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CRISPy-web: An online resource to design sgRNAs for CRISPR applications

Synthetic and Systems Biotechnology 2016年第2期1卷 118-121页

作者： Kai Blin Lasse Ebdrup Pedersen TilmannWeber Sang Yup Lee The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKogle Alle 62970 HosholmDenmark Metabolic and Biomolecular Engineering National Research Laboratory Department of Chemical and Biomolecular Engineering(BK21 Plus Program)Center for Systems and Synthetic BiotechnologyInstitute for the BioCenturyKorea Advanced Institute of Science and Technology(KAIST)Daejeon 305-701Republic of Korea

CRISPR/Cas9-based genome editing has been one of the major achievements of molecular biology,allowing the targeted engineering of a wide range of *** system originally evolved in prokaryotes as an adaptive immune system against bacteriophage *** now sees widespread application in genome engineering workflows,especially using the Streptococcus pyogenes endonuclease *** utilize Cas9,so-called single guide RNAs(sgRNAs)need to be designed for each target *** there are many tools available to design sgRNAs for the popular model organisms,only few tools that allow designing sgRNAs for non-model organisms ***,we present CRISPy-web(http://***/),an easy to use web tool based on CRISPy to design sgRNAs for any userprovided microbial ***-web allows researchers to interactively select a region of their genome of interest to scan for possible *** checks for potential off-target matches,the resulting sgRNA sequences are displayed graphically and can be exported to text *** steps and information are accessible from a web browser without the requirement to install and use command line scripts.

关键词： CRISPR Cas9 sgRNA Guide RNA Genome editing Genome engineering

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Droplet Dynamics: Dynamically Actuated Liquid‐Infused Poroelastic Film with Precise Control over Droplet Dynamics (Adv. Funct. Mater. 39/2018)

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Advanced Functional Materials 2018年第39期28卷

作者： Inkyu Oh Christoph Keplinger Jiaxi Cui Jiehao Chen George M. Whitesides Joanna Aizenberg Yuhang Hu Department of Mechanical Science and Engineering University of Illinois at Urbana‐Champaign Urbana IL 61801 USA Department of Mechanical Engineering University of Colorado Boulder CO 80309 USA Materials Science and Engineering Program University of Colorado Boulder CO 80309 USA INM – Leibniz Institute for New Materials Campus D2 2 66123 Saarbrücken Germany Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02318 USA Wyss Institute for Biologically Inspired Engineering Harvard University Cambridge MA 02138 USA Kavli Institute for Bionano Science and Technology Harvard University Cambridge MA 02138 USA John A. Paulson School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA The George W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta GA 30332 USA

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LncRNA CamK-A Regulates Ca²⁺-Signaling-Mediated Tumor Microenvironment Remodeling

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MOLECULAR CELL 2018年第3期72卷 601-601页

作者： Sang, Ling-jie Ju, Huai-qiang Liu, Guang-ping Tian, Tian Ma, Guo-lin Lu, Yun-xin Liu, Ze-xian Pan, Ruo-lang Li, Rui-hua Piao, Hai-long Marks, Jeffrey R. Yang, Luo-jia Yan, Qingfeng Wang, Wenqi Shao, Jianzhong Zhou, Yubin Zhou, Tianhua Lin, Aifu College of Life Sciences Zhejiang University Hangzhou Zhejiang 310058 China Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou Guangdong 510060 China College of Life Sciences Yan’an University Yan’an Shaanxi 716000 China Center for Translational Cancer Research Institute of Biosciences and Technology Texas A&M University Health Science Center Houston TX 77030 USA CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian Liaoning 116023 China Department of Surgery Division of Surgical Science School of Medicine Duke University Durham NC 27710 USA Department of Developmental and Cell Biology University of California Irvine Irvine CA 92697 USA Department of Cell Biology and Program in Molecular Cell Biology School of Medicine Zhejiang University Hangzhou Zhejiang 310058 China Key Laboratory for Cell and Gene Engineering of Zhejiang Province Hangzhou Zhejiang 310058 China The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou Zhejiang 310058 China

Cancer cells entail metabolic adaptation and microenvironmental remodeling to survive and progress. Both calcium (Ca2+) flux and Ca2+-dependent signaling play a crucial role in this process, although the underlying mechanism has yet to be elucidated. Through RNA screening, we identified one long noncoding RNA (lncRNA) named CamK-A (lncRNA for calcium-dependent kinase activation) in tumorigenesis. CamK-A is highly expressed in multiple human cancers and involved in cancer microenvironment remodeling via activation of Ca2+-triggered signaling. Mechanistically, CamK-A activates Ca2+/calmodulin-dependent kinase PNCK, which in turn phosphorylates IκBα and triggers calcium-dependent nuclear factor κB (NF-κB) activation. This regulation results in the tumor microenvironment remodeling, including macrophage recruitment, angiogenesis, and tumor progression. Notably, our human-patient-derived xenograft (PDX) model studies demonstrate that targeting CamK-A robustly impaired cancer development. Clinically, CamK-A expression coordinates with the activation of CaMK-NF-κB axis, and its high expression indicates poor patient survival rate, suggesting its role as a potential biomarker and therapeutic target.

关键词： LncRNA Ca2+ NF-κB PDX tumor microenvironment glycolysis cancer metabolism signal transduction

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Exploring low internal reorganization energies for silicene nanoclusters

arXiv

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arXiv 2017年

作者： Pablo-Pedro, Ricardo Lopez-Rios, Hector Mendoza-Cortes, Jose-L Kong, Jing Fomine, Serguei van Voorhis, Troy Dresselhaus, Mildred S. Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue CambridgeMA02139 United States Instituto de Investigaciones en Materiales Universidad Nacional Autónoma de México Apartado Postal 70-360 CU Coyoacán Ciudad de México04510 Mexico Department of Chemical & Biomedical Engineering Florida A&M University Florida State University Joint College of Engineering Tallahassee FL32310 United States Scientific Computing Department Materials Science and Engineering Program High Performance Material Institute Condensed Matter Theory National High Magnetic Field Laboratory Florida State University TallahasseeFL32310 United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States

High-performance materials rely on small reorganization energies to facilitate both charge separation and charge transport. Here, we performed DFT calculations to predict small reorganization energies of rectangular silicene nanoclusters with hydrogen-passivated edges denoted by H-SiNC. We observe that across all geometries, H-SiNCs feature large electron affinities and highly stabilized anionic states, indicating their potential as n-type materials. Our findings suggest that fine-tuning the size of H-SiNCs along the "zigzag" and "armchair" directions may permit the design of novel n-type electronic materials and spinctronics devices that incorporate both high electron affinities and very low internal reorganization energies. Copyright © 2017, The Authors. All rights reserved.

关键词： Silicene

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Exploring Low Internal Reorganization Energies for Silicene Nanoclusters

arXiv

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arXiv 2017年

关键词： Silicene

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Improved discrete element method model to predict coating layer mechanical properties

Improved discrete element method model to predict coating la...

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Paper Conference and Trade Show, PaperCon 2016

作者： Varney, Daniel H. Bousfield, Douglas W. Omya Inc. 48 Oak St. ProctorVT05765 United States Paper Surface Science Program University of Maine Department of Chemical and Biological Engineering OronoME04469 United States

ISBN: (纸本)9781510831193

The mechanical properties of coated papers can have a significant impact on how well they survive post coating application steps. Processes such as calendering, printing, and folding can cause the following quality problems respectively: cracking, picking, and crack-at-the fold (CAF). The Discrete Element Method (DEM) has the potential to describe the mechanics of the coating layer on a microscopic scale. Recent models have given insight into the strength properties of coatings, but a good comparison with experimental results is lacking. In this paper, a DEM model is improved to account for the non-linear deformation behavior seen with most binders. In addition, a new method to convert the latex volume fraction to a latex bridge radius is proposed. The model results are compared to recent in-plane tension type experimental data in the literature that include starch-latex mixtures. The elastic modulus, ultimate tensile stress, and strain-to-failure compare well with the experimental results.

关键词： Finite difference method

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Recent advances in “living”/controlled radical polymerization of phosphorus-containing monomers and their potential applications

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science China Chemistry 2015年第11期58卷 1633-1640页

作者： Tianchi Xu Lifen Zhang Zhenping Cheng Xiulin Zhu Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Department of Polymer Science and Engineering College of Chemistry Chemical Engineering and Materials ScienceSoochow University

Special research attention has been paid to phosphorus-containing materials and their corresponding applications. This mini review considers recent publications devoted to the "living"/controlled radical(co)polymerization of phosphorus-containing monomers. In addition, different properties of the polymers involved in the phosphonate group in various chemical environments are demonstrated, and their potential applications are briefly discussed.

关键词： living radical polymerization nitroxide-mediated polymerization （NMP） atom transfer radical polymerization （ATRP） reversible addition-fragmentation chain transfer （RAFT） phosphorus-containing monomer

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The sensing properties of fuzzy carbon nanotube based silica fibers 5

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Advances in Materials science for Environmental and Energy Technologies V - Materials science and Technology 2015 Conference and Exhibition, MS and T 2015

作者： Radetic, M. Cortes, P. Kubas, G. Cook, Jim Gade, Ravi Chandra Reddy Oder, T. Department of Civil/Envtl. and Chemical Engineering Youngstown State University YoungstownOH44555 United States Materias Science and Engineering Program Youngstown State University YoungstownOH44555 United States Department of Electrical and Computer Engineering Youngstown State University YoungstownOH44555 United States Department of Physics and Astronomy Youngstown State University YoungstownOH44555 United States

ISBN: (纸本)9781119323617

The present research program investigates the mechanical sensing properties of fuzzy silica fibers either coated with carbon nanotubes (CNTs), or with a CNT-Zinc Oxide (ZnO) layered arrangement. Here, the CNTs have been grown directly on the silica fiber using a chemical Vapor Deposition (CVD) process. In the case of the CNT-ZnO based Silica fibers, the semiconducting coating was performed using a sputter deposition system. The sensing properties of the manufactured fuzzy fibers have been investigated through a curing process on a thermoset resin as well as through a series of compressive tests. It has been observed, that the fuzzy fibers are capable of detecting the curing time of the polymeric resin as well as measuring the mechanical deformation of the cured resin after being subjected to a series of compressive tests.

关键词： Carbon nanotubes

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Designing a Perylene Diimide/Fullerene Hybrid as Effective Electron Transporting Material in Inverted Perovskite Solar Cells with Enhanced Efficiency and Stability

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Angewandte Chemie 2019年第25期131卷

作者： Zhenghui Luo Fei Wu Teng Zhang Xuan Zeng Yiqun Xiao Tao Liu Cheng Zhong Xinhui Lu Linna Zhu Shihe Yang Chuluo Yang Hubei Key Lab on Organic and Polymeric Optoelectronic Materials Department of Chemistry Wuhan University Wuhan 430072 P. R. China Shenzhen Key Laboratory of Polymer Science and Technology College of Materials Science and Engineering Shenzhen University Shenzhen 518060 P. R. China Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energy Faculty of Materials & Energy Southwest University Chongqing 400715 P. R. China Nano Science and Technology Program Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong P. R. China Department of Physics Chinese University of Hong Kong New Territories Hong Kong P. R. China Guangdong Key Lab of Nano-Micro Material Research School of Chemical Biology and Biotechnology Shenzhen Graduate School Peking University Xili University Town Shenzhen 518055 Guangdong P. R.China

Electron transport materials (ETM) play an important role in the improvement of efficiency and stability for inverted perovskite solar cells (PSCs). This work reports an efficient ETM, named PDI‐C 60 , by the combination of perylene diimide (PDI) and fullerene. Compared to the traditional PCBM, this strategy endows PDI‐C 60 with slightly shallower energy level and higher electron mobility. As a result, the device based on PDI‐C 60 as electron transport layer (ETL) achieves high power conversion efficiency (PCE) of 18.6 %, which is significantly higher than those of the control devices of PCBM (16.6 %) and PDI (13.8 %). The high PCE of the PDI‐C 60 ‐based device can be attributed to the more matching energy level with the perovskite, more efficient charge extraction, transport, and reduced recombination rate. To the best of our knowledge, the PCE of 18.6 % is the highest value in the PSCs using PDI derivatives as ETLs. Moreover, the device with PDI‐C 60 as ETL exhibits better device stability due to the stronger hydrophobic properties of PDI‐C 60 . The strategy using the PDI/fullerene hybrid provides insights for future molecular design of the efficient ETM for the inverted PSCs.

关键词： Elektronentransportmaterial Fullerene Perowskit-Solarzellen Perylendiimide Stromwandlungswirkungsgrad

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Fogging and water spray velocity to reduce dust cement widespread

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IOP Conference Series: Earth and Environmental science 2018年第1期200卷

作者： J Purwanta T Marnoto P Setyono A H Ramelan Doctoral Program in Environmental Science Graduate Program Universitas Sebelas Maret Jl. Ir. Sutami 36 A Kentingan Surakarta 57126 Indonesia Department of Chemical Engineering Universitas Pembangunan Nasional Veteran Yogyakarta Jl. SWK 104 Condongcatur Depok Sleman Yogyakarta 55283 Indonesia Faculty of Mathematics and Natural Science Universitas Sebelas Maret Jl. Ir. Sutami 36 A Kentingan Surakarta 57126 Indonesia

Climate change as the global issue should be analysed from mitigating especially in the cement industrial. This industry contributes up to 6% to the global warming. Cement plants must already take over management of the cement dust arising mainly on the production. However, there are still many who are exposed to cement dust into the surrounding environment, due to the dust cement contributes to air pollutant and give impact to climate change. This research aims to study the various strategies to catch a smooth dust using fogging methods with variable water speed. In such a device, as media dust catcher is mist generated from water which is converted into mist by sprayer. The dust catcher instrument installed at the location after the end of the cement factory chimneys. Of course, in order not to complicate the technical implementation in the chimney is curved downward so it is easier to install dust extraction tool such fogging method. The tool optimal conditions occur in the water velocity 110 ml per min with an efficiency of 63.60%. In the water velocity 110 ml per min it will form a mist with the optimal amount, if the water velocity is greater than 110 ml per min will tend to form droplets, on the contrary if the water velocity is less than 110 ml per min of the amount of haze formed is not maximized.

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