Article
Cell Biology
Xiaojun Wang, Hanqing Xiong, Yurong Liu, Tao Yang, Anan Li, Fei Huang, Fangfang Yin, Lei Su, Ling Liu, Ning Li, Longhui Li, Shenghua Cheng, Xiaoxiang Liu, Xiaohua Lv, Xiuli Liu, Jun Chu, Tonghui Xu, Fuqiang Xu, Hui Gong, Qingming Luo, Jing Yuan, Shaoqun Zeng
Summary: CSFT technique utilizing chemical switching of fluorescent proteins enables high-resolution imaging of brain structures for studying neuron connections and cellular compositions. It also allows quantitative acquisition at the single-neuron level.
Article
Optics
Qiuyuan Zhong, Chenyu Jiang, Dejie Zhang, Siqi Chen, Rui Jin, Hui Gong, Jing Yuan
Summary: This study introduces a new method for optical sectioning imaging that achieves higher image quality and throughput compared to traditional methods. By imaging large biological tissue samples, it opens up new possibilities for the development of high-throughput, high-resolution optical imaging methods.
Article
Microbiology
Maximilian W. D. Raas, Thiago P. Silva, Jhamine C. O. Freitas, Lara M. Campos, Rodrigo L. Fabri, Rossana C. N. Melo
Summary: The study utilized whole slide imaging (WSI) to visualize Candida biofilm formation, staining accumulated biofilms with fluorescent markers and scanning in both bright-field and fluorescence modes using a WSI digital scanner. WSI allowed for clear assessment of biofilm size and structural features, with quantitative analysis showing reductions in biofilm-covered surface area upon antifungal exposure. At the single-cell level, WSI proved to be adequate for evaluating morphometric parameters, demonstrating its reliability in visualizing Candida biofilms and making it an important addition to microscopic tools for fungal biofilm growth analysis.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Yiming Huang, Ravi U. Sheth, Shijie Zhao, Lucas A. Cohen, Kendall Dabaghi, Thomas Moody, Yiwei Sun, Deirdre Ricaurte, Miles Richardson, Florencia Velez-Cortes, Tomasz Blazejewski, Andrew Kaufman, Carlotta Ronda, Harris H. Wang
Summary: A machine learning isolation and genotyping platform allows for high-throughput bacterial culture generation. The platform utilizes colony morphology and genomic data to maximize microbial diversity and target specific genera for isolation. It has been successfully applied to generate personalized gut microbiome biobanks and has revealed important microbial interactions and strain evolution.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Akash Kumar Bhaskar, Salwa Naushin, Arjun Ray, Praveen Singh, Anurag Raj, Shalini Pradhan, Khushboo Adlakha, Towfida Jahan Siddiqua, Dipankar Malakar, Debasis Dash, Shantanu Sengupta
Summary: Lipid compositions are complex and challenging to identify, necessitating new comprehensive analysis methods. This study proposes a targeted-mass spectrometry method that can rapidly screen a large number of lipid species, and identifies alterations in plasma lipids due to vitamin B(12) deficiency.
Article
Biology
Wentao Yu, Lei Kang, Victor T. C. Tsang, Yan Zhang, Ivy H. M. Wong, Terence T. W. Wong
Summary: TRUST is a fast, cost-effective, and robust multicolor whole-organ 3D imaging method that achieves fluorescence imaging of exogenous molecular-specific and endogenous autofluorescence simultaneously. It offers fast and high-content multicolor 3D imaging capability for vital organs and developmental biology samples.
Article
Biochemical Research Methods
David J. J. Thomas, Jordan Rainbow, Laura E. E. Bartley
Summary: Microscopic analysis of plant anatomy requires high-quality sections for accurate measurements. The authors present a hand-sectioning method suitable for softer tissues and a novel microtome design called Rapid-Tome for sectioning both soft and tougher plant materials. The Rapid-Tome allows rapid sectioning, sample control, and is cost-effective compared to traditional microtomes. High school students were able to produce sections for comparative analyses with minimal training.
Article
Biotechnology & Applied Microbiology
Fang Xu, Yan Shen, Lufeng Ding, Chao-Yu Yang, Heng Tan, Hao Wang, Qingyuan Zhu, Rui Xu, Fengyi Wu, Yanyang Xiao, Cheng Xu, Qianwei Li, Peng Su, Li I. Zhang, Hong-Wei Dong, Robert Desimone, Fuqiang Xu, Xintian Hu, Pak-Ming Lau, Guo-Qiang Bi
Summary: This study introduces a new method combining primate-optimized tissue sectioning and clearing with high-speed fluorescence microscopy to achieve high-resolution imaging of the entire rhesus monkey brain. Researchers have also developed an efficient method for tracing sparse axonal fibers in large datasets, enabling connectome-scale mapping of large primate brains.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
Summary: We propose a deep-learning method for precise localization of spatially variant point emitters, covering the full chip of a modern sCMOS camera. By using a graphic processing unit-based vectorial point spread function fitter, we accurately model the spatially variant PSF of a high numerical aperture objective in the entire field of view. Combined with deformable mirror-based optimal PSF engineering, we demonstrate high-accuracy three-dimensional single-molecule localization microscopy over a large volume, enabling imaging of mitochondria and nuclear pore complexes in entire cells without hardware scanning, with a 100-fold increase in throughput compared to existing techniques.
Article
Multidisciplinary Sciences
Zunming Zhang, Rui Tang, Xinyu Chen, Lauren Waller, Alston Kau, Anthony A. Fung, Bien Gutierrez, Cheolhong An, Sung Hwan Cho, Lingyan Shi, Yu-Hwa Lo
Summary: We have developed a high-throughput technique that can relate the positions of individual cells to their three-dimensional imaging features. This technique is particularly useful for nonadherent cells and overcomes the limitations of existing spatial biology methodologies. Our approach involves recording 3D cell images at high throughput using a custom 3D imaging flow cytometer and dispensing cells in a FIFO manner using a robotic cell placement platform. Experiments with human cancer cell lines have demonstrated the feasibility of mapping 3D cell images to their locations on a membrane filter for a large number of cells in a short time. This technology and method bridge the gap between single-cell image analysis and single-cell molecular analysis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Feng Liu, Zexin Wang, Zi Wang, Jing Zhong, Lei Zhao, Liang Jiang, Runhua Zhou, Yong Liu, Lan Huang, Liming Tan, Yujia Tian, Han Zheng, Qihong Fang, Lijun Zhang, Lina Zhang, Hong Wu, Lichun Bai, Kun Zhou
Summary: This study proposes a high-throughput-based design strategy for high-temperature alloys, which can accelerate the selection of alloy composition with improved performance through calculating diffusion coefficients, refining physical models, and using machine learning. Experimental validation shows that this strategy has high accuracy and efficiency.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Materials Science, Ceramics
Premysl Stastny, Zdenek Chlup, Klara Castkova, Martin Trunec
Summary: In this study, high strength alumina thin tapes were prepared using a novel gel-tape casting method. The choice of dispersants and sintering conditions significantly affected the properties of the tapes, with as-sintered tapes showing high characteristic Weibull strength values.
CERAMICS INTERNATIONAL
(2021)
Article
Chemistry, Physical
Huihui Wen, Hongye Zhang, Runlai Peng, Chao Liu, Shuman Liu, Fengqi Liu, Huimin Xie, Zhanwei Liu
Summary: In this study, a scanning transmission electron microscopy (STEM) moire depth sectioning method is proposed, which can accurately evaluate the 3D strain field at the nanoscale. Through optimizing the scanning parameters of electron probes at different depths, a large field of view STEM-MFs sequence is obtained, and the 3D STEM moire information is constructed. The developed method realizes multi-scale 3D strain field measurements and accurately measures the 3D strain field near the heterostructure interface and single dislocation.
Article
Clinical Neurology
Andras Sziraki, Yu Zhong, Allison M. Neltner, Dana M. Niedowicz, Colin B. Rogers, Donna M. Wilcock, Geetika Nehra, Janna H. Neltner, Rebecca R. Smith, Anika M. Hartz, Junyue Cao, Peter T. Nelson
Summary: By analyzing single-cell RNA expression profiles derived from different regions of the human and mouse brain, we have identified specific gene markers for pericytes. These gene markers showed better immunolabeling for pericytes in human brain sections compared to existing markers.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2023)
Article
Biophysics
Jie Liu, Jian-Zhong Xu, Zhi-Ming Rao, Wei-Guo Zhang
Summary: We have developed an enzymatic colorimetric biosensor that allows direct identification of high-level lysine-producing strains by optimizing the export mechanism of L-lysine and the synthesis pathway of lycopene precursors.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Radiology, Nuclear Medicine & Medical Imaging
Noam Shemesh, Sune N. Jespersen, Daniel C. Alexander, Yoram Cohen, Ivana Drobnjak, Tim B. Dyrby, Jurgen Finsterbusch, Martin A. Koch, Tristan Kuder, Fredrik Laun, Marco Lawrenz, Henrik Lundell, Partha P. Mitra, Markus Nilsson, Evren Ozarslan, Daniel Topgaard, Carl-Fredrik Westin
MAGNETIC RESONANCE IN MEDICINE
(2016)
Review
Neurosciences
Hideyuki Okano, Partha Mitra
NEUROSCIENCE RESEARCH
(2015)
Article
Biology
Jia Liu, Hyun Joo Lee, Andrew J. Weitz, Zhongnan Fang, Peter Lin, ManKin Choy, Robert Fisher, Vadim Pinskiy, Alexander Tolpygo, Partha Mitra, Nicholas Schiff, Jin Hyung Lee
Article
Neurosciences
Piotr Majka, Tristan A. Chaplin, Hsin-Hao Yu, Alexander Tolpygo, Partha P. Mitra, Daniel K. Wojcik, Marcello G. P. Rosa
JOURNAL OF COMPARATIVE NEUROLOGY
(2016)
Article
Multidisciplinary Sciences
Minju Jeong, Yongsoo Kim, Jeongjin Kim, Daniel D. Ferrante, Partha P. Mitra, Pavel Osten, Daesoo Kim
SCIENTIFIC REPORTS
(2016)
Article
Neurosciences
Georg F. Striedter, T. Grant Belgard, Chun-Chun Chen, Fred P. Davis, Barbara L. Finlay, Onur Guentuerkuen, Melina E. Hale, Julie A. Harris, Erin E. Hecht, Patrick R. Hof, Hans A. Hofmann, Linda Z. Holland, Andrew N. Iwaniuk, Erich D. Jarvis, Harvey J. Karten, Paul S. Katz, William B. Kristan, Eduardo R. Macagno, Partha P. Mitra, Leonid L. Moroz, Todd M. Preuss, Clifton W. Ragsdale, Chet C. Sherwood, Charles F. Stevens, Maik C. Stuettgen, Tadaharu Tsumoto, Walter Wilczynski
JOURNAL OF COMPARATIVE NEUROLOGY
(2014)
Review
Neurosciences
Partha P. Mitra
Article
Multidisciplinary Sciences
Yanjie Li, Dingkang Wang, Giorgio A. Ascoli, Partha Mitra, Yusu Wang
Article
Multidisciplinary Sciences
Pascal Grange, Jason W. Bohland, Benjamin W. Okaty, Ken Sugino, Hemant Bokil, Sacha B. Nelson, Lydia Ng, Michael Hawrylycz, Partha P. Mitra
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Automation & Control Systems
Emma Tegling, Partha Mitra, Henrik Sandberg, Bassam Bamieh
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2019)
Article
Neurosciences
Hemanth Mohan, Xu An, X. Hermione Xu, Hideki Kondo, Shengli Zhao, Katherine S. S. Matho, Bor-Shuen Wang, Simon Musall, Partha Mitra, Z. Josh Huang
Summary: This study reveals that the cellular basis of cerebral cortex functional architecture is not well understood. The activity dynamics of subcortical-projecting and intratelencephalic-projecting neurons in the dorsal cortex of mice during different brain states and behaviors were monitored using genetic targeting and wide-field imaging. The results show that these projection neurons process information and their projection patterns are consistent with their activation patterns.
NATURE NEUROSCIENCE
(2023)
Review
Computer Science, Artificial Intelligence
Partha P. Mitra
Summary: This article discusses the good generalization ability of modern machine learning methods when interpolating noisy data, introduces the phenomenon of statistically consistent interpolation (SCI), explains the reasons for successful data interpolation, and compares the different approaches of modern machine learning, traditional physical theory, and biological brains in modeling natural phenomena.
NATURE MACHINE INTELLIGENCE
(2021)
Article
Biochemistry & Molecular Biology
Yongsoo Kim, Guangyu Robert Yang, Kith Pradhan, Kannan Umadevi Venkataraju, Mihail Bota, Luis Carlos Garcia del Molino, Greg Fitzgerald, Keerthi Ram, Miao He, Jesse Maurica Levine, Partha Mitra, Z. Josh Huang, Xiao-Jing Wang, Pavel Osten
Proceedings Paper
Engineering, Electrical & Electronic
Mohammad Ramezanali, Partha P. Mitra, Anirvan M. Sengupta
2016 24TH EUROPEAN SIGNAL PROCESSING CONFERENCE (EUSIPCO)
(2016)
