Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrieval of Thermal and Microphysical Variables in Observed Convective Storms.

Abstract The air flow in convective storms, the force that regulate the flow, and the processes that produce hydrometeors of various kinds are all being studied intensively by meteorologists using Doppler radar observations. The research reported here proceeds from the observed motion through accompanying thermodynamic and micro-physical processes to the analysis of hydrometer content and thermal fields in thunderstorms. A three-dimensional numerical kinematic cloud model employing Doppler wind fields is developed and used to diagnose temperature and mixing ratios within a thunderstorm. The microphysical parameterization includes stochastic coalescence effects in warm clouds as well as well- and variable-density dry hail growth. Known fields from a dynamically simulated cloud are used to establish the accuracy of the retrieval scheme. Real data tests indicate good agreement between retrieved and observed radar reflectivities, qualitative dynamic consistency between observed winds and retrieved buoyancies,.
Separation of Plutonium from Other Actinides and Fission Products in Ionic Liquid Medium

ABSTRACT Recovery of plutonium from spent nuclear fuels is very much indispensable in fast neutron reactor fuel reactor wherein, plutonium – 239 (239Pu) is used as the driving fuel. Separation of Pu(IV) from other metal ions present in the spent nuclear fuels by liquid–liquid extraction process is a difficult task in conventional solvent system. In this context, Ionic Liquids (ILs) could be considered as a suitable solvent/diluent in the separation of actinides and fission products due to their numerous fascinating properties, such as high solvating capability, high selectivity, and high radiation stability. Selective separation of a target metal ion from other metal ions is feasible in IL-based extraction by suitably designing their cation–anion combination to acquire the desired selectivity. The present review summarizes the work on Pu(IV) solvent extraction from nitric acid medium using ILs as the extraction phase and highlights suitability of IL-based solvents for the selective separation of Pu(IV) from other actinides and fission products. This review also emphasizes on remarkable separation factor (SF) for Pu(IV) from other metal ions. Details on extraction kinetics, extraction thermodynamics, and stripping profiles of Pu(IV) are also congregated and presented. Graphical abstract
Correcting the Record: A Response to Backman and Barker (2020)

ABSTRACT This article is a response to Backman and Barker’s Re-thinking Pedagogical Content Knowledge for Physical Education Teachers-Implications for Physical Education Teacher Education. It affords us an opportunity to correct their misrepresentation of our research. Multiple perspectives on teaching and teacher education are necessary to advance the field because they provide different lenses to help us understand a particular phenomenon. However, there is a critical difference between interpretation and misrepresentation. Interpretation is the right due to all researchers to draw inferences. Misrepresentation, in contrast, is the attributing of positions and outcomes that are not supported by the empirical record. In making their case for phronesis in a 2020 publication, Backman and Barker used our research as the basis for their critique and in doing so, they misrepresented our body of research as well as the epistemology of Radical Behaviorism. We identify misrepresentations in their paper and address them using the empirical record.
The Relationship Between Economic Growth and Income Inequality in Economies in Transition

ABSTRACT In this study, we focus solely on economies in transition. The classification of the countries into the low-income and high-income economies in transition are based on the classification of the World Bank and on our own classification based on an income threshold that is endogenously estimated by our model. We use fixed-effects and dynamic panel technique such as system generalized method of moments (GMM) estimation in our analysis to mitigate endogeneity problem. Our empirical study uses dynamic econometric models to examine the relationship between income inequality and economic growth in the economies in transition. We find a positive relationship between income inequality and economic growth in high-income economies in transition, which is in stark contrast with the negative relationship for low-income economies in transition. We also find that inflation rate negatively and significantly affects economic growth in the low-income economies in transition, while it positively and significantly affects economic growth in the high-income economies in transition. We estimate an income threshold endogenously and reestimate both regressions according to our own threshold. Importantly, the contrasting qualitative difference (between low-income economies in transition and high-income economies in transition) in the relationship between income inequality and economic growth is robust whether we follow the World Bank’s classification of economies in transition or whether we classify them accordingly to what the data in our sample suggest.
Aperture Synthesis C18O J = 1-0 Observations of L1551 IRS 5: Detailed Structure of the Infalling Envelope

We report aperture synthesis C18O J = 1-0 observations of L1551 IRS 5 with a spatial resolution of 2. ″8 × 2. ″5 using the Nobeyama Millimeter Array. We have detected an emission component centrally condensed around IRS 5, as well as a diffuse component extending in the north-south direction from the centrally condensed component. The centrally condensed component, 2380 × 1050 AU in size, is elongated in the direction perpendicular to the outflow axis, indicating the existence of a flattened circumstellar envelope around L1551 IRS 5. The mass of the centrally condensed component is estimated to be 0.062 M☉. The position-velocity (P-V) diagrams reveal that the velocity field in the centrally condensed component is composed of infall and slight rotation. The infall velocity in the outer part is equal to the free-fall velocity around a central mass of ~0.1 M☉, e.g., 0.5 km s-1 at r = 700 AU, whereas the rotation velocity, 0.24 km s-1 at the same radius, gets prominent at inner radii with a radial dependence of r-1. We make up P-V diagrams for the model envelopes with vertical structure, in which the matter falls under the gravity and eventually settles down in Keplerian rotation inside the centrifugal radius, and compare them with the observed P-V diagrams of the centrally condensed component. The main characteristics of the observed P-V diagrams are reproduced by either (1) an envelope with a moderately flattened density distribution, or (2) a spherical envelope with a bipolar cavity whose half-opening angle is about 50°. Detailed comparison of the observed and model P-V diagrams suggests that the C18O J = 1-0 emission from the outer part of the centrally condensed component is well reproduced with the models with the central mass ~0.15 M☉ and the mass infall rate ~6 × 10-6 M☉ yr-1. However, the higher velocity features of the emission near the star cannot be reproduced unless the central mass is taken to be ~0.5 M☉. These facts suggest either that the gas pressure and/or magnetic force dilute the effect of the gravity in the outer part of the envelope, or that the velocity structure inside the centrifugal radius deviates significantly from the Keplerian rotation.
The Use of Diethylpropion in the Treatment of Obesity

Claims have been made for the value of diethylpropion as an anorectic agent, but few controlled trials have been carried out and these have been mostly of short duration. Double blind cross-over trials have been carried out by Stevens (1961), Hadden and Lucey (1961) and Jones (1962), the trial lasting 2 months only in the first two instances and 4 months in the last. A double blind matched pair trial lasting 6 months was carried out by Seaton, Duncan, Rose and Scott (1961). A blind, alternating patient trial, lasting two months, was performed by Decina and Tanyol (1960). It is thought, therefore, that the results of a slightly longer double blind cross-over trial might be of interest.
Study Based on the AIAA Aerodynamic Design Optimization Discussion Group Test Cases

Three model problems associated with aerodynamic drag minimizations are studied. These test cases have been proposed by the aerodynamic design optimization discussion group, and they include an inviscid NACA0012 nonlifting airfoil, a viscous RAE2822 lifting airfoil, and a viscous lifting wing based on the NASA Common Research Model. Various optimization methods are used, including MDOPT, TRANAIR, SYN83, and SYN107. The resulting designed and associated baseline geometries are cross analyzed by several computational fluid dynamics codes, including OVERFLOW, TRANAIR, GGNS, and FLO82. Pathological issues are unveiled in both of the simple airfoil model problems. Designed geometries for the inviscid symmetric test case exhibit strong tendencies to permit nonsymmetric flow solutions. Designed airfoils for the viscous lifting case also support nonunique solutions and hysteresis loops at or near the design point in Reynolds-averaged Navier–Stokes and integral boundary-layer method simulations. These results prov.
Spatial pattern formation in a model of vegetation-climate feedback

We consider a spatial version of Watson and Lovelock's tutorial model of vegetation-climate feedbacks (Watson A J and Lovelock J E 1983 Biological homeostasis of the global environment: the parable of daisyworld Tellus B 35 284–9). Two simple plant types compete on a hypothetical planet, stabilizing the global temperature via an albedo feedback. Numerical solutions show an alternating pattern of the two plant types. A stability analysis shows that there are two mechanisms involved in the pattern formation. A Turing-like process causes the uniform equilibrium state to be unstable to non-constant perturbations and the solution tends towards a striped pattern. This solution is then modified by a mechanism which restricts stripe length and results in subdivision. By calculating the associated temperature function we show how the maximum stripe length can be determined and the stability of different patterns assessed.
Electron Acceleration at Reconnecting X-Points in Solar Flares

The acceleration of electrons in solar flares is simulated using an extended version of a full orbit test-particle code previously used to compute losses of fusion alpha particles from tokamaks and to study flare proton acceleration. The magnetic and electric fields in the model are obtained from solutions of the linearized MHD equations for reconnecting modes at a magnetic X-point with zero equilibrium current. The magnetic field is assumed to have a small finite component perpendicular to the plane of the X-point. The version of the code used in the simulations is fully relativistic and includes Coulomb collisions. It is demonstrated that electrons cross the system boundary at distinct footpoints with the relative numbers and energy distribution at each footpoint sensitive to the longitudinal magnetic field component and collision time. These results are discussed in the context of recent flare observations showing asymmetric hard X-ray emission from the chromospheric footpoints of magnetic loops.
Cloud‐Surface Coupling Alters the Morning Transition From Stable to Unstable Boundary Layer

Due to surface heating, the morning boundary layer transits from stable to neutral or convective conditions, exerting critical influences on low tropospheric thermodynamics. Low clouds closely interact with the boundary layer development, yet their interactions bear considerable uncertainties. Our study reveals that cloud‐surface coupling alters the morning transition from stable to unstable boundary layer and thus notably affects the diurnal variation of the boundary layer. Specifically, due to the reduction in surface fluxes, decoupled clouds can delay the process of eroding nocturnal inversion by 0.8‐hr and even prevent the transition of the boundary layer from happening for 12% of decoupled cases, keeping the boundary layer in a stable state during the noontime. On the other hand, when clouds are coupled with the surface, cloud‐top radiative cooling can directly cool the upper boundary layer to facilitate sub‐cloud convection, leading to an unstable boundary layer in the earlier morning.
Identification of mobile element insertion from whole genome sequencing data using deep neural network model

Mobile element insertions (MEIs) are a major contributor to genome evolution and play an essential role in the regulation of gene expression, as well as being implicated in various human diseases. This study introduces DeepMEI, a tool based on a convolutional neural network model that transforms the MEI identification process into an image recognition problem and automatically learns complex and abstract representations of MEI features in whole genome sequencing data. DeepMEI outperformed existing tools in the benchmark dataset from the Genome in a Bottle consortium, with a precision of 0.90 and recall of 0.70. Moreover, factors such as sequencing depth, ME integrity, and genome mappability can affect MEI identification accuracy. Using DeepMEI, we reanalyzed 3,202 high-coverage whole-genome sequencing samples from the 1000 Genome Project (1kGP) phase 4 release, discovering 1.71-fold more non-reference MEIs, totaling 6,218,088, with 92.2% of the increase coming from rare MEIs (allele frequency <1%). This enhances our understanding of MEIs’ role in human disease and evolution. The DeepMEI tool and the updated 1kGP MEI dataset can be accessed at https://github.com/xuxif/DeepMEI.
Orthogonal coupling of a 3D cytoskeletal scaffold coordinates cell morphogenesis and maintains tissue organization in the Drosophila pupal retina

How complex three-dimensional (3D) organs coordinate cellular morphogenetic events to achieve the correct final form is a central question in development. The question is uniquely tractable in the late Drosophila pupal retina where cells maintain stereotyped contacts as they elaborate the specialized cytoskeletal structures that pattern the apical, basal and longitudinal planes of the epithelium. In this study, we combined cell type-specific genetic manipulation of the cytoskeletal regulator Abelson (Abl) with 3D imaging to explore how the distinct cellular morphogenetic programs of photoreceptors and interommatidial pigment cells coordinately organize tissue pattern to support retinal integrity. Our experiments revealed an unanticipated intercellular feedback mechanism whereby correct cellular differentiation of either cell type can non-autonomously induce cytoskeletal remodeling in the other Abl mutant cell type, restoring retinal pattern and integrity. We propose that genetic regulation of specialized cellular differentiation programs combined with inter-plane mechanical feedback confers spatial coordination to achieve robust 3D tissue morphogenesis.
The ComRS-SigX pathway regulates natural transformation in Streptococcus ferus

The ability to take up and incorporate foreign DNA via natural transformation is a well-known characteristic of some species of Streptococcus, and is a mechanism that rapidly allows for the acquisition of antibacterial resistance. Here, we describe that the understudied species Streptococcus ferus is also capable of natural transformation and uses a system analogous to that identified in Streptococcus mutans. S. mutans natural transformation is under the control of the alternative sigma factor sigX (also known as comX), whose expression is induced by two types of peptide signals: CSP (competence stimulating peptide, encoded by comC) and XIP (sigX-inducing peptide, encoded by comS). These systems induce competence via either the two-component signal-transduction system ComDE or the RRNPP transcriptional regulator ComR, respectively. Protein and nucleotide homology searches identified putative orthologs of comRS and sigX in S. ferus, but not homologs of S. mutans blpRH (also known as comDE). We demonstrate that natural transformation in S. ferus is induced by a small, double-tryptophan containing competence-inducing peptide (XIP), akin to that of S. mutans, and requires the presence of the comR and sigX orthologs for efficient transformation. Additionally, we find that natural transformation is induced in S. ferus by both the native XIP and the XIP variant of S. mutans, implying that crosstalk between the two species is possible. This process has been harnessed to construct gene deletions in S. ferus and provides a method to genetically manipulate this understudied species. IMPORTANCE Natural transformation is the process by which bacteria take up DNA and allows for acquisition of new genetic traits, including those involved in antibiotic resistance. This study demonstrates that the understudied species Streptococcus ferus is capable of natural transformation using a peptide-pheromone system like that previously identified in Streptococcus mutans and provides a framework for future studies concerning this organism.
Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation

Biofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit submerged and intertidal substrata. The development of a unique form of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. Gliding motility is hypothesized to be driven by an intracellular actin-myosin motor and requires the secretion of polysaccharide- and protein-based adhesive materials. To date, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown. Proteomics analysis of the adhesive material from Craspedostauros australis revealed eight novel, diatom-specific proteins. Four of them constitute a new family of proteins, named Trailins, which contain an enigmatic domain termed Choice-of-Anchor-A (CAA). Immunostaining demonstrated that Trailins are only present in the adhesive trails required to generate traction on native substrata, but are absent from the extracellular matrix of biofilms. Phylogenetic analysis and Protein 3D structure prediction suggests that the CAA-domains in Trailins were obtained from bacteria by horizontal gene transfer, and exhibit a striking structural similarity to ice-binding proteins. Our work advances the understanding of the molecular basis for diatom underwater adhesion and biofilm formation providing evidence that there is a molecular switch between proteins required for initial surface colonization and those required for 3D biofilm matrix formation.
High Volume Rate 3-D Ultrasound Imaging Using Fast-Tilting and Redirecting Reflectors

3-D ultrasound imaging has many advantages over 2-D imaging such as more comprehensive tissue evaluation and less operator dependence. Although many 3-D ultrasound imaging techniques have been developed in the last several decades, a low-cost and accessible solution with high imaging volume rate and imaging quality remains elusive. Recently we proposed a new, high volume rate 3-D ultrasound imaging technique: Fast Acoustic Steering via Tilting Electromechanical Reflectors (FASTER), which uses a water-immersible and fast-tilting acoustic reflector to steer ultrafast plane waves in the elevational direction to achieve high volume rate 3-D ultrasound imaging with conventional 1-D array transducers. However, the initial implementation of FASTER imaging only involves a single fast-tilting acoustic reflector, which is inconvenient to use because the probe cannot be held in the regular upright position. Also, conventional FASTER imaging can only be performed inside a water tank because of the necessity of using water for acoustic conduction. To address these limitations of conventional FASTER, here we developed a novel ultrasound probe clip-on device that encloses a fast-tilting reflector, a redirecting reflector, and an acoustic wave conduction medium. The new FASTER 3-D imaging device can be easily attached to or removed from clinical ultrasound transducers, allowing rapid transformation from 2-D to 3-D ultrasound imaging. In vitro B-mode imaging studies demonstrated that the proposed method provided comparable imaging quality (e.g., spatial resolution and contrast-to-noise ratio) to conventional, mechanical-translation-based 3-D imaging while providing a much faster 3-D volume rate (e.g., 300 Hz vs ∼10 Hz). In addition to B-mode imaging, we also demonstrated 3-D power Doppler imaging and 3-D super-resolution ultrasound localization microscopy with the newly developed FASTER device. An in vivo imaging study showed that the FASTER device could clearly visualize the 3-D anatomy of the basilic vein of a healthy volunteer, and customized beamforming was implemented to accommodate the speed of sound difference between the acoustic medium and the imaging object (e.g., soft tissue). These results suggest that the newly developed redirecting reflector and the clip-on device could overcome key hurdles for future clinical translation of the FASTER 3-D imaging technology.
Asymmetric dust distribution in an eccentric protoplanetary disk as a signpost of a gas giant planet

Abstract The presence of a cavity in a protoplanetary disk revealed by dust continuum emissions is sometimes postulated as a signpost of an embedded gas giant planet. More peculiarly, dust emissions exterior to the cavity are often observed to be asymmetric. We explore the possibility of the asymmetry as a result of the asymmetric distribution of dust in an eccentric protoplanetary disk under the secular gravitational perturbation of an embedded massive gas giant planet. We find that the surface density of the dust well coupled to the disk gas is enhanced around the apocenter of the disk. In addition, the azimuthal distributions of particles of various sizes can deviate significantly due to different coupling to the gas. Overall, the asymmetric structure exhibits a phase correlation between the gas velocity field and dust density distribution. A Doppler map for an eccentric disk is also presented based on Cycle 1 ALMA observations. Our study potentially provides a reality check as to whether an asymmetric disk gap detected at sub-mm and cm wavelengths is a signpost of a massive gas giant planet.
Accurate modeling of peptide-MHC structures with AlphaFold

Major histocompatibility complex (MHC) proteins present peptides on the cell surface for T-cell surveillance. Reliable in silico prediction of which peptides would be presented and which T-cell receptors would recognize them is an important problem in structural immunology. Here, we introduce an AlphaFold-based pipeline for predicting the three-dimensional structures of peptide-MHC complexes for class I and class II MHC molecules. Our method demonstrates high accuracy, outperforming existing tools in class I modeling precision and class II peptide register prediction. We explore applications of this method towards improving peptide-MHC binding prediction.