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5th international Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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Rapid Escherichia coli Cloned DNA Detection in Serum Using an Electrical Double Layer-Gated Field-Effect Transistor-Based DNA Sensor

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Analytical Chemistry 2023年第17期95卷 6871-6878页

作者： Paulose, Akhil K. Hou, Yueh-Ju Huang, Yu-Shan Chakkalaparambil Dileep, Navyamol Chiu, Chia-Lin Pal, Arnab Kalaimani, Vishal Mani Lin, Zong-Hong Chang, Chuang-Rung Chen, Cheng-Pin Lin, Yi-Chun Cheng, Chien-Yu Cheng, Shu-Hsing Cheng, Chao-Min Wang, Yu-Lin Institute of Nanoengineering and Microsystems National Tsing Hua University Hsinchu30013 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu30013 Taiwan College of Semiconductor Research National Tsing Hua University Hsinchu30013 Taiwan Department of Life Sciences National University of Kaohsiung Kaohsiung811726 Taiwan Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biotechnology National Tsing Hua University Hsinchu30013 Taiwan Department of Infectious Diseases Taoyuan General Hospital Ministry of Health and Welfare Taoyuan32748 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu30013 Taiwan

In this study, a rapid diagnosis platform was developed for the detection of Escherichia coli O157:H7. An electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) as a point-of-care testing device is demonstrated with its high sensitivity, portability, high selectivity, quick response, and ease of use. The specially designed ssDNA probe was immobilized on the extended gate electrode to bind the target complementary DNA segment of E. coli, resulting in a sharp drain current change within minutes. The limit of detection for target DNA is validated to a concentration of 1 fM in buffer solution and serum. Meanwhile, the results of a Kelvin probe force microscope were shown to have reduced surface potential of the DNA immobilized sensors before and after the cDNA detection, which is consistent with the decreased drain current of the BioFET. A 1.2 kb E. coli duplex DNA synthesized in plasmid was sonicated and detected in serum samples with the sensor array. Gel electrophoresis was used to confirm the efficiency of sonication by elucidating the length of DNA. Those results show that the EDL-gated BioFET system is a promising platform for rapid identification of pathogens for future clinical needs. © 2023 American Chemical Society

关键词： DNA

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Facile synthesis of copper cobalt sulfide and nickel hydroxide tube-like composites as battery-type active material of energy storage devices

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Journal of Energy Storage 2023年 65卷

作者： Kuo, Tsung-Rong Fitriannisa, Istikhori Chung, Ren-Jei Lin, Kuan-Hsien Yougbaré, Sibidou Lin, Lu-Yin Wu, Yung-Fu International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan BP 218 11 Nanoro Burkina Faso Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan

Bimetallic sulfide has attracted much attentions as efficient electroactive materials of battery supercapacitor hybrid (BSH), because of numerous redox states, high conductivity and good energy efficiency. Developing composites having excellent chemical and electrochemical properties is necessary to enhance the energy storage features of bimetallic sulfides. In this study, CuCo2S4 and Ni(OH)2 composites (CuCo2S4@Ni(OH)2) are designed on Ni foam via the facial hydrothermal process and chemical bath deposition as the electroactive material of BSH at first time. Effects of Ni(OH)2 amounts on CuCo2S4 on electrochemical and physical properties of CuCo2S4@Ni(OH)2 are investigated. The physical mixed CuCo2S4 and Ni(OH)2 composite is also fabricated to verify synergistic effects of CuCo2S4@Ni(OH)2. A higher specific capacitance (CF) of 1583.9 F/g along with the capacity of 220.0 mAh/g are got for optimal CuCo2S4@Ni(OH)2 electrode, respectively comparing to 831.7 and 1063.3 F/g of CuCoS4 and Ni(OH)2 electrodes. A BSH is fabricated by the CuCo2S4@Ni(OH)2 electrode and the activated carbon electrode. The potential window of 1.6 V and maximum energy density of 32.1 Wh/kg at 1.1 kW/kg are achieved. The CF retention of 78% and Coulombic efficiency higher than 97% in 8000 charge/discharge cycles are also obtained for this BSH. © 2023

关键词： Sulfur compounds

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Modifying BiVO4 as a photocatalyst for water oxidation using constant-duration alkaline-etched post treatments

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New Journal of Chemistry 2023年第2期48卷 569-577页

作者： Hsu, Chuan-Chih Chuang, Kai-Jie Huang, Hsiao-Wen Pan, Bo-Jin Chen, Hung-Ming Husain, Sadang Yougbaré, Sibidou Hsiao, Yu-Cheng Wu, Yung-Fu Lin, Lu-Yin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Gingen Technology Co. Ltd. Rm. 7 10F. No. 189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin70124 Indonesia /Nanoro Ouagadougou03 Burkina Faso International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA94305-5428 United States Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan

BiVO4 with suitable band edges and a small band gap is considered an efficient photocatalyst for the oxygen evolution reaction (OER), but short charge-transfer lengths limit its photocatalytic ability. Increasing active sites can essentially enhance oxidation reactions and photocatalytic ability. The alkaline etching technique can refine the surface properties of BiVO4 by introducing oxygen vacancies and possibly establishing a heterojunction, but suitable alkaline etching methods are rarely discussed. In this study, three alkaline etching methods, including hydrothermal, soaking, and electrodeposition processes, are first applied for a constant duration to tailor the surface properties of BiVO4 as a photocatalyst for the OER. Alkaline-etched BiVO4 prepared using hydrothermal and soaking processes shows better photocatalytic abilities due to the generation of additional oxygen vacancies, while poor photocatalytic ability is found for that fabricated using electrodeposition due to the formation of less photocatalytic VO2. The highest photocurrent density of 2.38 mA cm−2 is obtained at 1.23 V versus a reversible hydrogen electrode in an electrolyte without a hole scavenger for the BiVO4 etched in the hydrothermal process, while the untreated BiVO4 presents a photocurrent density of 0.58 mA cm−2. A photocurrent retention of 92.3% is achieved after 5000 seconds of continuous illumination. The study supplies blueprints for establishing effective alkaline etching methods for enhancing the photocatalytic ability of BiVO4, with the exception of time costs. © 2024 The Royal Society of Chemistry.

关键词： Charge transfer

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YTHDF1 differentiates the contributing roles of mTORC1 in aging

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Molecular Cell 2025年

作者： Chenzhong Xu Cong Yu Jie Zhang Zhen Zhang Jin Zhang Yuan Meng Ming Wang Minting Wen Junhao Chen Yuping Ning Xinchun Chen Jinke Gu Wen Su Baohua Liu Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI) Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine (SKL-ARM) Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention Marshall Laboratory of Biomedical Engineering International Cancer Center School of Basic Medical Sciences Shenzhen University Medical School Shenzhen 518055 China Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program Friedrich Schiller Universität Jena 07743 Germany Department of Physiology Wannan Medical College Wuhu 241002 China Guangdong Provincial Key Laboratory of Regional Immunity and Diseases School of Basic Medical Sciences Shenzhen University Medical School Shenzhen 518055 China

The mechanistic target of rapamycin (mTOR) serves as an essential hub in sensing metabolic stress and regulating aging, although the differential contributions of mTOR-regulated protein and cholesterol synthesis are unclear. Post-transcriptional modifications of mRNAs, such as N6-methyladenosine (m6A), occur rapidly in response to acute environmental changes to maintain tissue homeostasis. Here, we showed that loss of YTH m6A RNA-binding protein 1 (YTHDF1) accelerated murine aging. Mechanistically, YTHDF1 is anchored to the lysosome surface by lysosome-associated membrane protein (LAMP2), whereby it recruits tuberous sclerosis complex (TSC2) to inhibit mTOR complex 1 (mTORC1). Ythdf1 loss activated mTORC1-sterol regulatory element-binding protein 2 (SREBP2)-axis-mediated cholesterol biosynthesis but not m6A-reader-regulated protein translation. Rapamycin restored murine healthspan in contrast to the maximum lifespan shortening caused by Ythdf1 depletion. Our data reveal an m6A-independent function of YTHDF1, which differentiates the contributing roles of mTORC1 in the regulation of aging.

关键词： YTHDF1 aging mTORC1 TSC2 SREBP2 m6A rapamycin

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Construction of Triboelectric Series and Chirality Detection of Amino Acids Using Triboelectric Nanogenerator

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Advanced Science 2024年第4期11卷 e2307266页

作者： Pal, Arnab Ganguly, Anindita Wei, Po-Han Barman, Snigdha Roy Chang, Chia-Chih Lin, Zong-Hong International Intercollegiate PhD Program National Tsing Hua University Hsinchu30013 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University 1001 University Road Hsinchu30010 Taiwan

Triboelectrification necessitates a frictional interaction between two materials, and their contact electrification is characteristically based on the polarity variance in the triboelectric series. Utilizing this fundamental advantage of the triboelectric phenomenon, different materials can be identified according to their contact electrification capability. Herein, an in-depth analysis of the amino acids present in the stratum corneum of human skin is performed and these are quantified regarding triboelectric polarization. The principal focus of this study lies in analyzing and identifying the amino acids present in copious amounts in the stratum corneum to explain their positive behavior during the contact electrification process. Thus, an augmented triboelectric series of amino acids with quantified triboelectric charging polarity by scrutinizing the transfer charge, work function, and atomic percentage is presented. Furthermore, the chirality of aspartic acid as it is most susceptible to racemization with clear consequences on the human skin is detected. The study is expected to accelerate research exploiting triboelectrification and provide valuable information on the surface properties and biological activities of these important biomolecules. © 2023 The Authors. Advanced Science published by Wiley-VCH GmbH.

关键词： Amino acids

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Improved camptothecin encapsulation and efficacy by environmentally sensitive block copolymer/chitosan/fucoidan nanoparticles for targeting lung cancer cells

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international Journal of Biological Macromolecules 2024年第Part2期277卷 133901页

作者： Don, Trong-Ming Hong, Yu-Ting Jheng, Pei-Ru Chuang, Er-Yuan Huang, Yi-Cheng Department of Chemical and Materials Engineering Tamkang University New Taipei City Taiwan College of Life Sciences Department of Food Science National Taiwan Ocean University Keelung Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering International PhD Program in Biomedical Engineering Taipei Medical University Taipei Taiwan Cell Physiology and Molecular Image Research Center Taipei Medical University–Wan Fang Hospital Taipei Taiwan

In this study, thermo-sensitive poly(N-isopropyl acrylamide) (PNP) was polymerized with pH-sensitive poly(acrylic acid) (PAA) to prepare a PAA-b-PNP block copolymer. Above its cloud point, the block copolymer self-assembled into nanoparticles (NPs), encapsulating the anticancer drug camptothecin (CPT) in situ. Chitosan (CS) and fucoidan (Fu) further modified these NPs, forming Fu-CPT-NPs to enhance biocompatibility, drug encapsulation efficiency (EE), and loading content (LC), crucially facilitating P-selectin targeting of lung cancer cells through a drug delivery system. The EE and LC reached 82 % and 3.5 %, respectively. According to transmission electron microscope observation, these Fu-CPT-NPs had uniform spherical shapes with an average diameter of ca. 250 nm. They could maintain their stability in a pH range of 5.0–6.8. In vitro experimental results revealed that the Fu-CPT-NPs exhibited good biocompatibility and had anticancer activity after encapsulating CPT. It could deliver CPT to cancer cells by targeting P-selectin, effectively increasing cell uptake and inducing cell apoptosis. Animal study results showed that the Fu-CPT-NPs inhibited lung tumor growth by increasing tumor cell apoptosis without causing significant tissue damage related to generating reactive oxygen species in lung cancer cells. This system can effectively improve drug-delivery efficiency and treatment effects and has great potential for treating lung cancer. © 2024 Elsevier B.V.

关键词： Nanoparticles

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Novel synthesis of ZIF67 derived cobalt and nickel oxides induced by ammonium tetrafluoroborate as electroactive material of battery supercapacitor hybrids

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Journal of Energy Storage 2023年 68卷

作者： Kuo, Tsung-Rong Draviana, Hanny Tika Hsu, Chia-Shuo Chung, Ren-Jei Chen, Min-Wen Wang, Su-Ching Lee, Pin-Yan Yougbaré, Sibidou Lin, Lu-Yin Wu, Yung-Fu International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Department of Chemical Engineering National Taiwan University of Science and Technology Taipei106 Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan BP 218 11 Nanoro Burkina Faso Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan

Cobalt and nickel oxides with large theoretical capacitance, high redox activity and low-cost features are widely applied as electroactive material of battery supercapacitor hybrids (BSH) to reduce energy consumption and create renewable energy. Synthesizing cobalt and nickel oxides using zeolitic imidazolate framework 67 (ZIF67) can enhance conductivity and electroactivity and maintain surface area and porosity of ZIF67. Structure directing agent (SDA) can control morphology and improve electrochemical performance. It is attractive to apply SDA for controlling morphology of oxidized ZIF67 and achieving excellent energy storage. In this work, ammonium tetrafluoroborate (NH4BF4) is firstly applied as SDA to synthesize ZIF67 derivative, which is then annealed to form leaf-like cobalt and nickel oxides as electroactive material. The optimal oxidized ZIF67 derivative shows a larger specific capacitance (CF) of 828.9 F/g than those of 519.9 and 5.0 F/g respectively for the oxidized ZIF67 and pristine ZIF67 electrodes, due to preferable leaf-like structure and (311) facet for the former case. A BSH with oxidized ZIF67 derivative positive electrode and graphene negative electrode shows maximum energy density of 10.2 Wh/kg at 357 W/kg, and CF retention of 91% and Coulombic efficiency of 97% after 10,000 cycles. The novel SDA of NH4BF4 is expected to design other efficient electroactive materials for effective energy storage. © 2023 Elsevier Ltd

关键词： Nickel oxide

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Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

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Nano Energy 2024年 125卷

作者： Cheng, Yu-Ying Ganguly, Anindita Cheng, Yi-Yun Ortiz, Christopher Llynard D. Pal, Arnab Shah, Pramod Kaswan, Kuldeep Yang, Lee-Wei Lin, Zong-Hong Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Internet of Senses Research Center National Tsing Hua University Hsinchu30013 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300044 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu300044 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu300044 Taiwan Biomedical Artificial Intelligence PhD Program National Tsing Hua University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei Taiwan

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available. © 2024 Elsevier Ltd

关键词： Nanosensors

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Multifaceted regenerative lives of ‘expired’ platelets

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ISBT Science Series 2018年第3期13卷

作者： T. Burnouf Graduate Institute of Biomedical Materials and Tissue Engineering & International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei Taiwan

There is great interest in using expired platelet concentrates for producing human platelet lysates (hPLs) for cell therapy procedures and, potentially, regenerative medicine. The scientific rationale lies in the richness of platelets in growth factors and cytokines and other cell growth-promoting biomolecules. The main use of hPL is to replace fetal bovine serum (FBS) for cell therapy protocols for clinical-grade xeno-free nutritional supplementation of propagation media. To improve consistency, hPLs may be currently manufactured by pooling the lysates from approximately 16 to 50 frozen platelet concentrates, depending upon jurisdiction. hPL is used as growth medium supplement to expand primary mesenchymal stromal cells (MSCs) from different tissues, as well as various differentiated primary cells. hPLs avoid immunological and zoonotic infectious risks linked to FBS, exhibit potent capacity at expanding cells, shortening the cell population doubling time while maintaining cell physiological, biochemical and functional properties, and, for MSCs, capacity to differentiate. Nonexpired autologous or allogeneic platelet-derived biomaterials are used in regenerative medicine to enhance the healing and repair of damaged or injured tissues. However, the variability in these products does not generally allow to draw evidence-based conclusions, and recommendations on best clinical practices remain needed. Future trends may include the development of large-scale virally inactivated hPLs manufactured following controlled conditions meeting specifications tailored-made for dedicated clinical applications. In conclusion, there is a scientific rationale for making optimal use of expired platelets to produce standardized growth factor preparations for both cell therapy procedures and dedicated regenerative medicine applications.

关键词： cellular therapy platelet concentrates platelet lysates regenerative medicine

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