Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT)

Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that is solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work, and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.
COLD-INDUCED HYPERPHAGIA REQUIRES AGRP NEURON ACTIVATION IN MICE 1

30 To maintain energy homeostasis during cold exposure, the increased energy demands of 31 thermogenesis must be counterbalanced by increased energy intake. To investigate the 32 neurobiological mechanisms underlying this cold-induced hyperphagia, we asked whether agouti-33 related peptide (AgRP) neurons are activated when animals are placed in a cold environment 34 and, if so, whether this response is required for the associated hyperphagia. We report that AgRP-35 neuron activation occurs rapidly upon acute cold exposure, as do increases of both energy 36 expenditure and energy intake, suggesting the mere perception of cold is sufficient to engage 37 each of these responses. We further report that silencing of AgRP neurons selectively blocks the 38 effect of cold exposure to increase food intake. Together, these findings establish a 39 physiologically important role for AgRP neurons in the hyperphagic response to cold exposure. 40
Integrated IVUS-OCT for Real-Time Imaging of Coronary Atherosclerosis

Accurate assessment of atherosclerotic plaque characteristics and the subsequent tailoring of optimal therapy holds great promise for preventing acute coronary syndromes (ACS) and life-threatening sequelae (1). Combined use of optical coherence tomography (OCT) and intravascular ultrasound (IVUS) was proposed as a potential method for accurate assessment of plaque characteristics and vulnerability (2,3). However, significant challenges remain in trying to adapt an integrated OCT-IVUS system for clinical applications. We report here a fully integrated intracoronary OCT-IVUS imaging technique to visualize atherosclerotic plaque in living animals and human coronary arteries from cadavers with high resolution and deep penetration capability simultaneously. First, we created lesions, similar to human atherosclerotic plaques, inmaleNewZealandwhite rabbits by feeding themahighcholesterol diet and subjecting them to de-endothelization procedures (4). We imaged plaques in rabbit aortas using the OCT-IVUS system with a 3.4-F integrated catheter (5) and a 10-ml Omnipaque (iohexol, 350 mgI/ml, GE Healthcare, Princeton,New Jersey) injection flushing into the artery atw3ml/s for blood clearance. A total of 10 volumetric datasets were obtained from 5 rabbits. Ten 2to 20-mm long aorta segments were imaged at 5 mm/s pull-back speed. A representative OCT-IVUS image pair and corresponding histology of a rabbit abdominal aorta with a thick-cap fibroatheroma is shown in Fig. 1 (row I). IVUS enables the visualization of the layer structure of the artery wall. Intimal thickening and a low-density acoustic signal region (denoted by the arrow inFig.1Ia)demonstrate plaque in the IVUSimage.However, this image also illustrates the inability of IVUS to determinate the plaque type and the plaque cap boundary. At the same site in the OCT image (Fig. 1Ib), a homogenous boundary and weak signal region under a high signal region indicates that this plaque is a necrotic/lipid plaque with an overlying fibrous cap. In addition, the minimum thickness of the cap can be easily measured to be w200 mm by using OCT, which is indicative of a thick-cap fibroatheroma. The classification of plaque type is validated by the corresponding histology photo (Fig. 1Ic), which shows loose necrotic material. This area is covered by smooth muscle and fibrous proliferations at the luminal surface, which is consistent with a fibrous cap. All IVUS-OCT images of rabbit aortas were matched with histology for correlation of accuracy. Linear regression showed a high correlation between plaque circumference percent (PCP) (defined as the circumference of lumen in which there is plaque divided by the entire lumen circumference) determined from histological analysis and the estimated PCP of OCT and IVUS (R 1⁄4 0.955, p < 0.001 between OCT and histology; R 1⁄4 0.970, p < 0.001 between IVUS and histology). Second, a female Yorkshire white swine was imaged by conventional femoral access and angiography guidance under
An efficient spectral‐Galerkin method based on a dimension reduction scheme for eigenvalue problems of Schrödinger equations

In this paper, we propose an efficient spectral‐Galerkin method based on a dimension reduction scheme for eigenvalue problems of Schrödinger equations. Firstly, we carry out a truncation from a three‐dimensional unbounded domain to a bounded spherical domain. By using spherical coordinate transformation and spherical harmonic expansion, we transform the original problem into a series of one‐dimensional eigenvalue problem that can be solved effectively. Secondly, we introduce a weighted Sobolev space to treat the singularity in the effective potential. Using the property of orthogonal polynomials in weighted Sobolev space, the error estimate for the approximate eigenvalues and corresponding eigenfunctions are proved. Error estimates show that our numerical method can achieve spectral accuracy for approximate eigenvalues and eigenfunctions. Finally, we give some numerical examples to demonstrate the efficiency of our algorithms and the correctness of the theoretical results.
Internet College Education Based on Artiﬁcial Intelligence and Social Computing

Internet education in colleges and universities is the inevitable result of the high popularization of college students’ network use, and it is an important strategy for colleges and universities to actively adapt to the networked education environment. With the rapid development of artiﬁcial intelligence, traditional Internet education technology is no longer suitable for the increasingly large infor-mationscaleofthemoderneducationsystem,andnewcomputertechnologiesneed tobeassistedinthecompletionofInterneteducation.Tosolvethischallenge,we proposeanovelinterneteducationplatformbasedonartiﬁcialintelligenceand socialcomputing,whichcanbeutilizedtominestudents’interactioninformation andpredicttheirfutureevolutions.Inparticular,weintroducethestate-of-the-art graphlearningmodelsasthepre-trainingmodelinourplatform.Suchmodels cangeneratenodeembeddingsinthestudentsocialgraph,andtheseembeddings usuallycontainimportantinformationforfutureprediction.Intheexperiments, wedemonstratethemodels’performanceandeffectiveness.Inaddition,wealso discusswhatdatasetscanbeusedinourplatformpre-training.
Jargon: Ngajaga Shalat, Ngajago Silat, Ngajaga Silaturahmi at Dhikr Al Fath Islamic Boarding School

Dhikr Al Fath Islamic Boarding School has advantages in dhikr activities, entrepreneurship, martial arts and known by Sundanese culture. The jargon of ngajaga shalat, ngajago silat, ngajaga silaturahmi is one of the local wisdom that lives in this school, which describes the values that are instilled in Santri through worship activities, martial arts, and maintaining positive relationships with others. This study's aim is to explore further into jargon's values. There are semi-structured interviews, non-participant observations, and documentation studies as the methods of this study. The study's findings show in jargon of ngajaga shalat includes religious values that connects God, mankind, and the cosmos (environment). So we may commemorate Allah while remembering mankind, said the leader of this school. Align with this school vision that understanding, teaching, practicing, maintaining, and preserving Allah's word and the Prophet's Sunnah . Additionally, in the jargon ngajago silat , there are values like honesty, discipline, bravery, and self-confidence. Previous research shows that martial arts improves children's self-control, fearlessness, and confidence. The coach in this school says Santri must be disciplined before warming up. After that, the jargon of ngajaga silaturahmi refers to the value of social education that comes from the view of Islam, including the value of brotherhood, forgiving others, and courage. So, silat means taking care of oneself by remembering God, so keep yourself away from the devil from the side of qolbu said the leader of the school. These all value are internalized through activities of worship and practicing martial arts.
1-1-2011 FSR : Formal Analysis and Implementation Toolkit for Safe Inter-domain Routing

Inter-domain routing stitches the disparate parts of the Internet together, making protocol stability a critical issue to both researchers and practitioners. Yet, researchers create safety proofs and counter-examples by hand, and build simulators and prototypes to explore protocol dynamics. Similarly, network operators analyze their router configurations manually, or using home-grown tools. In this paper, we present a comprehensive toolkit for analyzing and implementing routing policies, ranging from high-level guidelines to specific router configurations. Our Formally Safe Routing (FSR) toolkit performs all of these functions from the same algebraic representation of routing policy. We show that routing algebra has a natural translation to both integer constraints (to perform safety analysis with SMT solvers) and declarative programs (to generate distributed implementations). Our extensive experiments with realistic topologies and policies show how FSR can detect problems in an AS's iBGP configuration, prove sufficient conditions for BGP safety, and empirically evaluate convergence time. Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-11-10. Author(s) Anduo Wang, Limin Jia, Wenchao Zhou, Yiqing Ren, Boon Thau Loo, Jennifer Rexford, Vivek Nigam, Andre Scedrov, and Carolyn Talcott This technical report is available at ScholarlyCommons: http://repository.upenn. edu/cis_reports/954
Méthodologie d'étude et modélisation du transport de solutes en milieux poreux naturels : application à la migration du chrome dans la nappe alluviale du Drac (Isère)

On presente une methodologie d'etude du transport de solutes interactifs en milieu poreux naturel, basee sur l'experimentation et la modelisation. La modelisation s'effectue grâce a un code de calcul couplant hydrodynamique et geochimie, des ameliorations y sont apportees avec la prise en compte de corrections d'activite et surtout, avec la simulation d'effets cinetiques chimiques ou diffusionnels. La methodologie proposee a ete appliquee au cas de migration du chrome dans la nappe alluviale du Drac (Isere). L'etude du site experimental associee a la connaissance generale de la chimie du chrome, a permis de definir et de cadrer les experiences a mener au laboratoire pour caracteriser les interactions du chrome avec les alluvions. Ces experiences ont montre que c'est un phenomene d'adsorption qui impose la repartition du chrome hexavalent entre phases mobile et immobile. Ce phenomene a ensuite ete decrit a l'equilibre thermodynamique par deux modeles, le premier utilise un phenomene elementaire de type echange anionique entre chromate et bicarbonate, le second est resume a une loi de Langmuir. Les courbes experimentales ont ete simulees en considerant ces deux modeles avec des limitations cinetiques. Les experiences de tracage sur le site ont montre que le chrome hexavalent y a un comportement equivalent a un traceur d'eau. Ce resultat souligne que certains parametres capacitifs des interactions ne peuvent etre determines au laboratoire et doivent faire l'objet de mesures in-situ
Tracking Sound Sources for Object-based Spatial Audio in 3D Audio-visual Production

In 3D audio-visual production, the positioning of sound sources relative to the visual display requires careful attention. This can be achieved with object-based audio which also allows the producer to maintain control over individual elements within the mix. However, each object’s metadata is needed to deﬁne its position over time. Therefore, a 3D multiple-target tracking system relying on the fusion of audio and visual modalities using iterated-corrector probability hypothesis density (IPHD) ﬁltering framework is proposed for tracking unknown and varying number of audio objects. Video data is analyzed to form a 3D reconstruction of a scene, and human ﬁgure detection is applied to the 2D frames of a camera-array. The steered response power of the acoustical signals at a microphone-array is used, with the phase transform (SRP-PHAT), to determine the dominant source position(s) at any time. Both position estimates from audio and visual processing are then fused using an IPHD ﬁlter and the re-liabilities from each modality are utilized to provide more robust tracking performance. We apply the proposed 3D audio-visual IPHD (3DAV-IPHD) tracker for tracking audio objects in six degree-of-freedom (6DOF) virtual reality (VR) production and in our case, audio-visual measurements are captured using a compact audio-visual sensing platform consisting of 16-element microphone-array and 11-element light-ﬁeld camera-array. Our experimental re-sults show that audio information can successfully compensate the missed detections from visual-only tracking and hence, demonstrate the effectiveness of fusing audio and visual information using the proposed 3DAV-IPHD tracker. This gives an initial promising indication that such an approach may open the door to object-based VR production
(2020). Opportunities, Challenges and Potential Solutions in the Application of Fast-Switching Silicon Carbide (SiC) Power Devices and Converters. IEEE Transactions on Power Electronics

-Power devices based on wide-bandgap (WBG) material such as silicon-carbide (SiC) can operate at higher switching speeds, higher voltages and higher temperatures compared to those based on silicon (Si) material. This paper highlights some opportunities brought by SiC devices in existing and emerging applications in terms of efficiency and power density improvement. While the opportunities are clear, there are also design challenges that must be met in order to realize their full potential. For example, the fast switching speeds and high d v /d t of SiC devices can cause increased electromagnetic interference (EMI), current overshoot, cross-talk effect and have a negative impact on loads such as motors. This paper presents several potential solutions to tackle the application challenges and to fully exploit the superior characteristics of SiC devices and converters while attenuating their negative side-effects. This paper provides an overview of recent SiC device research and development activities based on academic literature, work carried out by the authors and collaborators as well as input from industry. It aims to provide benchmark results and a timely and useful reference to accelerate the adoption and deployment of SiC devices and converters.
The Inhibitor Preincubation Effect Is Universal to SLC Transporter Assays and Is Only Partially Eliminated in the Presence of Extracellular Protein

Variation in the methodology of in vitro transporter inhibition assays causes wide divergence in reported IC50/Ki data. Notably, although potentiation of transporter inhibition by preincubation (PTIP) has been described, current guidelines do not specifically recommend inhibitor preincubation; they only encourage sponsors to follow emerging literature. To clarify how generally preincubation should be considered in transporter inhibition studies and whether PTIP can be solely explained by protein binding of the respective inhibitors, we performed in vitro inhibition assays on solute carrier (SLC) and ATP-binding cassette transporters scarcely or not covered in prior research and examined the effect of extracellular protein in preincubation and washout experiments. In SLC assays without extracellular protein, a 30-minute preincubation caused significant > twofold change of IC50 in 21/33 transporter-inhibitor combinations involving 19 evolutionarily disparate transporters. The preincubation effect correlated with inhibitor properties like protein binding and aqueous solubility. In vesicular transport assays of multidrug resistance protein 1, breast cancer resistance protein, multidrug resistance-associated protein 2, and bile salt export pump, sizable PTIP was observed for only 2/23 combinations, and preincubation was practically inconsequential in breast cancer resistance protein or multidrug resistance protein 1 monolayer assays. In SLC assays, PTIP partly persisted in the presence of 5% albumin, indicating that the absence of extracellular protein does not fully explain PTIP. The presence of protein, however, complicated the interpretation of results. Overall, while preincubating without protein may overpredict inhibitory potency, adding protein compromises clarity, and omitting preincubation altogether may miss clinically relevant inhibitors. Therefore, we propose that protein-free preincubation should be considered in all SLC inhibition assays. ATP-binding cassette transporter inhibition seems less commonly affected by preincubation, but conclusions require further investigation. SIGNIFICANCE STATEMENT Drugs may inhibit transporter proteins in the body, which may precipitate drug interactions. In vitro transporter inhibition assays help predict such drug interactions. Some inhibitors act more potently when preincubated with the transporter prior to the assay. Here we argue that this effect is not a mere in vitro artifact due to the lack of plasma proteins and should be considered in all uptake inhibition assays to model the worst-case scenario. Preincubation in efflux transporter inhibition assays is likely dispensable.
Evaluation of hygroscopic cloud seeding in warm-rain processes by a hybrid microphysics scheme using a Weather Research and Forecasting (WRF) model: a real case study

Abstract. To evaluate the hygroscopic cloud seeding in reality, this study develops a hybrid microphysics scheme using a Weather Research and Forecasting (WRF) model, WDM6-NCU (WDM6 modified by National Central University), which involves 43 bins of seeded cloud condensation nuclei (CCN) in the WDM6 bulk method scheme. This scheme can describe the size distribution of seeded CCN and explain the process of the CCN imbedding and cloud and raindrop formation in detail. Furthermore, based on the observational CCN size distribution applied in the modelling, a series of tests on cloud seeding were conducted during the seeding periods of 21–22 October 2020 with stratocumulus clouds. The model simulation results reveal that seeding in in-cloud regions with an appropriate CCN size distribution can yield greater rainfall and that spreading the seeding agents over an area of 40–60 km2 is the most efficient strategy to create a sufficient precipitation rate. With regard to the microphysical processes, the main process that causes the enhancement of precipitation is the strengthening of the accretion process of raindrops. In addition, hygroscopic particles larger than 0.4 µm primarily contribute to cloud-seeding effects. The study results could be used as references for model development and warm-cloud-seeding operations.
Orthonormal bases for anisotropic -modulation spaces

A bstract . In this article we construct orthonormal bases for bi-variate anisotropic α -modulation spaces. The construction is based on generating a nice anisotropic α -covering and using carefully selected tensor products of univariate brushlet functions with regards to this covering. As an application, we show that n -term nonlinear approximation with the orthonormal bases in certain anisotropic α -modulation spaces can be completely characterized.
Examining the use of lipid analysis as an indicator of fish habitat condition and overwinter survival of chinook salmon in large rivers of central British Columbia

Lipid and triglyceride levels have the potential to be indicators of the status of individuals and populations of fish because they may affect overwinter survival and energy allocation strategies. Identification of (1) seasonal lipid levels in juvenile fish, and (2) the relationship between fish lipid levels and fish habitat may provide managers with a tool for monitoring the quality of fish habitat in rivers. I assessed seasonal and spatial variation in lipid and triglyceride levels for young-of-the-year stream-type chilnook salmon (Oncorhynchus tshawytscha) throughout central British Columbia, Canada. I found triglyceride levels were highest in fish from the Bridge River, a flow-regulated river, with maximum levels occurring in November. I related triglyceride levels to environmental variables, and found a significant positive relationship between triglyceride levels and food availability. My research supports the potential for using triglyceride analysis as an evaluative tool in freshwater monitoring programs.
Risk bounds for purely uniformly random forests

Random forests, introduced by Leo Breiman in 2001, are a very effective statistical method. The complex mechanism of the method makes theoretical analysis difficult. Therefore, a simplified version of random forests, called purely random forests, which can be theoretically handled more easily, has been considered. In this paper we introduce a variant of this kind of random forests, that we call purely uniformly random forests. In the context of regression problems with a one-dimensional predictor space, we show that both random trees and random forests reach minimax rate of convergence. In addition, we prove that compared to random trees, random forests improve accuracy by reducing the estimator variance by a factor of three fourths.