Microstructural analysis of skeletal muscle force generation during aging.

Human aging results in a progressive decline in the active force generation capability of skeletal muscle. While many factors related to the changes of morphological and structural properties in muscle fibers and the extracellular matrix (ECM) have been considered as possible reasons for causing age-related force reduction, it is still not fully understood why the decrease in force generation under eccentric contraction (lengthening) is much less than that under concentric contraction (shortening). Biomechanically, it was observed that connective tissues (endomysium) stiffen as ages, and the volume ratio of connective tissues exhibits an age-related increase. However, limited skeletal muscle models take into account the microstructural characteristics as well as the volume fraction of tissue material. This study aims to provide a numerical investigation in which the muscle fibers and the ECM are explicitly represented to allow quantitative assessment of the age-related force reduction mechanism. To this end, a fiber-level honeycomb-like microstructure is constructed and modeled by a pixel-based Reproducing Kernel Particle Method (RKPM), which allows modeling of smooth transition in biomaterial properties across material interfaces. The numerical investigation reveals that the increased stiffness of the passive materials of muscle tissue reduces the force generation capability under concentric contraction while maintains the force generation capability under eccentric contraction. The proposed RKPM microscopic model provides effective means for the cellular-scale numerical investigation of skeletal muscle physiology. NOVELTY STATEMENT: A cellular-scale honeycomb-like microstructural muscle model constructed from a histological cross-sectional image of muscle is employed to study the causal relations between age-associated microstructural changes and age-related force loss using Reproducing Kernel Particle Method (RKPM). The employed RKPM offers an effective means for modeling biological materials based on pixel points in the medical images and allow modeling of smooth transition in the material properties across interfaces. The proposed microstructure-informed muscle model enables quantitative evaluation on how cellular-scale compositions contribute to muscle functionality and explain differences in age-related force changes during concentric, isometric and eccentric contractions

Neural-Integrated Meshfree (NIM) Method: A differentiable programming-based hybrid solver for computational mechanics

We present the neural-integrated meshfree (NIM) method, a differentiable programming-based hybrid meshfree approach within the field of computational mechanics. NIM seamlessly integrates traditional physics-based meshfree discretization techniques with deep learning architectures. It employs a hybrid approximation scheme, NeuroPU, to effectively represent the solution by combining continuous DNN representations with partition of unity (PU) basis functions associated with the underlying spatial discretization. This neural-numerical hybridization not only enhances the solution representation through functional space decomposition but also reduces both the size of DNN model and the need for spatial gradient computations based on automatic differentiation, leading to a significant improvement in training efficiency. Under the NIM framework, we propose two truly meshfree solvers: the strong form-based NIM (S-NIM) and the local variational form-based NIM (V-NIM). In the S-NIM solver, the strong-form governing equation is directly considered in the loss function, while the V-NIM solver employs a local Petrov-Galerkin approach that allows the construction of variational residuals based on arbitrary overlapping subdomains. This ensures both the satisfaction of underlying physics and the preservation of meshfree property. We perform extensive numerical experiments on both stationary and transient benchmark problems to assess the effectiveness of the proposed NIM methods in terms of accuracy, scalability, generalizability, and convergence properties. Moreover, comparative analysis with other physics-informed machine learning methods demonstrates that NIM, especially V-NIM, significantly enhances both accuracy and efficiency in end-to-end predictive capabilities

A Physics-Constrained Data-Driven Approach Based on Locally Convex Reconstruction for Noisy Database

Physics-constrained data-driven computing is an emerging hybrid approach that integrates universal physical laws with data-driven models of experimental data for scientific computing. A new data-driven simulation approach coupled with a locally convex reconstruction, termed the local convexity data-driven (LCDD) computing, is proposed to enhance accuracy and robustness against noise and outliers in data sets in the data-driven computing. In this approach, for a given state obtained by the physical simulation, the corresponding optimum experimental solution is sought by projecting the state onto the associated local convex manifold reconstructed based on the nearest experimental data. This learning process of local data structure is less sensitive to noisy data and consequently yields better accuracy. A penalty relaxation is also introduced to recast the local learning solver in the context of non-negative least squares that can be solved effectively. The reproducing kernel approximation with stabilized nodal integration is employed for the solution of the physical manifold to allow reduced stress-strain data at the discrete points for enhanced effectiveness in the LCDD learning solver. Due to the inherent manifold learning properties, LCDD performs well for high-dimensional data sets that are relatively sparse in real-world engineering applications. Numerical tests demonstrated that LCDD enhances nearly one order of accuracy compared to the standard distance-minimization data-driven scheme when dealing with noisy database, and a linear exactness is achieved when local stress-strain relation is linear

Physics-informed neural networks of the Saint-Venant equations for downscaling a large-scale river model

Large-scale river models are being refined over coastal regions to improve the scientific understanding of coastal processes, hazards and responses to climate change. However, coarse mesh resolutions and approximations in physical representations of tidal rivers limit the performance of such models at resolving the complex flow dynamics especially near the river-ocean interface, resulting in inaccurate simulations of flood inundation. In this research, we propose a machine learning (ML) framework based on the state-of-the-art physics-informed neural network (PINN) to simulate the downscaled flow at the subgrid scale. First, we demonstrate that PINN is able to assimilate observations of various types and solve the one-dimensional (1-D) Saint-Venant equations (SVE) directly. We perform the flow simulations over a floodplain and along an open channel in several synthetic case studies. The PINN performance is evaluated against analytical solutions and numerical models. Our results indicate that the PINN solutions of water depth have satisfactory accuracy with limited observations assimilated. In the case of flood wave propagation induced by storm surge and tide, a new neural network architecture is proposed based on Fourier feature embeddings that seamlessly encodes the periodic tidal boundary condition in the PINN's formulation. Furthermore, we show that the PINN-based downscaling can produce more reasonable subgrid solutions of the along-channel water depth by assimilating observational data. The PINN solution outperforms the simple linear interpolation in resolving the topography and dynamic flow regimes at the subgrid scale. This study provides a promising path towards improving emulation capabilities in large-scale models to characterize fine-scale coastal processes

A multi-resolution physics-informed recurrent neural network: formulation and application to musculoskeletal systems

Abstract: This work presents a multi-resolution physics-informed recurrent neural network (MR PI-RNN), for simultaneous prediction of musculoskeletal (MSK) motion and parameter identification of the MSK systems. The MSK application was selected as the model problem due to its challenging nature in mapping the high-frequency surface electromyography (sEMG) signals to the low-frequency body joint motion controlled by the MSK and muscle contraction dynamics. The proposed method utilizes the fast wavelet transform to decompose the mixed frequency input sEMG and output joint motion signals into nested multi-resolution signals. The prediction model is subsequently trained on coarser-scale input–output signals using a gated recurrent unit (GRU), and then the trained parameters are transferred to the next level of training with finer-scale signals. These training processes are repeated recursively under a transfer-learning fashion until the full-scale training (i.e., with unfiltered signals) is achieved, while satisfying the underlying dynamic equilibrium. Numerical examples on recorded subject data demonstrate the effectiveness of the proposed framework in generating a physics-informed forward-dynamics surrogate, which yields higher accuracy in motion predictions of elbow flexion–extension of an MSK system compared to the case with single-scale training. The framework is also capable of identifying muscle parameters that are physiologically consistent with the subject’s kinematics data

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD) followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes) and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes) hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.Published versio