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At least 343 records · Page 19

TransPlatformer

We propose TransPlatformer for translating toxicogenomics from one platform to another. Transcriptomic profiling has evolved through multiple generations of technology, from microarrays (e.g., Affymetrix, CodeLink) to more recent high-throughput sequencing and targeted panels such as S1500+. Microarrays, which dominated gene expression studies in the early 2000s, provided affordable and high-throughput transcript quantification but suffered from cross-hybridization issues and limited dynamic range . RNA-Seq, introduced in the late 2000s, revolutionized transcriptomics by enabling unbiased and comprehensive gene expression analysis, albeit at higher costs and computational demands . Despite advances, many studies rely on historical microarray data, necessitating the translation of legacy data into modern platforms to ensure continuity and comparability. This translation is complicated by factors such as platform-specific probe design, differences in transcript coverage, and batch effects . Existing methods for cross-platform mapping include statistical normalization, machine learning models, and biological anchoring approaches. The ability to translate transcriptomic data between platforms has broad implications, including enhanced meta-analyses, improved toxicological modeling, and better integration of historical datasets with contemporary research. TransPlatformer seeks to contribute to this effort by evaluating translation methodologies and proposing novel strategies to improve cross-platform gene expression harmonization. In this repository there are code examples for TransPlatformer implementation

Cong, Guojing↗

Discovery of an Afterglow Extension of the Prompt Phase of Two Gamma Ray Bursts Observed by Swift

Contemporaneous BAT and XRT observations of two recent well-covered GRBs observed by Swift, GRB 050315 and GRB 050319, show clearly a prompt component joining the onset of the afterglow emission. The rapid slewing capability of the spacecraft enables X-ray observations immediately after the burst, typically ~ 100 s following the initiation of the prompt y-ray phase. By fitting a power law form to the y-ray spectrum, we extrapolate the time dependent fluxes measured by the BAT, in the energy band 15 - 350 keV, into the spectral regime observed by the XRT 0.2 - 10 keV, and examine the functional form of the rate of decay of the two light curves. We find that the BAT and XRT light curves merge to form a unified curve. There is a period of steep decay up to ~ 300 s, followed by a flatter decay. The duration of the steep decay, ~ 100 s in the source frame after correcting for cosmological time dilation, agrees roughly with a theoretical estimate for the deceleration time of the relativistic ejecta as it interacts with circumstellar material. For GRB 050315, the steep decay can be characterized by an exponential form, where one e-folding decay time Te (BAT)~ = 24 f 2 s, and Te,(XRT)~ = 35 f 2 s. For GRB 050319, a power law decay - d l n f / d l n t = n, where n approx. ~ = 3, provides a reasonable fit. The early time X-ray fluxes are consistent with representing the lower energy tail of the prompt emission, and provide our first quantitative measure of the decay of the prompt y-ray emission over a large dynamic range in flux. The initial steep decay is expected due to the delayed high latitude photons from a curved shell of relativistic plasma illuminated only for a short interval. The overall conclusion is that the prompt phase of GRBs remains observable for hundreds of seconds longer than previously thought.

Bathelmy, S. D.↗

Global Evolution of Solar Magnetic Fields and Prediction of Solar Activity Cycles

Prediction of solar activity cycles is challenging because the physical processes inside the Sun involve a broad range of multiscale dynamics that no model can reproduce, and the available observations are highly limited and cover mostly surface layers. Helioseismology makes it possible to probe solar dynamics in the convective zone, but variations in the differential rotation and meridional circulation are currently available for only two solar activity cycles. It has been demonstrated that sunspot observations, which cover over 400 years, can be used to calibrate the Parker-Kleeorin-Ruzmaikin model and that the Ensemble Kalman Filter (EnKF) method can be used to link the model magnetic fields to sunspot observations to make reliable predictions of a following cycle. However, for more accurate predictions, it is necessary to use actual observations of the solar magnetic fields, which are available for only four solar cycles. This raises the question of how limitations in observational data and model uncertainties affect predictive capabilities and implies the need for the development of new forecast methodologies and validation criteria. In this presentation, I will discuss the influence of the limited number of available observations on the accuracy of EnKF estimates of solar cycle parameters.

Kitiashvili, Irina N.↗

Dynamics of the Terrestrial Radiation Belts: a Review of Recent Results During the VarSITI (Variability of the Sun and Its Terrestrial Impact) Era, 2014–2018

The Earth’s magnetosphere is region that is carved out by the solar wind as it flows past and interacts with the terrestrial magnetic field. The inner magnetosphere is the region that contains the plasmasphere, ring current, and the radiation belts all co-located within about 6.6 Re, nominally taken to be bounding this region. This region is highly dynamic and is home to a variety of plasma waves and particle populations ranging in energy from a few eV to relativistic and ultra-relativistic electrons and ions. The interplanetary magnetic field (IMF) embedded in the solar wind via the process of magnetic reconnection at the sub-solar point sets up plasma convection and creates the magnetotail. Magnetic reconnection also occurs in the tail and is responsible for explosive phenomena known as substorms. Substorms inject low-energy particles into the inner magnetosphere and help generate and sustain plasma waves. Transients in the solar wind such as coronal mass ejections (CMEs), co-rotating interaction regions (CIRs), and interplanetary shocks compress the magnetosphere resulting in geomagnetic storms, energization, and loss of energetic electrons in the outer radiation belt and enhance the ring current, thereby driving the geomagnetic dynamics. The Specification and Prediction of the Coupled Inner-Magnetospheric Environment (SPeCIMEN) is one of the four elements of VarSITI (Variability of the Sun and Its Terrestrial Impact) program which seeks to quantitatively predict and specify the inner magnetospheric environment based on Sun/solar wind driving inputs. During the past 4 years, the SPeCIMEN project has brought together scientists and researchers from across the world and facilitated their efforts to achieve the project goal. This review provides an overview of some of the significant scientific advances in understanding the dynamical processes and their interconnectedness during the VarSITI era. Major space missions, with instrument suites providing in situ measurements, ground-based programs, progress in theory, and modeling are briefly discussed. Open outstanding questions and future directions of inner magnetospheric research are explored.

Shrikanth Kanekal↗

Experimental Measurement of Frozen and Partially Melted Water Droplet Impact Dynamics

High-speed video of single frozen water droplets impacting a surface was acquired. The droplets diameter ranged from 0.4 mm to 0.9 mm and impacted at velocities ranging from 140 m/sec to 309 m/sec. The techniques used to freeze the droplets and launch the particles against the surfaces is described in this paper. High-speed video was used to quantify the ice accretion area to the surface for varying impact angles (30 deg, 45 deg, 60 deg), impacting velocities, and break-up angles. An oxygen /acetylene cross-flow flame used to ensure partial melting of the traveling frozen droplets is also discussed. A linear relationship between impact angle and ice accretion is identified for fully frozen particles. The slope of the relationship is affected by impact speed. Perpendicular impacts, i.e. 30 deg, exhibited small differences in ice accretion for varying velocities, while an increase of 60% in velocity from 161 m/sec to 259 m/sec, provided an increase on ice accretion area of 96% at an impact angle of 60 deg. The increase accretion area highlights the importance of impact angle and velocity on the ice accretion process of ice crystals. It was experimentally observed that partial melting was not required for ice accretion at the tested velocities when high impact angles were used (45 and 60 deg). Partially melted droplets doubled the ice accretion areas on the impacting surface when 0.0023 Joules were applied to the particle. The partially melted state of the droplets and a method to quantify the percentage increase in ice accretion area is also described in the paper.

Impact Dynamics↗

A comparison between theoretical prediction and experimental measurement of the dynamic behavior of spur gears

A comparison was made between computer model predictions of gear dynamics behavior and experimental results. The experimental data were derived from the NASA gear noise rig, which was used to record dynamic tooth loads and vibration. The experimental results were compared with predictions from the DSTO Aeronautical Research Laboratory's gear dynamics code for a matrix of 28 load speed points. At high torque the peak dynamic load predictions agree with the experimental results with an average error of 5 percent in the speed range 800 to 6000 rpm. Tooth separation (or bounce), which was observed in the experimental data for light torque, high speed conditions, was simulated by the computer model. The model was also successful in simulating the degree of load sharing between gear teeth in the multiple tooth contact region.

Rebbechi, Brian↗

High fidelity, radiation tolerant analog-to-digital converters

Techniques for an analog-to-digital converter (ADC) using pipeline architecture includes a linearization technique for a spurious-free dynamic range (SFDR) over 80 deciBels. In some embodiments, sampling rates exceed a megahertz. According to a second approach, a switched-capacitor circuit is configured for correct operation in a high radiation environment. In one embodiment, the combination yields high fidelity ADC (>88 deciBel SFDR) while sampling at 5 megahertz sampling rates and consuming <60 milliWatts. Furthermore, even though it is manufactured in a commercial 0.25-.mu.m CMOS technology (1 .mu.m=12.sup.-6 meters), it maintains this performance in harsh radiation environments. Specifically, the stated performance is sustained through a highest tested 2 megarad(Si) total dose, and the ADC displays no latchup up to a highest tested linear energy transfer of 63 million electron Volts square centimeters per milligram at elevated temperature (131 degrees C.) and supply (2.7 Volts, versus 2.5 Volts nominal).

Wang, Charles Chang-I↗

Imaging Science Requirements for a Uranus Flagship Mission

Introduction: Our presentation will summarize the requirements for UV/Visible/Near-IR remote-sensing imaging science instruments (including mapping spectrometers) envisioned for the Uranus Orbiter and Probe (UOP) mission recommended by the recent planetary decadal survey. The Uranus system offers many targets for imaging investigations. Imaging science investigations are crucial to answering fundamental questions about various physical processes that shape the Uranian system and drive its evolution. Each science objective addressed through imaging has requirements for observation and illumination geometries as well as coverage and resolution in the spatial, spectral and temporal dimensions. By combining the requirements for the diverse science targets in the Uranian system, we present a set of overarching imaging science requirements for UOP. Atmospheric Science: The study of Uranus’ atmosphere is crucial in understanding the planet's energy balance and interior heat flux. Imaging observations map how the atmosphere scatters incident solar radiation. Imaging is key to characterizing planetary-scale energy/material transport though global atmospheric dynamics and local meteorology. Hyperspectral mapping combined with radiative transfer analysis reveals the vertical distribution of clouds and hazes. Chronicling temporal variabilities of atmospheric features is key to understanding the various processes that operate within the dynamic Uranian atmosphere. A comprehensive understanding of Uranus' atmosphere is essential in deciphering the planet's origins and evolution as well as providing insight into the broader field of planetary and exoplanetary science. Magnetospheric Interactions: Imaging science is critical to understand the elusive Uranian aurorae. Mapping the aurorae and their temporal dynamics will reveal the interaction of Uranus’ complex magnetosphere with the solar wind. The apparent decades-long cooling of Uranus’ upper atmosphere is thought to be due to changes in energy input from the overlying magnetosphere, and so mapping and quantifying the auroral evidence for this energy flux is particularly relevant for upper atmospheric science In addition, Uranus’ large moons may generate auroral footprints, which can be used to constrain the planet’s unusual magnetic field structure. Satellite Interiors: Imaging science can address the potential habitability of the larger moons of Uranus by measuring their shapes and rotational states (including librations), which combined with gravity data are crucial to understanding their internal density structure. Satellite Origins: Origin markers such as organics and volatiles may be preserved on the satellite surfaces, which may be sensed by UV/IR mapping. Imaging combined with the moons’ densities may reveal whether the moons formed in Uranus’ circumplanetary disk, rings, or from ejecta of a giant impact on Uranus. Satellite Geology: Imaging investigations, including stereo imaging to obtain topography, will enable constraining each satellite’s geologic history by investigating the distributions and morphologies of impact craters, tectonic and potential cryovolcanic features, and regolith and mass wasting deposits. These records will help unravel the past complex history of orbital resonances that occurred between Uranian satellites, which may have driven geologic activity. Analyses of these features will also point to resurfacing styles and modification processes important for understanding each moon’s thermal evolution, and any present-day geological activity, including potential subsurface deep oceans or possible current activity. Additionally, hyperspectral imaging will enable mapping the surface composition and identifying the potential presence of material that may point to a subsurface ocean, such as ammonia-bearing species. Rings and Small Moons: Imaging observations elucidate the physical processes that contribute to the complex ring-moon system’s inferred unstable state. Imaging surveys will seek smaller moons and other debris that could provide evidence of past collisions, while precise astrometric data of moons will determine the current dynamical state of the system. Many of Uranus' rings are exceptionally narrow, and images of the rings covering a broad range of longitudes, and high-resolution images of features within the rings will reveal how these rings are confined and maintained, as well as illustrating the rings' internal structure and dynamics. Images of the rings and moons obtained at a variety of wavelengths and lighting conditions are also needed to quantify the composition and the size distribution of the small satellites and ring particles.

K M Sayanagi↗

On the Recoverability of Reactor Dynamics from Point Kinetics Data using SINDYc

Data driven models for reactor dynamics tend to face a few notable challenges. First, the broad range of timescales present across the various feedback mechanisms. Next, high standards for safety and importance of model performance in all operational domains. Finally, the correlations between state variables observed in most transients leads to difficulties when methods attempt to attribute certain dynamic phenomena to a particular cause. The current paper seeks to support efforts towards incorporating physics knowledge into one particular data-driven method for finding reactor dynamics called ``Sparse Identification of Nonlinear Dynamics with Control (SINDYc). The incorporation of physical knowledge into SINDYc will help address the challenges listed above by giving the model an initial understanding of the system being modeled. The demonstration of an exact representation of a set of point reactor dynamics equations in SINDYc is provided. Then, this allows for further discussion with mathematical justification as to why SINDYc, and other data-driven methods, may be difficult to apply to nuclear reactor dynamics due to correlations in the state variables. A particularly useful result of this work is the set of candidate functions required in SINDYc to exactly represent the reactor dynamics under a point approximation. In the future, SINDYc can be integrated with point models for reactor dynamics before being applied to the physical system to yield higher accuracy.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Flight Investigation using Variable-Stability Airplanes of Minimum Stability Requirements for High-Speed, High-Altitude Vehicles

The pilot opinion of the flying qualities of vehicles covering a wide range of longitudinal dynamic characteristics has been determined by the use of a variable-stability airplane. Particular emphasis has been placed on determining the minimum level of stability and control characteristics that the pilot can cope with. There was considerable pilot learning associated with operation in the regions of poor stability characteristics. In the statically stable region the maximum acceptable value of time to damp to half amplitude of the longitudinal mode for normal operation was about 1 second. For emergency conditions the damping could be reduced to zero over most of the frequency range. The extreme lim it of controllability corresponded to a time to double amplitude of the oscillation of about 1 - 1/2 seconds. In the statically unstable region somewhat shorter times to double amplitude were acceptable to the pilots. The boundary for emergency operation corresponded roughly to time to double amplitude of about 2/3 second and the limit of controllability of about l/3 second.

McFadden, Norman M.↗

Continuously bounds-preserving discontinuous Galerkin methods for hyperbolic conservation laws

For finite element approximations of transport phenomena, it is often necessary to apply a form of limiting to ensure that the discrete solution remains well-behaved and satisfies physical constraints. However, these limiting procedures are typically performed at discrete nodal locations, which is not sufficient to ensure the robustness of the scheme when the solution must be evaluated at arbitrary locations (e.g., for adaptive mesh refinement, remapping in arbitrary Lagrangian–Eulerian solvers, overset meshes, etc.). In this work, a novel limiting approach for discontinuous Galerkin methods is presented which ensures that the solution is continuously bounds-preserving (i.e., across the entire solution polynomial) for any arbitrary choice of basis, approximation order, and mesh element type. Through a modified formulation for the constraint functionals, the proposed approach requires only the solution of a single spatial scalar minimization problem per element for which a highly efficient numerical optimization procedure is presented. Here, the efficacy of this approach is shown in numerical experiments by enforcing continuous constraints in high-order unstructured discontinuous Galerkin discretizations of hyperbolic conservation laws, ranging from scalar transport with maximum principle preserving constraints to compressible gas dynamics with positivity-preserving constraints.

97 MATHEMATICS AND COMPUTING↗

Gravitational collapse of small-scale structure as the origin of the Lyman-alpha forest

If gravitational clustering is a hierarchical process, the present large-scale structure of the galaxy distribution implies that structures on smaller scales must have formed at high redshift. We simulate the formation of small-scale structure (average cell mass: (delta) bar m(sub b) = 10(sup 4.2) solar mass) and the evolution of photoionized gas, in the specific case of the CDM + Lambda model. The photoionized gas has a natural minimal scale of collapse, the Jeans scale (m(sub b,J) is approximately equal to 10(exp 9) solar mass). We find that low column density (N(sub HI) is less than or equal to 10(exp 14)/sq cm) lines originate in regions resembling Zel'dovich pancakes, where gas with overdensities in the range 3-30 is enclosed by two shocks but is typically reexpanding at approximately the Hubble velocity. However, higher column density lines stem from more overdense regions where the shocked gas is cooling. We show that this model can probably account for the observed number of lines, their distribution in column density and b-parameters, as well as the cloud physical sizes as observed in gravitationally lensed quasars. We find a redshift evolution that is too steep; however, this may be due to insufficient dynamical range in the simulation or because the specific model is incorrect. The model predicts that high signal-to-noise observations should find systematic deviations from Voigt profiles, mainly in the form of broad wings in the line profiles, and that a fluctuating Gunn-Peterson effect will be detected, which can be modeled as a superposition of weak lines with a wide range of b-parameters.

Cen, Renyue↗

Characterization of lateral amorphous selenium photodetectors for low-photon and VUV detection at cryogenic temperatures

The performance of amorphous selenium (a-Se) as a cryogenic photodetector material is evaluated through a series of experiments using laterally structured devices operated in a custom optical test stand. These studies investigate the response of a-Se detectors to low-photon fluxes at high electric fields near avalanche conditions, the linearity of the photoconductive response over a wide dynamic range and the direct detection of narrowband 130 nm vacuum ultraviolet (VUV) illumination. At 87 K, matched-filter analysis shows reliable single-shot detection with efficiencies ≥80% and area under the curve (AUC) ≥ 0.85 using as few as ∼ 6800 incident 401 nm photons, corresponding to ∼ 3400 photons within field-active regions after accounting for geometric constraints. Measurements are performed at cryogenic temperatures using calibrated photon fluxes derived from a silicon photomultiplier reference and a characterized optical filter stack. Additional experiments using a tellurium-doped a-Se (a-SeTe) device explore the material's behavior under identical test conditions and demonstrate that avalanche is achievable in a-SeTe at cryogenic temperatures. The results demonstrate reproducible low-noise operation, VUV sensitivity and field-dependent gain behavior in a lateral a-Se architecture, representing the first reported observation of avalanche multiplication in laterally structured a-Se and a-SeTe devices at cryogenic temperatures. These findings support the potential integration of laterally structured a-Se devices into next-generation pixelated liquid-argon time projection chambers (TPCs) requiring scalable, high-field-compatible photon detection systems.

Amorphous selenium↗

Dominant balance-based adaptive mesh refinement for incompressible fluid flows

This work introduces a novel adaptive mesh refinement (AMR) method that utilizes dominant balance analysis (DBA) for efficient and accurate grid adaptation in computational fluid dynamics (CFD) simulations. The proposed method leverages a Gaussian mixture model (GMM) to classify grid cells into active and passive regions based on the dominant physical interactions within the equation space. By modeling truncation error probabilistically from discretized terms, the method identifies regions of high interaction where numerical accuracy is most sensitive to resolution. Unlike traditional AMR strategies, this approach does not rely on heuristic-based sensors or user-defined thresholds, providing a fully automated and problem-independent framework for AMR. Applied to the incompressible Navier-Stokes equations for steady and unsteady flow past a cylinder, the DBA-based AMR method achieves comparable accuracy to high-resolution grids while reducing computational costs by up to 70 %. The validation highlights the method’s effectiveness in capturing complex flow features while minimizing grid cells, directing computational resources toward regions with the most critical dynamics. This modular and scalable strategy is adaptable to a wide range of applications, presenting a promising tool for efficient high-fidelity simulations in CFD and other multiphysics domains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Characterization of Lateral Amorphous Selenium Photodetectors for Low-Photon and VUV Detection at Cryogenic Temperatures

The performance of amorphous selenium (a-Se) as a cryogenic photodetector material is evaluated through a series of experiments using laterally structured devices operated in a custom optical test stand. These studies investigate the response of a-Se detectors to low-photon fluxes at high electric fields near avalanche conditions, the linearity of the photoconductive response over a wide dynamic range and the direct detection of narrowband 130 nm vacuum ultraviolet (VUV) illumination. At 87 K, matched-filter analysis shows reliable single-shot detection with efficiencies greater than or equal to 80 percent and area under the curve (AUC) greater than or equal to 0.85 using as few as approximately 6800 incident 401 nm photons, corresponding to approximately 3400 photons within field-active regions after accounting for geometric constraints. Measurements are performed at cryogenic temperatures using calibrated photon fluxes derived from a silicon photomultiplier reference and a characterized optical filter stack. Additional experiments using a tellurium-doped a-Se (a-SeTe) device explore the material's behavior under identical test conditions and demonstrate that avalanche is achievable in a-SeTe at cryogenic temperatures. The results demonstrate reproducible low-noise operation, VUV sensitivity and field-dependent gain behavior in a lateral a-Se architecture, representing the first reported observation of avalanche multiplication in laterally structured a-Se and a-SeTe devices at cryogenic temperatures. These findings support the potential integration of laterally structured a-Se devices into next-generation pixelated liquid-argon time projection chambers (TPCs) requiring scalable, high-field-compatible photon detection systems.

FOS: Physical sciences↗

High Power Intermodulation Measurements up to 30 W of High Temperature Superconducting Filters

We have demonstrated a high power intermodulation measurement set-up capable of delivering 30 W in each of two fundamental tones. For closely spaced frequencies (less than 35 MHz), the dynamic range of the measurement is limited by the nonlinear performance of the mixer in the front end of the HP71210C spectrum analyzer. A tunable TE(sub 011) mode copper cavity was fabricated in which one of the endwalls could be adjusted shifting its resonant frequency between 5.7 and 6.6 GHz. Since the Q-value of this cavity is high, greater than 10(exp 4), and its bandwidth is small, less than 1 MHz, it can be used to attenuate the two fundamental tones relative to one of the harmonic tones, which greatly enhances the dynamic range of the measurement. This set-up can be used to measure the two-tone intermodulation distortion of any passive microwave device, e.g. a HTS filter, a connector, a cable, etc., over a frequency range of 5.9 to 6.4 GHz and a power range of 0.1 to 30 W. The third order intercept (TOI) of a prototype HTS filter measured at powers up to 30 W was +81.3 dBm.

Wilker, Charles↗

A versatile detector system to measure the change states, mass compositions and energy spectra of interplanetary and magnetosphere ions

An instrument is described for measuring the mass and charge state composition as well as the energy spectra and angular distributions of 0.5 to 350 kev/charge ions in interplanetary space and in magnetospheres of planets such as Jupiter and earth. Electrostatic deflection combined with a time-of-flight and energy measurement allows three-parameter analysis of output signals from which the mass, charge states, and energy are determined. Post-acceleration by 30 kV extends the energy range of the detector system into the solar wind and magnetosphere plasma regime. Isotopes of H and He are easily resolved as are individual elements up to Ne and the dominant elements up to and including Fe. This instrument has an extremely large dynamic range in intensity and is sensitive to rare elements even in the presence of high intensity radiation, and is adapted for interplanetary, deep-space, and out-of-the-ecliptic missions, as well as for flights on spacecraft orbiting Jupiter and earth.

Gloeckler, G.↗

Detector noise statistics in the non-linear regime

The statistical behavior of an idealized linear detector in the presence of threshold and saturation levels is examined. It is assumed that the noise is governed by the statistical fluctuations in the number of photons emitted by the source during an exposure. Since physical detectors cannot have infinite dynamic range, our model illustrates that all devices have non-linear regimes, particularly at high count rates. The primary effect is a decrease in the statistical variance about the mean signal due to a portion of the expected noise distribution being removed via clipping. Higher order statistical moments are also examined, in particular, skewness and kurtosis. In principle, the expected distortion in the detector noise characteristics can be calibrated using flatfield observations with count rates matched to the observations. For this purpose, some basic statistical methods that utilize Fourier analysis techniques are described.

Shopbell, P. L.↗