Article
Neurosciences
Yarmo Mackenbach, J. Gerard G. Borst
Summary: The medial superior olive (MSO) is a specialized binaural nucleus that detects the relative arrival times of sounds at both ears. Excitatory inputs to MSO neurons from different ears are segregated to different dendrites, and the neurons can phase-lock to multiple tones within a stimulus. The ability to phase-lock is linearly related to the size of the subthreshold response.
JOURNAL OF NEUROSCIENCE
(2023)
Article
Mathematics, Applied
Zahra Dayani, Fatemeh Parastesh, Fahimeh Nazarimehr, Karthikeyan Rajagopal, Sajad Jafari, Eckehard Schoell, Juergen Kurths
Summary: In this paper, a time-varying coupling function is proposed to enhance synchronization in complex networks of oscillators. The stability of synchronization is analyzed using the master stability approach, considering the largest Lyapunov exponent of the linearized variational equations as the master stability function dependent on the network eigenvalues. Diffusive single-variable coupling is assumed for the oscillators, and the coupling with the smallest local Lyapunov exponent is selected for each time interval. The obtained coupling function decreases the critical coupling parameter, leading to enhanced synchronization. Moreover, it achieves faster synchronization and increased robustness. Illustratively, the optimal coupling function is found for three networks of chaotic Rossler, Chen, and Chua systems, showing enhanced synchronization.
Article
Mathematics, Applied
Yuanyuan Liu, Zhongkui Sun, Xiaoli Yang, Wei Xu
Summary: The use of asymmetric feedback enhances the rhythmicity of coupled systems, while reducing asymmetric feedback helps to improve dynamical robustness. Strong coupling benefits dynamic activity, whereas normal diffusive interactions may compromise dynamical robustness.
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2021)
Article
Computer Science, Information Systems
Huan Zhang, Zhaoquan Gu, Hao Tan, Le Wang, Ziqi Zhu, Yushun Xie, Jianxin Li
Summary: The vulnerability of DNNs to adversarial attacks has been a concerning issue, and researchers are looking for methods to improve their robustness. Most existing methods are empirical and can only handle known attack environments and specific conditions, while certified defense methods provide theoretical proofs and worst-case adversarial robustness. However, the study on certified defenses is currently limited, and the existing certified defense methods rely on unrealistic prior knowledge and assumptions. In this paper, a model-agnostic and attack-agnostic certified defense method is proposed, which implements denoising and refactoring of input samples. The proposed method shows superior performance in balancing prediction accuracy and robustness against adversarial attacks compared to state-of-the-art defense methods.
INFORMATION SCIENCES
(2023)
Article
Computer Science, Information Systems
Huan Zhang, Zhaoquan Gu, Hao Tan, Le Wang, Ziqi Zhu, Yushun Xie, Jianxin Li
Summary: This paper proposes a model-agnostic and attack-agnostic certified defense method that implements denoising and refactoring of input samples through the Makser and the Purifier. The method shows superior performance in balancing robustness and prediction accuracy compared to other methods, as demonstrated by theoretical proofs and experiments.
INFORMATION SCIENCES
(2023)
Article
Agronomy
Bo-Yan Zhang, Sen Dou, Dan Guo, Song Guan
Summary: The study investigates the effects of soil water repellency and agglomeration stability on soil organic carbon mineralization, examining different methods of straw return to the field. Results show that deep burying of straw can improve soil water repellency and increase the content of organic carbon in macroaggregates and microaggregates. Additionally, deep straw burial leads to significant increases in CO2-C emissions and SOC mineralization.
Article
Engineering, Multidisciplinary
Phablo R. Carvalho, Marcelo A. Savi
Summary: This paper investigates the synchronization robustness of a network of pendulum-chart oscillators under random aspects, parameter changes, and initial conditions. Results show that the asynchronous region decreases with increased dissipation, and a chimera state may occur under parametric asymmetry. Energetic arguments are used to explain the pattern robustness in relation to randomness and asymmetries.
INTERNATIONAL JOURNAL OF NONLINEAR SCIENCES AND NUMERICAL SIMULATION
(2021)
Article
Automation & Control Systems
Bao-Zhu Guo, Tingting Meng
Summary: This article discusses two-dimensional robust output tracking for a Timoshenko beam equation using an observer-based error feedback control approach to handle disturbances and references produced by an external exosystem. By following certain steps, the control problem is addressed and theoretical results are validated through numerical simulations.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2021)
Article
Physics, Fluids & Plasmas
Nirmal Punetha, Lucas Wetzel
Summary: The production process of integrated electronic circuitry leads to heterogeneities on the component level, which affects the synchronization dynamics. Using a phase-model description, the study shows that heterogeneity can enhance the stability of synchronized states in networks of Kuramoto oscillators. This optimization of phase differences between clocks is not limited to electronic systems.
Article
Nanoscience & Nanotechnology
Mingshu Li, Li Gao, Jason C. White, Christy L. Haynes, Tana L. O'Keefe, Yukui Rui, Sami Ullah, Zhiling Guo, Iseult Lynch, Peng Zhang
Summary: Increasing the capacity of biological nitrogen fixation (BNF) is an effective strategy to enhance food security and reduce the carbon and nitrogen footprint of agriculture. Nanotechnology offers several pathways to successfully enhance BNF.
NATURE NANOTECHNOLOGY
(2023)
Review
Biology
Eugene Mamontov
Summary: Neutron scattering is highly suitable for studying molecular-level dynamics due to its wavelength and energy characteristics. The field has progressed from studying solids to liquids, protein complexes, and biomembranes, and now reaches the level of cells, tissues, and whole multicellular organisms.
Article
Computer Science, Artificial Intelligence
Risto Miikkulainen, Stephanie Forrest
Summary: Evolutionary computation, inspired by biological evolution, has discovered creative solutions but still falls short compared to biology in aspects such as small populations, strong selection, and direct genotype-to-phenotype mappings. Advancements in these areas can lead to evolutionary computation that approaches the complexity and flexibility of biology.
NATURE MACHINE INTELLIGENCE
(2021)
Article
Chemistry, Multidisciplinary
Pierre Picchetti, Stefano Volpi, Maria Sancho-Albero, Marianna Rossetti, Michael D. Dore, Tuan Trinh, Frank Biedermann, Martina Neri, Alessandro Bertucci, Alessandro Porchetta, Roberto Corradini, Hanadi Sleiman, Luisa De Cola
Summary: Organosilica nanoparticles with responsive organic building blocks offer promising opportunities for drug formulation, biomolecule delivery, and diagnostics. In this study, the researchers combined nucleic acid interactions with sol-gel chemistry to create dynamic supramolecular bridging units in the silica-based nanoparticles. These nanoparticles exhibit programmable responses to temperature and biological inputs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Mathematical & Computational Biology
Yu Zhang, Haitao Wu, Jinfeng Gao, Yongtao Zhang, Ruxian Yao, Yuxiang Zhu
Summary: This paper introduces a pattern-based ontology debugging method, DOBP, and a more efficient approach of calculating the minimal axiom sets for unsatisfiable classes by extracting modules. The experimental results show that the Module-DOBP method produces smaller modules compared to the original ontology, making the debugging process more efficient for large-scale ontologies with numerous unsatisfiable classes.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Article
Computer Science, Artificial Intelligence
Jie Yao, Weiwei Xing, Dongdong Wang, Jintao Xing, Liqiang Wang
Summary: This study introduces a new method (ActDB) to enhance the robustness of deep network training while maintaining accuracy. By combining active learning with DropBlock, the method effectively enhances defense against adversarial attacks and reduces model performance degradation.
Article
Biology
Shixuan Liu, Miriam Bracha Ginzberg, Nish Patel, Marc Hild, Bosco Leung, Zhengda Li, Yen-Chi Chen, Nancy Chang, Yuan Wang, Ceryl Tan, Shulamit Diena, William Trimble, Larry Wasserman, Jeremy L. Jenkins, Marc W. Kirschner, Ran Kafri
Article
Multidisciplinary Sciences
Ye Guan, Shiyuan Wang, Minjun Jin, Haotian Xu, Qiong Yang
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2018)
Article
Chemistry, Multidisciplinary
Meng Sun, Zhengda Li, Qiong Yang
JOURNAL OF CHEMICAL EDUCATION
(2019)
Article
Cell Biology
Wael L. Demian, Avinash Persaud, Chong Jiang, Etienne Coyaud, Shixuan Liu, Andras Kapus, Ran Kafri, Brian Raught, Daniela Rotin
Article
Chemistry, Analytical
Meng Sun, Zhengda Li, Shiyuan Wang, Gembu Maryu, Qiong Yang
ANALYTICAL CHEMISTRY
(2019)
Article
Immunology
Michelle A. Francisco, Siyi Wanggou, Jerry J. Fan, Weifan Dong, Xin Chen, Ali Momin, Namal Abeysundara, Hyun-Kee Min, Jade Chan, Rochelle McAdam, Marian Sia, Ronwell J. Pusong, Shixuan Liu, Nish Patel, Vijay Ramaswamy, Noriyuki Kijima, Lu-Yang Wang, Yuanquan Song, Ran Kafri, Michael D. Taylor, Xuejun Li, Xi Huang
JOURNAL OF EXPERIMENTAL MEDICINE
(2020)
Review
Nanoscience & Nanotechnology
Alessandro Groaz, Hossein Moghimianavval, Franco Tavella, Tobias W. Giessen, Anthony G. Vecchiarelli, Qiong Yang, Allen P. Liu
Summary: Constructing synthetic cells is a cutting-edge and challenging area of research. Two key features necessary for recreating cellular processes are compartmentalization and self-organization/spatiotemporal dynamics.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Meng Sun, Gembu Maryu, Shiyuan Wang, Qiong Yang, Ryan C. Bailey
Summary: This unique microfluidic technique utilizes a membrane filter and plug-in tubes to remove oil and pack water-in-oil droplets for controlled incubation of droplet-based assays. The system allows for extended and controllable incubation of droplets in microchannels, and can be easily integrated into most droplet-generation devices without altering their original designs. Additionally, the technique is evaluated and confirmed to be efficient for time-dependent enzyme assays with a fluorometric readout, and can be generalized to control inter-droplet distance for studying droplet communication and pattern formation.
Article
Cell Biology
Ceryl Tan, Miriam B. Ginzberg, Rachel Webster, Seshu Iyengar, Shixuan Liu, David Papadopoli, John Concannon, Yuan Wang, Douglas S. Auld, Jeremy L. Jenkins, Hannes Rost, Ivan Topisirovic, Andreas Hilfinger, W. Brent Derry, Nish Patel, Ran Kafri
Summary: This study demonstrates that cell size is determined by size checkpoints, and p38 and CDK4 cooperate to regulate cell size akin to a thermostat.
DEVELOPMENTAL CELL
(2021)
Article
Biology
Julia Eve Olivieri, Roozbeh Dehghannasiri, Peter L. Wang, SoRi Jang, Antoine de Morree, Serena Y. Tan, Jingsi Ming, Angela Ruohao Wu, Tabula Sapiens Consortium, Stephen R. Quake, Mark A. Krasnow, Julia Salzman
Summary: The study utilized a new statistical approach called SpliZ to detect and validate cell-type-specific splicing in multiple human tissues, demonstrating that splicing is regulated at the level of cell type.
Article
Biotechnology & Applied Microbiology
Sevahn K. Vorperian, Mira N. Moufarrej, Stephen R. Quake
Summary: Cell types affected by diseases can be identified by analyzing cell-free RNA, allowing the determination of their tissue of origin. By utilizing various databases and transcriptomic cell atlases, cell type signature scores can be used to infer cell types contributing to cell-free RNA in different diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Minjun Jin, Franco Tavella, Shiyuan Wang, Qiong Yang
Summary: The cell cycle oscillator can maintain stable oscillations in response to changes in cytoplasmic density. Dilution or concentration of the cytoplasm arrests the cell cycle in low or high steady states, and the direction of tuning forms a hysteresis loop.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Ajai J. Pulianmackal, Dan Sun, Kenji Yumoto, Zhengda Li, Yu-Chih Chen, Meha V. Patel, Yu Wang, Euisik Yoon, Alexander Pearson, Qiong Yang, Russell Taichman, Frank C. Cackowski, Laura A. Buttitta
Summary: The decision between proliferation and quiescence in the cell cycle is a dynamic process with high heterogeneity, even among clonal cell lines. Spontaneous entry into G0 states, which can lead to tumor dormancy and cancer recurrence, is influenced by both intrinsic and extrinsic signals, including asymmetric proliferation-quiescence decisions after mitosis. Dormant cancer cells exhibit altered expression of certain pathways and stem cell markers, potentially increasing the risk of cancer recurrence.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Robert C. Jones, Jim Karkanias, Mark A. Krasnow, Angela Oliveira Pisco, Stephen R. Quake, Julia Salzman, Nir Yosef, Bryan Bulthaup, Phillip Brown, William Harper, Marisa Hemenez, Ravikumar Ponnusamy, Ahmad Salehi, Bhavani A. Sanagavarapu, Eileen Spallino, Waldo Concepcion, Ksenia A. Aaron, James M. Gardner, Burnett Kelly, Nikole Neidlinger, Zifa Wang, Sheela Crasta, Saroja Kolluru, Maurizio Morri, Serena Y. Tan, Kyle J. Travaglini, Chenling Xu, Marcela Alcantara-Hernandez, Nicole Almanzar, Jane Antony, Benjamin Beyersdorf, Deviana Burhan, Kruti Calcuttawala, Matthew M. Carter, Charles K. F. Chan, Charles A. Chang, Stephen Chang, Alex Colville, Rebecca N. Culver, Gaetano D'Amato, Camille Ezran, Francisco X. Galdos, Astrid Gillich, William R. Goodyer, Yan Hang, Alyssa Hayashi, Sahar Houshdaran, Xianxi Huang, Juan C. Irwin, SoRi Jang, Julia Vallve Juanico, Aaron M. Kershner, Soochi Kim, Bernhard Kiss, William Kong, Maya E. Kumar, Angera H. Kuo, Rebecca Leylek, Baoxiang Li, Gabriel B. Loeb, Wan-Jin Lu, Sruthi Mantri, Maxim Markovic, Patrick L. McAlpine, Antoine de Morree, Karim Mrouj, Shravani Mukherjee, Tyler Muser, Patrick Neuhofer, Thi D. Nguyen, Kimberly Perez, Ragini Phansalkar, Nazan Puluca, Zhen Qi, Poorvi Rao, Hayley Raquer-McKay, Nicholas Schaum, Bronwyn Scott, Bobak Seddighzadeh, Joe Segal, Sushmita Sen, Shaheen Sikandar, Sean P. Spencer, Lea C. Steffes, Varun R. Subramaniam, Aditi Swarup, Michael Swift, Will Van Treuren, Emily Trimm, Stefan Veizades, Sivakamasundari Vijayakumar, Kim Chi Vo, Sevahn K. Vorperian, Wanxin Wang, Hannah N. W. Weinstein, Juliane Winkler, Timothy T. H. Wu, Jamie Xie, Andrea R. Yung, Yue Zhang, Angela M. Detweiler, Honey Mekonen, Norma F. Neff, Rene Sit, Michelle Tan, Jia Yan, Gregory R. Bean, Vivek Charu, Erna Forgo, Brock A. Martin, Michael G. Ozawa, Oscar Silva, Angus Toland, Venkata N. P. Vemuri, Shaked Afik, Kyle Awayan, Olga Borisovna Botvinnik, Ashley Byrne, Michelle Chen, Roozbeh Dehghannasiri, Adam Gayoso, Alejandro A. Granados, Qiqing Li, Gita Mahmoudabadi, Aaron McGeever, Julia Eve Olivieri, Madeline Park, Neha Ravikumar, Geoff Stanley, Weilun Tan, Alexander J. Tarashansky, Rohan Vanheusden, Peter Wang, Sheng Wang, Galen Xing, Rebecca Culver, Les Dethlefsen, Po-Yi Ho, Shixuan Liu, Jonathan S. Maltzman, Ross J. Metzger, Koki Sasagawa, Rahul Sinha, Hanbing Song, Bruce Wang, Steven E. Artandi, Philip A. Beachy, Michael F. Clarke, Linda C. Giudice, Franklin W. Huang, Kerwyn Casey Huang, Juliana Idoyaga, Seung K. Kim, Mark Krasnow, Christin S. Kuo, Patricia Nguyen, Thomas A. Rando, Kristy Red-Horse, Jeremy Reiter, David A. Relman, Justin L. Sonnenburg, Albert Wu, Sean M. Wu, Tony Wyss-Coray
Summary: The molecular characterization of cell types using single-cell transcriptome sequencing has led to a revolution in cell biology and provided new insights into the physiology of human organs. In this study, a human reference atlas was created, consisting of nearly 500,000 cells from 24 different tissues and organs, allowing for the molecular characterization of over 400 cell types, their tissue distribution, and tissue-specific variation in gene expression. By using multiple tissues from the same donor, the clonal distribution of T cells, tissue-specific mutation rate in B cells, and the analysis of cell cycle state and proliferative potential of shared cell types across tissues were identified. Additionally, cell type-specific RNA splicing was discovered and analyzed within an individual.
Article
Cell Biology
Gembu Maryu, Qiong Yang
Summary: The nucleocytoplasmic compartmentalization significantly modulates the spatiotemporal dynamics of Cdk1, which is important for the oscillation robustness of the cell cycle. Nucleus-absent cells display highly tunable frequency while nucleus-present cells maintain constant frequency against variations in cyclin B1. The biphasic activation of Cdk1 and the spatial compartmentalization may coordinate the accurate ordering of different downstream events.