Basic research and opportunities for translational advancement in the field of mammalian ∼12-hour ultradian chronobiology

Authors: William Dion, Bokai Zhu

Source: Frontiers in Physiology, Vol 15 (2024)

Subject Terms: circadian rhythm, ultradian rhythm, proteostasis, NAFLD/MAFLD, nuclear speckles, XBP1s, Physiology, QP1-981

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Relation: https://www.frontiersin.org/articles/10.3389/fphys.2024.1497836/full; https://doaj.org/toc/1664-042X

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MAPS: pathologist-level cell type annotation from tissue images through machine learning

Authors: Muhammad Shaban, Yunhao Bai, Huaying Qiu, Shulin Mao, Jason Yeung, Yao Yu Yeo, Vignesh Shanmugam, Han Chen, Bokai Zhu, Jason L. Weirather, Garry P. Nolan, Margaret A. Shipp, Scott J. Rodig, Sizun Jiang, Faisal Mahmood

Source: Nature Communications, Vol 15, Iss 1, Pp 1-11 (2024)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

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Epigenetically active chromatin in neonatal iWAT reveals GABPα as a potential regulator of beige adipogenesis

Authors: Raja Gopal Reddy Mooli, Bokai Zhu, Saifur R. Khan, Veerababu Nagati, Kulandaimanuvel Antony Michealraj, Michael J. Jurczak, Sadeesh K. Ramakrishnan

Source: Frontiers in Endocrinology, Vol 15 (2024)

Subject Terms: beige adipocyte, neonatal adipose tissue, epigenetic modification, GABPA, subcutaneous adipose tissue, Diseases of the endocrine glands. Clinical endocrinology, RC648-665

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Relation: https://www.frontiersin.org/articles/10.3389/fendo.2024.1385811/full; https://doaj.org/toc/1664-2392

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Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology

Authors: Yunhao Bai, Bokai Zhu, John-Paul Oliveria, Bryan J. Cannon, Dorien Feyaerts, Marc Bosse, Kausalia Vijayaragavan, Noah F. Greenwald, Darci Phillips, Christian M. Schürch, Samuel M. Naik, Edward A. Ganio, Brice Gaudilliere, Scott J. Rodig, Michael B. Miller, Michael Angelo, Sean C. Bendall, Xavier Rovira-Clavé, Garry P. Nolan, Sizun Jiang

Source: Nature Communications, Vol 14, Iss 1, Pp 1-18 (2023)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

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High‐Resolution Mapping Nanoscale Hydrophobicity for Fine Structures and Dynamic Evolution of Nanomaterial Surface

Authors: Yuyao Zhang, Xiaoying Zhu, Bokai Zhu, Chiheng Chu, Baoliang Chen

Source: Small Structures, Vol 5, Iss 1, Pp n/a-n/a (2024)

Subject Terms: atomic force microscopy, chemical force microscopy, graphene oxides, nanomaterials, surface hydrophobicity, Physics, QC1-999, Chemistry, QD1-999

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Relation: https://doaj.org/toc/2688-4062

Access URL: https://doaj.org/article/e29beb3199844e1da7cfbb4ab9de30a1

T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response

Authors: John W. Hickey, Maximillian Haist, Nina Horowitz, Chiara Caraccio, Yuqi Tan, Andrew J. Rech, Marc-Andrea Baertsch, Xavier Rovira-Clavé, Bokai Zhu, Gustavo Vazquez, Graham Barlow, Eran Agmon, Yury Goltsev, John B. Sunwoo, Markus Covert, Garry P. Nolan

Source: Cell Reports, Vol 42, Iss 12, Pp 113494- (2023)

Subject Terms: CP: Immunology, CP: Cancer, Biology (General), QH301-705.5

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Relation: http://www.sciencedirect.com/science/article/pii/S2211124723015061; https://doaj.org/toc/2211-1247

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Activation of Peroxisome Proliferator-Activated Receptor-β/δ (PPARβ/δ) in Keratinocytes by Endogenous Fatty Acids

Authors: Bokai Zhu, Xiaoyang Zhu, Michael G. Borland, Douglas H. Ralph, Christopher R. Chiaro, Kristopher W. Krausz, James M. Ntambi, Adam B. Glick, Andrew D. Patterson, Gary H. Perdew, Frank J. Gonzalez, Jeffrey M. Peters

Source: Biomolecules, Vol 14, Iss 6, p 606 (2024)

Subject Terms: peroxisome proliferator-activated receptor, ligands, cell cycle, fatty acids, UVB-induced non-melanoma skin cancer, Microbiology, QR1-502

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Relation: https://www.mdpi.com/2218-273X/14/6/606; https://doaj.org/toc/2218-273X

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Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock

Authors: Bokai Zhu, Silvia Liu

Source: Frontiers in Physiology, Vol 14 (2023)

Subject Terms: ultradian and circadian rhythms, proteostasis, mRNA metabolism, X-box binding protein 1 (XBP1), Drosophila S2 cell, Physiology, QP1-981

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Relation: https://www.frontiersin.org/articles/10.3389/fphys.2023.1195001/full; https://doaj.org/toc/1664-042X

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Twelve-hour rhythms in transcript expression within the human dorsolateral prefrontal cortex are altered in schizophrenia

Authors: Madeline R. Scott, Wei Zong, Kyle D. Ketchesin, Marianne L. Seney, George C. Tseng, Bokai Zhu, Colleen A. McClung

Source: PLoS Biology, Vol 21, Iss 1 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9873190/?tool=EBI; https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

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Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging

Authors: Xavier Rovira-Clavé, Sizun Jiang, Yunhao Bai, Bokai Zhu, Graham Barlow, Salil Bhate, Ahmet F. Coskun, Guojun Han, Chin-Min Kimmy Ho, Chuck Hitzman, Shih-Yu Chen, Felice-Alessio Bava, Garry P. Nolan

Source: Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/18ad42beb0ae47dfab30d767ad938893

Restoration of the molecular clock is tumor suppressive in neuroblastoma

Authors: Myrthala Moreno-Smith, Giorgio Milazzo, Ling Tao, Baharan Fekry, Bokai Zhu, Mahmoud A. Mohammad, Simone Di Giacomo, Roshan Borkar, Karthik Reddy Kami Reddy, Mario Capasso, Sanjeev A. Vasudevan, Pavel Sumazin, John Hicks, Nagireddy Putluri, Giovanni Perini, Kristin Eckel-Mahan, Thomas P. Burris, Eveline Barbieri

Source: Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/36f78ce6f76041c49c8161f0733a70f4

XBP1 links the 12-hour clock to NAFLD and regulation of membrane fluidity and lipid homeostasis

Authors: Huan Meng, Naomi M. Gonzales, David M. Lonard, Nagireddy Putluri, Bokai Zhu, Clifford C. Dacso, Brian York, Bert W. O’Malley

Source: Nature Communications, Vol 11, Iss 1, Pp 1-16 (2020)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/163c3b3fcdb943638dd992aefa6a597d

Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism

Authors: Huan Meng, Naomi M. Gonzales, Sung Yun Jung, Yue Lu, Nagireddy Putluri, Bokai Zhu, Clifford C. Dacso, David M. Lonard, Bert W. O’Malley

Source: Cell Reports, Vol 38, Iss 10, Pp 110491- (2022)

Subject Terms: 12-h clock, lipid metabolism, transcriptional coactivation, lipid homeostasis, energy metabolism, stress rhythms, Biology (General), QH301-705.5

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Relation: http://www.sciencedirect.com/science/article/pii/S2211124722002248; https://doaj.org/toc/2211-1247

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Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers

Authors: Tsuguhisa Nakayama, Ivan T. Lee, Sizun Jiang, Matthias S. Matter, Carol H. Yan, Jonathan B. Overdevest, Chien-Ting Wu, Yury Goltsev, Liang-Chun Shih, Chun-Kang Liao, Bokai Zhu, Yunhao Bai, Peter Lidsky, Yinghong Xiao, David Zarabanda, Angela Yang, Meena Easwaran, Christian M. Schürch, Pauline Chu, Han Chen, Anna K. Stalder, David R. McIlwain, Nicole A. Borchard, Phillip A. Gall, Sachi S. Dholakia, Wei Le, Le Xu, Chih-Jaan Tai, Te-Huei Yeh, Elizabeth Erickson-Direnzo, Jason M. Duran, Kirsten D. Mertz, Peter H. Hwang, Jasmin D. Haslbauer, Peter K. Jackson, Thomas Menter, Raul Andino, Peter D. Canoll, Adam S. DeConde, Zara M. Patel, Alexandar Tzankov, Garry P. Nolan, Jayakar V. Nayak

Source: Cell Reports Medicine, Vol 2, Iss 10, Pp 100421- (2021)

Subject Terms: SARS-CoV-2, COVID-19, ACE2, TMPRSS2, ciliated epithelial cell, IFN-β1, Medicine (General), R5-920

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Relation: http://www.sciencedirect.com/science/article/pii/S2666379121002834; https://doaj.org/toc/2666-3791

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Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images

Authors: Yunhao Bai, Bokai Zhu, Xavier Rovira-Clave, Han Chen, Maxim Markovic, Chi Ngai Chan, Tung-Hung Su, David R. McIlwain, Jacob D. Estes, Leeat Keren, Garry P. Nolan, Sizun Jiang

Source: Frontiers in Immunology, Vol 12 (2021)

Subject Terms: multiplexed tissue imaging, spatial proteomics, signal spillover, image correction, single-cell biology, cell annotation, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2021.652631/full; https://doaj.org/toc/1664-3224

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12-h clock regulation of genetic information flow by XBP1s.

Authors: Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C Dacso, Colleen A McClung, Bert W O'Malley, Silvia Liu, Bokai Zhu

Source: PLoS Biology, Vol 18, Iss 1, p e3000580 (2020)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000580&type=printable; https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/c2dd094cb87d4a129031aa33f2653b0a

Correction: SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer.

Authors: Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A Comerford, Chao Xing, Xian-Jin Xie, Brian York, Kathryn A O'Donnell

Source: PLoS Genetics, Vol 14, Iss 4, p e1007344 (2018)

Subject Terms: Genetics, QH426-470

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Relation: http://europepmc.org/articles/PMC5894952?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

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A novel mathematical method for disclosing oscillations in gene transcription: A comparative study.

Authors: Athanasios C Antoulas, Bokai Zhu, Qiang Zhang, Brian York, Bert W O'Malley, Clifford C Dacso

Source: PLoS ONE, Vol 13, Iss 9, p e0198503 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC6145530?pdf=render; https://doaj.org/toc/1932-6203

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SRC-2 Is an Essential Coactivator for Orchestrating Metabolism and Circadian Rhythm

Authors: Erin Stashi, Rainer B. Lanz, Jianqiang Mao, George Michailidis, Bokai Zhu, Nicole M. Kettner, Nagireddy Putluri, Erin L. Reineke, Lucas C. Reineke, Subhamoy Dasgupta, Adam Dean, Connor R. Stevenson, Natarajan Sivasubramanian, Arun Sreekumar, Francesco DeMayo, Brian York, Loning Fu, Bert W. O’Malley

Source: Cell Reports, Vol 6, Iss 4, Pp 633-645 (2014)

Subject Terms: Biology (General), QH301-705.5

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Relation: http://www.sciencedirect.com/science/article/pii/S2211124714000448; https://doaj.org/toc/2211-1247

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SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer.

Authors: Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A Comerford, Chao Xing, Xian-Jin Xie, Brian York, Kathryn A O'Donnell

Source: PLoS Genetics, Vol 13, Iss 3, p e1006650 (2017)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5362238?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

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