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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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Waste-battery-derived multifunctional zinc catalysts for glycolysis and decolorization of polyethylene terephthalate

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Applied Catalysis B: Environmental 2023年第1期325卷

作者： Chiao, Yu-Wen Liao, Weisheng Krisbiantoro, Philip Anggo Yu, Bor-Yih Wu, Kevin C.-W. Department of Chemical Engineering National Taiwan University Taipei10617 Taiwan Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan International Graduate Program of Molecular Science and Technology National Taiwan University Taipei10617 Taiwan

In this study, novel and easily recyclable catalysts were prepared from waste batteries for efficient glycolysis and decolorization of polyethylene terephthalate (PET) to obtain bis(2-hydroxyethyl) terephthalate (BHET). At 190 °C and 5 h, the PET conversion and BHET yield reach 89.7 and 77.7%, respectively, which are comparable to the values obtained for the commonly used catalyst zinc acetate. Species generated from the reaction between ethylene glycol (EG) and zinc plates (e.g., Zn-glycolate, ZnO, and other metal species on zinc plates) demonstrate excellent catalytic performance. Furthermore, dye molecules released from several commercial-colored PET bottles during glycolysis can be degraded to colorless molecules using zinc plates, thereby facilitating BHET purification. The exposed zero-valent zinc from the zinc plates in EG is responsible for degrading the dye molecules. Finally, the scaled-up PET glycolysis process is conceptually designed using Aspen Plus software. The simulation results suggest that reducing the energy requirement in distillation is necessary for further improvement. © 2022 Elsevier B.V.

关键词： Polyethylene terephthalates

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Heat stress priming enhanced conidial germination, insect virulence and metabolic adaptation in Beauveria bassiana

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Fungal Biology 2025年

作者： Somsiri Udompaisarn Jiraporn Jirakkakul Thanawat Duangfoo Wachiraporn Toopaang Alongkorn Amnuaykanjanasin National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA) 113 Thailand Science Park Paholyothin Rd. Tambon Khlong Nueng Amphoe Khlong Luang Pathum Thani 12120 Thailand Pilot Plant Development and Training Institute King Mongkut’s University of Technology Thonburi Bangkok 10150 Thailand Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program Academia Sinica and National Chung Hsing University Taipei 11529 Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei 11529 Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung 40227 Taiwan

Beauveria bassiana strains are commercially available as mycoinsecticides and are widely used for insect control. However, its effectiveness is often hindered by vulnerability to environmental stressors such as UV radiation, drought, and heat. Exposure to moderate heat, which is considered a triggering stimulus, partially inhibits the germination of conidia. This study investigated the impact of heat stress and priming on conidial germination, radial growth, sporulation, virulence to insects, and metabolic profiling in B . bassiana BCC 2660. The conidial germination significantly suppressed and declined from 82 to 34% at 45 °C after 180 min. Here, we introduced a priming state to enhance the fungus's tolerance to the triggering stimulus. Comparative analysis revealed that conidia subjected to heat-induced priming at 35 °C for 40 min exhibited a significant increase in germination from 32 to 65%, compared to non-primed conidia. The primed conidia also demonstrated a reduction in the LT 50 by 10 h in comparison to their non-primed counterparts. While priming improved germination, it did not significantly affect radial growth or sporulation rates under heat stress. We further explored the memory time of priming, finding that the fungus retained the priming state for up to 4 h. To elucidate the molecular mechanisms underlying the heat stress response, we identified candidate metabolites using LC-MS. Metabolomic analysis identified 34 metabolites, with significant alterations in metabolic pathways related to spermidine biosynthesis, coenzyme A synthesis, fungal wall development and various cellular process among primed conidia. These results underscored the complex metabolic adjustments in B. bassiana conidia, highlighting the potential of priming strategies to enhance fungal tolerance to environmental stresses and improve biocontrol efficacy in agricultural applications.

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Maturation of human induced pluripotent stem cell-derived cardiomyocytes promoted by Brachyury priming

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Scientific Reports 2025年第1期15卷 1-13页

作者： Kargaran, Parisa K. Garmany, Armin Garmany, Ramin Stutzman, Marissa J. Sadeghian, Maryam Ackerman, Michael J. Perez-Terzic, Carmen M. Terzic, Andre Behfar, Atta Department of Cardiovascular Medicine Mayo Clinic Rochester MN United States Center for Regenerative Biotherapeutics Mayo Clinic Rochester MN United States Van Cleve Cardiac Regenerative Medicine Program Mayo Clinic Rochester MN United States Marriott Heart Disease Research Program Mayo Clinic Rochester MN United States Mayo Clinic Alix School of Medicine Mayo Clinic Rochester MN United States Mayo Clinic Graduate School of Biomedical Sciences Mayo Clinic Rochester MN United States Windland Smith Rice Sudden Death Genomics Laboratory Windland Smith Rice Genetic Heart Rhythm Clinic Mayo Clinic Rochester MN United States Department of Molecular Pharmacology & Experimental Therapeutics Mayo Clinic Rochester MN United States Department of Physiology and Biomedical Engineering Mayo Clinic Rochester MN United States Department of Physical Medicine and Rehabilitation Mayo Clinic Rochester MN United States Department of Medical Genetics Mayo Clinic Rochester MN United States

Cardiac differentiation of human induced pluripotent stem cells is readily achievable, yet derivation of mature cardiomyocytes has been a recognized limitation. Here, a mesoderm priming approach was engineered to boost the maturation of cardiomyocyte progeny derived from pluripotent stem cells under standard cardiac differentiation conditions. Functional and structural hallmarks of maturity were assessed through multiparametric evaluation of cardiomyocytes derived from induced pluripotent stem cells following transfection of the mesoderm transcription factor Brachyury prior to initiation of lineage differentiation. Transfection with Brachyury resulted in earlier induction of a cardiopoietic state as hallmarked by early upregulation of the cardiac-specific transcription factors NKX2.5, GATA4, TBX20. Enhanced sarcomere maturity following Brachyury conditioning was documented by an increase in the proportion of cells expressing the ventricular isoform of myosin light chain and an increase in sarcomere length. Mesoderm primed cells displayed increased reliance on mitochondrial respiration as determined by increased mitochondrial size and a greater basal oxygen consumption rate. Further, Brachyury priming drove maturation of calcium handling enabling transfected cells to maintain calcium transient morphology at higher external field stimulation rates and augmented both calcium release and sequestration kinetics. In addition, transfected cells displayed a more mature action potential morphology with increased depolarization and repolarization kinetics. Derived cells transfected with Brachyury demonstrated increased toxicity response to doxorubicin as determined by a compromise in calcium transient morphology. Thus, Brachyury pre-treatment here achieved a streamlined strategy to promote maturity of human pluripotent stem cell-derived cardiomyocytes establishing a generalizable platform ready for deployment. © The Author(s) 2025.

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EMMC technology for treatment/reuse of dilute dairy wastewater

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Clean Technologies and Environmental Policy 2009年 1-9页

作者： Lin, Rhoda Luo-Ting Irvine, Joshua Lelemia Kao, J. C. M. Yang, P. Y. Graduate Program in Bioengineering Department of Molecular Biosciences and Bioengineering University of Hawaii at Manoa Honolulu USA Graduate Institute of Environmental Engineering National Sun Yat-San University Kaohsiung Taiwan

A rural dairy farm located on the island of Oahu, Hawaii needed to upgrade current lagoon treatment system for further reuse as floor flushing and crop irrigation. This is a comprehensive bench scale and pilot plant study to evaluate the potential biological treatment and reuse systems. Systems evaluated include: (1) pre-existing lagoon system, (2) integrated anaerobic BIO-NEST/aerobic EMMC (entrapped mixed microbial cell) system, (3) aerobic EMMC reactor only system. Based upon a comprehensive economic evaluation and sensitivity analysis, the EMMC-only system achieved the best effluent quality for simultaneous removal of carbon and nitrogen. The pilot study of the EMMC-only reactor achieved an overall of 78% TCOD, 63% SCOD, 65% TN, and 96% soluble NH3-N removal efficiencies (HRT 12 h, continuous aeration). Implementing this system would cost about $0.25 a cow/day to remove a ton of organic TCOD ($88.10/cow/year). The information presented provides a model for animal producers to consider in evaluating alternatives to upgrade existing waste management facilities.

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BPS2025 - Surface remodeling and inversion of matrix-cell interaction underlies community recognition and dispersal in biofilms

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Biophysical Journal 2025年第3期124卷 181a-181a页

作者： Alexis P. Moreau Danh Nguyen Alex Hinbest Anthony Zamora Ranjuna Weerasekera Katherine Matej Xuening Zhou Sandra Sanchez Carey D. Nadell Wai-leung Ng Vernita D. Gordon Natalia L. Komarova Rich A. Olson Ying Li Jing Yan Department of Molecular Cellular and Developmantal Biology Yale University New Haven CT USA Department of Mechanical Engineering University of Wisconsin Madison Madison WI USA Wesleyan University Middletown CT USA Department of Mathematics University of California Irvine Irvine CA USA Department of Molecular Biology and Biochemistry Wesleyan University Middletown CT USA Interdisciplinary Life Sciences Graduate Program The University of Texas at Austin Austin TX USA Department of Molecular Biology and Microbiology Tufts University School of Medicine Boston MA USA Department of Biological Sciences Dartmouth College Hanover NH USA Department of Physics The University of Texas at Austin Austin TX USA

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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

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Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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Sugar coated stealth carbon nanotubes

Sugar coated stealth carbon nanotubes

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4th IEEE International Conference on Nano/molecular Medicine and engineering, IEEE NANOMED 2010

作者： Kotagiri, Nalinikanth Kim, Jin-Woo Bio/Nano Technology Laboratory Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR United States Bio/Nano Technology Laboratory Institute for Nanoscale Materials Science and Engineering University of Arkansas Fayetteville AR United States

ISBN: (纸本)9781612841533

Single walled carbon nanotubes (SWNT) have shown tremendous promise as agents for diagnostic and therapeutic intervention in vivo. We demonstrate how Dextran sulfate (DS) can render SWNT transparent to macrophages, a vital component of the innate immunity. We also demonstrate a site specific attachment strategy to conjugate antibodies to DS for downstream applications. DS was compared to Polyethylene Glycol (PEG) coated SWNT, a trusted standard for rendering nanoparticles immune to opsonization. © 2010 IEEE.

关键词： Polyethylene glycols

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Human identification using X-Ray image matching

Human identification using X-Ray image matching

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2017 International MultiConference of Engineers and Computer Scientists, IMECS 2017

作者： Ishigami, Ryudo Thi Zin, Thi Shinkawa, Norihiro Nishii, Ryuichi Department of Electrical and Systems Engineering Graduate School of Engineering University of Miyazaki Miyazaki Japan Department of Electrical and Systems Engineering Faculty of Engineering University of Miyazaki Miyazaki Japan Department of Radiology Faculty of Medicine University of Miyazaki Miyazaki Japan Department of Diagnostic Imaging Program Molecular Imaging Center National Institute of Radiological Sciences Chiba Japan

ISBN: (纸本)9789881404732

Human identification both prior to death and after death is becoming one of the major worldwide issues nowadays for law enforcement aspect as well as social and security aspects. General identification prior to death is possible through comparison of many biometric identifiers. However identification after death is impossible using behavioral biometric such as speech and actions. Moreover, in many circumstances such as natural disasters, air plane crash or a case of identification a couple of weeks later, most of physical biometrics may not be useful for identification due to the decay of some soft tissues. A lot of research has been done in the field of different biometric modalities like Finger-print, Iris, Hand-Veins, Dental biometrics etc. to identify humans. However only a little has been known the chest X-Ray biometric which was very powerful method for identification especially during the mass disasters in which most of other biometrics are unidentifiable. Therefore in this paper, we propose a stochastic modelling approach for human identification after death by using chest X- Ray prior to death database. Some experimental results are shown based on real life dataset and confirmed.

关键词： Biometrics

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Plasmonic Nanolaser by Silver Nanowire Embedded in CsPbBr3 Quantum Dots

Plasmonic Nanolaser by Silver Nanowire Embedded in CsPbBr3 Q...

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JSAP-OSA Joint Symposia, JSAP 2021

作者： Xing, Di Lin, Cheng-Chieh Won, Phillip Xiang, Rong Chen, Tzu-Pei A. Kamal, A. Syazwan Lee, Yang-Chun Ho, Ya-Lun Maruyama, Shigeo Ko, Seung Hwan Chen, Chun-Wei Delaunay, Jean-Jacques School of Engineering The University of Tokyo Japan International Graduate Program of Molecular Science and Technology National Taiwan University Taiwan Department of Materials Science and Engineering National Taiwan University Taiwan Department of Mechanical Engineering Seoul National University Korea Republic of Center of Atomic Initiative for New Materials National Taiwan University Taiwan

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