Leveraging Numerical Methods for Efficient Scientific Machine Learning
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Firestone Walker Brewing Company (FWBC), Paso Robles, California, owns a 1-million-barrel (BBL) brewery that requires up to 5 MW of process heat in form of saturated steam. Firestone Walker Brewery has set a goal of reducing carbon emissions by 50% for our 1 million BBL brewery.
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Test systems must be capable of classifying measured data as expected or anomalous in real time. Anomalous results may portend system failure, and, if undetected, may result in damage to the unit, test equipment, or potential harm to personnel. This report investigates the use of Gaussian Mixture Models (GMMs) as a clustering tool in classifying time-series data.
Roadway “corners†are common for pedestrian use, whether designated with markings or not. Different types of markings have been deployed, ranging from simple parallel lines to more complex designs. Understanding the impact of different types of crosswalks is important for public safety. In this work we explore methods to improve the logging of marked crosswalk types. We used the Roadway Information Database from the Second Strategic Highway Research Project and used active learning methods with transfer learning to identify the crosswalk types (marked or unmarked). Upon completion we found our classifiers were unable to perform above roughly 94% correct classifications. To improve their efficacy, we separated the crosswalks into their “fine grained†types and used Gradient-Weighted Class Activation Mapping to isolate and study the features that classified the crosswalks. We compared this with sampled manually marked crosswalks and present findings. We believe this use case can represent a process to improve the active learning method for some visual machine learning applications.
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The aim of this study was to identity variation in drought tolerance across genotypes of Populus deltoides, Populus trichocarpa, and hybrids of the two species. A panel of 102 Populus genotypes, comprising 37 genotypes of P. trichocarpa, 37 of P. deltoides and 28 unique hybrid genotypes (P. trichocarpa x P. deltoides and P. deltoides x P. trichocarpa) were evaluated in the greenhouse under two treatments, well-watered (WW) and drought (DS). Plant physiological data were collected throughout the experiment once the drought treatment began. Throughout the experiment, we tracked soil volumetric water content, pot weight, stomatal conductance, quantum yield of photosystem II, and electron transport rate. In addition to those measurements, upon completion of the experiment, we assessed above and belowground plant biomass, plant height and stem diameter, leaf number, specific leaf area, relative water content, total protein, and total chlorophyll. We obtained hyperspectral signatures of one leaf from each plant at the end of the experiment. Columns BC – LL are hyperspectral averages for one leaf from each plant at each wavelength as described in the column header.
Ace-SABRE and PETALUTE to Detect and Image Hyperpolarized [1-13C]pyruvate Metabolism in Yeast
Digital Imagine and Communications in Medicine (DICOM) images, although most commonly used in medical settings, have been widely adopted by the United States Department of Energy (DOE) for capturing images of the internal components in a nuclear weapon. DICOMs, a lesser-known file format that combine nested metadata structures with complex image data-including multiple planes, frames, and high resolution-require the creation of access copies to support usability within the DOE. Used primarily for ensuring the safety, security, and reliability of the U.S. nuclear stockpile, the Los Alamos National Laboratory (LANL)’s DICOM images and corresponding image metadata must be accessible to scientists and researchers via our institutional centralized databases. This paper describes the author's creation of a Python script that converts DICOM images into accessible, archive-friendly TIFF files while preserving key image data and metadata.
As new highly productive strains of algae are discovered and developed to meet the energy, chemical, and food requirements of the future, genetic engineering of those strains in a manner that yields deployable transformants is paramount. This study introduces the novel CRoxP ($\underline{\textrm{C}}$$\textrm{as9}$ $\underline{\textrm{R}}$$\textrm{NPs}$ coupled with an inducible $\underline{\textrm{CR}}$$\textrm{e}$-$\textrm{l}\underline{\textrm{oxP}}$) system for rapid generation of marker- and transgene-free strains of Picochlorum celeri. The CRoxP system allows reuse of selection markers without Cas9 expression in vivo, eliminating many of the bottlenecks associated with conventional CRISPR Cas9 use for precise genome editing. In P. celeri, transformants were generated with a turnaround time as short as 21 days between transformation and being ready for another round of transformation with the same selection marker by using the CRoxP system. As a use-case for CRoxP, depigmented strains of P. celeri were generated by multiplexed Cas9 disruption of major LHCII genes followed by either a second round of LHCII targeting, or knockout of an LHCI gene. One transformant tested in flask culture (R6) exhibited similar biomass production to the wild type with 46% less Chl a + b on a biomass basis. In photobioreactors and under diel light simulating a solar day, a transformant (LhcBM31) exhibited 34 g AFDW m –2 d –1 with 54% less Chl a + b on a biomass basis vs. wild type.
Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis , using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (Δ fadN ) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA- fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n 16:0 to a 15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.