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At least 271 records · Page 15

Transplatformer: translating toxicogenomic profiles between generations of platforms

Background Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. Results We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation ( ≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra Conclusions TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

59 BASIC BIOLOGICAL SCIENCES↗

In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots

Abstract Background Nitrate (NO 3 − ) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good ( in-vivo ) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ . Results As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5–10 mM). These results were validated through destructive measurement of nitrate concentration. Conclusions We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.

Fernández González, Alma↗

Comparison of pyrometry and thermography for thermal analysis of thermite reactions

This article examines the thermal behavior of a laser ignited thermite composed of aluminum and bismuth trioxide. Temperature data were collected during the reaction using a four-color pyrometer and a high-speed color camera modified for thermography. The two diagnostics were arranged to collect data simultaneously, with similar fields of view and with similar data acquisition rates, so that the two techniques could be directly compared. Results show that at initial and final stages of the reaction, a lower signal-to-noise ratio affects the accuracy of the measured temperatures. Both diagnostics captured the same trends in transient thermal behavior, but the average temperatures measured with thermography were about 750 K higher than those from the pyrometer. This difference was attributed to the lower dynamic range of the thermography camera’s image sensor, which was unable to resolve cooler temperatures in the field of view as well as the photomultiplier tube sensors in the pyrometer. Overall, while the camera could not accurately capture the average temperature of a scene, its ability to capture peak temperatures and spatial data make it the preferred method for tracking thermal behavior in thermite reactions.

36 MATERIALS SCIENCE↗

Frequency-domain terahertz spectroscopy using long-carrier-lifetime photoconductive antennas

We present a telecommunication-compatible frequency-domain terahertz spectroscopy system realized by novel photoconductive antennas without using short-carrier-lifetime photoconductors. Built on a high-mobility InGaAs photoactive layer, these photoconductive antennas are designed with plasmonics-enhanced contact electrodes to achieve highly confined optical generation near the metal/semiconductor surface, which offers ultrafast photocarrier transport and, hence, efficient continuous-wave terahertz operation including both generation and detection. Consequently, using two plasmonic photoconductive antennas as a terahertz source and a terahertz detector, we successfully demonstrate frequency-domain spectroscopy with a dynamic range more than 95 dB and an operation bandwidth of 2.5 THz. Moreover, this novel approach to terahertz antenna design opens up a wide range of new possibilities for many different semiconductors and optical excitation wavelengths to be utilized, therefore bypassing short-carrier-lifetime photoconductors with limited availability.

36 MATERIALS SCIENCE↗

High-speed fiber-coupled terahertz time-domain spectroscopy system using a bias-free plasmonic source

We demonstrate a high-speed fiber-coupled terahertz time-domain spectroscopy (THz-TDS) system using a bias-free plasmonic terahertz source. The system is powered by a compact, low-power femtosecond fiber laser oscillator that drives a dual-branch fiber amplifier to pump and probe a plasmonic terahertz source and detector, respectively. A polarization-maintaining, fiber-coupled optical delay line is employed to precisely control the temporal offset between the pump and probe beams through a compact, robust platform. Operating in the self-similar amplification regime, the fiber amplifiers are engineered to mitigate nonlinear pulse distortion and dispersion while delivering robust, high-energy pulses at a 1560-nm wavelength, with an output power exceeding 326 mW. In reflection mode, the THz-TDS system achieves a peak dynamic range of 81 dB and a bandwidth greater than 3.5 THz at a scan rate of 3.75 Hz. The utility of the system for rapid sensing is further demonstrated by quantifying the porosity and density of pharmaceutical tablets through measurements of their physical thickness and effective refractive index.

Jiang, Xinghe [University of California, Los Angel↗

Distributed Brillouin fiber laser sensor

Brillouin fiber sensors can provide distributed strain and temperature measurements over long distances in standard off-the-shelf fiber by measuring the Brillouin frequency shift as a function of position along a fiber. The primary drawback of these systems is their limited sensitivity, which results from the challenge in identifying the Brillouin frequency shift to within a small fraction of the Brillouin linewidth. In this work, we introduce a technique that overcomes this fundamental limitation by establishing a series of lasing modes that experience Brillouin amplification at discrete spatial locations in the test fiber. The linewidth narrowing and high intensity associated with the lasing transition enable precise measurements of this lasing frequency. As an initial demonstration, we present a sensor that simultaneously excites 40 lasing modes in a 400 m fiber, providing a measurement of the strain at 40 discrete locations with a spatial resolution of 4 m. Each sensor exhibits a minimum detectable strain as low as 4 nε/Hz 1/2 with a dynamic range of >5 mε and a bandwidth of ~10 kHz. As the first demonstration that Brillouin lasing can be used for distributed fiber sensing, this work establishes an approach that could enable ultra-high strain sensitivity using off-the-shelf fiber.

47 OTHER INSTRUMENTATION↗

Temporal and spatial tuning of optical constants in praseodymium doped ceria by electrochemical means

Abstract Temporal and spatial tuning of the refractive index of optical thin films is desired for flat optics applications. The redistribution of mobile ions in mixed ionic-electronic conductors (MIEC) has been demonstrated to serve as a viable means for achieving optical tuning down to the nanoscale. Here we studied the dynamic range of the optical tuning achievable in the refractive index, in the MIEC oxide – Pr x Ce 1− x O 2− δ (PCO), for x = 0.1, 0.2 and 0.4, at 500 °C, by in-situ spectrophotometry. Significant increases in the modulation of both the imaginary and real optical constants in the visible and the adjacent spectra were obtained for increased doping levels. Device employing an electrochemical titration method was implemented to modulate the oxygen concentration, and thereby the optical transmission of PCO. Incorporation of a patterned top electrode allowed for the demonstration of spatial control of PCO thin film properties by in-situ video imaging of the optical switching process. The electrochemically induced optical state is shown to remain non-volatile upon quenching the device to room temperature under applied bias.

36 MATERIALS SCIENCE↗

Extraction of the electron excess temperature in terahertz quantum cascade lasers from laser characteristics

Abstract We propose a method to extract the upper laser level’s (ULL’s) excess electronic temperature from the analysis of the maximum light output power ( P max ) and current dynamic range Δ J d = ( J max − J th ) of terahertz quantum cascade lasers (THz QCLs). We validated this method, both through simulation and experiment, by applying it on THz QCLs supporting a clean three-level system. Detailed knowledge of electronic excess temperatures is of utmost importance in order to achieve high temperature performance of THz QCLs. Our method is simple and can be easily implemented, meaning an extraction of the excess electron temperature can be achieved without intensive experimental effort. This knowledge should pave the way toward improvement of the temperature performance of THz QCLs beyond the state-of-the-art.

47 OTHER INSTRUMENTATION↗

Fiber-Optic Sensing for Earthquake Hazards Research, Monitoring, and Early Warning

The use of fiber‐optic sensing systems in seismology has exploded in the past decade. Despite an ever‐growing library of ground‐breaking studies, questions remain about the potential of fiber‐optic sensing technologies as tools for advancing if not revolutionizing earthquake‐hazards‐related research, monitoring, and early warning systems. A working group convened to explore these topics; we comprehensively examined the application of fiber optics in various aspects of earthquake hazards, encompassing earthquake source processes, crustal imaging, data archiving, and technological challenges. There is great potential for fiber‐optic systems to advance earthquake monitoring and understanding, but to fully unlock their capabilities requires continued progress in key areas of research and development, including instrument testing and validation, increased dynamic range for applications focused on larger earthquakes, and continued improvement in subsurface and source imaging methods. A key current stumbling block results from the lack of clear data archiving requirements, and we propose an initial strategy that balances data volume requirements with preserving key data for a broad range of future studies. In addition, we demonstrate the potential for fiber‐optic sensing to impact monitoring efforts by documenting the data completeness in a number of long‐term experiments. Finally, we outline the features of a instrument testing facility that would enable progress toward reliable and standardized distributed acoustic sensing data. Overcoming these current obstacles would facilitate progress in fiber‐optic sensing and unlock its potential application to a broad range of earthquake hazard problems.

58 GEOSCIENCES↗

Measurements at peak operational beam current in the SNS beam test facility

Work at the SNS beam test facility has focused on high dimensional and high dynamic range measurements of the medium energy (2.5 Mev) beam distribution. This is motivated by the need to understand and predict beam losses down to one-part-per-million. The initial demonstration of full-and-direct 6D phase space measurement was done at a current of 40 mA transported through the RFQ. Since that demonstration, more detailed studies have been performed at lower transported currents (in the range 30 mA and below). This is due to a hardware change - recent runs utilize the original SNS RFQ, which after a decade of service in the SNS achieves transmission significantly below design (50-60%, vs >80%). A short run in 2023 with a newly-commissioned RFQ enables maximum transmission. Preliminary results from beam distribution measurements during this run are discussed.

Ruisard, Kiersten↗

Recent progress in laser wire-based H- beam diagnostics at the SNS linac

Laser wire has been used for nonintrusive profile and emittance measurements of operational hydrogen ion (H-) beam at the SNS linac. In this talk, we will describe the following recent developments in the laser wire system. 1) An upgraded light source and laser transport line which enables novel measurement capabilities including longitudinal profile measurement and high-energy proton beam extraction over potentially an entire macropulse. 2) A dual-detector emittance measurement scheme that boosted the dynamic range by an order of magnitude. 3) Design and implementation laser-wire-based nonintrusive longitudinal phase space measurement system.

Liu, Yun↗

2019 Hyperion 5313A and 5119A Infrasound Sensor Type Approval Evaluation

Sandia National Laboratories has tested and evaluated two variations of a new model of infrasound sensor, the Hyperion 5313A and 5119A. The purpose of this infrasound sensor evaluation is to measure the performance characteristics in such areas as power consumption, sensitivity, full scale, self-noise, dynamic range, response, passband, sensitivity variation due to changes in static pressure and temperature, and sensitivity to vertical acceleration. The Hyperion infrasound sensors are being evaluated for potential use in the International Monitoring System (IMS) of the Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Evaluation of the Nanometrics Centaur Digitizer

Sandia National Laboratories has tested and evaluated a new digitizer, the Centaur, manufactured by Nanometrics, Inc. This digitizer is used to record sensor output for seismic and infrasound monitoring applications. The purpose of the digitizer evaluation was to measure the performance characteristics in such areas as power, sensitivity, self-noise, dynamic range, system noise, modified noise power ration, relative transfer function, analog bandwidth, harmonic distortion, common mode, cross talk, timing tag accuracy and timing drift. The Centaur provides six channels of 24 bit digitization, three of which may be transmitted utilizing CD1.1 protocol.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Kinemetrics Q330M+ Digitizer Evaluation

Sandia National Laboratories has tested and evaluated a new digitizer, the Q330M+, manufactured by Quanterra, a division of Kinemetrics Inc. This digitizer is used to record sensor output for seismic and infrasound monitoring applications. The purpose of the digitizer evaluation was to measure the performance characteristics in such areas as sensitivity, input impedance, power consumption, self noise, dynamic range, system noise, relative transfer function, analog bandwidth, modified noise power ratio, harmonic distortion, common mode, cross talk, timing tag accuracy and timing drift. The Q330M+ provides six channels of 24 bit digitization, all of which may be transmitted utilizing CD1.1 protocol, at multiple sample rates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Guralp Affinity Digitizer Evaluation

Sandia National Laboratories has tested and evaluated a new digitizer, the Affinity, manufactured by Guralp Systems. This digitizer is used to record sensor output for seismic and infrasound monitoring applications. The purpose of the digitizer evaluation was to measure the performance characteristics in such areas as sensitivity, power, self-noise, dynamic range, system noise, relative transfer function, modified noise power ratio, analog bandwidth, harmonic distortion, common mode, cross talk, timing tag accuracy and timing drift. The Affinity provides eight, rather the typical six, channels of 24 bit high sample rate digitization, all of which may be transmitted utilizing the CD1.1 protocol, at multiple sample rates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Nonproliferation Legacy Technology and Artifact Collection: NASA Space Shuttle Tiles

The NASA Space Shuttle Tiles were used by Sandia in the process of developing the Laser Dynamic Range Imager (LDRI) in support of NASA's Return to Flight following the 2003 Space Shuttle Columbia disaster. The heat shield tiles, provided to Sandia by NASA, are identical to those that were located on the underbelly of the Space Shuttle Columbia's orbiter. Sandia used the tiles to test the efficacy of the LDRI's imaging capabilities. The LDRI was utilized during every space shuttle mission between 2005 and 2011. The tiles are currently located in Building 891 and need to be moved to free up space for operational use. Given their technical significance, Sandia would like to archive them as historically significant items in long-term storage until such time as they can be appropriately displayed or employed as a demonstration artifact. This document provides basic information about the provenance of this artifact.

42 ENGINEERING↗

Quantitative Determination of Total Cesium in Savannah River Site (SRS) Tank Waste by Inductively Coupled Plasma Emission Spectroscropy

Utilization of the significant and unique wavelength dynamic range (165 to 1100 nm) available on the Leeman Prodigy Inductively Coupled Plasma Emission Spectroscopy (ICP-ES) allows for quantification of cesium using the emission line 894.347 nm without the potential of Barium interference in nuclear waste samples. Samples are added to a Sodium Peroxide Fusion and Lithium Carbonate buffer in 2% nitric acid solution to increase sensitivity of the easily ionizable (<6 eV) cesium for quantitation to 5 pbb. Through direct comparison of analytical data results, the method is proven to be complementary to the Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis (LOQ 100 ppt) in support of the Department of Energy’s (DOE) Nuclear Waste Mission.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗