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This is a python package used to fit an unknown function from data that potential contains systematic biases related to metadata. The model fits the unknown function and uses a Bayesian horseshoe prior model to impose sparsity on the bias terms. This code has been generalized from research code developed for AIACHNE into a package that should have more general application in a wider class of statistical models.
Abstract Background While clinical trials are considered the gold standard for detecting adverse events, often these trials are not sufficiently powered to detect difficult to observe adverse events. We developed a preliminary approach to predict 135 adverse events using post-market safety data from marketed drugs. Adverse event information available from FDA product labels and scientific literature for drugs that have the same activity at one or more of the same targets, structural and target similarities, and the duration of post market experience were used as features for a classifier algorithm. The proposed method was studied using 54 drugs and a probabilistic approach of performance evaluation using bootstrapping with 10,000 iterations. Results Out of 135 adverse events, 53 had high probability of having high positive predictive value. Cross validation showed that 32% of the model-predicted safety label changes occurred within four to nine years of approval (median: six years). Conclusions This approach predicts 53 serious adverse events with high positive predictive values where well-characterized target-event relationships exist. Adverse events with well-defined target-event associations were better predicted compared to adverse events that may be idiosyncratic or related to secondary target effects that were poorly captured. Further enhancement of this model with additional features, such as target prediction and drug binding data, may increase accuracy.
Background: Technology to assess tissue perfusion is exciting with translational potential, although data supporting its clinical applications have been lagging. Patients who have undergone radiation are at particular risk of poor tissue perfusion and would benefit from this expanding technology. We designed a prospective clinical trial using intraoperative indocyanine green angiography to evaluate for wound-healing complications in patients undergoing salvage laryngectomy after radiation failure. Patients and Methods: This prospective trial included patients undergoing salvage laryngectomy at a National Cancer Institute-designated tertiary cancer center between 2016 and 2018. After tumor extirpation and prior to reconstruction, 10 mg indocyanine green dye was infused and the fluorescence (F{sub HYPO}) and ingress rate of the pharyngeal mucosa recorded. The primary outcome measure was formation of a pharyngocutaneous fistula (PCF). Results: Patients who developed a PCF had significantly lower F{sub HYPO} (87 vs 172, p < 0.001) and ingress rates (6.7 vs 15.8, p = 0.043) compared with those who did not develop a fistula. There were no fistulas in patients with F{sub HYPO} > 150 (n = 21) or ingress > 15 (n = 15). There was a 50% fistula rate in patients with F{sub HYPO} ≤ 103 (n = 10) and ingress rate ≤ 6 (n = 6). Conclusions: Intraoperative indocyanine green angiography can assess hypoperfusion in patients and predict risk of PCFs after salvage laryngectomy, and can thus intraoperatively risk-stratify patients for postoperative wound-healing complications.
The selection of pretreatment methods is critical to achieving high product yields during bioconversion of lignocellulosic biomass. Hydrothermal, soaking-in-aqueous ammonia, and ionic liquid pretreatment methods are viable candidates for minimizing sugar decomposition, permitting the effective hydrolysis of structural carbohydrates, and producing a fermentable substrate suitable for achieving industrial ethanol titers and yields. In this study, the effect of these three pretreatment methods on non-modified sugarcane cultivar CP88-1762 and two transgenic lipid-accumulating sugarcane lines, oilcane 1565 and oilcane 1566, were investigated and compared in terms of lipid recovery, sugar yield, and ethanol yields within the lignocellulosic biomass conversion pipeline. Fed-batch enzymatic hydrolysis at high solid loading yielded hydrolysates capable of supporting industrial bioethanol titers across all conditions. The highest sugar yields were obtained on ammonia-pretreated biomass hydrolysate (253.73 g L−1), followed by hydrothermally pretreated hydrolysate (213.10 g L−1) and ionic liquid-pretreated hydrolysate (154.20 g L−1). Commercially viable ethanol titers of 100.62 g L−1, 64.47 g L−1, and 52.95 g L−1 were achieved from ammonia, hydrothermal, and ionic liquid pretreated hydrolysate with the corresponding ethanol productivities of 2.08 g L−1 h−1, 0.53 g L−1 h−1, and 0.36 g L−1 h−1. The lower acetic acid concentration in ammonia-pretreated hydrolysate may have enhanced its fermentability relative to the hydrothermal pretreatment condition, as indicated by the differences in ethanol titer and productivity. Lower sugar yields and ethanol productivities under the ionic liquid conditions likely resulted from the inhibitory effect of cholinium lysinate. Oilcane 1565 and oilcane 1566 bagasse accumulated over 16- and 3 times higher lipids than the non-modified sugarcane CP88-1762. The total fatty acid content in the oilcane samples was reduced in ammonia and ionic liquid-pretreated bagasse relative to the hydrothermal pretreatment condition. While all pretreatment techniques tested are industrially viable, the observed differences in titer, productivity, and lipid content indicate that careful selection and validation of upstream processing methods can contribute to improved economic and environmental outcomes.
This presentation, based on research at Lawrence Berkeley National Laboratory and the National Renewable Energy Laboratory, provides a high-level overview of historical, recent, and projected near-term PV pricing trends in the United States focusing on the installed price of PV systems. It also attempts to provide clarity surrounding the wide variety of potentially conflicting data available about PV system prices. This PowerPoint is the fourth edition from this series.
This white paper was requested by the Core Team (United States Department of Energy [USDOE], United States Environmental Protection Agency [USEPA], and South Carolina Department of Health and Environmental Control [SCDHEC]) at the P-Area Groundwater (PAGW) Operable Unit (OU) Scoping Meeting held in January 2017 to discuss recent data and potential alternatives in support of a focused Corrective Measures Study/Feasibility Study (CMS/FS). This white paper presents an overview of the problem, and a range of technical and administrative options for addressing the tritium contamination in groundwater and Steel Creek. As tritium cannot be treated practicably, alternatives are limited to media transfer, containment and natural attenuation principally relying on radioactive decay. Using other groundwater OU decisions involving tritium as precedent, Savannah River Nuclear Solutions (SRNS) recommends that final tritium alternatives be evaluated in a CMS/FS, understanding that the likely preferred remedy will include natural attenuation with land use controls (LUCs). This is based on the inability to significantly reduce tritium impact to Steel Creek using an engineered solution as compared to natural attenuation. The timing of this evaluation could be conducted concurrently with the final remedy evaluation for volatile organic compounds (VOCs).
This report describes the aggregation and mapping of certain building characteristics data available in the most recent Commercial Building Energy Consumption Survey (CBECS) (DOE EIA 2012) to describe most typical building construction practices. This report provides summary data for potential use in the support of modifications to the Pacific Northwest National Laboratory’s commercial building prototypes used for building energy code analysis. Specifically, this report outlines findings and most typical design choices for certain building envelope and heating, ventilating, and air-conditioning (HVAC) system choices.
Hydrogen Risk Assessment Models (HyRAM) is a software toolkit that provides a basis for quantitative risk assessment and consequence modeling for hydrogen infrastructure and transportation systems. HyRAM integrates validated, analytical models of hydrogen behavior, statistics, and a standardized QRA approach to generate useful, repeatable data for the safety analysis of various hydrogen systems. HyRAM is a software developed by Sandia National Laboratories for the U.S. Department of Energy. This document demonstrates how to use HyRAM to recreate a hydrogen system and obtain relevant data regarding potential risk. Specific examples are utilized throughout this document, providing detailed tutorials of HyRAM features with respect to hydrogen system safety analysis and risk assessment.
The entirety of the report that follows this brief Executive Summary Chapter is the product of a Funding Announcement by the US Department of Energy (DOE), Office of Fossil Energy, originally issued 09/28/2016, otherwise known as Funding Opportunity Number: DE-FOA-0001627, under the title of “Production of Rare Earth Elements from Domestic U.S. Coal and Coal By-Products” The solicitation was subsequently amended several times ending in amendment 000005. Ultimately a consortium designated “Minerals Refining and Rare Earth Consortium” (to which many of the remaining participants recited in this report joined) filed a proposal on December 8, 2016. On June 9, 2017, the contracting office of the US DOE, National Energy Technology Laboratory (NETL), alerted Dr. Keim, the Authorized Representative of the December 08, 2016, proposal, that the consortium proposal had been selected. In summary, this report presents the results of the efforts in meeting the stated project objectives as outlined in DE-FOA-0001627 to wit: “The main objective of the proposed work is to design and construct a demonstration plant that can extract rare earth elements (REEs) from domestic U.S. coal and coal by-products. The plant will produce salable rare earth elements and intermediates, including at a minimum three individual REEs (preferably heavy rare earths) at 90-99% purities, with output capacities in excess of 10 pounds per day of composite rare earth products (reported as oxides). In addition, the plant will produce high value premium solid fuels, magnetite and other materials to increase the economic viability of the plant and to create jobs. If successful, the proposed work will help develop a domestic supply chain of the critical materials that are essential for the development of renewable energy resources, high-tech industries and a strong national defense.” The principal investigators immediately launched the tasks outlined in the Statement of Project Objectives (SOPO) in accordance to its Project Management Plan (PMP) based on their collective knowledge of the subject matter and the expectations generated by preliminary laboratory results. Events and circumstances related in part to the vagaries of the coal mining, processing, and marketing industry triggered a series of carefully deliberated step-wise transitions from the original Lower Kittanning coal source in West Virginia to an ultimate stopping point with the Fire Clay Seam (Hazard No. 4) rejects from Blue Diamond Coal Company in Kentucky (Operated by Blackhawk Mining LLC). These transitional steps are discussed in substantial detail in the body of this report. Notably, substantial data of potential future significance, both in terms of sample collection, processing, and testing, were collected in the process. Unfortunately, as reported in the Techno-Economic Chapter of this report, none of these efforts resulted in an anticipated economically viable venture. Thus, the principals associated with this project elected not to transition into a “Pilot Plant” operation. A proposal for funding that pilot plant was therefore not requested. The outcome of this initiative under DE-FOA-0001627 notwithstanding, the following portions of this Executive Summary outline the activities of the investigators. That said, the reader is encouraged to examine the main body of this report in which each chapter is assembled as a free-standing product, complete with Table of Contents, for practical and easy reference purposes.
Based on review of the related NEPA documents, and consideration of the potential gaps in NEPA coverage, a number of questions have been generated. These questions are generally higher level (less detailed) questions that should help to establish the applicability of analyses in existing NEPA documents and the ability of these documents to provide NEPA coverage for the Proposed Action. These questions do not request detailed information about SRS facilities/activities and the Proposed Action like typically would be requested when performing impacts analyses for an EIS. We do not believe detail information is needed; if it is needed, it may be an indication that an SA is not the appropriate level of NEPA documentation for the Proposed Action.
As the current global pandemic makes abundantly clear, we need a better understanding of infectious disease to safeguard human health, the economy and global security. Modern omics techniques hold the promise of providing a comprehensive understanding of the molecular mechanisms of life, including causes of pathogenesis from infectious disease at the molecular level, but we there is a serious gap in annotation of gene function. For as much as half of the genes and gene products encoded in genomes the molecular and/or cellular function is unknown or only partially understood. Recent innovations in fluorescence microscopy for live cell imaging and genetic engineering make it possible to determine the temporal correlation between molecular events, such as a gene being expressed due to host-pathogen interaction, and cellular events, such as bacterial invasion of immune cells. This is turn allows us to gain new insight as to the molecular and cellular role of individual genes and will enable the discovery and validation of new molecular mechanisms essential for infectious disease. Knowing the molecular mechanisms of disease processes will provide new therapeutic targets or novel countermeasure strategies. We aimed to develop a lattice light sheet fluorescence microscope as a unique resource at LLNL for long time course live cell imaging experiments; to develop the reagents and cell lines needed to monitor molecular events during the course pathogenic bacteria infecting mammalian immune cells; and to demonstrate that we could capture molecular events during an infection. We fully commissioned the LLNL lattice light sheet microscope and conducted initial proof of principle imaging experiments on mammalian immune cells and pathogenic bacteria. It is clear from the experience gained that long time course live cell imaging has tremendous potential to help elucidate molecular mechanisms of host-pathogen interactions and to help annotate gene function, which would establish a basis for new countermeasures. It is also clear that if live cell imaging is to realize its full potential new data processing and analysis tools will need to be developed to facilitate analysis of molecular events within cells; new sample chambers and stages could facilitate studies with a wider range of cell and tissue types; and alternative molecular tagging methods need to be explored to enable more facile engineering of cells labeled with molecular specificity.
Hydrogen Risk Assessment Models (HyRAM) is a software toolkit that provides a basis for quantitative risk assessment and consequence modeling for hydrogen infrastructure and transportation systems. HyRAM integrates validated, analytical models of hydrogen behavior, statistics, and a standardized QRA approach to generate useful, repeatable data for the safety analysis of various hydrogen systems. HyRAM is a software developed by Sandia National Laboratories for the U.S. Department of Energy. This document demonstrates how to use HyRAM to recreate a hydrogen system and obtain relevant data regarding potential risk. Specific examples are utilized throughout this document, providing detailed tutorials of HyRAM features with respect to hydrogen system safety analysis and risk assessment.
Large-scale cultivation of macroalgae is one of the most promising biofuel sources that could reduce our consumption of fossil fuels and would be particularly economically competitive when grown for the co-production of additional goods such as food and textiles. Current production of biofuel from algal biomass is limited by labor costs and lack of data on potential impacts of cultivation and harvesting on marine and coastal environments as well as a comprehensive characterization of the impact of environmental conditions on macroalgal feedstock and their bioproduct and biofuel yield and quality. Awarded by the United States (U.S.) Department of Energy Advanced Research Projects Agency-Energy (ARPA-E) Macroalgae Research Inspiring Novel Energy Resources (MARINER) program, which seeks to enable the U.S. as a global leader in the production of marine biomass, the Marine Biological Laboratory (MBL) has been developing a test system for tropical seaweed cultivation in the Gulf of Mexico and the Caribbean. An integral step in designing macroalgae cultivation farms is to adequately characterize the hydrodynamic climate at potential growth sites. In regions like the Gulf of Mexico and the Caribbean, which are highly exposed to tropical cyclones, it is critical to not only consider the day-to-day hydrodynamic conditions but to also assess the risk of extreme sea states to ensure the survivability of future macroalgae farms. Under these considerations, the Pacific Northwest National Laboratory (PNNL) is providing modeling support for MBL to inform the design and siting of the farm systems that have been proposed for their ARPA-E MARINER project. This report describes the development of a high-resolution coupled storm surge and wave model to simulate the hydrodynamics and wave climate at proposed macroalgae cultivation sites selected by MBL in Florida and Puerto Rico. Model results, including model validation, water level, current distributions, and sea states, are discussed for both selected sites in Florida and Puerto Rico coast. These simulations provide an accurate insight into the hydrodynamic conditions that a macroalgae farm is likely to experience during its operational lifetime, including current information to support fine-scale hydrodynamic load modeling, risk analysis and system design.
In the 1970’s and 1980’s, researchers at Sandia National Laboratories produced electron albedo data for a range of materials. Since that time, the electron albedo data has been used for a wide variety of purposes including the validation of Monte Carlo electron transport codes. This report was compiled to examine the electron albedo experiment results in the context of Integrated Tiger Series (ITS) validation. The report presents tables and figures that could provide insight into the underlying model form uncertainty present in the ITS code. Additionally, the report provides data on potential means to reduce these model form errors by highlighting potential refinements in the cross-section generation process.
In collaboration with the U.S. Nuclear Regulatory Commission (NRC) the LLNL has developed a computationally efficient simulation platform designed to perform physics-based ground motion simulations for crustal earthquakes in the Stable Continental Regions of Central and Eastern US (CEUS), using high-performance computing. The main objective of the earthquake simulations was to use synthetic ground motion to provide constrains to refinements of existing ergodic Ground Motion Models (GMMs), for large magnitude earthquakes and near-fault distances, for which these models are less reliable. Physics-based broadband (0-10Hz) ground motion simulations were used to estimate the near-fault ground motion amplitudes and within event and between-event variabilities associated with fault rupture characteristics. In our simulations we used a 3D regional velocity model that was based on Saikia’s 1D velocity model (1994). In simulations performed during the first stage of this project the Saikia’s velocity model demonstrated better performance in modelling high frequency regional wave propagation for the CEUS region recorded during the Mw5.0 November 7, 2016, Cushing Oklahoma (Taylor et al., 2017), and Mw5.8 September 3, 2016, Pawnee Oklahoma earthquakes. The proposed regional 3D model includes random perturbations to the 1D background model using the stochastic scheme of Pitarka and Mellors (2021). In addition, validation analysis of the rupture generator and regional wave propagation models, using comparisons with different GMMs for Mw6.5 and Mw7.0 scenario earthquakes in the CEUS region resulted in a very good match between the simulated and empirical ground motion models. For the purposes of seismic hazard assessment at the existing and planned nuclear power plants, NRC is interested in studies aimed at improving the current ground motion models (GMM) for both Stable Continental Regions (SCR) in the Central and Eastern US and Active Crustal Regions (ACR) in the Western US. Due to lack of recorded data, these improvements require synthetic data for short fault distances and large magnitude earthquakes for which the existing recorded data is not enough to uniquely constrain the GMMs. The need for simulations and strong motion data is especially critical for the CEUS region where we do not have recorded data from potentially large damaging earthquakes with moment magnitudes 6.0 and higher. In this the project, we focused on 10Hz simulations of Mw7.0 scenario earthquakes with strike slip and thrust faulting mechanisms. We used more than 50 Mw7.0 earthquake rupture scenarios to investigate the ground motion uncertainty due to unknown earthquake rupture parameters, in particular, the slip distribution, rupture velocity, and faulting mechanism, and their implication on ground motion amplification due to forward rupture directivity effects.
Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.
In China, Platycladus orientalis has a lifespan of thousands of years. The long lifespan of these trees may be relevant for the characterization of plant aging at the molecular level. However, the molecular mechanism of the aging process of P. orientalis is still unknown. To explore the relationship between age and growth of P. orientalis , we analyzed physiological changes during P. orientalis senescence. The malondialdehyde content was greater in 200-, 700-, and 1100-year-old ancient trees than in 20-year-old trees, whereas the peroxidase and superoxide dismutase activities, as well as the soluble protein content, exhibited the opposite trend. Furthermore, we performed a de novo transcriptome assembly using RNA-Seq and obtained 48,044 unigenes with an average length of 896 bp. A total of 418 differentially expressed genes were identified in different stages of aging of P. orientalis . Clustering analysis revealed distinct timepoints at which the oxidation–reduction and photosynthesis pathways changed. Eight clusters with distinct expression patterns were identified. The expression levels of photosynthesis-, oxidation–reduction-, and transporter-related genes were down-regulated, whereas those of transcription-, signaling-, and senescence-related genes were up-regulated during aging. In addition, consistent with the most obviously down-regulated genes of photosynthesis-related genes, the photosynthetic indexes including chlorophyll a and b levels decreased steadily during P. orientalis aging. This study combined transcriptome with physiological and biochemical data, revealing potential candidate genes influencing senescence during P. orientalis aging.
This paper presents the design, fabrication, and characterization of a novel fiber optic ultrasonic sensing system based on the photoacoustic (PA) ultrasound generation principle and Fabry-Perot interferometer principle for high temperature monitoring applications. The velocity of a sound wave traveling in a medium is proportional to the medium’s temperature. The fiber optic ultrasonic sensing system was applied to measure the change of the velocity of sound. A fiber optic ultrasonic generator and a Fabry-Perot fiber sensor were used as the signal generator and receiver, respectively. A carbon black-polydimethylsiloxane (PDMS) material was utilized as the photoacoustic material for the fiber optic ultrasonic generator. Two tests were performed. The system verification test proves the ultrasound sensing capability. The high temperature test validates the high temperature measurement capability. The sensing system survived 700 °C. It successfully detects the ultrasonic signal and got the temperature measurements. The test results agreed with the reference sensor data. Two potential industry applications of fiber optic ultrasonic sensing system are, it could serve as an acoustic pyrometer for temperature field monitoring in an industrial combustion facility, and it could be used for exhaust gas temperature monitoring for a turbine engine.