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Genetic biosensors for small-molecule products: Design and applications in high-throughput screening

Qingzhuo Wang,Shuang-Yan Tang,Sheng Yang

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 15-26 doi: 10.1007/s11705-017-1629-z

摘要： Overproduction of small-molecule chemicals using engineered microbial cells has greatly reduced the production cost and promoted environmental protection. Notably, the rapid and sensitive evaluation of the concentrations of the desired products greatly facilitates the optimization process of cell factories. For this purpose, many genetic components have been adapted into biosensors of small molecules, which couple the intracellular concentrations of small molecules to easily detectable readouts such as fluorescence, absorbance, and cell growth. Such biosensors allow a high-throughput screening of the small-molecule products, and can be roughly classified as protein-based and RNA-based biosensors. This review summarizes the recent developments in the design and applications of biosensors for small-molecule products.

关键词： biosensor small molecule product transcription factor riboswitch high-throughput screening

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Imaging technologies for plant high-throughput phenotyping: a review

Yong ZHANG, Naiqian ZHANG

《农业科学与工程前沿（英文）》 2018年第5卷第4期页码 406-419 doi: 10.15302/J-FASE-2018242

摘要：

Phenomics studies a variety of phenotypic plant traits and is the key to understanding genetic functions and environmental effects on plants. With the rapid development of genomics, many plant phenotyping platforms have been developed to study complex traits related to the growth, yield, and adaptation to biotic or abiotic stress, but the ability to acquire high-throughput phenotypic data has become the bottleneck in the study of plant genomics. In recent years, researchers around the world have conducted extensive experiments and research on high-throughput, image-based phenotyping techniques, including visible light imaging, fluorescence imaging, thermal imaging, spectral imaging, stereo imaging, and tomographic imaging. This paper considers imaging technologies developed in recent years for high-throughput phenotyping, reviews applications of these technologies in detecting and measuring plant morphological, physiological, and pathological traits, and compares their advantages and limitations.

关键词： high-throughput phenotyping imaging technology morphological traits pathological traits physiological traits

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Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

《环境科学与工程前沿（英文）》 2022年第16卷第8期 doi: 10.1007/s11783-022-1521-z

摘要：

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

关键词： UV/chlorine process Pathogen Antibiotic resistance genes High-throughput qPCR Reclaimed water

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METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORNSTRAW UNDER THERMOPHILIC AND HIGH OLR

《农业科学与工程前沿（英文）》 2023年第10卷第3期页码 403-423 doi: 10.15302/J-FASE-2022471

摘要：

● Methane production from fresh straw was 7.50% higher than dry straw.

关键词： fresh corn straw high solid anaerobic digestion metagenomics microbial communities thermophilic

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Combination of ARTP mutagenesis and color-mediated high-throughput screening to enhance 1-naphthol yield

Chenggang Qiu, Alei Zhang, Sha Tao, Kang Li, Kequan Chen, Pingkai Ouyang

《化学科学与工程前沿（英文）》 2020年第14卷第5期页码 793-801 doi: 10.1007/s11705-019-1876-2

摘要： Strain QCG of the aerobic bacteria is capable of producing 1-naphthol from naphthalene, this strain was first isolated and characterized in this study. Strain QCG was mutagenized to enhance 1-naphthol production, using atmospheric and room temperature plasma (ARTP) technology. Then, a microbial clone screening system was used to accelerate the operation. Meanwhile, a novel color-mediated high-throughput screening using 4-aminoantipyrine was performed to screen mutants. The optimal mutant strain QCG4 produced 19.58±0.34 mg∙L 1-naphthol from naphthalene that was 47.32% higher than that of the original strain (13.29±0.28 mg∙L ). In addition, the optimal conditions for 1-naphthol production via whole-cell catalysis of strain QCG4 were determined to be an OD of 40, 150 mg∙L naphthalene, and 7.5% dimethyl formamide as a co-solvent at pH 7.5 and 26°C for 3 h, resulting in 41.18±0.12 mg∙L 1-naphthol, i.e., the mutant strain produces a 2.1-fold higher yield compared to the original strain.

关键词： Bacillus cereus QCG naphthalene 1-naphthol ARTP mutagenesis high-throughput screening 4-aminoantipyrine

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Rapid alloying of CoCrFeMnNi high-entropy alloy from elemental feedstock toward high-throughput synthesis

《机械工程前沿（英文）》 2023年第18卷第1期 doi: 10.1007/s11465-022-0727-x

摘要： High-entropy alloys (HEAs) are considered alternatives to traditional structural materials because of their superior mechanical, physical, and chemical properties. However, alloy composition combinations are too numerous to explore. Finding a rapid synthesis method to accelerate the development of HEA bulks is imperative. Existing in situ synthesis methods based on additive manufacturing are insufficient for efficiently controlling the uniformity and accuracy of components. In this work, laser powder bed fusion (L-PBF) is adopted for the in situ synthesis of equiatomic CoCrFeMnNi HEA from elemental powder mixtures. High composition accuracy is achieved in parallel with ensuring internal density. The L-PBF-based process parameters are optimized; and two different methods, namely, a multi-melting process and homogenization heat treatment, are adopted to address the problem of incompletely melted Cr particles in the single-melted samples. X-ray diffraction indicates that HEA microstructure can be obtained from elemental powders via L-PBF. In the triple-melted samples, a strong crystallographic texture can be observed through electron backscatter diffraction, with a maximum polar density of 9.92 and a high ultimate tensile strength (UTS) of (735.3 ± 14.1) MPa. The homogenization heat-treated samples appear more like coarse equiaxed grains, with a UTS of (650.8 ± 16.1) MPa and an elongation of (40.2% ± 1.3%). Cellular substructures are also observed in the triple-melted samples, but not in the homogenization heat-treated samples. The differences in mechanical properties primarily originate from the changes in strengthening mechanism. The even and flat fractographic morphologies of the homogenization heat-treated samples represent a more uniform internal microstructure that is different from the complex morphologies of the triple-melted samples. Relative to the multi-melted samples, the homogenization heat-treated samples exhibit better processability, with a smaller composition deviation, i.e., ≤ 0.32 at.%. The two methods presented in this study are expected to have considerable potential for developing HEAs with high composition accuracy and composition flexibility.

关键词： laser powder bed fusion (L-PBF) in situ alloying high-entropy alloys heat treatment rapid synthesis

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使用傅里叶变换红外成像进行高通量筛选 Article

Erdem Sasmaz, Kathleen Mingle, Jochen Lauterbach

《工程（英文）》 2015年第1卷第2期页码 234-242 doi: 10.15302/J-ENG-2015040

摘要：

组合库的有效平行筛选是高通量(HT) 多相催化工作流中最具挑战性的难题之一。目前，已有包括各种光学、质谱分析以及气相色谱技术在内的大量方法用于高通量催化剂研究。在这些技术中，快速扫描傅里叶变换红外(FTIR) 成像是最快、最通用的筛选技术。本文介绍了16 通道高通量反应器的新设计，并给出了其准确性和重复性试验结果。该系统的性能，通过在不同的还原剂–还原剂摩尔比、表面活性剂类型、金属和表面活性剂浓度、合成温度和升温速率下合成的商用Pd/Al₂O₃和氧化钴纳米粒子的一氧化碳氧化反应进行评估。

关键词：高通量傅里叶变换红外成像筛选氧化钴一氧化碳氧化

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高通量计算的兴起 None

Ning-hui SUN, Yun-gang BAO, Dong-rui FAN

《信息与电子工程前沿（英文）》 2018年第19卷第10期页码 1245-1250 doi: 10.1631/FITEE.1800501

摘要：近年来，云计算、人工智能和物联网等新兴计算应用的出现，对计算机系统设计提出3个共同要求：高利用率、高吞吐量和低延迟。在这里，这些被称为“高通量计算”的要求。我们进一步提出一种新指标，称为“系统熵”，用于测量计算机系统的混乱程度和不确定性。我们认为，与追求高性能和低功耗的传统计算系统的设计不同，高通量计算应致力于实现低并发性。然而，从计算机体系结构角度看，高通量计算面临两大挑战：（1）如何充分利用应用程序数据的并行和并发执行来实现高吞吐量；（2）如何获得低延迟，即便在具有高利用率的数据路径中发生严重争用的情况下。为应对这两个挑战，引入两种技术：片上数据流体系结构和标签化冯诺依曼体系结构。构建了两个可以实现高吞吐量和低延迟的原型，显著降低了系统熵。

关键词：高通量计算；系统熵；信息高铁

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用于材料探索与优化的高通量多羽流脉冲激光沉积 Article

Samuel S. Mao,Xiaojun Zhang

《工程（英文）》 2015年第1卷第3期页码 367-371 doi: 10.15302/J-ENG-2015065

摘要：

笔者设计并实现了高通量多羽流脉冲激光沉积 (MPPLD) 系统，而且与传统的高通量薄膜材料合成技术进行了比较。目前大多数组合式脉冲激光沉积 (PLD) 系统为了使沉积的薄膜厚度均匀而采用掩膜法多层薄膜沉积和沉积后退火的工艺，MPPLD则同时利用了多个PLD羽流的方向性和沉积速率的空间变化，在一个衬底上直接沉积不同成分的化合物以形成薄膜材料库。这个新系统更适合以高通量的手段制备多组分化合物薄膜材料。

关键词：脉冲激光沉积高通量

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Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput

Yiwen LIN,Dan LI,Siyu ZENG,Miao HE

《环境科学与工程前沿（英文）》 2016年第10卷第3期页码 539-547 doi: 10.1007/s11783-016-0830-5

摘要： This study employed 454-pyrosequencing to investigate microbial and pathogenic communities in two wastewater reclamation and distribution systems. A total of 11972 effective 16S rRNA sequences were acquired from these two reclamation systems, and then designated to relevant taxonomic ranks by using RDP classifier. The Chao index and Shannon diversity index showed that the diversities of microbial communities decreased along wastewater reclamation processes. was the most dominant phylum in reclaimed water after disinfection, which accounted for 83% and 88% in two systems, respectively. Human opportunistic pathogens, including , , and , were selected and enriched by disinfection processes. The total chlorine and nutrients (TOC, NH -N and NO -N) significantly affected the microbial and pathogenic communities during reclaimed water storage and distribution processes. Our results indicated that the disinfectant-resistant pathogens should be controlled in reclaimed water, since the increases in relative abundances of pathogenic bacteria after disinfection implicate the potential public health associated with reclaimed water.

关键词： wastewater reclamation systems microbial community pathogenic community 454-pyrosequencing

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双层高通量计算——包括翘曲情况下的有效质量计算 Article

Andrew Supka, Nicholas A. Mecholsky, Marco Buongiorno Nardelli, Stefano Curtarolo, Marco Fornari

《工程（英文）》 2022年第10卷第3期页码 74-80 doi: 10.1016/j.eng.2021.03.031

摘要：

本文使用了双层高通量计算。在涉及改变晶体结构和（或）化学成分的第一层中，本文分析了选定的IIIV半导体、填充和未填充的方钴矿，以及岩盐和层状硫属化物。第二层在整个布里渊区（BZ）中搜索费米能级1.5 eV (1 eV = 1.602176×10−19 J)范围内的临界点，并通过计算有效质量来表征这些点。本文介绍了几种从第一原理计算有效质量的方法并对它们进行了比较。本文使用的方法还包括计算翘曲临界点的态密度有效质量，由于临界点存在潜在非解析性，传统方法无法给出一致的结果。本文证明了考虑能带结构的全部复杂性以及计算有效质量的互补方法价值的必要性。本文还通过计算证明翘曲仅发生在有退化性的情况下。

关键词：高通量电子结构能带翘曲有效质量

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机器学习辅助的高通量虚拟筛选用于实现先进含能材料按需定制 Article

宋思维, 王毅, 陈方, 晏蜜, 张庆华

《工程（英文）》 2022年第10卷第3期页码 99-109 doi: 10.1016/j.eng.2022.01.008

摘要：

受限于试错法较低的研发效率，寻找具有特定性能的含能材料始终是一个极具挑战性的工作。本文展示了基于领域知识、机器学习算法和实验验证的含能材料研发新模式。设计了一个集成分子生成和机器学习模型的高通量虚拟筛选（HTVS）系统，该系统可预测分子性能，并对晶体堆积模式进行评估。在该系统指导下，快速生成了25 112 个分子，并从中确认了具有理想性能和晶体堆积模式的候选分子。对目标分子进行实验合成，后续的晶体结构和性质研究表明，目标分子良好的综合性能与预测结果一致；验证了本文中研发模式的有效性。本研究展示了一种用于发现新型含能材料的新的研究范式，并且可以无障碍地
将其用于其他有机功能材料的探索。

关键词：含能材料机器学习高通量虚拟筛选分子性能合成

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Bioaerosolization behavior along sewage sludge biostabilization

《环境科学与工程前沿（英文）》 2021年第15卷第3期 doi: 10.1007/s11783-020-1339-5

摘要：

• Aerosolization behavior during a lab-scale sludge biostabilization was determined.

关键词： Sludge Composting Bioaerosol Bioaerosolization index High-throughput sequencing 4′ 6-diamidino-2-phenylindole (DAPI)

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高通量统计映射表征技术研究进展及其应用 Review

王海舟, 赵雷, 贾云海, 李冬玲, 杨丽霞, 卢毓华, 冯光, 万卫浩

《工程（英文）》 2020年第6卷第6期页码 621-636 doi: 10.1016/j.eng.2020.05.005

摘要：

实际材料是非均匀的、多元的、复杂的，任何材料在特定尺度下都不可能是绝对均匀的或者绝对规则的，可视为“自然芯片”，一个材料每个位置上的成分、组织结构和性能都存在着微小差异，而这种微小差异的组合形成了材料整体性能，本文综述了基于材料非均匀性本质的高通量统计映射表征技术的研究及应用进展。高通量统计映射表征技术采用一系列跨尺度快速表征技术，从宏观到微观逐级分析，快速获取实际大尺寸试样每个位置上的成分、组织结构和各种性能参量的数据集；通过准确的位置坐标信息，将这些数据集按照点对点的对应关系，形成组合映射点阵数据仓库；根据材料研发的设计需求，从数据仓库中筛选出符合要求的目标区间内的映射数据集；通过对目标区间内映射数据集的统计解析，筛查出接近设计需求的映射数据集，再经过反复验证最终获得反映材料性能的基本单元（组）；通过确定的工艺优化指向参量，验证这些基本单元（组）在介观尺度的组装，最终建立微观-介观-宏观-常规试样-构件跨尺度的成分-组织结构-特性间的量化相关性。高通量统计映射表征技术已在各种钢铁、高温合金、镀层板、铁硅合金等材料体系得到应用，有效地指导了工艺的优化及材料的改性。

关键词：材料非均匀性高通量表征统计映射原位统计分布分析

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Assessment of antibiotic resistance genes in dialysis water treatment processes

Xuan Zhu, Chengsong Ye, Yuxin Wang, Lihua Chen, Lin Feng

《环境科学与工程前沿（英文）》 2019年第13卷第3期 doi: 10.1007/s11783-019-1136-1

摘要：

• Quantitative global ARGs profile in dialysis water was investigated.

• Totally 35 ARGs were found in the dialysis treatment train.

• 29 ARGs (highest) were found in carbon filtration effluent.

• erm and mtrD-02 occurred in the final effluent.

• The effluent was associated with health risks even after RO treatment.

关键词： Dialysis water Treatment process Antibiotic resistance gene High-throughput quantitative PCR Horizontal gene transfer

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标题作者时间类型操作

Genetic biosensors for small-molecule products: Design and applications in high-throughput screening

Qingzhuo Wang,Shuang-Yan Tang,Sheng Yang

期刊论文

Imaging technologies for plant high-throughput phenotyping: a review

Yong ZHANG, Naiqian ZHANG

期刊论文

Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

期刊论文

METAGENOMICS COMBINED WITH HIGH-THROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORNSTRAW UNDER THERMOPHILIC AND HIGH OLR

期刊论文

Combination of ARTP mutagenesis and color-mediated high-throughput screening to enhance 1-naphthol yield

Chenggang Qiu, Alei Zhang, Sha Tao, Kang Li, Kequan Chen, Pingkai Ouyang

期刊论文

Rapid alloying of CoCrFeMnNi high-entropy alloy from elemental feedstock toward high-throughput synthesis

期刊论文

使用傅里叶变换红外成像进行高通量筛选

Erdem Sasmaz, Kathleen Mingle, Jochen Lauterbach

期刊论文

高通量计算的兴起

Ning-hui SUN, Yun-gang BAO, Dong-rui FAN

期刊论文

用于材料探索与优化的高通量多羽流脉冲激光沉积

Samuel S. Mao,Xiaojun Zhang

期刊论文

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput

Yiwen LIN,Dan LI,Siyu ZENG,Miao HE

期刊论文

双层高通量计算——包括翘曲情况下的有效质量计算

Andrew Supka, Nicholas A. Mecholsky, Marco Buongiorno Nardelli, Stefano Curtarolo, Marco Fornari

期刊论文

机器学习辅助的高通量虚拟筛选用于实现先进含能材料按需定制

宋思维, 王毅, 陈方, 晏蜜, 张庆华

期刊论文

Bioaerosolization behavior along sewage sludge biostabilization

期刊论文

高通量统计映射表征技术研究进展及其应用

王海舟, 赵雷, 贾云海, 李冬玲, 杨丽霞, 卢毓华, 冯光, 万卫浩

期刊论文

Assessment of antibiotic resistance genes in dialysis water treatment processes

Xuan Zhu, Chengsong Ye, Yuxin Wang, Lihua Chen, Lin Feng

期刊论文

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