Review
Physics, Multidisciplinary
Ying Tang, Alexander Hoffmann
Summary: In this review, we explore the use of information-theoretic approaches to quantify information transmission by signaling pathways. We also discuss how recent advances in machine learning have helped address the challenges posed by complex temporal trajectory datasets, leading to a better understanding of how cells employ temporal coding to adapt to environmental perturbations.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Review
Plant Sciences
Claudia Allan, Richard J. Morris, Claudia-Nicole Meisrimler
Summary: This review discusses recent technological advances and computational frameworks for studying the specificity of calcium signaling in plant cells. Calcium plays a role in signal and information transmission in all eukaryotes, and there are various mechanisms and proteins involved in the encoding, transmission, and decoding of calcium signals. Recent developments in imaging technology and genetically encoded sensors have provided new insights into intra- and intercellular calcium signaling. The review highlights the current gaps in understanding and proposes techniques and approaches for unraveling the underlying mechanisms.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Cell Biology
Johannes Nicolaus Wibisana, Mariko Okada
Summary: The NF-kB signaling pathway plays a crucial role in cellular responses to environmental factors. This pathway encodes and decodes extracellular information through complex regulatory mechanisms and nuclear dynamics of the NF-kB transcription factor, resulting in distinct transcriptional responses. This review summarizes recent advances in understanding how cells encode and decode different environmental stimuli, as well as the important analytical techniques used in NF-kB research.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Xiangzhen Zan, Ranze Xie, Xiangyu Yao, Peng Xu, Wenbin Liu
Summary: Synthetic DNA is considered as a potential medium for digital data storage, but the errors in read sequences remain a challenge. Inspired by modulation techniques, a new DNA storage architecture is proposed to modulate binary data into DNA sequences with the same AT/GC patterns, making it easier to detect errors. Experiments show that modulation encoding complies with biological constraints and can correct up to 40% of errors.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Physics, Multidisciplinary
Jean L. L. Rintoul, Esra Neufeld, Chris Butler, Robin O. O. Cleveland, Nir Grossman
Summary: In this study, it is discovered that heterodyning occurs between acoustic and electric fields in liquid electrolytes. The researchers predicted and experimentally validated this effect and demonstrated the control of electric field distribution and the detection of multi-frequency ionic currents at distant focal locations. Acoustoelectric heterodyning could have potential applications in non-invasive biomedical and bioelectronics.
COMMUNICATIONS PHYSICS
(2023)
Article
Automation & Control Systems
Wei Chen, Zidong Wang, Jun Hu, Guo-Ping Liu
Summary: This article investigates the differentially private average consensus problem for multiagent systems with quantized communication. A logarithmic dynamic encoding-decoding scheme is developed to eliminate the influence of quantization errors on consensus accuracy. The article establishes a unified framework integrating convergence analysis, accuracy evaluation, and privacy level for the developed DPAC algorithm. Sufficient conditions for the almost sure convergence, convergence accuracy, and privacy level are derived, and simulation results verify the correctness and validity of the algorithm.
IEEE TRANSACTIONS ON CYBERNETICS
(2023)
Article
Multidisciplinary Sciences
Bingchen Che, Wei Zhao, Yanan Liu, Dan Sun, Guangyin Jing, Jintao Bai, Xiqiao Feng, Ce Zhang
Summary: The study reveals that under specific conditions, cells are able to collectively respond to stimulation frequencies higher than their intrinsic values by translating chemical stimulation into dynamic mechanical cues through cell-cell connections and cytoskeleton reorganizations.
Article
Psychology, Experimental
Kazuma Mori
Summary: Research shows that music can evoke emotional responses, with chills and tears being the peak emotional responses. The study examines whether computational acoustic and lyrical features can decode these responses. The results suggest that acoustic features related to early responses and rhythm expectation violations may trigger chills, while the harmonious overlapping of acoustic spectra and sad farewell lyrics may evoke tears.
Article
Computer Science, Hardware & Architecture
Yiping Duan, Qiyuan Du, Xin Fang, Zhipeng Xie, Zhijin Qin, Xiaoming Tao, Chengkang Pan, Guangyi Liu
Summary: This article discusses key technologies for semantic communications, including semantic representation, semantic encoding and decoding, and transmission of semantic information. Existing work on semantic communications is presented, such as sketch graph structure representation of images, semantic reconstruction, and end-to-end semantic communication systems. Challenges in semantic communication systems are identified, and unified semantic representations, semantic codecs, and multiple access techniques are proposed to support the transmission of semantic information. The results of semantic encoding and decoding methods and the coexistence of semantics and bits transmission supported by the non-orthogonal multiple access technique (NOMA) are presented.
Article
Neurosciences
A. Pastore, A. Tomassini, I. Delis, E. Dolfini, L. Fadiga, A. D'Ausilio
Summary: Speech processing involves the interplay between bottom-up and top-down computations. The brain is able to reconstruct articulatory patterns associated with speech production during speech listening, and tongue movements provide unique and synergistic information.
Article
Automation & Control Systems
Bo Jiang, Yuxuan Shen, Hongli Dong, Fei Han, Gongfa Li
Summary: This paper addresses the dynamic event-based recursive filtering problem for a class of time-varying networked systems under the encoding-decoding mechanism. It introduces a dynamic event-triggered protocol and a dynamic-quantization-based encoding-decoding mechanism to save energy consumption and encrypt the transmitted measurements. The paper develops a recursive filtering algorithm to derive a minimal upper bound on the filtering error covariance and analyzes the boundedness of the filtering error in mean square sense.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2022)
Article
Engineering, Electrical & Electronic
Yanbo Liu, Guo Cao, Hao Shi, Yingxiang Hu
Summary: Crowd counting is an important task in intelligent applications, but traditional methods often require large resources and have limited practical applications. In this paper, we propose a lightweight encoding-decoding crowd counting network named Lw-Count, which achieves an optimal trade-off between counting performance and running speed through optimizing the network structure and designing a new loss function.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Jingyuan Li, Wenfang Sun, Xiulong Feng, Gang Xing, Karen M. von Deneen, Wen Wang, Yi Zhang, Guangbin Cui
Summary: The study proposed a DSC-Net model and an image preprocessing method, demonstrating improved performance in thymoma segmentation, enhancing accuracy and efficiency. Experimental results showed the robustness and stability of the DSC-Net model in segmentation of different patients and different types of thymoma classified by the WHO histological classification criteria.
Article
Nanoscience & Nanotechnology
Hao Song, Ran Zhang, Zihan Zhao, Xiuping Wu, Yanjie Zhang, Jinlong Wang, Bing Li
Summary: A multimodal dynamic optical information coding strategy using red, green, and blue (RGB) tricolors has been developed, and the traditional quick response (QR) code mechanism has been integrated into the design of multi-information encrypted RGB tricolor anti-counterfeiting devices.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Dirk Benzinger, Serguei Ovinnikov, Mustafa Khammash
Summary: Cells employ dynamic signaling pathways to decode and process signals for gene regulation. Researchers have developed networked optogenetic pathways to achieve dynamic signal processing functions that mimic cellular information processing. The study shows that dynamic multiplexing significantly increases the information transmission capacity from signal to gene expression state and enables precise multidimensional regulation of metabolic pathways.
Article
Gastroenterology & Hepatology
Veronica Massey, Austin Parrish, Josepmaria Argemi, Montserrat Moreno, Aline Mello, Mar Garcia-Rocha, Jose Altamirano, Gemma Odena, Laurent Dubuquoy, Alexandre Louvet, Carlos Martinez, Anna Adrover, Silvia Affo, Oriol Morales-Ibanez, Pau Sancho-Bru, Cristina Millan, Edilmar Alvarado-Tapias, Dalia Morales-Arraez, Juan Caballeria, Jelena Mann, Sheng Cao, Zhaoli Sun, Vijay Shah, Andrew Cameron, Phillipe Mathurin, Natasha Snider, Candid Villanueva, Timothy R. Morgan, Joan Guinovart, Rajanikanth Vadigepalli, Ramon Bataller
Summary: Metabolomic and transcriptomic analyses revealed extensive reprogramming of glucose metabolism in alcoholic hepatitis, with up-regulated expression of HKDC1 contributing to dysregulation of glucose metabolism. HKDC1 may serve as a novel biomarker and therapeutic target for AH.
Article
Cardiac & Cardiovascular Systems
Peter Hanna, Michael J. Dacey, Jaclyn Brennan, Alison Moss, Shaina Robbins, Sirisha Achanta, Natalia P. Biscola, Mohammed A. Swid, Pradeep S. Rajendran, Shumpei Mori, Joseph E. Hadaya, Elizabeth H. Smith, Stanley G. Peirce, Jin Chen, Leif A. Havton, Zixi (Jack) Cheng, Rajanikanth Vadigepalli, James Schwaber, Robert L. Lux, Igor Efimov, John D. Tompkins, Donald B. Hoover, Jeffrey L. Ardell, Kalyanam Shivkumar
Summary: This study provides an in-depth examination of the innervation of the sinoatrial node by the right atrial ganglionated plexus in porcine and human hearts. It demonstrates the significant phenotypic diversity of neurons in the ganglionated plexus and their role in modulating cardiac function. The findings suggest that intrinsic cardiac neurons play a crucial role in controlling specific regions of the heart and could pave the way for targeted therapies in the future.
CIRCULATION RESEARCH
(2021)
Article
Immunology
Michael Prosniak, Larry A. Harshyne, Jonathan Gorky, Mark T. Curtis, Lawrence C. Kenyon, James S. Schwaber, Aurore Lebrun, Rhonda B. Kean, David W. Andrews, D. Craig Hooper
Summary: Patients with grade III anaplastic astrocytomas (AA) can be categorized into distinct immune bias profiles based on the presence or absence of mutations in isocitrate dehydrogenase (IDH). Two different immune biases were identified in patients with different IDH mutational status, with type 2 bias more common in IDH wild-type AA and type 1 bias more common in patients with IDH1R132H mutation. Additionally, the patient's immune profile was found to be more closely associated with tumor vascular enhancement on imaging rather than IDH mutational status.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Jonathan Gorky, Alison Moss, Marina Balycheva, Rajanikanth Vadigepalli, James S. Schwaber
Summary: The study found that under homeostasis, DMV neuronal states can be organized into distinguishable signal processing units, while remote ischemic preconditioning and chronic cardiac ischemic injury both induce significant shifts in neuronal states, affecting inhibitory inputs and neurosecretory function respectively. This suggests a potential molecular network mechanism in the DMV that integrates neurotransmitter inputs and humoral signals to modulate cardiac health.
Editorial Material
Multidisciplinary Sciences
Rajanikanth Vadigepalli, James S. Schwaber
Review
Behavioral Sciences
Sean J. O'Sullivan, James S. Schwaber
Summary: Alcohol and opioids, despite their distinct effects on mammalian systems, share commonalities in withdrawal syndromes, indicating potential similar addiction mechanisms. Neurovisceral feedback may generate antireward effects for both substances. Gut dysbiosis may contribute to alcohol and opioid withdrawal syndromes by stimulating peripheral and neuroinflammation pathways.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Michelle Gee, Eden Hornung, Alison Moss, Lakshmi Kuttippurathu, James S. Schwaber, Babatunde Ogunnaike, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Eden Hornung, Shaina Robbins, Sirisha Achanta, Ankita Srivastava, Alison Moss, James Schwaber, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Suranjana Gupta, Jessica M. Feldman, Adam J. H. Newton, Lakshmi Kuttippurathu, Alison Moss, James S. Schwaber, Rajanikanth Vadigepalli, William W. Lytton
Meeting Abstract
Biochemistry & Molecular Biology
Sirisha Achanta, Eden Hornung, Alison Moss, James Schwaber, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Ankita Srivastava, Shaina Robbins, Sirisha Achanta, James S. Schwaber, Rajanikanth Vadigepalli
Article
Engineering, Chemical
Michelle M. Gee, Abraham M. Lenhoff, James S. Schwaber, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Summary: This paper developed a computational model that incorporates the intrinsic cardiac nervous system into the computational model of blood pressure regulation. The central and local contributions to the control of heart rate, ventricular functions, and respiratory sinus arrhythmia were studied. The simulations matched the experimental observations and predicted the relative contributions of sensory and motor neuron pathways to heart rate changes. This closed-loop cardiovascular control model is important for evaluating bioelectronic interventions to treat heart failure and renormalize cardiovascular physiology.
Article
Engineering, Chemical
Daniel Cook, Alexandra Manchel, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Summary: Recent experiments on liver homeostatic renewal have found that hepatocyte populations with high replication capacity are primarily responsible for maintaining liver mass. However, the processes controlling liver homeostatic renewal are still unknown. To address this, a mathematical model was developed that describes the interactions of cellular networks underlying liver homeostatic renewal. Simulation results showed that without feedback control, basic homeostatic renewal is not robust and can lead to tissue loss under persistent/repetitive injury. Incorporating putative regulatory interactions in the model improved its robustness, but simulations indicated that repeated injury can still destabilize liver homeostasis over several months, contrasting with the slower decay of liver function observed in epidemiological studies. Further extending the model to include feedback control by liver nonparenchymal cells suggested that achieving robust liver homeostatic renewal requires intrinsic stability in hepatocellular networks combined with feedback control by nonparenchymal cells.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Alexandra Manchel, Radhakrishnan Mahadevan, Ramon Bataller, Jan B. Hoek, Rajanikanth Vadigepalli
Summary: Metabolic pathways in the liver of patients with alcoholic hepatitis vary in activity, with increasing disease severity resulting in sequential dysregulation of solute transport mechanisms underlying the glutathione metabolic pathway. Targeting solute transporters in the glutathione pathway to mimic healthy liver state flux activity may be a potential therapeutic intervention for alcoholic hepatitis.
Review
Physiology
Michelle M. Gee, Eden Hornung, Suranjana Gupta, Adam J. H. Newton, Zixi Jack Cheng, WilliamW. Lytton, Abraham M. Lenhoff, James S. Schwaber, Rajanikanth Vadigepalli
Summary: The vagus nerve plays an important role in brain-heart signaling and is crucial for cardiovascular health. Studying the neural regulation of cardiac function has been challenging due to the complexity of the data and its distribution across different systems. Computational modeling based on molecular-scale and physiological data can provide insights into the fast and slow regulation of the vagus nerve in the cardiovascular system. These insights can guide future experimental research on neuromodulation and cardiovascular health.
EXPERIMENTAL PHYSIOLOGY
(2023)