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DOE OSTI2026

In-line measurements of below-the-surface food deformation during drying with an interference-based optical fiber strain sensor

Real-time measurements of food deformation are important for quality control in drying, yet they pose significant challenges. In this study, we developed an interference-based optical fiber strain sensor to enable in-line, continuous, below-the-surface strain measurements in drying of soft food samples. Compared to a strain resolution of 8 × 10 -4 at zero strain and 7.2 × 10 -3 at 0.20 strain reported in our previously published work, the present study achieves markedly improved resolutions of 1.3 × 10 -4 at zero strain and 7.8 × 10 -4 at 0.25 strain, which strains are the lower and higher boundaries of the dynamic range, respectively. This nearly order-of-magnitude improvement is attributed to the unique interference-based sensing mechanism, no need for calibration to convert optical signals to strain, and the system-design-enabled immunity to fiber-disk misalignments and light source intensity fluctuations. To demonstrate the in-line process monitoring, deformation measurements of fresh banana slices and sugar cookie doughs were carried out in a benchtop oven and an industrial-scale hot-air pilot dryer, respectively. In both dryers, strain measurements were continuously measured during the whole drying process at various depths and radii below the sample surfaces, with the strains up to 25%. Computer vision was used only in the benchtop drying to confirm the faithfulness of the fiber sensor measurements and cannot provide below-the-surface measurements. The measured spatiotemporal deformation allowed us to confirm the shell-hardening effect and to determine the speed and location of large deformation changes in the whole drying process, the latter of which is related to the sample cracking. To the best of the authors’ knowledge, this study is the first to report on an interferometry-based fiber sensor to measure food deformation. This sensor and the sensing mechanism have high potential for real-time process monitoring and control to prevent over-drying or cracking during drying processes.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

The ABC130 barrel module prototyping programme for the ATLAS strip tracker

For the Phase-II Upgrade of the ATLAS Detector [1], its Inner Detector, consisting of silicon pixel, silicon strip and transition radiation sub-detectors, will be replaced with an all new 100% silicon tracker, composed of a pixel tracker at inner radii and a strip tracker at outer radii. The future ATLAS strip tracker will include 11,000 silicon sensor modules in the central region (barrel) and 7,000 modules in the forward region (end-caps), which are foreseen to be constructed over a period of 3.5 years. The construction of each module consists of a series of assembly and quality control steps, which were engineered to be identical for all production sites. In order to develop the tooling and procedures for assembly and testing of these modules, two series of major prototyping programs were conducted: an early program using readout chips designed using a 250 nm fabrication process (ABCN-250) [2,2] and a subsequent program using a follow-up chip set made using 130 nm processing (ABC130 and HCC130 chips). This second generation of readout chips was used for an extensive prototyping program that produced around 100 barrel-type modules and contributed significantly to the development of the final module layout. This paper gives an overview of the components used in ABC130 barrel modules, their assembly procedure and findings resulting from their tests.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

The upgrade of the ALICE TPC with GEMs and continuous readout

The upgrade of the ALICE TPC will allow the experiment to cope with the high interaction rates foreseen for the forthcoming Run 3 and Run 4 at the CERN LHC. In this article, we describe the design of new readout chambers and front-end electronics, which are driven by the goals of the experiment. Gas Electron Multiplier (GEM) detectors arranged in stacks containing four GEMs each, and continuous readout electronics based on the SAMPA chip, an ALICE development, are replacing the previous elements. The construction of these new elements, together with their associated quality control procedures, is explained in detail. Finally, the readout chamber and front-end electronics cards replacement, together with the commissioning of the detector prior to installation in the experimental cavern, are presented. After a nine-year period of R&D, construction, and assembly, the upgrade of the TPC was completed in 2020.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Production and testing of the powerboard for ATLAS ITk Strip barrel modules

The upgrade of the ATLAS ITk strips detector for HL-LHC will employ a custom PCB (powerboard) for on-module DC-DC conversion, HV switching, and monitoring. Production of about 14100 of such PCBs with high reliability is a big challenge. In this paper we will present the production procedure and quality control (QC) testing system for the powerboards to be installed on ITk Strip barrel modules. During production, about 150 powerboards will be produced every week. Each powerboard will need to pass QC tests before they are assembled to module. The QC tests include thermal cycling between -35 °C and 40 °C, soak test (continuous running of DC-DC converter at high load at 20 °C), and basic functionality and characterization electrical tests of the low voltage (LV), high voltage (HV), and monitoring functions of the powerboard. A custom QC test system is described, which is based on a reusable PCB (active board) with all testing circuits, a one-time powerboard carrier card, and a Z-turn SoC board which hosts and runs the testing program. The production procedure and QC test system has been tested with 400 powerboards during pre-production, and the system has been proven ready for production with the desired testing program, speed, safety, and cost. Performance and typical failures of powerboards observed during the QC test of pre-production powerboards is also presented.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Construction of precision sMDT detector for the ATLAS Muon Spectrometer upgrade

Here, this paper describes the small-diameter monitored drift-tube detector construction at the University of Michigan as a contribution to the ATLAS Muon Spectrometer upgrade for the high-luminosity Large Hadron Collider at CERN. Measurements of the first 30 chambers built at Michigan show that the drift tube wire position accuracy meets the specification of 20 μm. The positions of the platforms for alignment and magnetic field sensors are all installed well within the required precision. The cosmic ray test measurements show single wire tracking resolution of 100 ± 7 μm with an average detection efficiency above 99%. The infrastructure, tooling, techniques, and procedures for chamber production are described in detail. The results from the chamber quality control tests of the first 30 constructed chambers are reported.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Establishing the Quality Assurance programme for the strip sensor production of the ATLAS tracker upgrade including irradiation with neutrons, photons and protons to HL-LHC fluences

The successful pre-production delivery of strip sensors for the new Inner Tracker (ITk) for the upgraded ATLAS detector at the High Luminosity LHC (HL-LHC) at CERN was completed and based on their performance full production has commenced. The overall delivery period is anticipated to last 4 years to complete the approximately 22000 sensors required for the ITk. For Quality Assurance (QA), a number of test structures designed by the collaboration, along with a large area diode and miniature version of the main sensor, are produced in every wafer by the foundry Hamamatsu Photonics K.K (HPK). As well as Quality Control (QC) checks on every main sensor, samples of the QA pieces from each delivery batch are tested both before and after irradiation with results after exposure to neutrons, gammas or protons to fluences and doses corresponding to those anticipated after operation at the HL-LHC to roughly 1.5 times the ultimate integrated luminosity of 4000 fb -1 . In this paper the procedures are presented and the studies carried out to establish that the seven ITk QA Strip Sensor irradiation and test sites meet all the requirements to support this very extensive programme throughout the strip sensor production phase for the ITk project.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Production and testing of the large-area photon detector ArCLight

Compact large-area dielectric photon detectors that ensure modular noble liquid detectors can sense scintillation light signals for triggering and reconstruction purposes with minimal impact to the overall target volume. ArCLight is a small-volume, sizeable sensitive-area detector that consists of a light trap covered in a thin layer of TPB that can be placed inside a time projection chamber's electric field. These sensors are used in the Deep Underground Neutrino Experiment Near Detector liquid argon (DUNE ND-LAr). They are constructed and tested at the University of Bern and will be deployed in the prototype experiment ProtoDUNE-ND. The talk discusses the details of assembling ArCLights, the quality control methods, and the test studies done with LEDs to assess their performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

An extreme thermal cycling reliability test of ATLAS ITk Strips barrel modules

At the end of Run 3 of the Large Hadron Collider (LHC), the accelerator complex will be upgraded to the High-Luminosity LHC (HL-LHC) in order to increase the total amount of data provided to its experiments. To cope with the increased rates of data, radiation, and pileup, the ATLAS detector will undergo a substantial upgrade, including a replacement of the Inner Detector with a future Inner Tracker, called the ITk. The ITk will be composed of pixel and strip sub-detectors, where the strips portion will be composed of 17,888 silicon strip detector modules. During the HL-LHC running period, the ITk will be cooled and warmed a number of times from about -35°C to room temperature as part of the operational cycle, including warm-ups during yearly shutdowns. To ensure ITk Strips modules are functional after these expected temperature changes, and to ensure modules are mechanically robust, each module must undergo ten thermal cycles and pass a set of electrical and mechanical criteria before it is placed on a local support structure. This paper describes the thermal cycling Quality Control (QC) procedure, and results from the barrel pre-production phase (about 5% of the production volume). Additionally, in order to assess the headroom of the nominal QC procedure of 10 cycles and to ensure modules don't begin failing soon after, four representative ITk Strips barrel modules were thermally cycled 100 times — this study is also described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Using additive manufacturing technologies in high-field accelerator magnet coils

Recent advances with additive manufacturing (AM) technologies using various materials allow them to be considered for the manufacture of precise and complicated metal parts of the magnet coils of high field accelerator magnets from aluminum bronze, titanium alloy, stainless steel, etc. The 3D printing technology is also being used to fabricate prototype models of real parts to test and optimize their geometry. This paper discusses the designs of the complex stress-management coil parts developed at Fermilab, their fabrication using AM technologies, and quality control methods and results.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Uncertainty analysis of Raman spectra for measuring ortho-parahydrogen compositions

Determining ortho-parahydrogen compositions at cryogenic temperatures is an important quality control for liquid hydrogen custody exchange. High orthohydrogen compositions lead to an exothermic reaction resulting in increased boil off and increased venting losses of liquid hydrogen product by either the supplier or consumer. Traditional methods for measuring ortho-parahydrogen compositions such as hot-wire anemometry, nuclear magnetic resonance, and infrared spectroscopy are typically inconvenient at best. As the number of cryogenic hydrogen systems continue to increase, there is an increased need for flexible, standardized techniques for post processing composition measurements. A Raman spectrometer implemented in the Cryo-Catalysis Hydrogen Experimental Facility (CHEF) has demonstrated incredible flexibility for composition measurements of cryogenic hydrogen flows through a wide range of temperatures and pressures with the Raman probe in-situ at cryogenic temperatures. This article analyzes the uncertainty of Raman spectroscopy data of cryogenic hydrogen equilibrated at temperatures in IONEX catalyst. Spectra from hydrogen catalyzed to the equilibrium ortho-parahydrogen composition are processed and compared to expected statistical distributions for method verification.

08 HYDROGEN↗

DOE OSTI2022

‘Flux+Mutability’: a conditional generative approach to one-class classification and anomaly detection

Abstract Anomaly Detection is becoming increasingly popular within the experimental physics community. At experiments such as the Large Hadron Collider, anomaly detection is growing in interest for finding new physics beyond the Standard Model. This paper details the implementation of a novel Machine Learning architecture, called Flux+Mutability, which combines cutting-edge conditional generative models with clustering algorithms. In the ‘flux’ stage we learn the distribution of a reference class. The ‘mutability’ stage at inference addresses if data significantly deviates from the reference class. We demonstrate the validity of our approach and its connection to multiple problems spanning from one-class classification to anomaly detection. In particular, we apply our method to the isolation of neutral showers in an electromagnetic calorimeter and show its performance in detecting anomalous dijets events from standard QCD background. This approach limits assumptions on the reference sample and remains agnostic to the complementary class of objects of a given problem. We describe the possibility of dynamically generating a reference population and defining selection criteria via quantile cuts. Remarkably this flexible architecture can be deployed for a wide range of problems, and applications like multi-class classification or data quality control are left for further exploration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

First detection of the BAO signal from early DESI data

We present the first detection of the baryon acoustic oscillations (BAOs) signal obtained using unblinded data collected during the initial 2 months of operations of the Stage-IV ground-based Dark Energy Spectroscopic Instrument (DESI). From a selected sample of 261 291 luminous red galaxies spanning the redshift interval 0.4 < z < 1.1 and covering 1651 square degrees with a 57.9 per cent completeness level, we report a ∼5σ level BAO detection and the measurement of the BAO location at a precision of 1.7 per cent. Using a bright galaxy sample of 109 523 galaxies in the redshift range 0.1 < z < 0.5, over 3677 square degrees with a 50.0 per cent completeness, we also detect the BAO feature at ∼3σ significance with a 2.6 per cent precision. These first BAO measurements represent an important milestone, acting as a quality control on the optimal performance of the complex robotically actuated, fibre-fed DESI spectrograph, as well as an early validation of the DESI spectroscopic pipeline and data management system. Based on these first promising results, we forecast that DESI is on target to achieve a high-significance BAO detection at sub-per cent precision with the completed 5-yr survey data, meeting the top-level science requirements on BAO measurements. This exquisite level of precision will set new standards in cosmology and confirm DESI as the most competitive BAO experiment for the remainder of this decade.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

IGM damping wing constraints on the tail end of reionization from the enlarged XQR-30 sample

ABSTRACT The attenuation of Lyα photons by neutral hydrogen in the intergalactic medium (IGM) at z ≳ 5 continues to be a powerful probe for studying the epoch of reionization. Given a framework to estimate the intrinsic (true) Lyα emission of high-z sources, one can infer the ionization state of the IGM during reionization. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high signal-to-noise quasar spectra between $5.8\lesssim \, z\lesssim \, 6.6$ obtained with VLT/X-shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Lyα emission profiles (obtained via covariance matrix reconstruction of the Lyα and N v emission lines from unattenuated high-ionization emission line profiles; C iv, Si iv + O iv], and C iii]) and (ii) distribution of ionized regions within the IGM using synthetic damping wing profiles drawn from a 1.63 Gpc3 reionization simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionization. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14 -0.12}$ and $0.29\substack{+0.14 -0.13}$ at z = 6.15 and 6.35. Further, we also report 68th percentile upper limits of $\bar{x}_{\mathrm{H\, {\small I}}{}} \lt 0.21$, 0.20, 0.21, and 0.18 at z = 5.8, 5.95, 6.05, and 6.55. These results imply reionization is still ongoing at $5.8\lesssim \, z\lesssim \, 6.55$, consistent with previous results from XQR-30 (dark fraction and Lyα forest) along with other observational probes considered in the literature.

Greig, B. (ORCID:0000000240852094)↗

DOE OSTI2021

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗

DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Self-consistent quasiparticle G W and hybrid functional calculations for Al/InAs/Al heterojunctions: Band offset and spin-orbit coupling effects

The electronic structure of surfaces and interfaces plays a key role in the properties of quantum devices. Here, we study the electronic structure of realistic Al/InAs/Al heterojunctions using a combination of density functional theory with hybrid functionals and state-of-the-art quasiparticle G W (QSGW) calculations. We find a good agreement between QSGW calculations and hybrid functional calculations, which themselves compare favorably well with angle-resolved photoemission spectroscopy experiments. Our paper confirms the need for well-controlled quality of the interfaces to obtain the needed properties of InAs/Al heterojunctions. A detailed analysis of the effects of spin-orbit coupling on the spin splitting of the electronic states shows a linear scaling in k space, related to the two-dimensional nature of some interface states. The good agreement by QSGW and hybrid functional calculations opens the door towards trustable use of an effective approximation to QSGW for studying very large heterojunctions. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗