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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Likelihood analysis of the sub-GUT MSSM in light of LHC 13-TeV data

We describe a likelihood analysis using MasterCode of variants of the MSSM in which the soft supersymmetry-breaking parameters are assumed to have universal values at some scale M in below the supersymmet-ric grand unification scale M GUT , as can occur in mirage mediation and other models. In addition to M in , such ‘sub-GUT’ models have the 4 parameters of the CMSSM, namely a common gaugino mass m 1/2 , a common soft supersymmetry-breaking scalar mass m 0 , a common trilinear mixing parameter A and the ratio of MSSM Higgs vevs tan β, assuming that the Higgs mixing parameter μ> 0. We take into account constraints on strongly- and electroweakly-interacting sparticles from ~ 36/fb of LHC data at 13 TeV and the LUX and 2017 PICO, XENON1T and PandaX-II searches for dark matter scattering, in addition to the previous LHC and dark matter constraints as well as full sets of flavour and electroweak constraints. We find a preference for Min ~ 10 5 to 10 9 GeV, with M in ~ M GUT disfavoured by Δχ 2 ~ 3 due to the BR(B s,d → μ + μ - ) constraint. The lower limits on strongly-interacting sparticles are largely determined by LHC searches, and similar to those in the CMSSM. We find a preference for the LSP to be a Bino or Higgsino with m$\mathbb -0\atop{X1} $ ~ 1 TeV, with annihilation via heavy Higgs bosons H/A and stop coannihilation, or chargino coannihilation, bringing the cold dark matter density into the cosmological range. We find that spin-independent dark matter scattering is likely to be within reach of the planned LUX-Zeplin and XENONnT experiments. We probe the impact of the (g - 2) μ constraint, finding similar results whether or not it is included.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Challenges in Firmware Re-Hosting, Emulation, and Analysis

System emulation and firmware re-hosting have become popular techniques to answer various security and performance related questions, such as determining whether a firmware contain security vulnerabilities or meet timing requirements when run on a specific hardware platform. While this motivation for emulation and binary analysis has previously been explored and reported, starting to either work or research in the field is difficult. To this end, we provide a comprehensive guide for the practitioner or system emulation researcher. Here, we layout common challenges faced during firmware re-hosting, explaining successive steps and surveying common tools used to overcome these challenges. We provide classification techniques on five different axes, including emulator methods, system type, fidelity, emulator purpose, and control. These classifications and comparison criteria enable the practitioner to determine the appropriate tool for emulation. We use our classifications to categorize popular works in the field and present 28 common challenges faced when creating, emulating, and analyzing a system from obtaining firmwares to post emulation analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

I/O Access Patterns in HPC Applications: A 360-Degree Survey

The high-performance computing I/O stack has been complex due to multiple software layers, the inter-dependencies among these layers, and the different performance tuning options for each layer. In this complex stack, the definition of an “I/O access pattern” has been reappropriated to describe what an application is doing to write or read data from the perspective of different layers of the stack, often comprising a different set of features. It has become common to have to redefine what is meant when discussing a pattern in every new study, as no assumption can be made. This survey aims to propose a baseline taxonomy, harnessing the I/O community’s knowledge over the past 20 years. This definition can serve as a common ground for high-performance computing I/O researchers and developers to apply known I/O tuning strategies and design new strategies for improving I/O performance. We seek to summarize and bring a consensus to the multiple ways to describe a pattern based on common features already used by the community over the years.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Unexpected Voltage Fade in LMR-NMC Oxides Cycled below the “Activation” Plateau

A common feature of lithium-excess layered oxides, nominally of composition xLi 2 MnO 3 •(1-x)LiMO 2 (M = transition metal) is a high-voltage plateau (~4.5 V vs. Li/Li + ) in their capacity-voltage profile during the first delithiation cycle. This plateau is believed to result from activation of the Li 2 MnO 3 component, which makes additional lithium available for electrochemical cycling. However, oxides cycled beyond this activation plateau are known to display voltage fade which is a continuous reduction in their equilibrium potential. In this article we show that these oxides display gradual voltage fade even on electrochemical cycling in voltage ranges well below the activation plateau. The average fade is ~0.08 mV-cycle-1 for Li 1.2 Ni 0.15 Mn 0.55 Co 0.1 O 2 vs. Li cells after 20 cycles in the 2–4.1 V range at 55°C; a ~54 mV voltage hysteresis, expressed as the difference in average cell voltage between charge and discharge cycles, is also observed. The voltage fade results from a gradual accumulation of local spinel environments in the crystal structure. Some of these spinel sites result from lithium deficiencies during oxide synthesis and are likely to be at the particle surfaces; other sites result from the migration of transition metal atoms in the partially-delithiated LiMO 2 component into the lithium planes during electrochemical cycling. The observed rate of voltage fade depends on a combination of factors that includes the phase equilibrium between the layered and spinel components and the kinetics of transition metal migration.

Li, Yan↗
DOE OSTI2014

Screening of Viral Pathogens from Pediatric Ileal Tissue Samples after Vaccination

In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technology was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae , Bacteroidaceae , and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PyOECP: A flexible open-source software for the measurement and modeling of the dielectric spectrum from the reflection coefficient

We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to complex permittivity is performed based on two different models, including the capacitance model and the antenna model. The software library contains dielectric spectra of common reference liquids, which can be used to transform the reflection coefficient into the dielectric spectra. Several Python routines that are commonly employed (e.g., SciPy and NumPy) are only required so that the users can alter the software structure depending on their needs. The modeling algorithm exploits the Markov chain Monte Carlo method for the data regression. The discrete relaxation models can be built by a proper combination of well-known relaxation models. In addition to these models, the electrode polarization, which is a common measurement artifact for interpreting the dielectric spectra, can be incorporated in the modeling algorithm. A continuous relaxation model, which solves the Fredholm integral equation of the first kind (a mathematically ill-posed problem) is also included.

Yoon, Tae-Jun↗
DOE OSTI2023

RadSim: Math, Utility & RTK

This package includes three parts, (1) gov.llnl.math, (2)gov.llnl.utility and (3)gov.llnl.rtk, which are utilized in the development of Radiation Detector Simulator (RadSim) project. RadSim is being developed to provide the capability to: (1) simulate radiation source emissions, (2) interpolate results from radiation transport tools into a common format to prepare incident flux, and (3) model radiation detector response to rapidly produce synthetic radiation measurement templates. RadSim is targeted for open-source release, which will enable researchers and industry partners to model gamma-ray detectors response to simulated flux from the transport tool of their choice. The techniques and implementation will be entirely transparent, which will allow for improvements and boutique modifications by future researchers beyond the lifespan of this specific project. The first tool of the package, gov.llnl.math, includes classes and functions to define and perform basic math operations. Some of the example features available in the package include defining statistical distributions and performing algebra and matrix operations, all of which are already accessible on publicly available software packages such as MATLAB and ROOT. The second package gov.llnl.utility includes tools commonly used to enable optimization and readability of various data structures such as Java lists and external xml files. Lastly, the gov.llnl.rtk package includes classes and functions to implement methods commonly used in radiation physics, such as data structures to represent and characterize photon spectra and tools to apply well-defined and published methods to calibrate a given spectra.

Cheung, Hoi Sing↗
DOE OSTI2021

Altered Cardiac Energetics and Mitochondrial Dysfunction in Hypertrophic Cardiomyopathy

Background: Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure–function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. Here, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM. Methods: We performed a comprehensive multiomics profile of the molecular (transcripts, metabolites, and complex lipids), ultrastructural, and functional components of HCM energetics using myocardial samples from 27 HCM patients and 13 normal controls (donor hearts). Results: Integrated omics analysis revealed alterations in a wide array of biochemical pathways with major dysregulation in fatty acid metabolism, reduction of acylcarnitines, and accumulation of free fatty acids. HCM hearts showed evidence of global energetic decompensation manifested by a decrease in high energy phosphate metabolites (ATP, ADP, and phosphocreatine) and a reduction in mitochondrial genes involved in creatine kinase and ATP synthesis. Accompanying these metabolic derangements, electron microscopy showed an increased fraction of severely damaged mitochondria with reduced cristae density, coinciding with reduced citrate synthase activity and mitochondrial oxidative respiration. These mitochondrial abnormalities were associated with elevated reactive oxygen species and reduced antioxidant defenses. However, despite significant mitochondrial injury, HCM hearts failed to upregulate mitophagic clearance. Conclusions: Overall, our findings suggest that perturbed metabolic signaling and mitochondrial dysfunction are common pathogenic mechanisms in patients with HCM. These results highlight potential new drug targets for attenuation of the clinical disease through improving metabolic function and reducing mitochondrial injury.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Opinion: Lighting Research During and After the Pandemic

For many lighting researchers, the recent restrictions related to COVID-19 have paused most in-person laboratory or field experiments. In certain countries, regulatory institutions have allowed such experiments to resume but issued safety recommendations like pre-checking participants for disease symptoms and excluding those that are especially vulnerable. To avoid potential complications and delays, researchers are likely to resort to other research designs that enable remote research — eliminating the need for the experimenter and subjects to be in the same room. While unanticipated, this shift to remote research methods is an opportunity to revisit and further develop remote experimental techniques, which can have beneficial long-lasting implications on lighting research during and after the pandemic. Perhaps the most common type of remote research is online experiments; which can greatly benefit from improved techniques to allow for greater control or characterization of experimental conditions, like those proposed by Villa and Labayrade . These techniques require validation specific to the type of response collected and context, e.g. space type and attributes. New research techniques continue to emerge and will enable remote collection of objective measures such as gaze direction and high dynamic range images (HDRIs) without specialized equipment. In fact, many of these methods and techniques are commonly used in other disciplines, like vision science and psychology, and can be adapted for lighting research. Not all lighting studies can be conducted online, but in the age of ubiquitous and connected technologies, there is a largely missed opportunity to utilize crowdsourced responses to lighting conditions in real environments where people live and go about their daily lives without the research being limited to a certain time and laboratory locations. For instance, outdoor street luminaires can be rated by passersby using ecological momentary assessments on mobile phones. While this approach does not provide laboratory-level control over experimental conditions, it can provide more contextual responses resulting from ‘normal’ dynamic gaze, behavior, and interactions. Further, it can also reduce bias related to the experimental setting. Further development of remote research methods and their use in lighting research can improve the quality of lighting research. Given that sample sizes in most lighting research are relatively small, remote research can substantially increase sample sizes, reduce research costs, and shorten study duration, all while reducing interaction between experimenter and subjects. Another benefit is reaching a wider audience and including under-represented individuals who typically are not reachable using common recruitment methods. The pandemic has set back our plans for in-lab experiments, but can it inspire us to think of new and creative ways to expand lighting research?

Abboushi, Belal K.↗
DOE OSTI2014

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled “unconferences” (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Stepwise approach to SNP-set analysis illustrated with the Metabochip and colorectal cancer in Japanese Americans of the Multiethnic Cohort

Background: Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome scans. Because of low frequency (low statistical power), less-common variants are best analyzed using SNP-set methods such as gene-set or pathway-based analyses. However, there is as yet no clear consensus regarding how to focus in on potential risk variants following set-based analyses. We used a stepwise, telescoping approach to analyze commonand rare-variant data from the Illumina Metabochip array to assess genomic association with colorectal cancer (CRC) in the Japanese sub-population of the Multiethnic Cohort (676 cases, 7180 controls). We started with pathway analysis of SNPs that are in genes and pathways having known mechanistic roles in colorectal cancer, then focused on genes within the pathways that evidenced association with CRC, and finally assessed individual SNPs within the genes that evidenced association. Pathway SNPs downloaded from the dbSNP database were cross-matched with Metabochip SNPs and analyzed using the logistic kernel machine regression approach (logistic SNP-set kernel-machine association test, or sequence kernel association test; SKAT) and related methods. Results: The TGF-β and WNT pathways were associated with all CRC, and the WNT pathway was associated with colon cancer. Individual genes demonstrating the strongest associations were TGFBR2 in the TGF-β pathway and SMAD7 (which is involved in both the TGF-β and WNT pathways). As partial validation of our approach, a known CRC risk variant in SMAD7 (in both the TGF-β and WNT pathways: rs11874392) was associated with CRC risk in our data. We also detected two novel candidate CRC risk variants (rs13075948 and rs17025857) in TGFBR2, a gene known to be associated with CRC risk. Conclusions: A stepwise, telescoping approach identified some potentially novel risk variants associated with colorectal cancer, so it may be a useful method for following up on results of set-based SNP analyses. Further work is required to assess the statistical characteristics of the approach, and additional applications should aid in better clarifying its utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

COVID-19 prevention at institutions of higher education, United States, 2020–2021: implementation of nonpharmaceutical interventions

Background, In early 2020, following the start of the coronavirus disease 2019 (COVID-19) pandemic, institutions of higher education (IHEs) across the United States rapidly pivoted to online learning to reduce the risk of on-campus virus transmission. We explored IHEs’ use of this and other nonpharmaceutical interventions (NPIs) during the subsequent pandemic-affected academic year 2020–2021. Methods, From December 2020 to June 2021, we collected publicly available data from official webpages of 847 IHEs, including all public (n = 547) and a stratified random sample of private four-year institutions (n = 300). Abstracted data included NPIs deployed during the academic year such as changes to the calendar, learning environment, housing, common areas, and dining; COVID-19 testing; and facemask protocols. We performed weighted analysis to assess congruence with the October 29, 2020, US Centers for Disease Control and Prevention (CDC) guidance for IHEs. For IHEs offering ≥50% of courses in person, we used weighted multivariable linear regression to explore the association between IHE characteristics and the summated number of implemented NPIs. Results, Overall, 20% of IHEs implemented all CDC-recommended NPIs. The most frequently utilized NPI was learning environment changes (91%), practiced as one or more of the following modalities: distance or hybrid learning opportunities (98%), 6-ft spacing (60%), and reduced class sizes (51%). Additionally, 88% of IHEs specified facemask protocols, 78% physically changed common areas, and 67% offered COVID-19 testing. Among the 33% of IHEs offering ≥50% of courses in person, having < 1000 students was associated with having implemented fewer NPIs than IHEs with ≥ 1000 students. Conclusions, Only 1 in 5 IHEs implemented all CDC recommendations, while a majority implemented a subset, most commonly changes to the classroom, facemask protocols, and COVID-19 testing. IHE enrollment size and location were associated with degree of NPI implementation. Additional research is needed to assess adherence to NPI implementation in IHE settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The formation of spinel-group minerals in contaminated soils: the sequestration of metal(loid)s by unexpected incidental nanoparticles

Mineralogical studies of contaminated soils affected by smelter emission and dust from mining activities indicate that minerals of the spinel group are one of the common hosts of metal-bearing contaminants. Spinel group minerals typically originate from high temperature processes, but an increasing number of studies indicate that metal-bearing spinel group minerals can also form under ambient Earth surface conditions in surficial soils. In this contribution to honor Donald Sparks, we show that the spinels Zn-bearing magnetite (Zn 0.5 Fe 2.5 O 4 ) and minium (Pb 3 O 4 ) form during low temperature alteration of Pb-bearing silica glass in surficial organic rich soils in proximity to a former Cu-smelter in Timmins, Ontario, Canada. The glass most likely formed during high-temperature processes and has been either emitted by the smelter or wind-blown from waste rock piles to near-by soils. The alteration of the glass by percolating pore solutions has resulted in the formation of large micrometer-size dendritic etch features and in nanometer-size dendritic alteration halos composed of nano-size prismatic crystals of Zn-rich magnetite and spherical nanoparticles of minium. Both spinel-type phases are embedded in an amorphous silica matrix which formed during the alteration of the glass at low temperature. A review on the occurrence of spinel-group minerals in smelter-affected soils or mine tailings indicates that the formation of these minerals under ambient Earth surface conditions is quite common and often results in the sequestration of contaminants such as Cu, Ni, Zn and Sb. The pedogenic spinels often occur as euhedral crystals in nano-size mineral assemblages within alteration features such as dendritic etch patterns, mineral surface coatings and mineralized organic matter. Their well-developed crystal forms indicate that (a) they have not formed during a rapid cooling process in a smelter or refinery which typically creates spherical particulate matter, and (b) they have not been part of particulate matter added via fluvial or Aeolian processes which most commonly yield anhedral morphologies. The formation of nano-size spinel-group minerals in low temperature environmental settings may lead to the long-term storage of metal(loid)s in mineral phases and their transport over vast distances via fluvial, alluvial and Aeolian processes.

58 GEOSCIENCES↗
DOE OSTI2023

The rapid-tome, a 3D-printed microtome, and an updated hand-sectioning method for high-quality plant sectioning

Abstract Background Microscopic analysis of plant anatomy is a common procedure in biology to study structure and function that requires high-quality sections for accurate measurements. Hand sectioning of specimens is typically limited to moderately soft tissue while harder samples prohibit sectioning by hand and/or result in inconsistent thicknesses. Results Here we present both a clearly described hand-sectioning method and a novel microtome design that together provide the means to section a variety of plant sample types. The described hand-sectioning method for herbaceous stems works well for softer subjects but is less suitable for samples with secondary growth (e.g., wood production). Instead, the “Rapid-Tome” is a novel tool for sectioning both soft and tougher high-aspect-ratio samples, such as stems and roots, with excellent sample control. The Rapid-Tome can be 3D-printed in approximately 18 h on a mid-quality printer common at university maker spaces. After printing and trimming, Rapid-Tome assembly takes a few minutes with five metal parts common at hardware stores. Users sectioned a variety of plant samples including the hollow internodes of switchgrass ( Panicum virgatum ), fibrous switchgrass roots containing aerenchyma, and woody branches of eastern red cedar ( Juniperus virginiana ) and American sycamore ( Platanus occidentalis ). A comparative analyses with Rapid-Tome-produced sections readily revealed a significant difference in seasonal growth of sycamore xylem vessel area in spring (49%) vs. summer (23%). Additionally, high school students with no prior experience produced sections with the Rapid-Tome adequate for comparative analyses of various plant samples in less than an hour. Conclusions The described hand-sectioning method is suitable for softer tissues, including hollow-stemmed grasses and similar samples. In addition, the Rapid-Tome provides capacity to safely produce high-quality sections of tougher plant materials at a fraction of the cost of traditional microtomes combined with excellent sample control. The Rapid-Tome features rapid sectioning, sample advancement, blade changes, and sample changes; it is highly portable and can be used easily with minimal training making production of thin sections accessible for classroom and outreach use, in addition to research.

3D-printing↗
DOE OSTI2017

Established patterns of animal study design undermine translation of disease-modifying therapies for Parkinson’s disease

Translation of disease-modifying therapies in neurodegenerative disease has been disappointing. Parkinson’s disease (PD) was used to compare patterns of preclinical study design for symptomatic and potentially disease-modifying interventions. We examined the relationship of model, intervention type and timing, outcomes and outcome measures in 543 animal and human studies (1973–2015) across a contemporary cohort of animal and human interventional studies (n = 445), animal studies for approved interventions (n = 28), animal and human studies for those that failed to translate (n = 70). Detailed study design data were collected for 216 studies in non-human primate (NHP) and rodent toxin-induced models. Species-specific patterns of study design prevailed regardless of whether interventions were symptomatic or potentially disease-modifying. In humans and NHPs, interventions were typically given to both sexes well after the PD phenotype was established, and clinical outcome measures were collected at single (symptomatic) or multiple (disease-modifying) time-points. In rodents, interventions often preceded induction of the model, acute toxic protocols were common, usually given to young males, clinical outcome measures were used less commonly, and outcomes were less commonly assessed at multiple time points. These patterns were more prevalent in mice than rats. In contrast, study design factors such as randomization and blinding did not differ appreciably across symptomatic and disease-modifying intervention categories. The translational gap for potentially disease-modifying interventions in PD in part results from study designs, particularly in mice, that fail to model the progressive nature and relatively late intervention characteristic of PD, or that anchor mechanistic and neuropathologic data to longitudinal clinical outcomes. Even if measures to improve reproducibility are broadly adopted, perpetuation of these norms will continue to impede effective translation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ESS-DIVE Reporting Format for Amplicon Abundance Table

While standardized sequencing data is available in public repositories and efforts such as MIxS for common sample collection and processing metadata are well established, the lack of common bioinformatic processing metadata has hindered the ability to do large-scale metaanalyses and the potential for data re-use by non-experts such as ecosystem, watershed, or earth system modelers. To address this need for Department of Energy researchers, we have developed an amplicon reporting format which captures both sample preparation and bioinformatic processing metadata and stores processed amplicon data as a paired abundance table and sequencing file to maximize the potential for re-use of these data. To aid in the adoption of accessible and reproducible analysis workflows, this reporting format was developed in concert with amplicon functionality within the Department of Energy’s Systems Biology Knowledgebase (KBase) to ensure common data and metadata requirements and facilitate seamless transfer between these platforms.This dataset contains support documentation for the amplicon reporting format (README.md and instructions.md), templates for both bioinformatic and sequencing metadata (amplicon_bioinformatic_metadata_template_2021_10_03.csv and amplicon_sequencing_metadata_template_2021_10_03.csv), a crosswalk indicating how this reporting format relates to the current MIxS format (ESSDIVE-MIxS_crosswalk.csv), a list of available instrument terms (amplicon_seq_instrument_terms_2021_10_03.csv), a map between QIIME2 parameter settings and metadata fields (amplicon_qiime2_plugin_metadata_map.csv), a data dictionary (amplicon_CSV_dd.csv), and file-level metadata (amplicon_FLMD.csv).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Differentiating Vaccine-Related Fowl Cholera from Naturally Occurring Disease

Vaccine-related fowl cholera must be considered when flock mortality increases after use of a live Pasteurella multocida vaccine product. All registered live vaccines serotype as Heddleston 3,4; however, in some regions this is also the most common serotype of outbreak isolates in broiler breeders and turkeys. Therefore, serotyping may not be useful for diagnosing vaccine-related fowl cholera. This project sought to apply a vaccine-specific test to differentiate vaccine-related disease from naturally occurring outbreaks. Results indicate that vaccine strains were commonly isolated from broiler breeders exhibiting signs of fowl cholera post vaccination, but some of these isolates exhibited only serotype 4 antigenicity. The isolates’ lipopolysaccharides, the target antigen for serotyping, contained compositional changes that may explain the varying serotype results and virulence of the commercial preparations. Furthermore, these results suggest that vaccine-related disease may be common in broiler breeders, and live commercial vaccine preparations need to be assessed for serotype and titer prior to use in order to reduce vaccine-related fowl cholera.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

AmeriFlux US-CF1 CAF-LTAR Cook East

This is the AmeriFlux version of the carbon flux data for the site US-CF1 CAF-LTAR Cook East. Site Description - CF1 has operated since May 2017 at the R.J. Cook Agronomy Farm outside of Pullman, Washington, and monitors the no-till side of a paired-catchment study that is part of the Longterm Agroecosystem Research (LTAR) site common experiment. CF1 is located in “Cook East,” a field that has been in no-till management since 1998, and represents the Alternative treatment of the LTAR common experiment. It is paired with the CF2 tower location in “Cook West,” which has been in conventional tillage since prior to 1998 and represents the Prevalent treatments of the common experiment. Cook Agronomy Farm is in the high precipitation agroecological zone of the Columbia Plateau’s dryland cropping region. Crop rotations are wheat-based and include winter wheat, spring wheat, chickpea, spring canola, and winter peas. Wheat is the principal cash crop, with other crops grown in rotation for diversity, nutrient, and pest management. Soils are predominantly silt loam texture Mollisols in the Palouse, Thatuna, Naff soil series. The CF1 tower replaced US-RC1, which operated 2012-2016 in a neighboring field that was also in no-till management since 1998. CF1 and RC1 have distinct footprints, aspects, and soil series compositions.

Phillips, Claire L.↗