Article
Biology
Ryan S. Phillips, Hidehiko Koizumi, Yaroslav Molkov, Jonathan E. Rubin, Jeffrey C. Smith
Summary: This study experimentally confirmed the roles of neuronal persistent sodium current (I-NaP) and calcium-activated non-selective cation current (I-CAN) in the respiratory oscillator. The results showed that I-NaP is essential for rhythm generation, while I-CAN plays a crucial role in determining the amplitude of rhythmic output.
Article
Mathematics, Applied
Anna Ivagnes, Giovanni Stabile, Andrea Mola, Traian Iliescu, Gianluigi Rozza
Summary: In this paper, hybrid data-driven ROM closures for fluid flows are proposed. These closures combine two fundamentally different strategies: purely data-driven closures and physically based, eddy viscosity data-driven closures. The hybrid model is applied to investigate a two-dimensional flow past a circular cylinder at Re = 50,000, and the numerical results show that it is more accurate than both the purely data-driven ROM and the eddy viscosity ROM.
APPLIED MATHEMATICS AND COMPUTATION
(2023)
Article
Computer Science, Information Systems
Caetano M. Ranieri, Jhielson M. Pimentel, Marcelo R. Romano, Leonardo A. Elias, Roseli A. F. Romero, Michael A. Lones, Mariana F. P. Araujo, Patricia A. Vargas, Renan C. Moioli
Summary: This study introduces a biophysical computational model based on biological data for investigating the mechanisms of Parkinson's Disease and supporting the development of new therapies. The model successfully simulates spectral features of healthy and Parkinsonian brain data by fitting various parameters using a data-driven approach.
Article
Biochemical Research Methods
Daniele Linaro, Matthew J. Levy, David L. Hunt
Summary: The transformation of synaptic input into action potential output is a fundamental process in cellular computation, which is determined by cellular morphology and the expression profile of ion channels. This study uses high-resolution morphological reconstructions and patch-clamp electrophysiology data to build biophysically detailed models of hippocampal neurons, and successfully matches the firing phenotypes of different cell types by adjusting the expression pattern of ion channel genes.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Neurosciences
Manisha Sinha, Rishikesh Narayanan
Summary: Neurons and glial cells have membranes that express ion channels, transporters, and receptors, which generate voltage fluctuations. The high frequency components of the voltage signal reflect neuronal activity, while the low frequency components, known as the local field potential (LFP), provide information about synaptic inputs. This review emphasizes the importance of considering active dendritic mechanisms in understanding the genesis and location-dependent dynamics of LFPs.
Article
Materials Science, Multidisciplinary
P. Carrara, M. Ortiz, L. De Lorenzis
Summary: This study extends the model-free data-driven paradigm to rate-dependent fracture and sub-critical fatigue. The problem is formulated by combining governing equations from variational principles with a set of data points encoding fracture constitutive behavior. The solution is found by satisfying meta-stability conditions and minimizing distances based on closest-point projection. Testing involved different setups with various rate-dependent fracture and fatigue models, with or without white noise.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2021)
Article
Engineering, Mechanical
Liang Li, Qian Shao, Yichen Yang, Zengtao Kuang, Wei Yan, Jie Yang, Ahmed Makradi, Heng Hu
Summary: A new method combining computational homogenization and artificial neural network (ANN) is proposed to efficiently construct elastoplastic composites database for data-driven computational mechanics (DDCM). Numerical calculations are performed to collect high-fidelity data on the representative volume element (RVE) of elastoplastic composites, which are then enhanced using ANN. The proposed method shows good accuracy and efficiency in reducing computational cost for database construction in DDCM of composites.
INTERNATIONAL JOURNAL OF MECHANICAL SCIENCES
(2023)
Review
Cardiac & Cardiovascular Systems
Ahmed Qureshi, Gregory Y. H. Lip, David A. Nordsletten, Steven E. Williams, Oleg Aslanidi, Adelaide de Vecchi
Summary: Atrial fibrillation (AF) is a major cause of ischemic stroke, and the left atrial appendage (LAA) is recognized as the primary source of embolism. Current stroke risk stratification methods mainly rely on clinical factors, rather than thrombogenic mechanisms. Cardiac imaging and image-based biophysical modeling have emerged as valuable tools for understanding thrombogenesis. However, neither technique alone is sufficient to fully assess thrombogenicity in AF. Future development integrating cardiac imaging, in-silico modeling, and machine learning approaches may improve personalized stroke risk stratification in AF patients.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Biology
Ruben A. Tikidji-Hamburyan, Gubbi Govindaiah, William Guido, Matthew T. Colonnese
Summary: The developing visual thalamus and cortex refine connectivity by extracting positional information through synaptic plasticity. However, developing synapses and circuits have evolved mechanisms to compensate for detrimental parasitic correlations.
Article
Astronomy & Astrophysics
Takafumi Kaneko, Sung-Hong Park, Kanya Kusano
Summary: Solar flares and plasma eruptions are sudden releases of magnetic energy from the plasma atmosphere, and to better understand the physical mechanisms behind these events, studying three-dimensional magnetic fields from the photosphere up to the corona is crucial. As coronal magnetic fields are unmeasurable directly, a data-driven simulation approach utilizing observational data of photospheric magnetic fields is employed to infer the coronal magnetic fields, leading to a better reproduction of phenomena such as helical flux ropes formation and eruptions.
ASTROPHYSICAL JOURNAL
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Tinsu Pan, M. Allan Thomas, Dershan Luo
Summary: A new automated DDG CT method was developed to address misregistration and tumor motion issues in PET/CT imaging. DDG CT showed greater consistency in selecting end-expiratory phase images compared to the clinical standard of 4D CT. It appeared to be more robust in regions prone to misregistration and tumor motion, and provided improved attenuation correction for DDG PET relative to D4D CT. DDG CT offered the benefits of 4D CT without the need for external device gating, making it a promising tool in PET/CT imaging.
Article
Geochemistry & Geophysics
Renan Rojas-Gomez, Jihyun Yang, Youzuo Lin, James Theiler, Brendt Wohlberg
Summary: Seismic full-waveform inversion is a computational imaging technique that provides detailed estimates of subsurface geophysical properties. This study develops a hybrid computational approach that combines physics-based models with data-driven methodologies to improve inversion accuracy. Validation using synthetic data demonstrates the method's accuracy and generalization ability.
IEEE GEOSCIENCE AND REMOTE SENSING LETTERS
(2022)
Article
Biochemical Research Methods
Sam F. L. Windels, Noel Malod-Dognin, Natasa Przulj
Summary: This study proposes a method to identify cancer pathways based on changes in pathway-pathway relationships. By learning the embedding space of relationships between pathways in a healthy cell, the study predicts genes and pathways involved in cancer, and identifies druggable targets.
Article
Multidisciplinary Sciences
Kshitiz Parihar, Jonathan Nukpezah, Daniel Iwamoto, Paul A. Janmey, Ravi Radhakrishnan
Summary: Biomechanical signals from remodeled extracellular matrix (ECM) promote tumor progression. Cellular communication and interaction between cell-matrix and cell-cell may be influenced by mechanosensitive biogenesis of trafficking vesicles. Through machine learning, a fingerprint of cytoskeleton-related proteins has been identified to accurately characterize cell stiffness in different ECM conditions. The expression of these genes is correlated with patient prognosis across different tumor types. Cortical tension mirrors the changes in cell stiffness with a change in ECM stiffness. A mechanistic biophysical model shows that curvature generation is highly dependent on cortical tension. This study highlights the effect of ECM stiffness, mediated by cortical tension, in modulating vesicle biogenesis.
Review
Chemistry, Multidisciplinary
Robert Pollice, Gabriel dos Passos Gomes, Matteo Aldeghi, Riley J. Hickman, Mario Krenn, Cyrille Lavigne, Michael Lindner-D'Addario, AkshatKumar Nigam, Cher Tian Ser, Zhenpeng Yao, Alan Aspuru-Guzik
Summary: The ongoing revolution in the natural sciences, driven by machine learning and artificial intelligence, has sparked significant interest in the material science community. To address the imminent climate catastrophe and transform to clean energy, the development of new materials is crucial. New materials, such as organic photovoltaics, show great potential in replacing existing materials and opening up new applications.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemical Research Methods
Ryan S. Phillips, Jonathan E. Rubin
PLOS COMPUTATIONAL BIOLOGY
(2019)
Article
Cell Biology
Ellen K. W. Brennan, Shyam Kumar Sudhakar, Izabela Jedrasiak-Cape, Tibin T. John, Omar J. Ahmed
Article
Neurosciences
Karine C. Flor, William H. Barnett, Marlusa Karlen-Amarante, Yaroslav Molkov, Daniel B. Zoccal
JOURNAL OF PHYSIOLOGY-LONDON
(2020)
Article
Physiology
William H. Barnett, Elizaveta M. Latash, Robert A. Capps, Thomas E. Dick, Erica A. Wehrwein, Yaroslav Molkov
JOURNAL OF APPLIED PHYSIOLOGY
(2020)
Article
Multidisciplinary Sciences
E. M. Latash, W. H. Barnett, H. Park, J. M. Rider, A. N. Klishko, B. I. Prilutsky, Y. I. Molkov
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Article
Biology
Ryan S. Phillips, Ian Rosner, Aryn H. Gittis, Jonathan E. Rubin
Article
Neurosciences
Elizaveta M. Latash, Charly Lecomte, Simon M. Danner, Alain Frigon, Ilya A. Rybak, Yaroslav Molkov
FRONTIERS IN NEUROSCIENCE
(2020)
Article
Physiology
William H. Barnett, David M. Baekey, Julian F. R. Paton, Thomas E. Dick, Erica A. Wehrwein, Yaroslav I. Molkov
Summary: Cardio-ventilatory coupling refers to the coordination between heartbeat and respiration, with studies suggesting that the pressure pulse from a heartbeat activates baroreceptors to modulate brainstem expiratory neuron activity and delay inspiration. This study used animal data, human data, and mathematical modeling to support the hypothesis that baroreflex activation controls the onset of inspiration through a neural activation loop, providing insights into the neural substrate mediating this coupling.
EXPERIMENTAL PHYSIOLOGY
(2021)
Article
Biology
Ryan S. Phillips, Jonathan E. Rubin
Summary: Inspiratory breathing rhythms are generated through synchronized neuronal activity in the preBotzinger complex, with low-amplitude oscillations known as burstlets persisting even at physiological levels. The burstlet theory of respiratory rhythm generation suggests that these subthreshold events contribute to motor output generation. Intracellular calcium dynamics and calcium-activated nonselective cationic current play crucial roles in recruiting rhythmic and non-rhythmic components of the preBotzinger complex for rhythm generation and motor output recruitment.
Article
Neurosciences
Nicholas J. Burgraff, Ryan S. Phillips, Liza J. Severs, Nicholas E. Bush, Nathan A. Baertsch, Jan -Marino Ramirez
Summary: The Ih current is important for maintaining the stability of respiratory rhythmogenesis and protecting breathing against perturbations. Loss of Ih slows down the inspiratory rhythm and destabilizes rhythm generation. Additionally, loss of Ih increases the susceptibility of breathing to opioid-induced respiratory depression and weakened excitatory synaptic interactions.
JOURNAL OF NEUROPHYSIOLOGY
(2022)
Article
Biology
Ryan S. Phillips, Hidehiko Koizumi, Yaroslav Molkov, Jonathan E. Rubin, Jeffrey C. Smith
Summary: This study experimentally confirmed the roles of neuronal persistent sodium current (I-NaP) and calcium-activated non-selective cation current (I-CAN) in the respiratory oscillator. The results showed that I-NaP is essential for rhythm generation, while I-CAN plays a crucial role in determining the amplitude of rhythmic output.
Article
Multidisciplinary Sciences
Dmitry V. Zaretsky, Maria V. Zaretskaia, Yaroslav I. Molkov
Summary: Senile plaques, composed mainly of beta-amyloid peptide, are the main characteristic of Alzheimer's disease. The concentration of soluble beta-amyloid-42 in cerebrospinal fluid and the density of amyloid deposits are strongly negatively correlated. However, Alzheimer's disease patients have lower levels of soluble beta-amyloid-42 in cerebrospinal fluid compared to individuals with normal cognition. The goal of this study was to infer deviations of beta-amyloid-42 metabolism parameters that underlie this difference using data from the Alzheimer's Disease Neuroimaging Initiative cohort.
Article
Neurosciences
S. R. John, W. H. Barnett, A. P. L. Abdala, D. B. Zoccal, J. E. Rubin, Y. I. Molkov
Summary: The Kolliker-Fuse nucleus (KF) plays a crucial role in both normal breathing and respiratory abnormalities, such as those seen in Rett syndrome. However, little is known about the dynamics of KF neurons and their synaptic connections. In this study, computational models were used to investigate the activity of KF and its interactions with other components of the respiratory neural circuitry. Two models were developed to simulate normal breathing and breathing abnormalities, and their properties were found to be consistent with experimental observations. These findings provide insights into the dynamics and local network interactions of KF, and offer predictions for future experimental testing.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
