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At least 541 records · Page 30

Mic-hackathon 2024: hackathon on machine learning for electron and scanning probe microscopy

Microscopy is one of the primary sources of information on materials structure and functionality at the nanometer and atomic scales. The data generated through microscopy is often contained in well-structured datasets, enriched with extensive metadata and sample histories, although not always with the same level of detail or storage format. The broad incorporation of data management plans by major funding agencies ensures the preservation and accessibility of this data. However, deriving insights from these rich datasets remains challenging due to the lack of established code ecosystems, standardized benchmarks, and integration strategies. Correspondingly, the efficiency of data usage is very low, and time expenditures at the analysis stage are enormous. In addition to post-acquisition data analysis, the emergence of application programming interfaces by major microscope manufacturers now creates opportunities for real-time ML-based data analytics to enable automated decision making, and particularly ML-agent controlled real-time microscope operation. Despite these opportunities, there is a significant gap in integrating the ML community with the broader microscopy community, limiting the value that these methods bring to physics and materials discovery and materials optimization. Hackathons address these challenges by fostering collaboration between ML experts and microscopy professionals, encouraging the development of innovative solutions that leverage ML for microscopy and preparing the workforce of the future both for microscopy-intensive domains areas, instrument manufacturers, and ML scientists interested in real world applications for fundamental research, materials optimization, and manufacturing. The hackathon generated benchmark datasets and digital twins of microscopes that further contribute to the development of the field and establish data analysis ecosystems. All the codes can be found at GitHub(https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1) and Zenodo (https://zenodo.org/records/15579940).

97 MATHEMATICS AND COMPUTING↗

The NBS data management technology program

The National Bureau of Standards (NBS) Data Management Technology Program is discussed. The NBS Data Management Technology Program addresses major problems encountered during the following stages of an application's lifetime: requirements analysis and data base design, system selection and implementation, operations management and conversion. Products developed include standard software specifications, guides to best practice, standard data elements and representations, and reports documenting the experiences of other organizations as they attempt to improve the management of their computing resources. Data base Laboratory facilities are maintained for the investigation and analysis of state of the art data base technology. These facilities support collaborative testing with researchers, vendors, users, and standards developers.

Wood, H. M.↗

Fission TPC FY2020 Report (Mid Q2 FY2021): Preliminary 235 U(n,f)/ 6 Li(n,t)α Cross Section Ratio Analysis & Update on the 239 Pu(n,f) Data Collection

Fission TPC L2 Milestone Description: The fission TPC experimental campaign is in its final stages of collecting high precision (n,f) cross section data aimed at improving our understanding of the 239 Pu fission process. During FY 2019 235 U(n,f)/ 6 Li(n,t) ratio data collection began at WNR/LANSCE. This data is the first step in demonstrating the efficacy of 6 Li(n,t) as a diagnostic standard for a 239 Pu(n,f) ratio measurement. In FY 2020 and FY2021, the NIFFTE Collaboration will analyze 235 U(n,f)/ 6 Li(n,t) data already collected to establish this technique in preparation for 239 Pu(n,f)/ 6 Li(n,t) ratio data. Additionally, the ability to vapor deposit 239 Pu was developed in 2019, greatly improving target quality. As access to experimental facilities allows, 239 Pu/ 235 U and 239 Pu/ 6 Li data will be collected to provide new inputs for evaluation of the 239 Pu(n,f) cross section.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Autoignition of cyclohexane at low-to-intermediate temperatures: Rapid compression machine experiments and improved comprehensive chemical kinetic model

Cycloalkanes are an important class of hydrocarbons found in conventional and alternative transportation fuels. Being one of the simplest practical cycloalkanes, cyclohexane is often used as a surrogate in studies to understand the oxidation, ignition, and sooting characteristics of cycloalkanes more broadly. Although cyclohexane has been extensively studied, very limited datasets for cyclohexane oxidation at low-to-intermediate temperatures are available in the literature. Moreover, the literature autoignition data from rapid compression machines (RCMs) did not provide information on volume histories or experimental heat transfer characteristics which can significantly impact model predictions, thereby hindering the detailed validation of chemical kinetic models. It has also been observed that the cyclohexane kinetic models developed so far are not able to predict the literature data across a wide range of operating and mixture conditions. Hence, further studies are recommended to understand and improve model predictions for cyclohexane oxidation. In this study, RCM experiments were conducted using cyclohexane/air mixtures at varying compressed pressures (P C =15, 20, and 30 bar), equivalence ratios (ϕ=0.5, 1.0, and 2.0), and compressed temperatures (T C =670–960 K). The current RCM results of cyclohexane were found to complement well with the literature data, with the first-stage IDTs at high pressures and volume histories at all test conditions being first reported for better development and validation of chemical kinetic models. Additionally, a detailed chemical kinetic model for the cyclohexane oxidation has been developed and validated using both newly acquired experimental IDTs in this study and literature experimental studies (IDTs in RCMs and STs, species profiles in jet-stirred reactors, and laminar burning velocities). Unlike literature models, the proposed model was observed to provide an overall better prediction for experimental results over a wide range of conditions. Chemical kinetic analysis of the developed model was further conducted to identify the reaction pathways controlling the autoignition of cyclohexane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-dimensional multivariate autoregressive model estimation of human electrophysiological data using fMRI priors

Multivariate autoregressive (MVAR) model estimation enables assessment of causal interactions in brain networks. However, accurately estimating MVAR models for high-dimensional electrophysiological recordings is challenging due to the extensive data requirements. Hence, the applicability of MVAR models for study of brain behavior over hundreds of recording sites has been very limited. Prior work has focused on different strategies for selecting a subset of important MVAR coefficients in the model to reduce the data requirements of conventional least-squares estimation algorithms. Here we propose incorporating prior information, such as resting state functional connectivity derived from functional magnetic resonance imaging, into MVAR model estimation using a weighted group least absolute shrinkage and selection operator (LASSO) regularization strategy. The proposed approach is shown to reduce data requirements by a factor of two relative to the recently proposed group LASSO method of Endemann et al (Neuroimage 254:119057, 2022) while resulting in models that are both more parsimonious and more accurate. The effectiveness of the method is demonstrated using simulation studies of physiologically realistic MVAR models derived from intracranial electroencephalography (iEEG) data. The robustness of the approach to deviations between the conditions under which the prior information and iEEG data is obtained is illustrated using models from data collected in different sleep stages. This approach allows accurate effective connectivity analyses over short time scales, facilitating investigations of causal interactions in the brain underlying perception and cognition during rapid transitions in behavioral state.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III

Abstract Plants make complex and potent therapeutic molecules 1,2 , but sourcing these molecules from natural producers or through chemical synthesis is difficult, which limits their use in the clinic. A prominent example is the anti-cancer therapeutic paclitaxel (sold under the brand name Taxol), which is derived from yew trees (Taxusspecies) 3 . Identifying the full paclitaxel biosynthetic pathway would enable heterologous production of the drug, but this has yet to be achieved despite half a century of research 4 . WithinTaxus’ large, enzyme-rich genome 5 , we suspected that the paclitaxel pathway would be difficult to resolve using conventional RNA-sequencing and co-expression analyses. Here, to improve the resolution of transcriptional analysis for pathway identification, we developed a strategy we term multiplexed perturbation × single nuclei (mpXsn) to transcriptionally profile cell states spanning tissues, cell types, developmental stages and elicitation conditions. Our data show that paclitaxel biosynthetic genes segregate into distinct expression modules that suggest consecutive subpathways. These modules resolved seven new genes, allowing a de novo 17-gene biosynthesis and isolation of baccatin III, the industrial precursor to Taxol, inNicotiana benthamianaleaves, at levels comparable with the natural abundance inTaxusneedles. Notably, we found that a nuclear transport factor 2 (NTF2)-like protein, FoTO1, is crucial for promoting the formation of the desired product during the first oxidation, resolving a long-standing bottleneck in paclitaxel pathway reconstitution. Together with a new β-phenylalanine-CoA ligase, the eight genes discovered here enable the de novo biosynthesis of 3’-N-debenzoyl-2’-deoxypaclitaxel. More broadly, we establish a generalizable approach to efficiently scale the power of co-expression analysis to match the complexity of large, uncharacterized genomes, facilitating the discovery of high-value gene sets.

Science & Technology - Other Topics↗

Experimental characterization of discharge plasma dynamics in a square capillary for prospective applications in laser wakefield acceleration

Research on plasma generated by electrical discharge in gas-filled capillaries plays an important role in advancing laser wakefield accelerators. We present a comprehensive study of the temporal and spatial distribution of plasma density within a short, 1 cm long, square-shaped capillary filled with hydrogen gas. Two transverse capillary sizes, 500 μm and 300 μm, were investigated achieving peak plasma densities of 0.9 × 10 18 cm −3 and 2.5 × 10 18 cm −3 , respectively, at the capillary center. In addition, we explore how these distributions depend on discharge parameters, specifically discharge current and gas flow through the capillary. Plasma density was determined by analyzing the Stark broadening of the hydrogen Balmer-alpha line. The results obtained were compared with the theoretical models and simulations. The comparison between the model predictions and the experimental data at the transient ionization stage of the discharge reveals a discrepancy of a factor of ∼1.3–2.1, depending on the capillary size, which is thoroughly discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Redshift space power spectrum beyond Einstein-de Sitter kernels

Abstract We develop a framework to compute the redshift space power spectrum (PS), with kernels beyond Einstein-de Sitter (EdS), that can be applied to a wide variety of generalized cosmologies. We build upon a formalism that was recently employed for standard cosmology in Chen, Vlah & White (2020), and utilize an expansion of the density-weighted velocity moment generating function that explicitly separates the magnitude of the k-modes and their angle to the line-of-sight direction dependencies. We compute the PS for matter and biased tracers to 1-loop Perturbation Theory (PT) and show that the expansion has a correct infrared and ultraviolet behavior, free of unwanted divergences. We also add Effective Field Theory (EFT) counterterms, necessary to account for small-scale contributions to PT, and employ an IR-resummation prescription to properly model the smearing of the BAO due to large scale bulk flows within Standard-PT. To demonstrate the applicability of our formalism, we apply it on the ΛCDM and the Hu-Sawicki f(R) models, and compare our numerical results against the elephant suite of N-body simulations, finding very good agreement up to k = 0.27 Mpc -1 h at z = 0.5 for the first three non-vanishing Legendre multipoles of the PS. To our knowledge, the model presented in this work is the most accurate theoretical EFT-PT for modified gravity to date, being the only one that accounts for beyond linear local biasing in redshift-space. Hence, we argue our RSD modeling is a promising tool to construct theoretical templates in order to test deviations from ΛCDM using real data obtained from the next stage of cosmological surveys such as DESI and LSST.

Astronomy & Astrophysics↗

‘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↗

SpectraCodec: A Hilbert curve-based method for encoding metadata in mass spectra for machine learning applications (SpectraCodec) v1

Machine learning approaches to mass spectrometry (MS) data analysis require structured metadata for optimal performance. However, current MS file formats necessitate external metadata sources, creating integration challenges that impede analytical workflows. Here, we present a novel approach for encoding metadata directly within mzML files using one-hot encoding of ASCII characters mapped via Hilbert space-filling curves. This strategy embeds metadata in the first spectrum's m/z-intensity space, ensuring persistence with the primary data, eliminating the need for external metadata files, and maintaining compatibility with existing MS software. We demonstrate that the Hilbert curve mapping efficiently utilizes the two-dimensional spectral space while maintaining robust data recovery. This method offers a practical solution for machine learning applications in mass spectrometry by ensuring metadata and spectral data remain unified through all stages of analysis.

Bowen, Benjamin [Lawrence Berkeley National Labora↗

The precession frequency measurement in the Muon $g - 2$ experiment at Fermilab

The Muon g-2 (E989) experiment aims to reduce the uncertainty on the muon magnetic anomaly value (aμ = g-22 ) by a factor four (0.14 ppm) compared to the previous experiment at Brookhaven National Laboratory (BNL) in order to clarify the difference (now greater than 3 σ) between the experimental value and the Standard Model (SM) prediction. E989 collected a dataset with the same statistical power of the BNL experiment during the Run 1 data taking (2018). The analysis of data is approaching the final stage and the first result should become available in2021. In this paper, I will briefly describe the experimental setup and discuss the measure of the muon’s spin anomalous precession frequency.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Post-DTL Beam Delivery

Ensuring that the beam delivered from the upgraded Front-End (FE) meets the Key Performance Parameters (KPPs) at each user facility is critical to the success of the LANSCE Accelerator Modernization Project (LAMP). For a high-intensity, multi-user facility like LANSCE, compliance with beam loss and radiation thresholds is as important as the charge delivered to each target. While early LAMPF/LANSCE operations relied on iterative tuning to minimize losses from beam halo and tail particles, the new FE may introduce different beam distributions and loss modes—making predictive modeling essential. To manage this, the F2E (Front-End to End) effort is developing detailed particle-tracking models that reflect realistic beamline conditions, including halo formation and expected diagnostic readings. These "snapshot" simulations aim to benchmark live machine performance at a given moment. This will help quantify how beam quality from the new FE will propagate downstream through the facility. Only by validating these models can we confidently assess and mitigate the potential impacts of the LAMP FE on beam delivery. Post-DTL, the beam splits to serve five major user facilities. Historically, low-energy beam transport has been modeled using TRACE, and higher-energy sections with TRANSPORT. These have now been unified into MAD-X format and validated with codes such as Elegant, pyOrbit, XSuite, Impact-Z, and HPSim. The primary focus now is on accurate modeling of full particle distributions (including beam halo) as they traverse the accelerator and beamlines to each experimental station. All models are at various stages of validation with empirical data.

43 PARTICLE ACCELERATORS↗

The effects of exercise training interventions on depression in hemodialysis patients

Purpose Depression considerably influences the clinical outcomes, treatment compliance, quality of life, and mortality of hemodialysis patients. Exercise plays a beneficial role in depressive patients, but its quantitative effects remain elusive. This study aimed to summarize the effects of exercise training on depression in patients with end-stage renal disease undergoing hemodialysis. Methods The PUBMED, EMBASE, and Cochrane Library databases were systematically searched from inception to April 2023 to identify published articles reporting the effect of exercise training on the depression level of patients with End-Stage Renal Disease undergoing hemodialysis. Data were extracted from the included studies using predefined data fields by two independent researchers. The Cochrane Handbook for Systematic Reviews of Interventions and Joanna Briggs Institute Critical Appraisal Checklist for Quasi-Experimental Studies were employed for quality evaluation. Results A total of 22 studies enrolling 1,059 patients who participated in exercise interventions were included. Hemodialysis patients exhibited superior outcomes with intradialytic exercise (SMD = −0.80, 95% CI: −1.10 to −0.49) and lower levels of depression following aerobic exercise (SMD = −0.93, 95%CI: −1.32 to −0.55) compared to combined exercise (c − 0.85, 95% CI: −1.29 to −0.41) and resistance exercise (SMD = −0.40, 95%CI: −0.96 to 0.17). Regarding exercise duration, patients manifested lower depression levels when engaging in exercise activities for a duration exceeding 6 months (SMD = −0.92, 95% CI: −1.67 to −0.17). Concerning the duration of a single exercise session, the most significant improvement was noted when the exercise duration exceeded 60 min (SMD = −1.47, 95% CI: −1.87 to −1.06). Conclusion Our study determined that exercise can alleviate depression symptoms in hemodialysis patients. This study established the varying impacts of different exercise parameters on the reduction of depression levels in hemodialysis patients and is anticipated to lay a theoretical reference for clinicians and nurses to devise tailored exercise strategies for interventions in patients with depression. Systematic review registration https://www.crd.york.ac.uk/prospero/ , This study was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database, with registration number CRD42023434181.

Yu, Huihui↗

Optimization of the Observing Cadence for the Rubin Observatory Legacy Survey of Space and Time: A Pioneering Process of Community-focused Experimental Design

Vera C. Rubin Observatory is a ground-based astronomical facility under construction, a joint project of the National Science Foundation and the U.S. Department of Energy, designed to conduct a multipurpose 10 yr optical survey of the Southern Hemisphere sky: the Legacy Survey of Space and Time. Significant flexibility in survey strategy remains within the constraints imposed by the core science goals of probing dark energy and dark matter, cataloging the solar system, exploring the transient optical sky, and mapping the Milky Way. The survey’s massive data throughput will be transformational for many other astrophysics domains and Rubin’s data access policy sets the stage for a huge community of potential users. To ensure that the survey science potential is maximized while serving as broad a community as possible, Rubin Observatory has involved the scientific community at large in the process of setting and refining the details of the observing strategy. The motivation, history, and decision-making process of this strategy optimization are detailed in this paper, giving context to the science-driven proposals and recommendations for the survey strategy included in this Focus Issue.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Data processing 1: Advancements in machine analysis of multispectral data

Multispectral data processing procedures are outlined beginning with the data display process used to accomplish data editing and proceeding through clustering, feature selection criterion for error probability estimation, and sample clustering and sample classification. The effective utilization of large quantities of remote sensing data by formulating a three stage sampling model for evaluation of crop acreage estimates represents an improvement in determining the cost benefit relationship associated with remote sensing technology.

Swain, P. H.↗

Fan noise and performance

Tradeoffs between aerodynamic and acoustic properties of various fan configurations led to the selection of a variety of fans that produce noise levels in the range of 100 to 120 PNdb. Fan configuration and design pressure ratio required for specific mission operations depend in part on the type of mission to be performed. Noise data obtained for single-stage low speed fans, single-stage high speed fans, and two-stage fan engines are presented in table form.

Kramer, J. J.↗

The interaction between an impact-produced neutral gas cloud and the solar wind at the lunar surface

On Apr. 15, 1970, the Apollo 13 S-IVB stage impacted the nighttime lunar surface. Beginning 20 sec after impact, the Suprathermal Ion Detector Experiment and the Solar Wind Spectrometer observed a large flux of positive ions (maximum flux of about 3 x 10 to the 8th ions/sq cm/sec/ster) and electrons. Two separate streams of ions were observed: a horizontal flux that appeared to be deflected solar wind ions and a smaller vertical flux of predominantly heavy ions (greater than 10 amu), which probably were material vaporized from the S-IVB stage. An examination of the data shows that collisions between neutral molecules and hot electrons (50 eV) were probably an important ionization mechanism in the impact-produced neutral gas cloud. These electrons, which were detected by the Solar Wind Spectrometer, are thought to have been energized in a shock front or some form of intense interaction region between the cloud and the solar wind. Thus strong ionization and acceleration are seen under conditions approaching a collisionless state.

Lindeman, R. A.↗