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Abstract This article addresses the kinematic control of a redundant soft robotic arm. Full pose kinematic control of soft robots is challenging because direct application of the classical controllers developed based on rigid robots to soft robots could lead to unreliable or infeasible motions. In this study, we explore the manipulability property of a soft robotic arm and develop an advanced resolved-rate controller that prioritizes position over orientation control and switches its modes and gains based on position and orientation manipulabilities, enabling stable motion even when the robot is close to the singular configurations. The simulation and experimental results indicate that our proposed method outperforms previous methods in terms of both accuracy and smoothness during operation. 

Alternative cleavage and polyadenylation within introns (intronic APA) generate shorter mRNA isoforms; however, their physiological significance remains elusive. In this study, we developed a comprehensive workflow to analyze intronic APA profiles using the mammalian target of rapamycin (mTOR)-regulated transcriptome as a model system. Our investigation revealed two contrasting effects within the transcriptome in response to fluctuations in cellular mTOR activity: an increase in intronic APA for a subset of genes and a decrease for another subset of genes. The application of this workflow to RNA-seq data from The Cancer Genome Atlas demonstrated that this dichotomous intronic APA pattern is a consistent feature in transcriptomes across both normal tissues and various cancer types. Notably, our analyses of protein length changes resulting from intronic APA events revealed two distinct phenomena in proteome programming: a loss of functional domains due to significant changes in protein length or minimal alterations in C- terminal protein sequences within unstructured regions. Focusing on conserved intronic APA events across 10 different cancer types highlighted the prevalence of the latter cases in cancer transcriptomes, whereas the former cases were relatively enriched in normal tissue transcriptomes. These observations suggest potential, yet distinct, roles for intronic APA events during pathogenic processes and emphasize the abundance of protein isoforms with similar lengths in the cancer proteome. Furthermore, our investigation into the isoform-specific functions of JMJD6 intronic APA events supported the hypothesis that alterations in unstructured C-terminal protein regions lead to functional differences. Collectively, our findings underscore intronic APA events as a discrete molecular signature present in both normal tissues and cancer transcriptomes, highlighting the contribution of APA to the multifaceted functionality of the cancer proteome. 

Abstract Alternative cleavage and polyadenylation within introns (intronic APA) generate shorter mRNA isoforms; however, their physiological significance remains elusive. In this study, we developed a comprehensive workflow to analyze intronic APA profiles using the mammalian target of rapamycin (mTOR)-regulated transcriptome as a model system. Our investigation revealed two contrasting effects within the transcriptome in response to fluctuations in cellular mTOR activity: an increase in intronic APA for a subset of genes and a decrease for another subset of genes. The application of this workflow to RNA-seq data from The Cancer Genome Atlas demonstrated that this dichotomous intronic APA pattern is a consistent feature in transcriptomes across both normal tissues and various cancer types. Notably, our analyses of protein length changes resulting from intronic APA events revealed two distinct phenomena in proteome programming: a loss of functional domains due to significant changes in protein length or minimal alterations in C-terminal protein sequences within unstructured regions. Focusing on conserved intronic APA events across 10 different cancer types highlighted the prevalence of the latter cases in cancer transcriptomes, whereas the former cases were relatively enriched in normal tissue transcriptomes. These observations suggest potential, yet distinct, roles for intronic APA events during pathogenic processes and emphasize the abundance of protein isoforms with similar lengths in the cancer proteome. Furthermore, our investigation into the isoform-specific functions of JMJD6 intronic APA events supported the hypothesis that alterations in unstructured C-terminal protein regions lead to functional differences. Collectively, our findings underscore intronic APA events as a discrete molecular signature present in both normal tissues and cancer transcriptomes, highlighting the contribution of APA to the multifaceted functionality of the cancer proteome. 

Abstract Soft robots can undergo large elastic deformations and adapt to complex shapes. However, they lack the structural strength to withstand external loads due to the intrinsic compliance of fabrication materials (silicone or rubber). In this paper, we present a novel stiffness modulation approach that controls the robot’s stiffness on-demand without permanently affecting the intrinsic compliance of the elastomeric body. Inspired by concentric tube robots, this approach uses a Nitinol tube as the backbone, which can be slid in and out of the soft robot body to achieve robot pose or stiffness modulation. To validate the proposed idea, we fabricated a tendon-driven concentric tube (TDCT) soft robot and developed the model based on Cosserat rod theory. The model is validated in different scenarios by varying the joint-space tendon input and task-space external contact force. Experimental results indicate that the model is capable of estimating the shape of the TDCT soft robot with an average root-mean-square error (RMSE) of 0.90 (0.56% of total length) mm and average tip error of 1.49 (0.93% of total length) mm. Simulation studies demonstrate that the Nitinol backbone insertion can enhance the kinematic workspace and reduce the compliance of the TDCT soft robot by 57.7%. Two case studies (object manipulation and soft laparoscopic photodynamic therapy) are presented to demonstrate the potential application of the proposed design.