Miracle-dz/UniFAR-FTUs huggingface dataset:
Apparatus, methods and recording medium for imaging a subsurface using the waveform inversion in the laplace-fourier domain

PURPOSE: An apparatus, a method and a recording medium for imaging an underground structure using waveform inversion of a Laplace-Fourier domain are provided to stably obtain a speed model with long wavelength information and middle wavelength information. CONSTITUTION: An apparatus for imaging an underground structure using waveform inversion of a Laplace-Fourier domain includes a receiver and a signal processing unit. The signal processing unit comprises an input unit, a converting unit(202), a modeling data generating unit(203), and a parameter update unit(206). The converting unit converts measurement data in a time domain into measurement data in a Laplace-Fourier domain using an attenuation constant of a complex number. The modeling data generating unit sets an equation including a parameter by receiving a parameter showing a feature of a measurement target region. The modeling data generating unit calculates the equation in the Laplace-Fourier domain to calculate modeling data.
Cell assembly analysis of neural circuits for innate behavior in Drosophila melanogaster using an immediate early gene stripe/egr-1

Significance Immediate early genes are genes whose expression is transiently up-regulated upon neural activity. In this study, we characterized stripe as an immediate early gene in vinegar fly Drosophila melanogaster. Utilizing the transcriptional activity of stripe, we established genetic methods that can activity-dependently label neural circuits. With these methods, we visualized neurons activated when males sexually interact with a female. Also, we enabled induction and inhibition of male sexual behavior in an experience-dependent manner. Furthermore, we demonstrate that neurons activated during two separate time windows can be differentially labeled by combining the detection of Stripe protein expression and activity-dependent transgenic labeling. These approaches provide powerful tools to analyze the cell population involved in instinctive behavior at single-cell resolution in insect brains.
Two-dimensional graphitic metal carbides: structure, stability and electronic properties

Via first-principles computational modeling and calculations, we propose a new class of two-dimensional (2D) atomically thin crystals that contain metal-C3 (MC3) moieties periodically distributed in a graphenic lattice, which we refer to as 2D graphitic metal carbides (g-MCs). Most g-MCs are dynamically stable as verified by the calculated phonon spectra. Our detailed chemical bonding analyzes reveal that the high stability of g-MCs can be attributed to a unique bonding feature, which manifests as the carbon-backbone-mediated metal–metal interactions. These analyzes provide new insights for understanding the stability of 2D materials. It is found that the calculated electronic band gaps and magnetic moments (per unit cell) of g-MCs can range from 0 to 1.30 eV and 0 to 4.40 μ B, respectively. Highly tunable electronic properties imply great potential of 2D g-MCs in various applications. As an example, we show that 2D g-MnC can be an excellent electrocatalyst towards CO2 reductive reaction for the formation of formic acid with an exceptionally high loading of Mn atoms (∼43 wt%). We expect this work to simulate new experiments for fabrication and applications of g-MCs.
Platelet-Derived Exosomes Alleviate Knee Osteoarthritis by Attenuating Cartilage Degeneration and Subchondral Bone Loss

Background: Osteoarthritis (OA) is the most prevalent chronic degenerative joint disease among the aged population. However, current treatments for OA are limited to alleviating symptoms, with no therapies that prevent and regenerate cartilage deterioration. Purpose: To assess the effects of platelet-derived exosomes (Plt-exos) on OA and then to explore the potential molecular mechanism. Study Design: Controlled laboratory study. Methods: Exosomes derived from human apheresis platelets were isolated and identified. The effects of Plt-exos in protecting chondrocytes under interleukin 1β stimulation were evaluated by analyzing the proliferation and migration in human primary chondrocytes. RNA sequencing was later performed in vitro for primary chondrocytes to reveal the underlying mechanisms of Plt-exo treatment. Anterior cruciate ligament transection was used to construct an OA mice model, and intra-articular injection of Plt-exos was given once a week for 6 weeks. Mice were sacrificed 4 weeks after the last injection. Histologic and immunohistochemistry staining and micro–computed tomography analysis were performed to assess alterations of articular cartilage and subchondral bone. Results: Plt-exos significantly promoted proliferation and migration of chondrocytes within a dose-dependent manner, as well as dramatically promoted cartilage regeneration and attenuated abnormal tibial subchondral bone remodeling, thus slowing the progression of OA. After being treated with Plt-exos, 1797 genes were differentially expressed in chondrocytes (923 upregulated and 874 downregulated genes). Functional enrichment results and hub genes were mainly involved in anti-inflammatory effects, mediating cell adhesion, stimulating cartilage repair, promoting anabolism, and inhibiting catabolism. Conclusion: Our results demonstrated that Plt-exos promoted chondrocyte proliferation and migration in vitro, as well as attenuated cartilage degeneration, improved the microarchitecture of subchondral bone, and retarded OA progression in vivo. Clinical Relevance: Our study illustrated that the administered Plt-exos could alleviate knee OA by attenuating cartilage degeneration and subchondral bone loss, possibly serving as a novel promising treatment for OA in the future.
Why fake death? Environmental and genetic control of tonic immobility in larval lacewings (Neuroptera: Chrysopidae)

Abstract Tonic immobility is a passive antipredator strategy employed late in the predation sequence that may decrease individual mortality in prey animals. Here, we investigate how energetic state and genetic predisposition influence antipredator decision-making in green lacewing larvae, Chrysoperla plorabunda (Fitch), using simulated predatory encounters. We demonstrate that tonic immobility is a plastic response influenced by energetic resource limitation. Larvae exposed to 1 or 2 days of food deprivation initiate tonic immobility more often and with less physical provocation than individuals fed ad libitum. Recently molted individuals exposed to food deprivation, the individuals most energetically challenged, engage in tonic immobility at a higher rate than any other group. We also find that variation in antipredator strategy between individuals is partly the result of within-population genetic variation. We estimate the propensity to enter tonic immobility to have a broad-sense heritability of 0.502. Taken together our results suggest that larval lacewings under energetic stress are more likely to engage in tonic immobility. Yet, energetic state does not explain all within-population variation, as individuals can have a genetic predisposition for tonic immobility.
A data-driven machine learning approach for discovering potent LasR inhibitors

ABSTRACT The rampant spread of multidrug-resistant Pseudomonas aeruginosa strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the las quorum sensing (QS) system remains an attractive therapeutic strategy to combat P. aeruginosa infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat P. aeruginosa-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate P. aeruginosa infections.
Transferts et stockages magmatiques au Piton de la Fournaise : approche sismologique et structurale

La sismicite associee a l'activite d'un volcan intraplaque tel que le Piton de la Fournaise se developpe, a priori, sans aucun controle tectonique regional. La complexite des structures internes et le fonctionnement des structures de stockage et de transfert magmatique declenchent une sismicite partiellement recurrente. Cette recurrence de la sismicite s'observe grâce aux formes d'ondes des seismes, quasiment identiques, et temoigne de la reactivation d'une meme source. Notre etude exploite la partie recurrente de la sismicite volcano-tectonique du Piton de la Fournaise entre 2000 et 2008, dans le but d'identifier les sources et de determiner la structure interne du volcan et son fonctionnement. En utilisant les donnees du reseau sismologique de l'Observatoire Volcanologique du Piton de la Fournaise, nous avons regroupe par familles les seismes ayant les memes formes d'ondes. Puis, nous avons mesure des differences de temps de trajet entre les seismes d'une meme famille. Ces derniers sont relocalises par la methode de double difference et leur mecanisme au foyer est determine synthetiquement en conservant l'hypothese de l'activite d'une meme source. Les determinations et les relocalisations sont utilisees pour extraire les orientations du plan de faille et du glissement cosismique de chaque famille. Nous avons ainsi pu cartographier les zones sismogenes et observer leur comportement lors des periodes de preparation des eruptions. Ces observations ont permis de construire un modele descriptif des phenomenes intrusifs sismogenes associes aux eruptions distales du Piton de la Fournaise. Le champ de contraintes induit par chaque objet de ce modele a ete modelise numeriquement en utilisant la methode des elements finis pour verifier la validite du modele descriptif. Notre etude est limitee par la non-exhaustivite des jeux de donnees utilises. Notre methode d'analyse de la sismicite a donc ete combinee a une methode de detection et d'estimation precise des temps d'arrivee des ondes P et S, ce qui a permis d'appliquer les apports de cette these a la surveillance en temps reel des volcans.
Mouse primary follicles experience slow growth rates after activation and progressive increases that influence the duration of the primary follicle phase

Abstract There are conflicting estimates of the duration of mouse primary follicle development. An accurate determination is needed for studies examining preantral follicle survival and mathematical modeling of folliculogenesis. Primary follicle granulosa cell proliferation rates are low and variable, which may explain the variation in duration estimates. In the present study, female C57Bl6/J mice were exposed to bromodeoxyuridine for 48 hours, to label the proliferating granulosa cells in a large proportion of primary follicles. The bromodeoxyuridine-containing water was then withdrawn and replaced with drug-free water and the mice were euthanized at 0, 1, 3, 6, 10, or 13 days post-bromodeoxyuridine withdrawal. Granulosa cells were bromodeoxyuridine labeled in 48% of primary follicles at day 0, but this decreased to 5% over the 13-day period, as the labeled primary follicles progressed to the secondary follicle stage. Curve-fitting estimated that the last of the bromodeoxyuridine-labeled primary follicles would progress to the secondary stage by 13.7 days. Mathematical models that assumed constant rates of primary follicle proliferation were fitted to the data, but the observed pattern of bromodeoxyuridine-labeled primary follicle disappearance could not be replicated. The level of immunoreactivity for bromodeoxyuridine and proliferating-cell nuclear antigen in primary follicles revealed follicles with no granulosa cell proliferation during the 48-h bromodeoxyuridine-exposure period had resumed proliferation 1 or 3 days later. Therefore, primary follicle granulosa cells proliferate after follicle activation, but proliferation rates gradually increase as the follicle develops. Prior estimates of primary follicle duration are inaccurate due to the assumption that follicles develop at a constant rate. Summary sentence The length of the primary follicle phase is 14–16 days in mice but follicle development pauses briefly, shortly after primordial follicle activation, and explains why prior mathematical model-based estimates were inaccurate.
Polarization rotation associated with phonon dynamics in monoclinic C phase near morphotropic phase boundary studied by diffuse and inelastic X-ray scattering from a Ti-composition-gradient Pb[(Mg1/3Nb2/3)1–xTix]O3 single crystal

ABSTRACT We have investigated polarization rotation associated with phonon dynamics in the relaxor ferroelectrics Pb[(Mg1/3Nb2/3)1–xTix]O3. The intensity distributions of the diffuse scattering patterns show intensity- crossover behavior in the monoclinic-C(MC) phase over a wide Ti composition range (29 < x < 32 mol%). The transverse acoustic (TA) mode of the crossover region along the [001] direction softens and is damped, strongly correlating with the central peak intensity, which originates in the polar regions. These results indicate that the lattice can easily deform in the MC phase, and the polarization can rotate easily by associating with the TA mode.
Planetary science in Australia

Research School of Earth Sciences, Australian National University, Canberra ACT 0200 Australia Department of Environmental Sciences, University of Technology Sydney, Broadway NSW 2007 Australia Department of Biological & Physical Sciences, University of Southern Queensland, Toowoomba Qld 4350, Australia Mars Society Australia, P.O. Box 327, Clifton Hill VIC 3068, Australia Department of Applied Physics, Curtin University, Perth WA 6845 Australia School of Mathematical Sciences, Monash University, Victoria 3800 Australia Dept. of Earth and Marine Sciences, Australian National University, Canberra ACT 0200 Australia School of Physics, University of Sydney, Sydney NSW 2006 Australia Department of Earth and Planetary Sciences, Macquarie University, North Ryde NSW 2109 Australia
A Novel Soft Glove Utilizing Honeycomb Pneumatic Actuators (HPAs) for Assisting Activities of Daily Living

Fabric-based pneumatic actuators (FPAs) are extensively employed in the design of lightweight and compliant soft wearable assistive gloves. However, conventional FPAs typically exhibit limited output force, thereby restricting the applications of such gloves. This paper presents the development of a novel honeycomb pneumatic actuator (HPA) constructed using flexible thermoplastic polyurethane (TPU) coating through hot pressing or ultrasonic welding techniques. Compared to the previously utilized double-layer fabric-based pneumatic actuators (DLFPAs), the HPAs yields a remarkable 862% increase in end output force. It can produce a tip force of 13.57 N at a pressure of 150 kPa. The integration of HPAs onto a soft pneumatic glove enables the facilitation of various activities of daily living. A series of trials involving nine patients were conducted to assess the effectiveness of the soft glove. The experimental results indicate that when assisted by the glove, the patients’ finger metacarpophalangeal (MCP) and proximal interphalangeal (PIP) joints achieved angles of 87.67 ± 19.27° and 64.2 ± 30.66°, respectively. Additionally, the average fingertip force reached 10.16 ± 4.24 N, the average grip force reached 26.04 ± 15.08 N, and the completion rate of daily functions for the patients increased from 39% to 76%. These outcomes demonstrate that the soft glove effectively aids in finger movements and significantly enhances the patients’ daily functioning.
Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling

Abstract Motivation The tertiary structures of an increasing number of biological macromolecules have been determined using cryo-electron microscopy (cryo-EM). However, there are still many cases where the resolution is not high enough to model the molecular structures with standard computational tools. If the resolution obtained is near the empirical borderline (3–4.5 Å), improvement in the map quality facilitates structure modeling. Results We report EM-GAN, a novel approach that modifies an input cryo-EM map to assist protein structure modeling. The method uses a 3D generative adversarial network (GAN) that has been trained on high- and low-resolution density maps to learn the density patterns, and modifies the input map to enhance its suitability for modeling. The method was tested extensively on a dataset of 65 EM maps in the resolution range of 3–6 Å and showed substantial improvements in structure modeling using popular protein structure modeling tools. Availability and implementation https://github.com/kiharalab/EM-GAN, Google Colab: https://tinyurl.com/3ccxpttx.
Confocal Microscopy Image Segmentation and Extracting Structural Information for Morphological Change Analysis of Dendritic Spine

The introduction of confocal microscopy makes it possible to observe the structural change of live neuronal cell. Neuro-degenerative disease, such as Alzheimer;s and Parkinson’s diseases are especially related to the morphological change of dendrite spine. That’s the reason for the study of segmentation and extraction from confocal microscope image. The difficulty comes from uneven intensity distribution and blurred boundary. Therefore, the image processing technique which can overcome these problems and extract the structural information should be suggested. In this paper, we propose robust structural information extracting technique with confocal microscopy images of dendrite in brain neurons. First, we apply the nonlinear diffusion filtering that enhance the boundary recognition. Second, we segment region of interest using iterative threshold selection. Third, we perform skeletonization based on Fast Marching Method that extracts centerline and boundary for analysing segmented structure. The result of the proposed method has been less sensitive to noise and has not been affected by rough boundary condition. Using this method shows more accurate and objective results.
NR-SLAM: Non-Rigid Monocular SLAM

In this paper we present NR-SLAM, a novel non-rigid monocular SLAM system founded on the combination of a Dynamic Deformation Graph with a Visco-Elastic deformation model. The former enables our system to represent the dynamics of the deforming environment as the camera explores, while the later allows us to model general deformations in a simple way. The presented system is able to automatically initialize and extend a map modeled by a sparse point cloud in deforming environments, that is refined with a sliding-window Deformable Bundle Adjustment. This map serves as base for the estimation of the camera motion and deformation and enables us to represent arbitrary surface topologies, overcoming the limitations of previous methods. To assess the performance of our system in challenging deforming scenarios, we evaluate it in several representative medical datasets. In our experiments, NR-SLAM outperforms previous deformable SLAM systems, achieving millimeter reconstruction accuracy and bringing automated medical intervention closer. For the benefit of the community, we make the source code public.
Quench Risk Increase With Radiation Damage

Superconducting magnets are often proposed to confine plasma in fusion reactors. Superconducting material enables the magnets to carry current densities that would melt materials with non-zero resistance. Quench occurs when superconductivity is lost and the current starts to generate heat. Unless prevented with a fast enough control system, the heat generated during a quench can cause catastrophic damage to the coils. This work describes a less-studied heating mechanism that increases the likelihood and aggressiveness of fusion magnet quenches. Defects accumulate in the magnet structural material under irradiation by the fusion process. The defects store energy in the material and change thermal and normal state electrical properties. Wigner energy is released when defects anneal. After a 0.9 mDPA neutron irradiation, a 10 K disturbance from 20 K is predicted to release enough energy to result in a final temperature of 40 K. Irradiation damage also reduces the quench time constant by increasing normal state resistivity and thus Ohmic heating. The continuous operation of a fusion reactor produces an increasingly unstable thermodynamic system in superconducting magnets by changing electrical and thermal properties with irradiation damage. The temperature margin between operation and quench runaway reduces with irradiation. The next steps are to include these observations in quench models and validate the predictions experimentally. Implications of this work is felt by all fusion powerplant projects planning to leverage superconducting magnets. Designs will recognize this risk with more stringent specifications on quench control systems and maximum duration of coil operation at cryogenic temperature between periodic releases of Wigner energy to avoid catastrophic quench failures.
Actor-Critic with variable time discretization via sustained actions

Reinforcement learning (RL) methods work in discrete time. In order to apply RL to inherently continuous problems like robotic control, a specific time discretization needs to be defined. This is a choice between sparse time control, which may be easier to train, and finer time control, which may allow for better ultimate performance. In this work, we propose SusACER, an off-policy RL algorithm that combines the advantages of different time discretization settings. Initially, it operates with sparse time discretization and gradually switches to a fine one. We analyze the effects of the changing time discretization in robotic control environments: Ant, HalfCheetah, Hopper, and Walker2D. In all cases our proposed algorithm outperforms state of the art.