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At least 991 records · Page 55

Predicting transcription factor activity using prior biological information

Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.

59 BASIC BIOLOGICAL SCIENCES↗

Subject-specific modeling framework for particle deposition using computational fluid dynamics

Quantifying particle deposition and dose in the respiratory tract requires a physiologically realistic representation and reproducible computational workflows. However, existing modeling frameworks, such as the International Commission on Radiological Protection (ICRP) compartmental models and the Multiple Path Particle Dosimetry (MPPD) tool, lack detailed deposition profiles and subject-specific capabilities. The combination of advances in computer vision algorithms applied to the respiratory tract and Computational Fluid and Particle Dynamics (CFPD) allows high-fidelity simulations of particle behavior in anatomically accurate geometries derived from individual CT scans. The segmentation, preprocessing, and file preparation task for a CFPD simulation was often time-consuming, and no prior studies to-date have yet presented a fully automated framework. This work presents a fully automated workflow to obtain individualized particle deposition profiles in the human respiratory tract. The pipeline starts with segmenting upper and lower airway geometries using morphological and deep learning-based methods, generating three-dimensional (3D) models from CT imaging data. Next, a series of algorithms are presented to quality check and prepare the 3D geometry for a CFD or CFPD simulation. The preprocessing step includes correcting geometric artifacts, enforcing a physically consistent mesh, and automatically identifying and capping multiple outlets, which is required for CFD/CFPD simulations. These processed models are then input into open-source (OpenFOAM) or commercial (StarCCM+) CFD solvers, where flow and transient particle transport equations — including turbulence and particle–wall interactions are solved under realistic breathing conditions. Finally, the resulting particle deposition profiles can be integrated with Monte Carlo radiation transport codes and state-of-the-art computational phantoms to assess organ-specific absorbed doses in scenarios of radioactive aerosol inhalation. The presented work streamlines respiratory tract segmentation, preprocessing for CFD/CFPD simulations, and integration with dose assessment workflows, reducing manual intervention and improving access to high-fidelity, subject-specific modeling. The high precision in predicted particle deposition and dose distributions can improve personalized treatment strategies in respiratory medicine and refine dose estimates for radiation protection.

AI↗

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

Chemical-Free Lithium Separation from High-Salinity Brines Using Model-Informed and Machine Learning-Optimized Multi-Column Zwitterionic Chromatography

Direct Lithium Extraction (DLE) technologies often struggle to produce high-purity lithium salts from high-salinity brines, as current approaches require chemical-based elution, regeneration, and precipitation steps, resulting in significant environmental footprints. A novel salt fractionation approach using carboxybetaine resin, known as zwitterionic chromatography (ZIC), has demonstrated that lithium ions can be separated from divalent cations under high-salinity conditions using only water as eluent, with no regeneration required. To enable continuous and scalable deployment of this approach, we developed a chemical-free Multi-column Zwitterionic Chromatography (MZC) process and its theoretical and process models. To predict and optimize this nontraditional separation system, we introduced a novel anti-Langmuir isotherm, and the isotherm parameters were estimated through a machine learning-driven optimization based on artificial neural network ensembles with numerical feasibility assessment. Using machine learning-driven optimization, the MZC process achieved 98.0% lithium recovery, 99.5 % Li/(Li + Mg + Ca) purity, a 31.3% productivity increase, and a 33% reduction in water use compared to batch operation. The proposed MZC process enables lithium separation at $0.6-1.2 kg-1 Li, with costs dominated by resin manufacturing, while offering lower separation costs and carbon footprint compared with conventional carbonation. Overall, these findings position the MZC process as an effective polishing step within scalable and sustainable lithium production pipelines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Techno-economic and life cycle analysis of synthetic natural gas production from low-carbon H 2 and point-source or atmospheric CO 2 in the United States

Synthetic natural gas (SNG) is of great interest in reducing fossil energy consumption while maintaining compatibility with existing NG infrastructure and end-use applications equipment. SNG can be produced using clean H 2 generated from renewable or nuclear energy and CO 2 captured from stationary sources or the atmosphere. In this study, we develop an engineering process model of SNG production using Aspen Plus® and production scales reported by the industry. We examine the levelized cost and life cycle greenhouse gas (GHG) emissions of SNG production under various CO 2 supply scenarios. Considering the higher cost of H 2 transportation compared with CO 2 transportation, we assume that CO 2 feedstock is transported via pipeline to the H 2 production location, which is collocated with the SNG plant. We also evaluate the cost of CO 2 captured from the atmosphere, assuming the direct air capture process can occur near the SNG facility. Depending on the CO 2 supply chain, the levelized cost of SNG is estimated to be in the range of $\$45–76$ per million British thermal units (MMBtu) on a higher heating value (HHV) basis. The SNG production cost may be reduced to $\$27–57$/MMBtu-HHV by applying a tax credit available in the United States for low-carbon H 2 production (45V). With a lower electricity price of 3¢/kWh for water electrolysis and accounting for a 45V tax credit, the SNG cost reaches parity with the cost of fossil NG. Depending on the CO 2 supply chain, SNG can reduce life cycle GHG emissions by 52–88% compared with fossil NG.

03 NATURAL GAS↗

Implementation of a Mesh refinement algorithm into the quasi-static PIC code QuickPIC

Plasma-based acceleration (PBA) has emerged as a promising candidate for the accelerator technology used to build a future linear collider and/or an advanced light source. In PBA, a trailing or witness particle beam is accelerated in the plasma wave wakefield (WF) created by a laser or particle beam driver. The WF is often nonlinear and involves the crossing of plasma particle trajectories in real space and thus particle-in-cell methods are used. The distance over which the drive beam evolves is several orders of magnitude larger than the wake wavelength. This large disparity in length scales is amenable to the quasi-static approach. Three-dimensional (3D), quasi-static (QS), particle-in-cell (PIC) codes, e.g., QuickPIC, have been shown to provide high fidelity simulation capability with 2-4 orders of magnitude speedup over 3D fully explicit PIC codes. In PBA, the witness beam needs to be matched to the focusing forces of the WF to reduce the emittance growth. In some linear collider designs, the matched spot size of the witness beam can be 2 to 3 orders of magnitude smaller than the spot size (and wavelength) of the wakefield. Such an additional disparity in length scales is ideal for mesh refinement where the WF within the witness beam is described on a finer mesh than the rest of the WF. A mesh refinement scheme is described that has been implemented into the 3D QS PIC code, QuickPIC. Very fine (high) resolution is used in a small spatial region that includes the witness beam and progressively coarser resolutions in the rest of the simulation domain. A fast multigrid Poisson solver has been implemented for the field solve on the refined meshes and a Fast Fourier Transform (FFT) based Poisson solver is used for the coarse mesh. The code has been parallelized with both MPI and OpenMP, and the parallel scalability has also been improved by using pipelining. A preliminary adaptive mesh refinement technique is described to optimize the computational time for simulations with an evolving witness beam size. Several test problems are used to verify that the mesh refinement algorithm provides accurate results. Additionally, the results are benchmarked against highly resolved simulations exhibiting near-azimuthal symmetry, performed using QPAD—a novel hybrid QS PIC code that uses a PIC description in the coordinates (r, ct – z) and a gridless description in the azimuthal angle, Φ.

Linear collider↗

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

In situ feature analysis for large-scale multiphase flow simulations

The study of multiphase flow is essential for designing chemical reactors such as fluidized bed reactors (FBR), as a detailed understanding of hydrodynamics is critical for optimizing reactor performance and stability. An FBR allows scientists to conduct different types of chemical reactions involving multiphase materials, especially interaction between gas and solids. During such complex chemical processes, the formation of void regions in the reactor, generally termed as bubbles, is an important phenomenon. The study of these bubbles has a deep implication in predicting the reactor’s overall efficiency. But physical experiments needed to understand bubble dynamics are costly and non-trivial due to the technical difficulties involved and harsh working conditions of the reactors. Therefore, to study such chemical processes and bubble dynamics, a state-of-the-art computational simulation MFIX-Exa is being developed. Despite the proven accuracy of MFIX-Exa in modeling bubbling phenomena, the large-scale output data prohibits the use of traditional post hoc analysis capabilities in both storage and I/O time. Herein, to address these issues and allow the application scientists to explore the bubble dynamics in an efficient and timely manner, we have developed an end-to-end analytics pipeline that enables in situ detection of bubbles, followed by a flexible post hoc visual exploration methodology of bubble dynamics. The proposed method enables interactive analysis of bubbles, along with quantification of several bubble characteristics, enabling experts to understand the bubble interactions in detail. Positive feedback from the experts has indicated the efficacy of the proposed approach for exploring bubble dynamics in very-large-scale multiphase flow simulations.

97 MATHEMATICS AND COMPUTING↗

Solar photovoltaics is ready to power a sustainable future

Thanks to fast learning and sustained growth, solar photovoltaics (PV) is today a highly cost-competitive technology, ready to contribute substantially to CO 2 emissions mitigation. However, many scenarios assessing global decarbonization pathways, either based on integrated assessment models or partial-equilibrium models, fail to identify the key role that this technology could play, including far lower future PV capacity than that projected by the PV community. In this perspective, we review the factors that lie behind the historical cost reductions of solar PV and identify innovations in the pipeline that could contribute to maintaining a high learning rate. We also aim at opening a constructive discussion among PV experts, modelers, and policymakers regarding how to improve the representation of this technology in the models and how to ensure that manufacturing and installation of solar PV- can ramp up on time, which will be crucial to remain in a decarbonization path compatible with the Paris Agreement.

14 SOLAR ENERGY↗

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗

Hierarchical median narrow band for level set segmentation of cervical cell nuclei

This paper presents a novel hierarchical nuclei segmentation algorithm for isolated and overlapping cervical cells based on a narrow band level set implementation. Our method applies a new multiscale analysis algorithm to estimate the number of clusters in each image region containing cells, which turns into the input to a narrow band level set algorithm. We assess the nuclei segmentation results on three public cervical cell image databases. Overall, our segmentation method outperformed six state-of-the-art methods concerning the number of correctly segmented nuclei and the Dice coefficient reached values equal to or higher than 0.90. We also carried out classification experiments using features extracted from our segmentation results and the proposed pipeline achieved the highest average accuracy values equal to 0.89 and 0.77 for two-class and three-class problems, respectively. Furthermore, these results demonstrated the suitability of the proposed segmentation algorithm to integrate decision support systems for cervical cell screening.

47 OTHER INSTRUMENTATION↗

Identifying multiple synergistic factors on the susceptibility to stress relaxation cracking in variously heat-treated weldments

The 347H austenitic stainless steel has been widely used for pressure vessels and pipeline (PVP) applications due to its excellent creep and corrosion resistance, which fit ideally to the harsh conditions in petrochemical industries, fossil fuel or nuclear power plants, and modern energy storages. However, a failure mode has been commonly observed with cracks emerging at the heat affected zone (HAZ) of weldments during post-weld heat treatment (PWHT) or under intermediate to high temperature service conditions. This phenomenon is termed as Stress Relaxation Cracking (SRC) since the purpose of PWHT is to relieve the welding-induced residual stress fields, or as Stress Age Cracking (SAC) if failure happens during service. A leading literature explanation of this failure suggests that the residual stress relaxation and the precipitation dissolution and/or re-precipitation occur in the same temperature range, which can lead to locally high strains and thus to crack at the grain boundaries. Since in situ spatial measurements of residual stress fields, microstructural evolution, and failure processes are nearly infeasible, this work recourses to a micromechanical finite element framework that models the high temperature failure as the nucleation and growth of grain boundary cavities, whereas various parameters such as thermomechanical loading history and its evolution, the competition of grain-interior dislocation creep and grain-boundary diffusion in failure lifetime, and microstructural heterogeneities (such as the precipitate free zone near grain boundaries) can be quantitatively incorporated. It can be concluded from these microstructure-explicit simulations that an accurate knowledge of residual stress evolution and a carefully calibrated set of material constitutive parameters are the essential prerequisites for lifetime predictions. The understanding of individual governing factors also leads to a mechanistic interpretation of the observed SRC susceptibility C-curves. In conclusion, these results suggest that the criticality of residual stress evolution, but not the precipitation-induced local strains, be the leading factor for SRC.

347H stainless steel weldments↗

NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Understanding the spatial interactions between the elements of the tumor microenvironment -i.e. tumor cells. fibroblasts, immune cells- and how these interactions relate to the diagnosis or prognosis of a tumor is one of the goals of computational pathology. We present NaroNet, a deep learning framework that models the multi-scale tumor microenvironment from multiplex-stained cancer tissue images and provides patient-level interpretable predictions using a seamless end-to-end learning pipeline. Trained only with multiplex-stained tissue images and their corresponding patient-level clinical labels, NaroNet unsupervisedly learns which cell phenotypes, cell neighborhoods, and neighborhood interactions have the highest influence to predict the correct label. To this end, NaroNet incorporates several novel and state-of-the-art deep learning techniques, such as patch-level contrastive learning, multi-level graph embeddings, a novel max-sum pooling operation, or a metric that quantifies the relevance that each microenvironment element has in the individual predictions. We validate NaroNet using synthetic data simulating multiplex-immunostained images where a patient label is artificially associated to the -adjustable- probabilistic incidence of different microenvironment elements. We then apply our model to two sets of images of human cancer tissues: 336 seven-color multiplex-immunostained images from 12 high-grade endometrial cancer patients; and 382 35-plex mass cytometry images from 215 breast cancer patients. In both synthetic and real datasets, NaroNet provides outstanding predictions of relevant clinical information while associating those predictions to the presence of specific microenvironment elements.

60 APPLIED LIFE SCIENCES↗

Solidification and crystallographic texture modeling of laser powder bed fusion Ti-6Al-4V using finite difference-monte carlo method

Laser powder bed fusion (LPBF) additive manufacturing makes near-net-shaped parts with reduced material cost and time, rising as a promising technology to fabricate Ti-6Al-4V, a widely used titanium alloy in aerospace and medical industries. However, LPBF Ti-6Al-4V parts produced with 67° rotation between layers, a scan strategy commonly used to reduce microstructure and property inhomogeneity, have varying grain morphologies and weak crystallographic textures that change depending on processing parameters. Here, this study predicts LPBF Ti-6Al-4V solidification at three energy levels using a finite difference-Monte Carlo method and validates the simulations with large-area electron backscatter diffraction (EBSD) scans. The developed model accurately shows that a <001> texture forms at low energy and a <111> texture occurs at higher energies parallel to the build direction but with a lower strength than the textures observed from EBSD. A validated and well-established method of combining spatial correlation and general spherical harmonics representation of texture is developed to calculate a difference score between simulations and experiments. The quantitative comparison enables effective fine-tuning of nucleation density (N 0 ) input, which shows a nonlinear relationship with increasing energy level. Future improvements in texture prediction code and a more comprehensive study of N 0 with different energy levels will further advance the optimization of LPBF Ti-6Al-4V components. These developments contribute a novel understanding of crystallographic texture formation in LPBF Ti-6Al-4V, the development of robust model validation and calibration pipeline methodologies, and provide a platform for mechanical property prediction and process parameter optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cascading economic losses from port disruptions under capacity constrained multimodal freight networks

This study quantifies how throughput disruptions at major seaports cascade through capacity-constrained multimodal freight networks and interregional production systems. We couple an agent-based model (ABM) multimodal freight simulation that resolves rerouting, terminal queueing, and inventory drawdown under binding modal and facility capacities with a multiregional output loss input-output (MRIIM) model that propagates realized delivery shortfalls across regions and sectors. The framework is demonstrated for the Port of Los Angeles using Freight Analysis Framework flows and Bureau of Economic Analysis input-output accounts and is evaluated over a 52-week horizon under deterministic sector targeted shocks and stochastic disruption realizations with uncertain severity and duration. Results indicate nonlinear amplification: realized national losses concentrate in manufacturing and transportation/warehousing even when exogenous port shocks are dispersed, suggesting that congestion spillback and limited short-run substitution can dominate the initial shock allocation. We further evaluate a tabular reinforcement-learning (Q-learning) intervention layer that selects among a small set of implementable system level levers (truck-to-rail and truck-to-barge shift settings) without overriding shipper routing, finding that such interventions reduce total losses for moderate disruptions but yield diminishing returns once substitute modes approach capacity. By linking operational freight behavior to system wide impacts under uncertainty, the proposed ABM-MRIIM pipeline provides a reusable workflow for port disruption stress testing, identification of structurally critical sectors/corridors, and evaluation of resilience interventions under realistic capacity limits.

42 ENGINEERING↗

A secure measurement unit for an inspection system used in nuclear arms-control verification

Verification of arms control treaties may require information barriers to protect sensitive data acquired during the verification process. These information barriers are commonly implemented in software, but must store and operate on data that are vulnerable to attack and tampering. Here, we present a new Secure Measurement Unit based on a modified pipeline SAR ADC architecture. The idea is to move the information barrier back into the digitization process so that prohibited data is never created. A prototype 65nm CMOS Secure Measurement Unit (SMU) was tested using U-235, U-238, Co-60, Cs-137 and Am-241 sources. Here, the prototype accurately digitized allowable signals while being immune to side-channel attacks on signals within preset forbidden regions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The GlueX beamline and detector

The GlueX experiment at Jefferson Lab has been designed to study photoproduction reactions with a 9-GeV linearly polarized photon beam. The energy and arrival time of beam photons are tagged using a scintillator hodoscope and a scintillating fiber array. The photon flux is determined using a pair spectrometer, while the linear polarization of the photon beam is determined using a polarimeter based on triplet photoproduction. Charged-particle tracks from interactions in the central target are analyzed in a solenoidal field using a central straw-tube drift chamber and six packages of planar chambers with cathode strips and drift wires. Electromagnetic showers are reconstructed in a cylindrical scintillating fiber calorimeter inside the magnet and a lead-glass array downstream. Charged particle identification is achieved by measuring energy loss in the wire chambers and using the flight time of particles between the target and detectors outside the magnet. The signals from all detectors are recorded with flash ADCs and/or pipeline TDCs into memories allowing trigger decisions with a latency of 3.3 $μs$. The detector operates routinely at trigger rates of 40 kHz and data rates of 600 megabytes per second. Here, we describe the photon beam, the GlueX detector components, electronics, data-acquisition and monitoring systems, and the performance of the experiment during the first three years of operation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗