Analyzing Graph Attention Network latent representations to uncover insights in temporal link prediction
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Simpson, Sarah Elizabeth [Sandia National Laborato↗
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Analyzing Graph Attention Network latent representations to uncover insights in temporal link prediction
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Doyle, Casey Lane↗
Laser Powder Bed Fusion (PBF) Additive Manufacturing (AM) of Polymethylpentene(PMP) Analyzing the Impact of Scan Strategy on the Powder Bed Fusion Process [Poster]
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McPhillips, Declan [Savannah River National Labora↗
Computer vision and statistical ML to analyze PBX microstructure and scale-invariance in explosive hotspots
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Maiti, Amitesh [Lawrence Livermore National Labora↗
Expandable Log Analyzing Framework
Prior to my internship, I was informed that a previous intern had built a tool to analyse MongoDB logs and look for invalid access attempts, which served as a great reference point for my project. I was initially tasked with expanding on her prototype and filling in the gaps such as integrating it with the main monitoring tool the lab uses. Eventually, the scope grew, expanding to support other databases and a growing collection of tools. I organized the framework around an observer pattern, meaning one point in the program sending updates to the rest of the framework. Every time a log was read and parsed, it was sent to be processed by the tools, using the type of event as a means to determine which tools should get a chance to act on the log. This decouples the tools from the log reader, making future updates and additions much easier. The framework processes MongoDB logs at ~135,000 entries per second and PostgreSQL logs at ~170,500 entries per second, accurately detecting anomalies such as slow queries and connections from unknown addresses. This framework serves to fill gaps in database monitoring tools currently implemented at the lab, such as tracking failed authentication for PostgreSQL and MongoDB which had very minimal or none before this framework. National labs such as Fermilab hold sensitive data and valuable computing resources, making them attractive targets. Monitoring intrusion attempts on databases is made much easier by this comprehensive monitoring suite.
Clark, Dylan [Unlisted, IL]↗
Expandable Log Analyzing Framework
Prior to my internship, I was informed that a previous intern had built a tool to analyse MongoDB logs and look for invalid access attempts, which served as a great reference point for my project. I was initially tasked with expanding on her prototype and filling in the gaps such as integrating it with the main monitoring tool the lab uses. Eventually, the scope grew, expanding to support other databases and a growing collection of tools. I organized the framework around an observer pattern, meaning one point in the program sending updates to the rest of the framework. Every time a log was read and parsed, it was sent to be processed by the tools, using the type of event as a means to determine which tools should get a chance to act on the log. This decouples the tools from the log reader, making future updates and additions much easier. The framework processes MongoDB logs at ~135,000 entries per second and PostgreSQL logs at ~170,500 entries per second, accurately detecting anomalies such as slow queries and connections from unknown addresses. This framework serves to fill gaps in database monitoring tools currently implemented at the lab, such as tracking failed authentication for PostgreSQL and MongoDB which had very minimal or none before this framework. National labs such as Fermilab hold sensitive data and valuable computing resources, making them attractive targets. Monitoring intrusion attempts on databases is made much easier by this comprehensive monitoring suite.
Clark, Dylan [Unlisted, IL]↗
Analyzing bolide shock source and propagation variability through a case study
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Silber, Elizabeth Allaryce [Sandia National Labora↗
Magnetic Analyzers for X-pinch Accelerated Electron and Ion Beams
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47 OTHER INSTRUMENTATION↗
Enhancing the Visualization of Laue Diffraction for Analyzing Strength Model Parameters
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Biswas, Ayan↗
AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women
Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.
Research & Experimental Medicine↗
Analyzing rotational bands in odd-mass nuclei using effective field theory and Bayesian methods
We recently developed an Effective Field Theory (EFT) for rotational bands in odd-mass nuclei. Here we use EFT expressions to perform a Bayesian analysis of data on the rotational energy levels of 99 Tc, 155,157 Gd, 159 Dy, 167,169 Er, 167,169 Tm, 183 W, 235 U and 239 Pu. The error model in our Bayesian analysis includes both experimental and EFT truncation uncertainties. It also accounts for the fact that low-energy constants (LECs) at even and odd orders are expected to have different sizes. We use Markov Chain Monte Carlo (MCMC) sampling to explore the joint posterior of the EFT and error-model parameters and show both the LECs and the breakdown scale can be reliably determined. We extract the LECs up to fourth order in the EFT and find that, provided we correctly account for EFT truncation errors in our likelihood, results for lower-order LECs are stable as we go to higher orders. LEC results are also stable with respect to the addition of higher-energy data. We extract the expansion parameter for all the nuclei listed above and find a clear correlation between the extracted and the expected value of the inverse breakdown scale, W, based on the single-particle and vibrational energy scales. However, the W that actually determines the convergence of the EFT expansion is markedly smaller than would be naively expected based on those scales.
EFT↗
A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense)
The lipidome comprises the total content of molecular species of each lipid class, and is measured using the analytical techniques of lipidomics. Many liquid chromatography-mass spectrometry (LC-MS) methods have previously been described to characterize the lipidome. However, many lipidomic approaches may not fully uncover the subtleties of lipid molecular species, such as the full fatty acid (FA) composition of certain lipid classes. Here, we describe a stepwise targeted lipidomics approach to characterize the polar and non-polar lipid classes using complementary LC-MS methods. Our “polar” method measures 260 molecular species across 12 polar lipid classes, and is performed using hydrophilic interaction chromatography (HILIC) on a NH2 column to separate lipid classes by their headgroup. Our “non-polar” method measures 254 molecular species across three non-polar lipid classes, separating molecular species on their FA characteristics by reverse phase (RP) chromatography on a C30 column. Five different extraction methods were compared, with an MTBE-based extraction chosen for the final lipidomics workflow. A state-of-the-art strategy to determine and relatively quantify the FA composition of triacylglycerols is also described. This lipidomics workflow was applied to developing, mature, and germinated pennycress seeds/seedlings and found unexpected changes among several lipid molecular species. During development, diacylglycerols predominantly contained long chain length FAs, which contrasted with the very long chain FAs of triacylglycerols in mature seeds. Potential metabolic explanations are discussed. The lack of very long chain fatty acids in diacylglycerols of germinating seeds may indicate very long chain FAs, such as erucic acid, are preferentially channeled into beta-oxidation for energy production.
59 BASIC BIOLOGICAL SCIENCES↗
Assessment of a reconfiguration of the InterSpread Plus US national FMD model as a potential tool to analyze a foot-and-mouth disease outbreak on a single large cattle feedlot in the United States
An incursion of foot-and-mouth disease (FMD) into the United States remains a concern of high importance and would have devastating socioeconomic impacts to the livestock and associated industries. This highly transmissible and infectious disease poses continual risk for introduction into the United States (US), due to the legal and illegal global movement of people, animals, and animal products. While stamping out has been shown to effectively control FMD, depopulation of large cattle feedlots (>50,000 head) presents a number of challenges for responders due to the resources required to depopulate and dispose of large numbers of animals in a timely and effective manner. However, evaluating alternative strategies for FMD control on large feedlots requires a detailed within-farm modeling approach, which can account for the unique structure of these operations. To address this, we developed a single feedlot, within-farm spread model using a novel configuration within the InterSpread Plus (ISP) framework. As proof of concept we designed six scenarios: (i) depopulation - the complete depopulation of the feedlot, (ii) burn-through – a managed “burn-through” where the virus is allowed to spread through the feedlot and only movement restriction and biosecurity are implemented, (iii) firebreak-NV – targeted depopulation of infected pens and adjacent pens without vaccination; (iv) firebreak - targeted depopulation of infected pens and adjacent pens with vaccination of remaining pens; (v) harvest-NV - selective harvest of pens where a 100% movement restriction is applied for 28-30 days, then pens are set for selection to be sent to slaughter, while allowing a controlled “burn-through” without vaccination; and (vi) harvest - selective harvest of pens with vaccination. Overall, the burn-through scenario (ii) had the shortest epidemic duration (31d (30, 33)) median (25th, 75th percentiles), while the firebreak scenario (iv) had the longest (47d (38,55)). Additionally, we found that scenarios implementing depopulation delayed the peak day of infection and reduced the total number of pens infected compared to non-depopulation scenarios.
60 APPLIED LIFE SCIENCES↗
Analyzing the Validity of Brazilian Testing Using Digital Image Correlation and Numerical Simulation Techniques
Characterizing the mechanical behavior of rocks plays a crucial role to optimize the fracturing process in unconventional reservoirs. However, due to the intrinsic anisotropy and heterogeneity in unconventional resources, fracture process prediction remains the most significant challenge for sustainable and economic hydrocarbon production. During the deformation tracking under compression, deploying conventional methods (strain gauge, extensometer, etc.) is insufficient to measure the deformation since the physical attachment of the device is restricted to the size of the sample, monitoring limited point-wise deformation, producing difficulties in data retrieval, and a tendency to lose track in failure points, etc. Where conventional methods are limited, the application of digital image correlation (DIC) provides detailed and additional information of strain evolution and fracture patterns under loading. DIC is an image-based optical method that records an object with a camera and monitors the random contrast speckle pattern painted on the facing surface of the specimen. To overcome the existing limitations, this paper presents numerical modeling of Brazilian disc tests under quasi-static conditions to understand the full-field deformation behaviors and finally, it is validated by DIC. As the direct tensile test has limitations in sample preparation and test execution, the Brazilian testing principle is commonly used to evaluate indirectly the tensile strength of rocks. The two-dimensional numerical model was built to predict the stress distribution and full-field deformation on Brazilian disc under compression based on the assumptions of a homogenous, isotropic and linear elastic material. The uniaxial compression test was conducted using the DIC technique to determine the elastic properties of Spider Berea sandstone, which were used as inputs for the simulation model. The model was verified by the analytical solution and compared with the digital image correlation. The numerical simulation results showed that the solutions matched reasonably with the analytical solutions where the maximum deviation of stress distribution was obtained as 14.59%. The strain evolution (normal and shear strains) and displacements along the central horizontal and vertical planes were investigated in three distinguishable percentages of peak loads (20%, 40%, and 90%) to understand the deformation behaviors in rock. The simulation results demonstrated that the strain evolution contours consistently matched with DIC generated contours with a reasonable agreement. The changes in displacement along the central horizontal and vertical planes showed that numerical simulation and DIC generated experimental results were repeatable and matched closely. In terms of validation, Brazilian testing to measure the indirect tensile strength of rocks is still an issue of debate. The numerical model of fracture propagation supported by digital image correlation from this study can be used to explain the fracturing process in the homogeneous material and can be extended to non-homogeneous cases by incorporating heterogeneity, which is essential for rock mechanics field applications.
58 GEOSCIENCES↗
A Framework to Analyze the Requirements of a Multiport Megawatt-Level Charging Station for Heavy-Duty Electric Vehicles
Widespread adoption of heavy-duty (HD) electric vehicles (EVs) will soon necessitate the use of megawatt (MW)-scale charging stations to charge high-capacity HD EV battery packs. Such a station design needs to anticipate possible station traffic, average and peak power demand, and charging/wait time targets to improve throughput and maximize revenue-generating operations. High-power direct current charging is an attractive candidate for MW-scale charging stations at the time of this study, but there are no precedents for such a station design for HD vehicles. We present a modeling and data analysis framework to elucidate the dependencies of a MW-scale station operation on vehicle traffic data and station design parameters and how that impacts vehicle electrification. This framework integrates an agent-based charging station model with vehicle schedules obtained through real-world vehicle telemetry data analysis to explore the station design and operation space. A case study applies this framework to a Class 8 vehicle telemetry dataset and uses Monte Carlo simulations to explore various design considerations for MW-scale charging stations and EV battery technologies. The results show a direct correlation between optimal charging station placement and major traffic corridors such as cities with ports, e.g., Los Angeles and Oakland. Corresponding parametric sweeps reveal that while good quality of service can be achieved with a mix of 1.2-megawatt and 100-kilowatt chargers, the resultant fast charging time of 35–40 min will need higher charging power to reach parity with refueling times.
33 ADVANCED PROPULSION SYSTEMS↗
Analyzing Potential Failures and Effects in a Pilot-Scale Biomass Preprocessing Facility for Improved Reliability
This study demonstrates a failure identification methodology applied to a preprocessing facility generating conversion-ready feedstocks from biomass meeting conversion process critical quality attribute (CQA) specifications. Failure Modes and Effects Analysis (FMEA) was used as an industrially relevant risk analysis approach to evaluate a logging residue preprocessing system to prepare feedstock for pyrolysis conversion. Risk evaluations considered both system-level and operation unit-level assessments considering process efficiency, product quality, cost, sustainability, and safety. Key outputs included estimations of semi-quantitative risk scores for each failure, identification of the failure impacts, identification of failure causes associated with material attributes and process parameters, ranking success rates of failure detection methods, and speculation of potential mitigation strategies for decreasing failure risk scores. Results showed that deviations from moisture specifications had cascading consequences for other CQAs along with process safety implications. Failures linked to fixed carbon specifications carried the highest risk scores for product quality and process efficiency impacts. As increased throughput can be inversely related to meeting product quality specifications; achieving throughput and other material-based CQAs simultaneously will likely require system optimization or prioritization based on system economics. Ultimately, this work successfully demonstrates FMEA as a risk analysis approach for other bioenergy process systems.
09 BIOMASS FUELS↗
Analyzing BMP2, FGFR, and TGF Beta Expressions in High-Grade Osteosarcoma Untreated and Treated Autografts Using Proteomic Analysis
In the last few decades, biological reconstruction techniques have improved greatly for treating high-grade osteosarcoma patients. To conserve the limb, and its function the affected tumor-bearing bones have been treated using liquid nitrogen and irradiation processes that enable the removal of entire tumors from the bone, and these treated autografts can be reconstructed for the patients. Here, we focus on the expressions of the growth factor family proteins from the untreated and treated autografts that play a crucial role in bone union, remodeling, and regeneration. In this proteomic study, we identify several important cytoskeletal, transcriptional, and growth factor family proteins that showed substantially low levels in untreated autografts. Interestingly, these protein expressions were elevated after treating the tumor-bearing bones using liquid nitrogen and irradiation. Therefore, from our preliminary findings, we chose to determine the expressions of BMP2, TGF-Beta, and FGFR proteins by the target proteomics approach. Using a newly recruited validation set, we successfully validate the expressions of the selected proteins. Furthermore, the increased growth factor protein expression after treatment with liquid nitrogen may contribute to bone regeneration healing, assist in faster recovery, and reduce local recurrence and metastatic spread in high-grade sarcoma patients.
60 APPLIED LIFE SCIENCES↗
New Insights on Plasmin Long Term Stability and the Mechanism of Its Activity Inhibition Analyzed by Quartz Crystal Microbalance
We used the research quartz crystal microbalance (RQCM) to monitor regulatory effects of plasmin and trypsin in the presence of their inhibitor α2-antiplasmin. The gold surface of quartz crystals was modified with a β-casein layer that served as a substrate for protease digestion. The addition of plasmin or trypsin as well as their mixtures with α2-antiplasmin resulted in an increase of resonant frequency, f, and in a decrease of motional resistance, Rm, depending on the molar ratio of protease: antiplasmin. At equimolar concentrations of protease and α2-antiplasmin (5 nM:5 nM) full inhibition of protease activity took place. Monitoring of plasmin activity on an hourly and daily basis revealed a prominent effect of autolysis and decrease of plasmin activity in freshly activated samples. The degree of inhibition as well as plasmin half-life (t1/2 = 2.48 ± 0.28 days) connected with its degradation was determined.
36 MATERIALS SCIENCE↗