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1. Fused ultrasound and electromyography-driven neuromuscular model to improve plantarflexion moment prediction across walking speeds

   https://doi.org/10.1186/s12984-022-01061-z  

   Zhang, Qiang ; Fragnito, Natalie ; Franz, Jason R. ; Sharma, Nitin ( August 2022 , Journal of NeuroEngineering and Rehabilitation)

   Improving the prediction ability of a human-machine interface (HMI) is critical to accomplish a bio-inspired or model-based control strategy for rehabilitation interventions, which are of increased interest to assist limb function post neurological injuries. A fundamental role of the HMI is to accurately predict human intent by mapping signals from a mechanical sensor or surface electromyography (sEMG) sensor. These sensors are limited to measuring the resulting limb force or movement or the neural signal evoking the force. As the intermediate mapping in the HMI also depends on muscle contractility, a motivation exists to include architectural features of the muscle as surrogates of dynamic muscle movement, thus further improving the HMI’s prediction accuracy.

   The purpose of this study is to investigate a non-invasive sEMG and ultrasound (US) imaging-driven Hill-type neuromuscular model (HNM) for net ankle joint plantarflexion moment prediction. We hypothesize that the fusion of signals from sEMG and US imaging results in a more accurate net plantarflexion moment prediction than sole sEMG or US imaging.

   Ten young non-disabled participants walked on a treadmill at speeds of 0.50, 0.75, 1.00, 1.25, and 1.50 m/s. The proposed HNM consists of two muscle-tendon units. The muscle activation for each unit was calculated as a weighted summation of the normalized sEMG signal and normalized muscle thickness signal from US imaging. The HNM calibration was performed under both single-speed mode and inter-speed mode, and then the calibrated HNM was validated across all walking speeds.

   On average, the normalized moment prediction root mean square error was reduced by 14.58 % ($$p=0.012$$$p=0.012$) and 36.79 % ($$p<0.001$$$p<0.001$) with the proposed HNM when compared to sEMG-driven and US imaging-driven HNMs, respectively. Also, the calibrated models with data from the inter-speed mode were more robust than those from single-speed modes for the moment prediction.

   The proposed sEMG-US imaging-driven HNM can significantly improve the net plantarflexion moment prediction accuracy across multiple walking speeds. The findings imply that the proposed HNM can be potentially used in bio-inspired control strategies for rehabilitative devices due to its superior prediction.

    

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2. Nontrivial nanostructure, stress relaxation mechanisms, and crystallography for pressure-induced Si-I → Si-II phase transformation

   https://doi.org/10.1038/s41467-022-28604-1  

   Chen, Hao ; Levitas, Valery I. ; Popov, Dmitry ; Velisavljevic, Nenad ( February 2022 , Nature Communications)

   Crystallographic theory based on energy minimization suggests austenite-twinned martensite interfaces with specific orientation, which are confirmed experimentally for various materials. Pressure-induced phase transformation (PT) from semiconducting Si-I to metallic Si-II, due to very large and anisotropic transformation strain, may challenge this theory. Here, unexpected nanostructure evolution during Si-I → Si-II PT is revealed by combining molecular dynamics (MD), crystallographic theory, generalized for strained crystals, and in situ real-time Laue X-ray diffraction (XRD). Twinned Si-II, consisting of two martensitic variants, and unexpected nanobands, consisting of alternating strongly deformed and rotated residual Si-I and third variant of Si-II, form$$\{111\}$$$\left\{111\right\}$interface with Si-I and produce almost self-accommodated nanostructure despite the large transformation volumetric strain of$$-0.237$$$-0.237$. The interfacial bands arrest the$$\{111\}$$$\left\{111\right\}$interfaces, leading to repeating nucleation-growth-arrest process and to growth by propagating$$\{110\}$$$\left\{110\right\}$interface, which (as well as$$\{111\}$$$\left\{111\right\}$interface) do not appear in traditional crystallographic theory.

    

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3. APA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data

   https://doi.org/10.1186/s12859-022-04939-w  

   Fahmi, Naima Ahmed ; Ahmed, Khandakar Tanvir ; Chang, Jae-Woong ; Nassereddeen, Heba ; Fan, Deliang ; Yong, Jeongsik ; Zhang, Wei ( September 2022 , BMC Bioinformatics)

   The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcripts with shorter or longer 3′-UTR. Often, 3′-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3′-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3′-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3′-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3′-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations.

   APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3′-UTR transcripts in the RNA-seq data. APA-Scan works in three major steps: (i) calculate the read coverage of the 3′-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3′-UTR annotation and read coverage on the 3′-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user’s manual are freely available athttps://github.com/compbiolabucf/APA-Scan.

   APA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3′-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3′-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3′-UTR APA events and improve genome annotation.

   APA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3′-UTR APA events. The pipeline integrates both RNA-seq and 3′-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.

    

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4. Dimension reduction through gamma convergence for general prestrained thin elastic sheets

   https://doi.org/10.1007/s00526-022-02262-z  

   Padilla-Garza, David ( July 2022 , Calculus of Variations and Partial Differential Equations)

   We study thin films with residual strain by analyzing the$$\Gamma -$$$\Gamma -$limit of non-Euclidean elastic energy functionals as the material’s thickness tends to 0. We begin by extending prior results (Bhattacharya et al. in Arch Ration Mech Anal 228: 143–181, 2016); (Agostiniani et al. in ESAIM Control Opt Calculus Var 25: 24, 2019); (Lewicka and Lucic in Commun Pure Appl Math 73: 1880–1932, 2018); (Schmidt in J de Mathématiques Pures et Appliquées 88: 107–122, 2007) , to a wider class of films, whose prestrain depends on both the midplate and the transversal variables. The ansatz for our$$\Gamma -$$$\Gamma -$convergence result uses a specific type of wrinkling, which is built on exotic solutions to the Monge-Ampere equation, constructed via convex integration (Lewicka and Pakzad in Anal PDE 10: 695–727, 2017). We show that the expression for our$$\Gamma -$$$\Gamma -$limit has a natural interpretation in terms of the orthogonal projection of the residual strain onto a suitable subspace. We also show that some type of wrinkling phenomenon is necessary to match the lower bound of the$$\Gamma -$$$\Gamma -$limit in certain circumstances. These results all assume a prestrain of the same order as the thickness; we also discuss why it is natural to focus on that regime by considering what can happen when the prestrain is larger.

    

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5. Anisotropic positive linear and sub-linear magnetoresistivity in the cubic type-II Dirac metal Pd3In7

   https://doi.org/10.1038/s41535-023-00601-7  

   Flessa Savvidou, Aikaterini ; Ptok, Andrzej ; Sharma, G. ; Casas, Brian ; Clark, Judith K. ; Li, Victoria M. ; Shatruk, Michael ; Tewari, Sumanta ; Balicas, Luis ( November 2023 , npj Quantum Materials)

   We report a transport study on Pd₃In₇which displays multiple Dirac type-II nodes in its electronic dispersion. Pd₃In₇is characterized by low residual resistivities and high mobilities, which are consistent with Dirac-like quasiparticles. For an applied magnetic field (μ₀H) having a non-zero component along the electrical current, we find a large, positive, and linear inμ₀Hlongitudinal magnetoresistivity (LMR). The sign of the LMR and its linear dependence deviate from the behavior reported for the chiral-anomaly-driven LMR in Weyl semimetals. Interestingly, such anomalous LMR is consistent with predictions for the role of the anomaly in type-II Weyl semimetals. In contrast, the transverse or conventional magnetoresistivity (CMR for electric fieldsE⊥μ₀H) is large and positive, increasing by 10³−10⁴% as a function ofμ₀Hwhile following an anomalous, angle-dependent power law$${\rho }_{{{{\rm{xx}}}}}\propto {({\mu }_{0}H)}^{n}$$${\rho }_{\mathrm{xx}}\propto {\left({\mu }_{0}H\right)}^n$withn(θ) ≤ 1. The order of magnitude of the CMR, and its anomalous power-law, is explained in terms of uncompensated electron and hole-like Fermi surfaces characterized by anisotropic carrier scattering likely due to the lack of Lorentz invariance.

    

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