adequately understand. The primary purpose of this work is to develop machine learning models capable of reliably predicting the shear strength of non-shear-reinforced slender beams (SB). A database encompassing 1118 experimental findings from the relevant literature was compiled, containing eight distinct factors. Gradient Boosting (GB) technique was developed and evaluated in combination with three different optimization algorithms, namely Particle Swarm Optimization (PSO), Random Annealing Optimization (RA), and Simulated Annealing Optimization (SA). The findings suggested that GB-SA could deliver strong prediction results and effectively generalizes the connection between the input and output variables. Shap values and two-dimensional PDP analysis were then carried out. Engineers may use the findings in this work to define beam's geometrical components and material used to achieve the desired shear strength of SB without reinforcement.

关键词： slender beam     shear strength     gradient boosting     optimization algorithms    

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Gradient-based compressive image fusion

Yang CHEN,Zheng QIN

《信息与电子工程前沿（英文）》 2015年 第16卷 第3期   页码 227-237 doi: 10.1631/FITEE.1400217

摘要： We present a novel image fusion scheme based on gradient and scrambled block Hadamard ensemble (SBHE) sampling for compressive sensing imaging. First, source images are compressed by compressive sensing, to facilitate the transmission of the sensor. In the fusion phase, the image gradient is calculated to reflect the abundance of its contour information. By compositing the gradient of each image, gradient-based weights are obtained, with which compressive sensing coefficients are achieved. Finally, inverse transformation is applied to the coefficients derived from fusion, and the fused image is obtained. Information entropy (IE), Xydeas’s and Piella’s metrics are applied as non-reference objective metrics to evaluate the fusion quality in line with different fusion schemes. In addition, different image fusion application scenarios are applied to explore the scenario adaptability of the proposed scheme. Simulation results demonstrate that the gradient-based scheme has the best performance, in terms of both subjective judgment and objective metrics. Furthermore, the gradient-based fusion scheme proposed in this paper can be applied in different fusion scenarios.

关键词： Compressive sensing (CS)     Image fusion     Gradient-based image fusion     CS-based image fusion    

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标题 作者 时间 类型 操作

Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

期刊论文

Seasonal microbial community shift in a saline sewage treatment plant

Qingmei YAN, Xuxiang ZHANG, Tong ZHANG, Herbert H P FANG

期刊论文

Interaction and independence on methane oxidation of landfill cover soil among three impact factors: water, oxygen and ammonium

Pinjing HE, Na YANG, Wenjuan FANG, Fan Lü, Liming SHAO

期刊论文

Cultivation of aerobic granular sludge in a conventional, continuous flow, completely mixed activated sludge system

Xi CHEN,Linjiang YUAN,Wenjuan LU,Yuyou LI,Pei LIU,Kun NIE

期刊论文

Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

期刊论文

PulseNet China, a model for future laboratory-based bacterial infectious disease surveillance in China

null

期刊论文

Removable Dyes—The Missing Link for In-Depth N-glycan Analysis via Multi-Method Approaches

Samanta Cajic,René Hennig,Valerian Grote,Udo Reichl,Erdmann Rapp,

期刊论文

可去除染料——N-聚糖多方法深入分析中的缺失环节

Samanta Cajic, René Hennig, Valerian Grote, Udo Reichl, Erdmann Rapp

期刊论文

prediction and optimization design of sustainable concrete based on squirrel search algorithm-extreme gradient

期刊论文

Vibration analysis of nano-structure multilayered graphene sheets using modified strain gradient theory

Amir ALLAHBAKHSHI,Masih ALLAHBAKHSHI

期刊论文

Visual chiral recognition of 1,1′-binaphthol through enantioselective collapse of gel based on an amphiphilic

Xuhong Zhang, Haimiao Li, Xin Zhang, Meng An, Weiwei Fang, Haitao Yu

期刊论文

Microstructural and photocatalytic characterization of cement-paste sol-gel synthesized titanium dioxide

Elena CERRO-PRADA,Miguel MANSO,Vicente TORRES,Jesús SORIANO

期刊论文

Velocity gradient elasticity for nonlinear vibration of carbon nanotube resonators

Hamid M. SEDIGHI, Hassen M. OUAKAD

期刊论文

Predicting shear strength of slender beams without reinforcement using hybrid gradient boosting trees

Thuy-Anh NGUYEN; Hai-Bang LY; Van Quan TRAN

期刊论文

Gradient-based compressive image fusion

Yang CHEN,Zheng QIN

期刊论文