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Author Correction: Effect of de novo transcriptome assembly on transcript quantification

Scientific reports 2019年第1期9卷 18041页

作者： Ping-Han Hsieh Yen-Jen Oyang Chien-Yu Chen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 10617 Taiwan. Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan. Department of Bio-Industrial Mechatronics Engineering National Taiwan University Taipei 10617 Taiwan. chienyuchen@ntu.edu.tw. Genome and Systems Biology Program National Taiwan University and Academia sinica Taipei 10617 Taiwan. chienyuchen@ntu.edu.tw.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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*** as digital platform for vegetation analysis and estimation of carbon stock in KEHATI aqua park

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AIP Conference Proceedings 2024年第1期3026卷

作者： Nanda Satya Nugraha Dian Pratama Putra Mohammad Prasanto Bimantio Amallia Ferhat Rama Zakaria Rudi Nirwantono Teddy Suparyanto Bens Pardamean Faculty of Forestry Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agriculture Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 PT. Tirta Investama Pabrik Klaten Klaten Central Java Indonesia 57474 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 1148 Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

KEHATI AQUA Park is one of the green areas managed by PT. Tirta Investama Klaten (Klaten Factory). This area is located in Wangen and Ponggok Villages, Polanharjo District, Klaten Regency, Central Java, and is an integral part of the company’s seriousness in carbon reduction movement. When maintenance of the area is important for the sustainability of the park, there is however no data on the trees inventory in the area. Therefore, this study aims to invent the trees at KEHATI AQUA Park and evaluate the potential of the area to become a carbon sink using *** application. This study was conducted at the KEHATI AQUA Park. The census method was performed to collect tree data, and the result was recorded in *** application. The carbon stock calculation was estimated using the application according to the tree data submitted in the application. The study included a total of 1048 plantation spots in 51 tree species. From those numbers, about 738 trees existed, and the remaining spots were blank spaces. Based on the condition of the trees, those were 660 good trees, 17 dry trees, and 61 under pest infection. The carbon stock estimation at KEHATI AQUA Park Klaten in the next five years (2026) is around 40 tons of carbon. Therefore, it can be concluded that the park is valuable as an area to preserve biodiversity and as a carbon sink.

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Transdermal nanolipoplex simultaneously inhibits subcutaneous melanoma growth and suppresses systemically metastatic melanoma by activating host immunity

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Nanomedicine: Nanotechnology, Biology, and Medicine 2023年 47卷 102628-102628页

作者： Chen, Chia-Hung Weng, Tzu-Han Chuang, Cheng-Hsun Huang, Kai-Yao Huang, Sih-Cheng Chen, Pin-Rong Huang, Hsiao-Hsuan Huang, Ling-Ya Shen, Pei-Chun Chuang, Po-Ya Huang, Hsiao-Yen Wu, Yi-Syuan Chang, Hao-Chiun Weng, Shun-Long Liao, Kuang-Wen Department of Medical Research Hsinchu MacKay Memorial Hospital Hsinchu City30071 Taiwan Dependent of Medical Education MacKay Memorial Hospital Taipei10449 Taiwan Institute of Molecular Medicine and Bioengineering National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan Industrial Development Graduate Program of College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan Department of Medicine MacKay Medical College New Taipei City25245 Taiwan Department of Obstetrics and Gynecology Hsinchu MacKay Memorial Hospital Hsinchu City30071 Taiwan MacKay Junior College of Medicine Nursing and Management Taipei City11260 Taiwan Drug Development and Value Creation Research Center College of Dental Medicine Kaohsiung Medical University School of Dentistry Graduate Institute of Medicine College of Medicine Center for Cancer Research Kaohsiung Medical University Kaohsiung City80708 Taiwan Center for Intelligent Drug Systems and Smart Bio-devices National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan Department of Biotechnology and Bioindustry Sciences National Cheng Kung University Tainan City70101 Taiwan Ph.D. Degree Program of Biomedical Science and Engineering National Yang Ming Chiao Tung University Hsinchu City30068 Taiwan

Benefit for clinical melanoma treatments, the transdermal neoadjuvant therapy could reduce surgery region and increase immunotherapy efficacy. Using lipoplex (Lipo-PEG-PEI-complex, LPPC) encapsulated doxorubicin (DOX) and carrying CpG oligodeoxynucleotide;the transdermally administered nano-liposomal drug complex (LPPC-DOX-CpG) would have high cytotoxicity and immunostimulatory activity to suppress systemic metastasis of melanoma. LPPC-DOX-CpG dramatically suppressed subcutaneous melanoma growth by inducing tumor cell apoptosis and recruiting immune cells into the tumor area. Animal studies further showed that the colonization and growth of spontaneously metastatic melanoma cells in the liver and lung were suppressed by transdermal LPPC-DOX-CpG. Furthermore, NGS analysis revealed IFN-γ and NF-κB pathways were triggered to recruit and activate the antigen-presenting-cells and effecter cells, which could activate the anti-tumor responses as the major mechanism responsible for the therapeutic effect of LPPC-DOX-CpG. Finally, we have successfully proved transdermal LPPC-DOX-CpG as a promising penetrative carrier to activate systemic anti-tumor immunity against subcutaneous and metastatic tumor. © 2022

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Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition

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Science Signaling 2022年第753期15卷 eabk1147页

作者： Pilo, Caila A. Baffi, Timothy R. Kornev, Alexandr P. Kunkel, Maya T. Malfavon, Mario Chen, Dong-Hui Rossitto, Leigh-Ana Chen, Daniel X. Huang, Liang-Chin Longman, Cheryl Kannan, Natarajan Raskind, Wendy H. Gonzalez, David J. Taylor, Susan S. Gorrie, George Newton, Alexandra C. Department of Pharmacology University of California La Jolla San Diego 92037 CA United States Biomedical Sciences Graduate Program University of California La Jolla San Diego 92037 CA United States Department of Neurology University of Washington Seattle 98195 WA United States Institute of Bioinformatics University of Georgia Athens 30602 GA United States Queen Elizabeth University Hospital Glasgow G51 4TF United Kingdom Department of Biochemistry and Molecular Biology University of Georgia Athens 30602 GA United States Department of Medicine/Medical Genetics University of Washington Seattle 98195 WA United States Department of Psychiatry and Behavioral Sciences University of Washington Seattle 98195 WA United States Mental Illness Research Education and Clinical Center Department of Veterans Affairs Seattle 98108 WA United States

Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progre...

Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca²⁺-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCγ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCγ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCγ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCγ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCγ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression. Copyright © 2022 The Authors, some rights reserved.

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An atlas of dynamic chromatin landscapes in mouse fetal development (vol 583, pg 744, 2020)

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NATURE 2021年第7842期589卷 E4-E4页

作者： Gorkin, David U. Barozzi, Iros Zhao, Yuan Zhang, Yanxiao Huang, Hui Lee, Ah Young Li, Bin Chiou, Joshua Wildberg, Andre Ding, Bo Zhang, Bo Wang, Mengchi Strattan, J. Seth Davidson, Jean M. Qiu, Yunjiang Afzal, Veena Akiyama, Jennifer A. Plajzer-Frick, Ingrid Novak, Catherine S. Kato, Momoe Garvin, Tyler H. Pham, Quan T. Harrington, Anne N. Mannion, Brandon J. Lee, Elizabeth A. Fukuda-Yuzawa, Yoko He, Yupeng Preissl, Sebastian Chee, Sora Han, Jee Yun Williams, Brian A. Trout, Diane Amrhein, Henry Yang, Hongbo Cherry, J. Michael Wang, Wei Gaulton, Kyle Ecker, Joseph R. Shen, Yin Dickel, Diane E. Visel, Axel Pennacchio, Len A. Ren, Bing Ludwig Institute for Cancer Research La Jolla CA USA Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Biomedical Sciences Graduate Program University of California San Diego School of Medicine La Jolla CA USA Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA Institute of Genomic Medicine University of California San Diego School of Medicine La Jolla CA USA Moores Cancer Center University of California San Diego School of Medicine La Jolla CA USA Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA Department of Surgery and Cancer Imperial College London London UK US Department of Energy Joint Genome Institute Berkeley CA USA School of Natural Sciences University of California Merced Merced CA USA Comparative Biochemistry Program University of California Berkeley Berkeley CA USA Genomic Analysis Laboratory Salk Institute for Biological Studies La Jolla CA USA Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA Department of Biochemistry and Molecular Biology Penn State School of Medicine Hershey PA USA Stanford University School of Medicine Department of Genetics Stanford CA USA Howard Hughes Medical Institute Salk Institute for Biological Studies La Jolla CA USA Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA Institute for Human Genetics and University of California San Francisco San Francisco CA USA Department of Neurology University of California San Francisco San Francisco CA USA

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A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration

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Cell Genomics 2023年第6期3卷 100302-100302页

作者： Orozco, Luz D. Owen, Leah A. Hofmann, Jeffrey Stockwell, Amy D. Tao, Jianhua Haller, Susan Mukundan, Vineeth T. Clarke, Christine Lund, Jessica Sridhar, Akshayalakshmi Mayba, Oleg Barr, Julie L. Zavala, Rylee A. Graves, Elijah C. Zhang, Charles Husami, Nadine Finley, Robert Au, Elizabeth Lillvis, John H. Farkas, Michael H. Shakoor, Akbar Sherva, Richard Kim, Ivana K. Kaminker, Joshua S. Townsend, Michael J. Farrer, Lindsay A. Yaspan, Brian L. Chen, Hsu-Hsin DeAngelis, Margaret M. Department of Bioinformatics and Computational Biology Genentech South San Francisco 94080 CA United States Department of Ophthalmology and Visual Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Population Health Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Obstetrics and Gynecology University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Ophthalmology Ross Eye Institute Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Pathology Genentech South San Francisco 94080 CA United States Department of Human Genetics Genentech South San Francisco 94080 CA United States Departments of Microchemistry Proteomics and Lipidomics Genentech South San Francisco 94080 CA United States Department of Human Pathobiology & OMNI Reverse Translation Genentech South San Francisco 94080 CA United States Neuroscience Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Biochemistry Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Veterans Administration Western New York Healthcare System Buffalo 14212 NY United States Department of Medicine Biomedical Genetics Boston University School of Medicine Boston 02118 MA United States Retina Service Massachusetts Eye & Ear Department of Ophthalmology Harvard Medical School Boston 02114 MA United States Genetics Genomics and Bioinformatics Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States

Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease. © 2023 The Authors

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Structural basis and synergism of ATP and Na⁺ activation in bacterial K⁺ uptake system KtrAB

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Nature Communications 2024年第1期15卷 3850页

作者： Chiang, Wesley Tien Chang, Yao-Kai Hui, Wei-Han Chang, Shu-Wei Liao, Chen-Yi Chang, Yi-Chuan Chen, Chun-Jung Wang, Wei-Chen Lai, Chien-Chen Wang, Chun-Hsiung Luo, Siou-Ying Huang, Ya-Ping Chou, Shan-Ho Horng, Tzyy-Leng Hou, Ming-Hon Muench, Stephen P. Chen, Ren-Shiang Tsai, Ming-Daw Hu, Nien-Jen Graduate Institute of Biochemistry National Chung Hsing University Taichung 402202 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115201 Taiwan Department of Civil Engineering National Taiwan University Taipei 106319 Taiwan Department of Biomedical Engineering National Taiwan University Taipei 10663 Taiwan Life Science Group Scientific Research Division National Synchrotron Radiation Research Center Hsinchu 30092 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung 402202 Taiwan Graduate Institute of Chinese Medical Science China Medical University Taichung 406040 Taiwan Department of Applied Mathematics Feng Chia University Taichung 407102 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung 402202 Taiwan School of Biomedical Sciences Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT United Kingdom Department of Life Science Tunghai University Taichung 407224 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106319 Taiwan Ph.D Program in Translational Medicine National Chung Hsing University Taichung 402202 Taiwan

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated...

The K⁺ uptake system KtrAB is essential for bacterial survival in low K⁺ environments. The activity of KtrAB is regulated by nucleotides and Na⁺. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na⁺ activates KtrAB and the Na⁺ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na⁺, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na⁺ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K⁺ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na⁺ in activating BsKtrAB is likely applicable to Na⁺-activated K⁺ channels in central nervous system. © The Author(s) 2024.

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Retraction Note: REHAB FUN: an assistive technology in neurological motor disorders rehabilitation of children with cerebral palsy

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Neural Computing and Applications 2024年第28期36卷 17757-17757页

作者： de Oliveira, Juliana M. Munoz, Roberto Ribeiro, Sidarta Wu, Wanqing de Albuquerque, Victor Hugo C. Graduate Program in Applied Informatics Laboratory of Bioinformatics University of Fortaleza Fortaleza Brazil Escuela de Ingeniería Civil Informática Centro de Investigación y Desarrollo en Ingeniería en Salud Universidad de Valparaíso Valparaíso Chile Brain Institute Federal University of Rio Grande do Norte (UFRN) Natal Brazil CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems Shenzhen Institute of Advanced Technology-Chinese Academy of Sciences (SIAT-CAS) Shenzhen China

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Correction: Resistance QTLs controlling leaf and neck blast disease identified in a doubled haploid rice population

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Euphytica 2023年第7期219卷 1-1页

作者： Korinsak, Siripar Sriprakhon, Saengchai Sirithunya, Kanyanat Sriwongchai, Tanee Wongsaprom, Chanakarn Plabpla, Anucha Vanavichit, Apichart Toojinda, Theerayut National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA) Khlong Luang Thailand Faculty of Science and Agricultural Technology Rajamangala University of Technology Lanna Chiangmai Thailand Department of Agronomy Faculty of Agriculture Kasetsart University Bangkok Thailand Interdisciplinary Graduate Program in Genetic Engineering and Bioinformatics Kasetsart University Bangkok Thailand Department of Agronomy Faculty of Agriculture at Kamphaeng Saen Kasetsart University Nakhon Pathom Thailand Rice Science Center Kasetsart University Nakhon Pathom Thailand

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Development and evaluation of a hospital-wide healthcare-associated surgical site infection detection algorithm

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Journal of Microbiology, Immunology and Infection 2015年第2期48卷 S43-S43页

作者： Yi-Ju Tseng Bo-Chiang Huang Hui-Chi Lin Ming-Yuan Chen Rung-Ji Shang Wang-Huei Sheng Yee-Chun Chen Feipei Lai Shan-Chwen Chang Children's Hospital Informatics Program Boston Children's Hospital Boston MA USA Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan Center for Infection Control National Taiwan University Hospital (NTUH) Taiwan Information Systems Office NTUH Taipei Taiwan Department of Internal Medicine NTUH and College of Medicine Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan Department of Computer Science and Information Engineering National Taiwan University Taiwan

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