Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “sequencer”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Abstract Background Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na V 1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and Na V 1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene, SCN1A . We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVR A1 , AVR A7 , AVR A9 , AVR A13 , and allelic AVR A10 /AVR A22 , which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVR A6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVR A1 , AVR A7 , AVR A10 /AVR A22 , and AVR A13 , suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVR A1 and AVR A6 as well as allelic AVR A10 and AVR A22 is largely determined by the receptors’ C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVR A10 and five specific AVR A22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVR A effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Carbon dioxide (CO2) flux, amplicon sequencing and liquid chromatography–mass spectrometry (LC-MS) data for pyrogenic organic matter (PYOM) amended soil incubations in lab, Madison, WI, 2021-22

This dataset comprises soil-pyrogenic organic matter (PyOM) incubation experiments conducted in a laboratory setting. The focus was on measuring carbon dioxide (CO2) flux emitted in the headspace of incubation jars over a one-month period. The aim was to estimate carbon mineralization from two different carbon fractions in PyOM, as well as carbon mineralization from soil organic carbon (SOC). Bacterial and fungal community profiles were tracked at various time points during the incubation to observe changes in the overall community and specific responders to PyOM. LC-MS analysis of soil samples was also performed to monitor changes in the soil's chemical composition.The provided dataset includes processed CO2 flux measurements obtained from the Picarro-multiplexer measurement setup for each sample incubation jar. This data is available in the "CO2Flux.csv" file. Additionally, the dataset includes CO2 flux data partitioned to estimate mean carbon mineralization from the two PyOM carbon fractions, bulk PyOM, and SOC. The cumulative carbon mineralization data is provided in "cml_respired.csv," while the rate of carbon mineralization data is in "rate_respired.csv." The file "cml_respired_lastcyc.csv" contains cumulative carbon mineralization data for the PyOM carbon fractions, bulk PyOM, and SOC throughout the entire incubation period.For the LC-MS analysis, the raw data can be found in the "20220721_NZ_PeakHeights_FinalAnalysis.csv" file, while sample metadata is provided in "20220721_NZpilot_Metadata.csv". Processed LC-MS data is available in the file "20220721_NZ_FINAL_msdat_sub3.csv". Lastly, the dataset includes the relative abundance data for bacterial genera that exhibited a significant positive response to the addition of PyOM produced at 350 degrees Celsius, which can be found in "resp_genera_350.csv".

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Factors That Influence Variability in Stress-Drop Measurements Using Spectral Decomposition and Spectral-Ratio Methods for the 2019 Ridgecrest Earthquake Sequence

Stress drop is a fundamental parameter related to earthquake source physics, but is hard to measure accurately. To better understand how different factors influence stress-drop measurements, we compare two different methods using the Ridgecrest stress-drop validation data set: spectral decomposition (SD) and spectral ratio (SR), each with different processing options. Here, we also examine the influence of spectral complexity on source parameter measurement. Applying the SD method, we find that frequency bandwidth and time-window length could influence spectral magnitude calibration, while depth-dependent attenuation is important to correctly map stress-drop variations. For the SR method, we find that the selected source model has limited influence on the measurements; however, the Boatwright model tends to produce smaller standard deviation and larger magnitude dependence than the Brune model. Variance reduction threshold, frequency bandwidth, and time-window length, if chosen within an appropriate parameter range, have limited influence on source parameter measurement. For both methods, wave type, attenuation correction, and spectral complexity strongly influence the result. The scale factor that quantifies the magnitude dependence of stress drop show large variations with different processing options, and earthquakes with complex source spectra deviating from the Brune-type source models tend to have larger scale factor than earthquakes without complexity. Based on these detailed comparisons, we make a few specific suggestions for data processing workflows that could help future studies of source parameters and interpretations.

58 GEOSCIENCES↗
DOE OSTI2023

How Good Is Your Location? Comparing and Understanding the Uncertainties in Location for the 1993 Rock Valley Sequence

Accurate event locations are important for many endeavors in seismology, and understanding the factors that contribute to uncertainties in those locations is complex. In this article, we present a case study that takes an in-depth look at the accuracy and precision possible for locating nine shallow earthquakes in the Rock Valley fault zone in southern Nevada. These events are targeted by the Rock Valley Direct Comparison phase of the Source Physics Experiment, as candidates for the colocation of a chemical explosion with an earthquake hypocenter to directly compare earthquake and explosion sources. For this comparison, it is necessary to determine earthquake hypocenters as accurately as possible so that different source types have nearly identical locations. Our investigations include uncertainty analysis from different sets of phase arrivals, stations, velocity models, and location algorithms. For a common set of phase arrivals and stations, we find that epicentral locations from different combinations of velocity models and algorithms are within 600 m of one another in most cases. Event depths exhibit greater uncertainties, but focusing on the S-P times at the nearest station allows for estimates within approximately 500 m.

58 GEOSCIENCES↗
DOE OSTI2020

The Brachypodium ENCODE Project – from sequence to function: Predicting physiological responses in grasses to facilitate engineering of biofuel crops

The overarching goal of this proposal was to gain deep knowledge of chromatin dynamics and gene networks related to stress responses in grasses. To accomplish this goal our Brachypodium ENCODE project (1) coupled drought-focused physiological analysis with multiple layers of ENCODE ‘omics’ profiling; (2) obtained fundamental information about the Brachypodium transcriptome, epigenome, chromatin dynamics, and gene regulatory networks; and (3) elucidated the regulatory dynamics of gene networks that can be manipulated to increase energy grass crop productivity.

09 BIOMASS FUELS↗
DOE OSTI2020

Impact of Inverter Based Resource Negative Sequence Current Injection on Transmission System Protection

This report documents the results of analysis performed to investigate the impact of inverter-based resource (IBR) response to unbalanced faults on transmission system protective relay dependability and security. Electromagnetic transient (EMT) simulations were performed to simulate IBR response to these faults using existing manufacturer-developed EMT models for four separate IBRs. The study team was composed of IBR manufacturers, relay manufacturers, transmission providers, reliability coordinators and industry consultants with experience in EMT simulation and system protection. The results indicate that under certain conditions, IBR response can result in protective relay misoperations if current protection practices, which were developed based on conventional power sources, are not adapted to the characteristics of IBRs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Predictive Skill of Deep Learning Models Trained on Limited Sequence Data

In this report we investigate the utility of one-dimensional convolutional neural network (CNN) models in epidemiological forecasting. Deep learning models, especially variants of recurrent neural networks (RNNs) have been studied for influenza forecasting, and have achieved higher forecasting skill compared to conventional models such as ARIMA models. In this study, we adapt two neural networks that employ one-dimensional temporal convolutional layers as a primary building block temporal convolutional networks and simple neural attentive meta-learner for epidemiological forecasting and test them with influenza data from the US collected over 2010-2019. We find that epidemiological forecasting with CNNs is feasible, and their forecasting skill is comparable to, and at times, superior to, RNNs. Thus CNNs and RNNs bring the power of nonlinear transformations to purely data-driven epidemiological models, a capability that heretofore has been limited to more elaborate mechanistic/compartmental disease models.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

KENO V.a Primer: Performing Calculations using SCALE’s Criticality Safety Analysis Sequence (CSAS5) with Fulcrum

The SCALE code system developed at Oak Ridge National Laboratory is widely used and accepted around the world for criticality safety analyses. The well-known KENO V.a three-dimensional Monte Carlo criticality computer code is one of the primary criticality safety analysis tools in SCALE. The KENO V.a primer is designed to help a new user understand and use the SCALE/KENO V.a Monte Carlo code for nuclear criticality safety analyses. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO V.a in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO V.a that are useful in criticality analyses. The primer is based on SCALE 6.2 and 6.3, which includes the Fulcrum graphical user interface (GUI). Each example uses Fulcrum to provide the framework for preparing input data and viewing output results. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO V.a input and allows the user to quickly run a simple criticality problem with SCALE/KENO V.a. The sections that follow Quickstart include a list of basic objectives at the beginning that identifies the goal of the section and the individual SCALE/KENO V.a features that are covered in detail in the sample problems in that section. Upon completion of the primer, a new user should be comfortable using Fulcrum to set up criticality problems in SCALE/KENO V.a. The primer provides a starting point for the criticality safety analyst who uses SCALE/KENO V.a. Complete descriptions are provided in the SCALE/KENO V.a manual. Although the primer is self-contained, it is intended as a companion volume to the SCALE/KENO V.a training and documentation. The SCALE manual and training schedule are available at https://scale.ornl.gov. The primer provides specific examples of using SCALE/KENO V.a for criticality analyses; the SCALE/KENO V.a manual provides information on the use of SCALE/KENO V.a and all its modules. The primer also contains an appendix with sample input files. In addition, this primer, its errata and sample inputs are also available at https://code.ornl.gov/scale/primers/kenova.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2020

KENO-VI Primer: Performing Calculations using SCALE’s Criticality Safety Analysis Sequence (CSAS6) with Fulcrum

The SCALE code system developed at Oak Ridge National Laboratory is widely used and accepted around the world for criticality safety analysis. The well-known KENO-VI three-dimensional Monte Carlo criticality computer code is one of the primary criticality safety analysis tools in SCALE. The KENO-VI primer is designed to help a new user understand and use the SCALE/KENO-VI Monte Carlo code for nuclear criticality safety analysis. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO-VI in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO-VI that are useful in criticality analysis. The primer is based on SCALE 6.2 and 6.3, which includes the Fulcrum graphical user interface. Each example uses Fulcrum to provide the framework for preparing input data and viewing output results. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO-VI input and allows the user to quickly run a simple criticality problem with SCALE/KENO-VI. Each following section begins with a list of basic objectives identifying the goal of the section and the individual SCALE/KENO-VI features covered in detail in the section’s sample problems. Upon completion of the primer, a new user should be comfortable using Fulcrum to set up criticality problems in SCALE/KENO-VI. The primer provides a starting point for the criticality safety analyst who uses SCALE/KENO-VI. Complete descriptions are provided in the SCALE/KENO-VI manual. Although the primer is self-contained, it is intended as a companion volume to the SCALE/KENO-VI training and documentation. The SCALE manual and training schedule are available at https://scale.ornl.gov. The primer provides specific examples of using SCALE/KENO-VI for criticality analysis; the SCALE/KENO-VI manual provides information on the use of SCALE/KENO-VI and all its modules. The primer also contains an appendix with sample input files. In addition, this primer, its errata, and sample inputs are also available at https://code.ornl.gov/scale/primers/kenovi/.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

A Spatiotemporal Sequence Forecasting Platform to Advance the Prediction of Changing Spatiotemporal Patterns of CO 2 Concentration by Incorporating Human Activity and Hydrological Extremes

Focal Areas (2): Predictive modeling using AI techniques and AI-derived model components. It describes the use of AI and other tools to design a prediction system comprising a hierarchy of models. Specifically, this white paper focuses on the development of a collaborative deep learning platform for evaluating and predicting spatiotemporal relationships between the hydrological and carbon cycles and includes capabilities for considering biogenic and anthropogenic inputs to these systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Validation and functional characterization of transcription factors in wheat using cell-free protein expression and high-throughput sequencing technologies

Transcription factors (TFs) are critical biomolecules that control and regulate gene expression in every organism. In wheat, there are 3,606 genes annotated as putative TFs which are primarily uncharacterized. In this work, using a DAP-seq approach, we have validated and characterized a select number of TFs (5bl and 5dl) belonging to GeBP family of proteins, responsible for plant cellular growth, development, and differentiation. We found that top DNA binding motifs for 5bl and 5dl are (G/T)N(T/G)GTGGT and (C/G)AA(C/G)AA respectively. These motifs/peaks are enriched in the promoter regions of the genes, which are associated with rRNA biogenesis and protein maturation pathways. This study is also a first demonstration that DAP-seq can be applied for such a complex and large genome such as wheat.

59 BASIC BIOLOGICAL SCIENCES↗