Miracle-dz/UniFAR-FTUs huggingface dataset:
DandelionTouch: High Fidelity Haptic Rendering of Soft Objects in VR by a Swarm of Drones

To achieve high fidelity haptic rendering of soft objects in a high mobility virtual environment, we propose a novel haptic display DandelionTouch. The tactile actuators are delivered to the fingertips of the user by a swarm of drones. Users of DandelionTouch are capable of experiencing tactile feedback in a large space that is not limited by the device’s working area. Importantly, they will not experience muscle fatigue during long interactions with virtual objects. Hand tracking and swarm control algorithm allow guiding the swarm with hand motions and avoid collisions inside the formation.Several topologies of impedance connection between swarm units were investigated in this research. The experiment, in which drones performed a point following task on a square trajectory in real-time, revealed that drones connected in a Star topology performed the trajectory with low mean positional error (RMSE decreased by 20.6% in comparison with other impedance topologies and by 40.9% in comparison with potential field-based swarm control). The achieved velocities of the drones in all formations with impedance behavior were 28% higher than for the swarm controlled with the potential field algorithm.Additionally, the perception of several vibrotactile patterns was evaluated in a user study with 7 participants. The study has shown that the proposed combination of temporal delay and frequency modulation allows users to successfully recognize the surface property and motion direction in VR simultaneously (mean recognition rate of 70%, maximum of 93%). Dandelion-Touch suggests a new type of haptic feedback in VR systems where no hand-held or wearable interface is required.
HyperPalm: DNN-based hand gesture recognition interface for intelligent communication with quadruped robot in 3D space

Nowadays, autonomous mobile robots support people in many areas where human presence either redundant or too dangerous. They have successfully proven themselves in expeditions, gas industry, mines, warehouses, etc. However, even legged robots may stuck in rough terrain conditions requiring human cognitive abilities to navigate the system. While gamepads and keyboards are convenient for wheeled robot control, the quadruped robot in 3D space can move along all linear coordinates and Euler angles, requiring at least 12 buttons for independent control of their DoF. Therefore, more convenient interfaces of control are required.In this paper we present HyperPalm: a novel gesture interface for intuitive human-robot interaction with quadruped robots. Without additional devices, the operator has full position and orientation control of the quadruped robot in 3D space through hand gesture recognition with only 5 gestures and 6 DoF hand motion.The experimental results revealed to classify 5 static gestures with high accuracy (96.5%), accurately predict the position of the 6D position of the hand in three-dimensional space. The absolute linear deviation Root mean square deviation (RMSD) of the proposed approach is 11.7 mm, which is almost 50% lower than for the second tested approach, the absolute angular deviation RMSD of the proposed approach is 2.6 degrees, which is almost 27% lower than for the second tested approach. Moreover, the user study was conducted to explore user’s subjective experience from human-robot interaction through the proposed gesture interface. The participants evaluated their interaction with HyperPalm as intuitive (2.0), not causing frustration (2.63), and requiring low physical demand (2.0).
Asynchronous Actor-Critic for Multi-Agent Reinforcement Learning

Synchronizing decisions across multiple agents in realistic settings is problematic since it requires agents to wait for other agents to terminate and communicate about termination reliably. Ideally, agents should learn and execute asynchronously instead. Such asynchronous methods also allow temporally extended actions that can take different amounts of time based on the situation and action executed. Unfortunately, current policy gradient methods are not applicable in asynchronous settings, as they assume that agents synchronously reason about action selection at every time step. To allow asynchronous learning and decision-making, we formulate a set of asynchronous multi-agent actor-critic methods that allow agents to directly optimize asynchronous policies in three standard training paradigms: decentralized learning, centralized learning, and centralized training for decentralized execution. Empirical results (in simulation and hardware) in a variety of realistic domains demonstrate the superiority of our approaches in large multi-agent problems and validate the effectiveness of our algorithms for learning high-quality and asynchronous solutions.
Application of the Chimera overlapped grid scheme to simulation of Space Shuttle ascent flows

Several issues relating to the application of Chimera overlapped grids to complex geometries and flowfields are discussed. These include the addition of geometric components with different grid topologies, gridding for intersecting pieces of geometry, and turbulence modeling in grid overlap regions. Sample results are presented for transonic flow about the Space Shuttle launch vehicle. Comparisons with wind tunnel and flight measured pressures are shown.
A T1R-independent mechanism for responses to hyperosmotic sugars involves a carbonic anhydrase-sensitive mechanism in Type III receptor cells

Recent findings from our laboratory demonstrated that the rostral nucleus of solitary tract (rNST) retains some responsiveness to glutamate (MSG+amiloride-MSGa) and sugars in mice lacking the canonical T1R receptors for these tastants. Here, we recorded from the parabrachial nucleus (PBN) in mice lacking the T1R1+T1R3 heterodimer (KO1+3), using warm stimuli to optimize sugar responses and employing extended concentrations and pharmacological agents to probe mechanisms. MSGa+IMP responses were not synergized in KO1+3 mice but responses to MSGa were similar to those in B6 (WT) mice. Glutamate responses in the neurons tested were unaffected by topical application of an mGluR4 antagonist. PBN T1R-independent sugar responses, including those to concentrated glucose, were more evident than in rNST. Sugar responses were undiminished by phlorizin, an inhibitor of SGLT, a component of a hypothesized alternative glucose-sensing mechanism. There were no sugar/umami “best” neurons in KO1+3 mice, and instead, sugars activated cells that displayed acid and amiloride-insensitive NaCl responses. In WTs, concentrated sugars activated “sugar/umami” cells but also electrolyte-sensitive neurons. The efficacy of hyperosmotic sugars for driving neurons broadly responsive to electrolytes implied an origin from Type III taste bud cells. To test this, we used the carbonic anhydrase (CA) inhibitor dorzolamide (DRZ), previously shown to inhibit amiloride-insensitive sodium responses arising from Type III cells. Dorzolamide had no effect on sugarelicited responses in WT sugar/umami PBN neurons but strongly suppressed them in WT and KO electrolyte-generalist neurons. These findings suggest a novel T1R-independent mechanism for hyperosmotic sugars, involving a CA-dependent mechanism in Type-III taste bud cells. Significance Statement Since the discovery of the Tas1r gene family that encodes receptors that lead to sweet and umami taste perception two decades ago, evidence has accrued that mice lacking these receptors maintain some degree of behavioral, physiological, and neural responsiveness to sugars and monosodium glutamate. But the basis for the remaining sensitivity to these nutritionally relevant compounds has remained elusive. Here we recorded from parabrachial nucleus taste neurons. Glutamate responses in mice lacking T1R1+T1R3 were unaffected by oral treatment of mGluR4 receptor antagonist suggesting that some T1R-independent glutamate responses are mediated by a different transduction pathway. Moreover, we identified a novel basis for T1R-independent responsiveness to hyperosmotic sugars that relies on carbonic anhydrase-mediated mechanism found in Type III taste bud cells.
Single and multi-trait genomic prediction for agronomic traits in Euterpe edulis

Popularly known as juçaizeiro, Euterpe edulis has been gaining prominence in the fruit growing sector and has demanded the development of superior genetic materials. As it is a native species and still little studied, the application of more sophisticated techniques can result in higher gains with less time. Until now, there are no studies that apply genomic prediction for this crop, especially in multi-trait analysis. In this sense, this study aimed to apply new methods and breeding techniques for the juçaizeiro, to optimize this breeding program through the application of genomic selection. This data consisted of 275 juçaizeiro genotypes from a population of Rio Novo do Sul-ES, Brazil. The genomic prediction was performed using the multi-trait (G-BLUP MT) and single-trait (G-BLUP ST) models and the selection of superior matrices was based on the selection index of Mulamba and Mock. Similar results for predictive ability were observed for both models. However, the G-BLUP ST model provided greater selection gains when compared to the G-BLUP MT. For this reason, the genomic estimated breeding values (GEBVs) from the G-BLUP ST were used to select the six superior genotypes (UFES.A.RN.390, UFES.A.RN.386, UFES.A.RN.080, UFES.A.RN.383, UFES.S.RN.098, and UFES.S.RN.093), to provide superior genetic materials for the development of seedlings and implantation of productive orchards, which will meet the demands of the productive, industrial and consumer market. Key message In the first genomic selection study for Euterpe edulis, substantial gains for multiple traits of fruit production was reported. This is a key factor for the sustainable use of the species in the Atlantic Forest.
Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are enzymes that produce isomers of cyclic ADPR (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate auto-active Thoeris TIRs and test the converse hypothesis: do prokaryotic Thoeris TIRs also cross-activate plant TIR-immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers, and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3’cADPR. This study demonstrates that the TIR-signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small molecule products.
SLC25A46 localizes to sites of mitochondrial fission and fusion and loss of function variants alter the oligomerization states of MFN2 and OPA1

Mutations in SLC25A46, coding for an outer mitochondrial membrane protein, underlie a wide spectrum of neurodegenerative diseases associated with alterations in mitochondrial morphology, but the precise role of the protein remains unknown. We established an SLC25A46 knock-out cell line in human fibroblasts and studied the pathogenicity of three different variants (p.T142I, p.R257Q, p.E335D) introduced into the null background. Mitochondria were fragmented in the knock-out cell line and hyperfused in all pathogenic variants. The loss of SLC25A46 led to impaired cellular proliferation and striking abnormalities in mitochondrial cristae ultrastructure that were not rescued by expression of the pathogenic variants. SLC25A46 was present in discrete puncta at mitochondrial branch points and at tips of mitochondrial tubules, co-localizing with DRP1 and OPA1. Virtually all fission/fusion events were demarcated by the presence of an SLC25A46 focus. SLC25A46 co-immunoprecipitated with the fusion machinery, and loss of function altered the oligomerization state of OPA1 and MFN2. Proximity interaction mapping identified components of the ER membrane, lipid transfer proteins, and mitochondrial outer membrane proteins indicating that it is present at interorganellar contact sites important for lipid exchange. Consistent with this, SLC25A46 loss of function led to altered mitochondrial lipid composition, suggesting that it may facilitate interorganellar lipid flux or play a role in membrane remodeling associated with mitochondrial fusion and fission.
Temporal asymmetries and interactions between dorsal and ventral visual pathways during object recognition

Despite their anatomical and functional distinctions, there is growing evidence that the dorsal and ventral visual pathways interact to support object recognition. However, the exact nature of these interactions remains poorly understood. Is the presence of identity-relevant object information in the dorsal pathway simply a byproduct of ventral input? Or, might the dorsal pathway be a source of input to the ventral pathway for object recognition? In the current study, we used high-density EEG – a technique with high temporal precision and spatial resolution sufficient to distinguish parietal and temporal lobes – to characterize the dynamics of dorsal and ventral pathways during object viewing. Using multivariate analyses, we found that category decoding in the dorsal pathway preceded that in the ventral pathway. Importantly, the dorsal pathway predicted the multivariate responses of the ventral pathway in a time-dependent manner, rather than the other way around. Together, these findings suggest that the dorsal pathway is a critical source of input to the ventral pathway for object recognition.
All-Aqueous Printing of Viscoelastic Droplets in Yield-Stress Fluids

All-aqueous printing of viscoelastic droplets (aaPVD) in yield-stress fluids is the core of an emerging voxelated bioprinting technology that enables the digital assembly of spherical bio-ink particles (DASP) to create functional tissue mimics. However, the mechanism of aaPVD is largely unknown. Here, by quantifying the dynamics of the whole printing process in real-time, we identify two parameters critical to aaPVD: (1) acceleration of print nozzle, and (2) droplet/nozzle diameter ratio. Moreover, we distinguish three stages associated with aaPVD: droplet generation, detachment, and relaxation. To generate a droplet of good roundness, the ink should be a highly viscous shear-thinning fluid. Using particle image velocimetry and scaling theory, we establish a universal description for the droplet displacements at various printing conditions. Along the direction of nozzle movement, the droplet displacement is determined by the detachment number, a dimensionless parameter defined as the ratio between the dragging force from the nozzle and the confinement force from the supporting matrix. Perpendicular to the direction of nozzle movement, the droplet displacement is determined by the Oldroyd number, a dimensionless parameter that describes the yielded area of the supporting matrix near the print nozzle. For a relaxed droplet, the droplet tail length is independent of droplet/nozzle diameter ratio but determined by the nozzle acceleration. We conclude that printing droplets of good fidelity requires a relatively large droplet/nozzle diameter ratio and intermediate nozzle accelerations. These ensure that the droplet is more solid-like to not flow with the nozzle to form a tadpole-like morphology and that the confinement force from the yield-stress fluid is large enough to prevent large droplet displacement. Our results provide the knowledge and tools for in situ generating and depositing highly viscoelastic droplets of good roundness at prescribed locations in 3D space, which help establish the foundational science for voxelated bioprinting. Statement of Significance Analogues of pixels to two-dimensional (2D) pictures, voxels – in the form of small cubes or spheres – are the basic units of three-dimensional (3D) objects. All-aqueous printing of viscoelastic droplets (aaPVD) is the core of voxelated bioprinting, an emerging technology that uses spherical bio-ink voxels as building blocks to create 3D tissue mimics. By quantifying the dynamics of the whole printing process in real-time, we distinguish the stages associated with aaPVD, identify parameters critical to aaPVD, and develop a universal understanding for in situ generating and depositing viscoelastic droplets of good roundness at prescribed locations in 3D space. Our results help establish the foundational science for voxelated bioprinting and provide a general approach for precisely manipulating viscoelastic voxels in 3D space.
Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials

Pseudoknots are key structure motifs of RNA and pseudoknotted RNAs play important roles in a variety of biological processes. Here, we present KnotFold, an accurate approach to the prediction of RNA secondary structure including pseudoknots. The key elements of Knot-Fold include a learned potential function and a minimum-cost flow algorithm to find the secondary structure with the lowest potential. KnotFold learns the potential from the RNAs with known structures using a self-attention-based neural network, thus avoiding the inaccuracy of hand-crafted energy functions. The specially-designed minimum-cost flow algorithm used by KnotFold considers all possible combinations of base pairs and selects from them the optimal combination. The algorithm breaks the restriction of nested base pairs required by the widely-used dynamic programming algorithms, thus facilitating the identification of pseudoknots. Using a total of 1605 RNAs as representatives, we demonstrate the successful application of KnotFold in predicting RNA secondary structures including pseudoknots with accuracy significantly higher than the state-of-the-art approaches. We anticipate that KnotFold, with its superior accuracy, will greatly facilitate the understanding of RNA structures and functionalities.
Genotypic variation in tolerance to salinity in Pakistani okra (Abelmoschus esculentus L.) varieties as assessed at seed germination, seedling growth and biochemical characters

Salt stress is one of the major abiotic stresses that causes reduction in crops yield. Okra (Abelmoschus esculentus L.) is a high-value nutraceutical vegetable because its various parts are used for different purposes. This study was conducted to calculate the salt tolerance among thirteen okra varieties. Different salt (NaCl) levels: 0, 50, 75 and 100 mM were selected to measure the response of the okra varieties to stress. The experimental data showed that all varieties were affected by salt level with a differential variation in their stress response, demonstrating the presence of genetic variability. Five varieties: “NAYAB-F1”, “Arka anamika”, “MALAV-27”, “Sarhad Green” and 051-F1 showed germination at all stress levels (0, 50, 75 and 100 mM), six varieties: “Feveeri Green”, “Punjab Selection”, “Local Multani”, “Shehzadi”, “Green Star” and “Hunza” showed germination at (0, 50 and 75 mM) and two: “Anmol” and “Sabz Pari” showed germination at (0 and 50 mM). As a result of salt stress, germination percentage (PG), leaf fresh and dry weight (LFW and LDW), shoot fresh and dry weight (SFW and SDW), root fresh and dry weight (RFW and RDW) were significantly reduced with increasing stress level. Based on the performance of variety to salt stress, five varieties were selected for biochemical analysis, concentrating on the determination of osmolytes. The values of sugar and proline were affected both by the varieties and salt levels. Variety “NAYAB-F1” showed higher sugar and proline content at all stress levels compared to varieties “Arka anamika”, “MALAV-27”, “051-F1” and Sarhad Green. Correspondingly, in the stressed seedling a decreasing trend in chlorophyll “a” and “b” were noted depending on the varieties and stress concentrations. After a series of experiment, it has been concluded that varieties “NAYAB-F1”, “Arka anamika”, “MALAV-27”, “Sarhad Green” and “051-F1” were recommended as salt tolerant varieties and could be utilized in the breeding program of salt tolerant okra.
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome

The analysis integrating immunoinformatics data mining models with large volumes of high-quality HLA-DQ specific immunopeptidomics data reveals trans-only HLA-DQ variants have a limited to no contribution to the overall HLA-DQ immunopeptidome. Human leukocyte antigen (HLA) class II antigen presentation is key for controlling and triggering T cell immune responses. HLA-DQ molecules, which are believed to play a major role in autoimmune diseases, are heterodimers that can be formed as both cis and trans variants depending on whether the α- and β-chains are encoded on the same (cis) or opposite (trans) chromosomes. So far, limited progress has been made for predicting HLA-DQ antigen presentation. In addition, the contribution of trans-only variants (i.e. variants not observed in the population as cis) in shaping the HLA-DQ immunopeptidome remains largely unresolved. Here, we seek to address these issues by integrating state-of-the-art immunoinformatics data mining models with large volumes of high-quality HLA-DQ specific mass spectrometry immunopeptidomics data. The analysis demonstrates highly improved predictive power and molecular coverage for models trained including these novel HLA-DQ data. More importantly, investigating the role of trans-only HLA-DQ variants reveals a limited to no contribution to the overall HLA-DQ immunopeptidome. In conclusion, this study furthers our understanding of HLA-DQ specificities and casts light on the relative role of cis versus trans-only HLA-DQ variants in the HLA class II antigen presentation space. The developed method, NetMHCIIpan-4.2, is available at https://services.healthtech. dtu.dk/services/NetMHCIIpan-4.2 .