GelSight Baby Fin Ray: A Compact, Compliant, Flexible Finger with High-Resolution Tactile Sensing

The synthesis of tactile sensing with compliance is essential to many fields, from agricultural usages like fruit picking, to sustainability practices such as sorting recycling, to the creation of safe home-care robots for the elderly to age with dignity. From tactile sensing, we can discern material properties, recognize textures, and determine softness, while with compliance, we are able to securely and safely interact with the objects and the environment around us. These two abilities can culminate into a useful soft robotic gripper, such as the original GelSight Fin Ray, which is able to grasp a large variety of different objects and also perform a simple household manipulation task: wine glass reorientation. Although the original GelSight Fin Ray solves the problem of interfacing a generally rigid, high-resolution sensor with a soft, compliant structure, we can improve the robustness of the sensor and implement techniques that make such camera-based tactile sensors applicable to a wider variety of soft robot designs. We first integrate flexible mirrors and incorporate the rigid electronic components into the base of the gripper, which greatly improves the compliance of the Fin Ray structure. Then, we synthesize a flexible and high-elongation silicone adhesive-based fluorescent paint, which can provide good quality 2D tactile localization results for our sensor. Finally, we incorporate all of these techniques into a new design: the Baby Fin Ray, which we use to dig through clutter, and perform successful classification of nuts in their shells. The supplementary video can be found here: https://youtu.be/_oD_QFtYTPMComment: Accepted to IEEE Conference of Soft Robotics (RoboSoft) 202

Exoskeleton-covered soft finger with vision-based proprioception and tactile sensing

Soft robots offer significant advantages in adaptability, safety, and dexterity compared to conventional rigid-body robots. However, it is challenging to equip soft robots with accurate proprioception and tactile sensing due to their high flexibility and elasticity. In this work, we describe the development of a vision-based proprioceptive and tactile sensor for soft robots called GelFlex, which is inspired by previous GelSight sensing techniques. More specifically, we develop a novel exoskeleton-covered soft finger with embedded cameras and deep learning methods that enable high-resolution proprioceptive sensing and rich tactile sensing. To do so, we design features along the axial direction of the finger, which enable high-resolution proprioceptive sensing, and incorporate a reflective ink coating on the surface of the finger to enable rich tactile sensing. We design a highly underactuated exoskeleton with a tendon-driven mechanism to actuate the finger. Finally, we assemble 2 of the fingers together to form a robotic gripper and successfully perform a bar stock classification task, which requires both shape and tactile information. We train neural networks for proprioception and shape (box versus cylinder) classification using data from the embedded sensors. The proprioception CNN had over 99\% accuracy on our testing set (all six joint angles were within 1 degree of error) and had an average accumulative distance error of 0.77 mm during live testing, which is better than human finger proprioception. These proposed techniques offer soft robots the high-level ability to simultaneously perceive their proprioceptive state and peripheral environment, providing potential solutions for soft robots to solve everyday manipulation tasks. We believe the methods developed in this work can be widely applied to different designs and applications.Comment: Accepted to ICRA202

Scalable, Simulation-Guided Compliant Tactile Finger Design

Compliant grippers enable robots to work with humans in unstructured environments. In general, these grippers can improve with tactile sensing to estimate the state of objects around them to precisely manipulate objects. However, co-designing compliant structures with high-resolution tactile sensing is a challenging task. We propose a simulation framework for the end-to-end forward design of GelSight Fin Ray sensors. Our simulation framework consists of mechanical simulation using the finite element method (FEM) and optical simulation including physically based rendering (PBR). To simulate the fluorescent paint used in these GelSight Fin Rays, we propose an efficient method that can be directly integrated in PBR. Using the simulation framework, we investigate design choices available in the compliant grippers, namely gel pad shapes, illumination conditions, Fin Ray gripper sizes, and Fin Ray stiffness. This infrastructure enables faster design and prototype time frames of new Fin Ray sensors that have various sensing areas, ranging from 48 mm $\times$ \18 mm to 70 mm $\times$ 35 mm. Given the parameters we choose, we can thus optimize different Fin Ray designs and show their utility in grasping day-to-day objects.Comment: Yuxiang Ma, Arpit Agarwal, and Sandra Q. Liu contributed equally to this work. Project video: https://youtu.be/CnTUTA5cfMw . 7 pages, 11 figures, 2024 IEEE International Conference on Soft Robotics (RoboSoft

Essential Genetic Interactors of SIR2 Required for Spatial Sequestration and Asymmetrical Inheritance of Protein Aggregates

Sir2 is a central regulator of yeast aging and its deficiency increases daughter cell inheritance of stress-and aging-induced misfolded proteins deposited in aggregates and inclusion bodies. Here, by quantifying traits predicted to affect aggregate inheritance in a passive manner, we found that a passive diffusion model cannot explain Sir2-dependent failures in mother-biased segregation of either the small aggregates formed by the misfolded Huntingtin, Htt103Q, disease protein or heat-induced Hsp104-associated aggregates. Instead, we found that the genetic interaction network of SIR2 comprises specific essential genes required for mother-biased segregation including those encoding components of the actin cytoskeleton, the actin-associated myosin V motor protein Myo2, and the actin organization protein calmodulin, Cmd1. Co-staining with Hsp104-GFP demonstrated that misfolded Htt103Q is sequestered into small aggregates, akin to stress foci formed upon heat stress, that fail to coalesce into inclusion bodies. Importantly, these Htt103Q foci, as well as the ATPase-defective Hsp104(Y662A)-associated structures previously shown to be stable stress foci, co-localized with Cmd1 and Myo2-enriched structures and super-resolution 3-D microscopy demonstrated that they are associated with actin cables. Moreover, we found that Hsp42 is required for formation of heat-induced Hsp104(Y662A) foci but not Htt103Q foci suggesting that the routes employed for foci formation are not identical. In addition to genes involved in actin-dependent processes, SIR2-interactors required for asymmetrical inheritance of Htt103Q and heat-induced aggregates encode essential sec genes involved in ER-to-Golgi trafficking/ER homeostasis

Macroscopic transport by synthetic molecular machines

Nature uses molecular motors and machines in virtually every significant biological process, but demonstrating that simpler artificial structures operating through the same gross mechanisms can be interfaced with—and perform physical tasks in—the macroscopic world represents a significant hurdle for molecular nanotechnology. Here we describe a wholly synthetic molecular system that converts an external energy source (light) into biased brownian motion to transport a macroscopic cargo and do measurable work. The millimetre-scale directional transport of a liquid on a surface is achieved by using the biased brownian motion of stimuli-responsive rotaxanes (‘molecular shuttles’) to expose or conceal fluoroalkane residues and thereby modify surface tension. The collective operation of a monolayer of the molecular shuttles is sufficient to power the movement of a microlitre droplet of diiodomethane up a twelve-degree incline.

Dorsal Periaqueductal gray ensembles represent approach and avoidance states

Animals must balance needs to approach threats for risk assessment and to avoid danger. The dorsal periaqueductal gray (dPAG) controls defensive behaviors, but it is unknown how it represents states associated with threat approach and avoidance. We identified a dPAG threatavoidance ensemble in mice that showed higher activity farther from threats such as the open arms of the elevated plus maze and a predator. These cells were also more active during threat avoidance behaviors such as escape and freezing, even though these behaviors have antagonistic motor output. Conversely, the threat approach ensemble was more active during risk assessment behaviors and near threats. Furthermore, unsupervised methods showed that avoidance/approach states were encoded with shared activity patterns across threats. Lastly, the relative number of cells in each ensemble predicted threat avoidance across mice. Thus, dPAG ensembles dynamically encode threat approach and avoidance states, providing a flexible mechanism to balance risk assessment and danger avoidance

Expression of Drug Targets in Patients Treated with Sorafenib, Carboplatin and Paclitaxel

Introduction: Sorafenib, a multitarget kinase inhibitor, targets members of the mitogen-activated protein kinase (MAPK) pathway and VEGFR kinases. Here we assessed the association between expression of sorafenib targets and biomarkers of taxane sensitivity and response to therapy in pre-treatment tumors from patients enrolled in ECOG 2603, a phase III comparing sorafenib, carboplatin and paclitaxel (SCP) to carboplatin, paclitaxel and placebo (CP). Methods: Using a method of automated quantitative analysis (AQUA) of in situ protein expression, we quantified expression of VEGF-R2, VEGF-R1, VEGF-R3, FGF-R1, PDGF-Rβ, c-Kit, B-Raf, C-Raf, MEK1, ERK1/2, STMN1, MAP2, EB1 and Bcl-2 in pretreatment specimens from 263 patients. Results: An association was found between high FGF-R1 and VEGF-R1 and increased progression-free survival (PFS) and overall survival (OS) in our combined cohort (SCP and CP arms). Expression of FGF-R1 and VEGF-R1 was higher in patients who responded to therapy ((CR+PR) vs. (SD+PD+ un-evaluable)). Conclusions: In light of the absence of treatment effect associated with sorafenib, the association found between FGF-R1 and VEGF-R1 expression and OS, PFS and response might reflect a predictive biomarker signature for carboplatin/paclitaxel-based therapy. Seeing that carboplatin and pacitaxel are now widely used for this disease, corroboration in another cohort might enable us to improve the therapeutic ratio of this regimen. © 2013 Jilaveanu et al

A Motif Unique to the Human Dead-Box Protein DDX3 Is Important for Nucleic Acid Binding, ATP Hydrolysis, RNA/DNA Unwinding and HIV-1 Replication

DEAD-box proteins are enzymes endowed with nucleic acid-dependent ATPase, RNA translocase and unwinding activities. The human DEAD-box protein DDX3 has been shown to play important roles in tumor proliferation and viral infections. In particular, DDX3 has been identified as an essential cofactor for HIV-1 replication. Here we characterized a set of DDX3 mutants biochemically with respect to nucleic acid binding, ATPase and helicase activity. In particular, we addressed the functional role of a unique insertion between motifs I and Ia of DDX3 and provide evidence for its implication in nucleic acid binding and HIV-1 replication. We show that human DDX3 lacking this domain binds HIV-1 RNA with lower affinity. Furthermore, a specific peptide ligand for this insertion selected by phage display interferes with HIV-1 replication after transduction into HelaP4 cells. Besides broadening our understanding of the structure-function relationships of this important protein, our results identify a specific domain of DDX3 which may be suited as target for antiviral drugs designed to inhibit cellular cofactors for HIV-1 replication

A Highly Conserved Poc1 Protein Characterized in Embryos of the Hydrozoan Clytia hemisphaerica: Localization and Functional Studies

Poc1 (Protein of Centriole 1) proteins are highly conserved WD40 domain-containing centriole components, well characterized in the alga Chlamydomonas, the ciliated protazoan Tetrahymena, the insect Drosophila and in vertebrate cells including Xenopus and zebrafish embryos. Functions and localizations related to the centriole and ciliary axoneme have been demonstrated for Poc1 in a range of species. The vertebrate Poc1 protein has also been reported to show an additional association with mitochondria, including enrichment in the specialized “germ plasm” region of Xenopus oocytes. We have identified and characterized a highly conserved Poc1 protein in the cnidarian Clytia hemisphaerica. Clytia Poc1 mRNA was found to be strongly expressed in eggs and early embryos, showing a punctate perinuclear localization in young oocytes. Fluorescence-tagged Poc1 proteins expressed in developing embryos showed strong localization to centrioles, including basal bodies. Anti-human Poc1 antibodies decorated mitochondria in Clytia, as reported in human cells, but failed to recognise endogenous or fluorescent-tagged Clytia Poc1. Injection of specific morpholino oligonucleotides into Clytia eggs prior to fertilization to repress Poc1 mRNA translation interfered with cell division from the blastula stage, likely corresponding to when neosynthesis normally takes over from maternally supplied protein. Cell cycle lengthening and arrest were observed, phenotypes consistent with an impaired centriolar biogenesis or function. The specificity of the defects could be demonstrated by injection of synthetic Poc1 mRNA, which restored normal development. We conclude that in Clytia embryos, Poc1 has an essentially centriolar localization and function

The Forkhead Transcription Factor Foxi1 Is a Master Regulator of Vacuolar H+-ATPase Proton Pump Subunits in the Inner Ear, Kidney and Epididymis

The vacuolar H+-ATPase dependent transport of protons across cytoplasmic membranes in FORE (forkhead related) cells of endolymphatic epithelium in the inner ear, intercalated cells of collecting ducts in the kidney and in narrow and clear cells of epididymis require expression of several subunits that assemble into a functional multimeric proton pump. We demonstrate that expression of four such subunits A1, B1, E2 and a4 all co-localize with the forkhead transcription factor Foxi1 in a subset of epithelial cells at these three locations. In cells, of such epithelia, that lack Foxi1 we fail to identify any expression of A1, B1, E2 and a4 demonstrating an important role for the transcription factor Foxi1 in regulating subunit availability. Promoter reporter experiments, electrophoretic mobility shift assays (EMSA) and site directed mutagenesis demonstrate that a Foxi1 expression vector can trans-activate an a4-promoter reporter construct in a dose dependent manner. Furthermore, we demonstrate using chromatin immunoprecipitation (ChIP) assays that Foxi1-dependent activation to a large extent depends on cis-elements at position −561/−547 in the a4 promoter. Thus, we provide evidence that Foxi1 is necessary for expression of at least four subunits in three different epithelia and most likely is a major determinant for proper assembly of a functional vacuolar H+-ATPase complex at these locations