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Brown, Ben

Publications and source records attributed to Brown, Ben.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Bioactivity Profiling of Chemical Mixtures for Hazard Characterization

Abstract The assessment and regulation of chemical toxicity to protect human health and the environment are done one chemical at a time and seldom at environmentally relevant concentrations. However, chemicals are found in the environment as mixtures, and their toxicity is largely unknown. Understanding the hazard posed by chemicals within the mixture is critical to enforce protective measures. Here, we demonstrate the application of bioactivity profiling of environmental water samples using the sentinel and ecotoxicology model species Daphnia to reveal the biomolecular response induced by exposure to real-world mixtures. We exposed a Daphnia strain to 30 sampled waters of the Chaobai River and measured the gene expression response profiles. Using a multiblock correlation analysis, we establish correlations between chemical mixtures identified in 30 water samples with gene expression patterns induced by these chemical mixtures. We identified 80 metabolic pathways putatively activated by mixtures of inorganic ions, heavy metals, polycyclic aromatic hydrocarbons, industrial chemicals, and a set of biocides, pesticides, and pharmacologically active substances. Our data-driven approach discovered both known bioactivity signatures with previously described modes of action and new pathways linked to undiscovered potential hazards. This study demonstrates the feasibility of reducing the complexity of real-world mixture toxicity to characterize the biomolecular effects of a defined number of chemical components based on gene expression monitoring of the sentinel species Daphnia.

Engineering↗
DOE OSTI2024

Nuclear Physics Network Requirements Review (Final Report)

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all its laboratories and facilities in the US and abroad. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet interconnects DOE national laboratories, user facilities, and major experiments so that scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large datasets, and access distributed data repositories. ESnet is specifically built to provide Between July 2023 and October 2023, ESnet and the Nuclear Physics program (NP) of the DOE SC organized an ESnet requirements review of NP-supported activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about its relationship to the NP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Learning epistatic polygenic phenotypes with Boolean interactions

Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1 , a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning

We present an ensemble transfer learning method to predict suicide from Veterans Affairs (VA) electronic medical records (EMR). A diverse set of base models was trained to predict a binary outcome constructed from reported suicide, suicide attempt, and overdose diagnoses with varying choices of study design and prediction methodology. Each model used twenty cross-sectional and 190 longitudinal variables observed in eight time intervals covering 7.5 years prior to the time of prediction. Ensembles of seven base models were created and fine-tuned with ten variables expected to change with study design and outcome definition in order to predict suicide and combined outcome in a prospective cohort. The ensemble models achieved c-statistics of 0.73 on 2-year suicide risk and 0.83 on the combined outcome when predicting on a prospective cohort of ~4.2 M veterans. The ensembles rely on nonlinear base models trained using a matched retrospective nested case-control (Rcc) study cohort and show good calibration across a diversity of subgroups, including risk strata, age, sex, race, and level of healthcare utilization. In addition, a linear Rcc base model provided a rich set of biological predictors, including indicators of suicide, substance use disorder, mental health diagnoses and treatments, hypoxia and vascular damage, and demographics. Similar content being viewed by others

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Influence of Molybdenum on Rapid Solidification Microstructure and Microsegregation in Primary Ferrite Solidified Stainless Steel

Due to the widespread use and familiarity of austenitic stainless steels in many industries these alloys are often the first materials used when adapting new processing techniques. The rapid cooling and solidification rates that occur during fusion based additive manufacturing processes like powder bed fusion cause a fundamental shift in the solidification behavior of the material. While the effects that Cr and Ni have on the microstructure have been fairly well documented across a range of solidification conditions, the impact of alloying elements like Mo are not as well understood at rapid solidification rates. For this study, four custom stainless steel alloy feedstocks were made with targeted modification of the Cr and Mo concentrations to maintain a constant Cr/Ni eq ratio of ~1.7. Two-piston splat quenching was used to produce rapidly solidified samples and the solidification mode, phase, and cell size were investigated. Solidification rates were estimated to be between 0.4 and 1.5m/s. A comparison of the microsegregation and partitioning behavior of Cr, Ni and Mo in ferrite solidified material was also performed for the different alloy compositions. Variations of the Mo concentration between each feedstock showed no measurable influence on the solidification/cooling rates, solidification morphology, or the partitioning of Mo. Furthermore, higher concentrations of Mo were found to significantly increase the amount of ferrite phase in the microstructure by suppressing the ferrite to austenite massive transformation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Investigation of the Effect of Chrome and Nickel Concentrations During Two-Piston Splat Quenching of Austenitic Stainless Steels

For solidification rates at or near equilibrium solidification conditions the effects of chrome (Cr) and nickel (Ni) on stainless steel solidification modes and microstructures are well detailed. However, fusion-based additive manufacturing (FBAM) processes that rely on faster, more rapid solidification rates call for a more in-depth understanding of the effects of rapid solidification on the solidification behavior and how these change with variations in alloy composition. Eleven custom stainless steel (SS) alloys with unique compositions based on 316L were made using targeted alloying element additions to generate feedstock with Cr/Ni eq ratios ranging from 0.9 to 2.1. Two-piston splat quenching (SQ) was used to produce rapid solidification conditions similar to those achieved in powder bed fusion processes in a fraction of the time and cost of traditional methods. Employing heat transfer simulations, SEM, TEM, and STEM characterization techniques, the SQ process was found to consistently produce solidification rates estimated to be between ~ 0.4 and 1.6 m/s. Five unique solidification microstructures were identified within the rapidly solidified SQ samples (primary austenite, massively transformed ferrite to austenite, primary austenite and massively transformed ferrite to austenite, primary ferrite, and primary ferrite and massively transformed ferrite to austenite). Both the primary ferrite solidification mode and primary ferrite phase were found to form at lower Cr/Ni eq values than previously predicted. SQ samples with compositions that were within the compositional specifications for 316L SS, an alloy which is commonly used in FBAM processes, demonstrated a wider range of potential solidification modes and microstructures that could form at rapid solidification rates than expected. Finally, by using SQ as a means to simulate rapid solidification conditions similar to those observed in FBAM processes, potential new alloy compositions can be screened faster and more cost effectively than purchasing and running test batches of the metallic powder.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A Comparison of Solidification Structures and Submicroscale Cellular Segregation in Rapidly Solidified Stainless Steels Produced via Two-Piston Splat Quenching and Laser Powder Bed Fusion

Fusion-based additive manufacturing techniques leverage rapid solidification (RS) conditions to create parts with complex geometries, unique microscale/nanoscale morphological features, and elemental segregation. Three custom composition stainless steel alloys with varying chromium equivalence to nickel equivalence ratio (Cr eq /Ni eq ) between 1.53 and 1.95 were processed using laser powder bed fusion (LPBF) and/or two-piston splat quenching (SQ) to produce solidification rates estimated between 0.4 and 0.8 m/s. Both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were utilized to collect high-resolution images, electron backscatter diffraction (EBSD) phase identification, and measure cellular segregation. Similar features were observed in both LPBF and SQ samples including phase and microstructure, nanoscale oxide particles, cell size, and segregation behavior. However, dislocation pileup was observed along the cell boundaries only in the LPBF austenite solidified microstructure. Targeted adjustment of the SQ feedstock Cr and Ni concentrations, within the ASTM A240 specification for 316L resulted in no observable impact on the cell size, oxide particle size, or magnitude of segregation. Also, the amount of Ni segregation in the ferrite solidified microstructures did not significantly differ, regardless of Cr/Ni eq or processing technique. Here, SQ is demonstrated as capable of simulating RS rates and microstructures similar to LPBF for use as an alternative screening tool for new RS alloy compositions.

42 ENGINEERING↗
DOE OSTI2022

Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans

Importance: Suicide is a leading cause of death; however, the molecular genetic basis of suicidal thoughts and behaviors (SITB) remains unknown. Objective: To identify novel, replicable genomic risk loci for SITB. Design, Setting, and Participants: This genome-wide association study included 633 778 US military veterans with and without SITB, as identified through electronic health records. GWAS was performed separately by ancestry, controlling for sex, age, and genetic substructure. Cross-ancestry risk loci were identified through meta-analysis. Study enrollment began in 2011 and is ongoing. Data were analyzed from November 2021 to August 2022. Main Outcome and Measures: SITB. Results: A total of 633 778 US military veterans were included in the analysis (57 152 [9%] female; 121 118 [19.1%] African ancestry, 8285 [1.3%] Asian ancestry, 452 767 [71.4%] European ancestry, and 51 608 [8.1%] Hispanic ancestry), including 121 211 individuals with SITB (19.1%). Meta-analysis identified more than 200 GWS (P < 5 × 10 -8 ) cross-ancestry risk single-nucleotide variants for SITB concentrated in 7 regions on chromosomes 2, 6, 9, 11, 14, 16, and 18. Top single-nucleotide variants were largely intronic in nature; 5 were independently replicated in ISGC, including rs6557168 in ESR1, rs12808482 in DRD2, rs77641763 in EXD3, rs10671545 in DCC, and rs36006172 in TRAF3. Associations for FBXL19 and AC018880.2 were not replicated. Gene-based analyses implicated 24 additional GWS cross-ancestry risk genes, including FURIN, TSNARE1, and the NCAM1-TTC12-ANKK1-DRD2 gene cluster. Cross-ancestry enrichment analyses revealed significant enrichment for expression in brain and pituitary tissue, synapse and ubiquitination processes, amphetamine addiction, parathyroid hormone synthesis, axon guidance, and dopaminergic pathways. Seven other unique European ancestry–specific GWS loci were identified, 2 of which (POM121L2 and METTL15/LINC02758) were replicated. Two additional GWS ancestry-specific loci were identified within the African ancestry (PET112/GATB) and Hispanic ancestry (intergenic locus on chromosome 4) subsets, both of which were replicated. Further, no GWS loci were identified within the Asian ancestry subset; however, significant enrichment was observed for axon guidance, cyclic adenosine monophosphate signaling, focal adhesion, glutamatergic synapse, and oxytocin signaling pathways across all ancestries. Within the European ancestry subset, genetic correlations (r > 0.75) were observed between the SITB phenotype and a suicide attempt-only phenotype, depression, and posttraumatic stress disorder. Additionally, polygenic risk score analyses revealed that the Million Veteran Program polygenic risk score had nominally significant main effects in 2 independent samples of veterans of European and African ancestry.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Fusion Energy Sciences Network Requirements Review. Final Report, April - October 2021

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all of its laboratories and facilities in the US and abroad. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. Throughout 2021, ESnet and the Office of Fusion Energy Sciences (FES) of the DOE SC organized an ESnet requirements review of FES-supported activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about their relationship to the FES program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Local prediction of Laser Powder Bed Fusion porosity by short-wave infrared imaging thermal feature porosity probability maps

We report that local thermal history can significantly vary in parts during metal Additive Manufacturing (AM), leading to local defects. However, the sequential layer-by-layer nature of AM facilitates in-situ part voxelmetric observations that can be used to detect and correct these defects for part qualification and quality control. The challenge is to relate this local radiometric data with local defect information to estimate process error likelihood in future builds. This paper uses a Short-Wave Infrared (SWIR) camera to record the temperature history for parts manufactured with Laser Powder Bed Fusion (LPBF) processes. The porosity from a cylindrical specimen is measured by ex-situ micro-computed tomography (μCT). Specimen data from the SWIR camera, combined with the μCT data, are used to generate thermal feature-based porosity probability maps. The porosity predictions made by various SWIR thermal feature-porosity probability maps of a specimen with a complex geometry are scored against the true porosity obtained via μCT. The receiver operating characteristic curves constructed from the predictions for the complex sample demonstrate the porosity probability mapping methodology’s potential for in-situ based porosity detection.

36 MATERIALS SCIENCE↗