FLIP: FLuorescence Imaging Pipeline for field-based chlorophyll fluorescence images
Not Available
97 MATHEMATICS AND COMPUTING↗
SEARCH · Engineering Papers
Results for “pipeline”
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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Could on-site fuel storage economically reduce power plant-gas grid dependence in pipeline constrained areas like New England?
In the Northeastern United States, natural gas supply constraints have led to periods when gas shortages have caused up to a quarter of all unscheduled power plant outages. Dual fuel oil/gas generators or local gas storage might mitigate gas supply shortages. We use historical power plant operational and availability data to develop a supply curve of the costs required for generators to mitigate fuel shortage failures in New England. Based on 2012–2018 data, we find that the historical fuel shortages at approximately 2 GW worth of gas-fired capacity could be mitigated using on-site fuel storage. For comparison, New England’s average reserve margin was 1.7–2.8 GW over our sample period. Oil dual fuel plants would recoup their investment if compensated with a reliability adder of $\$ 3-7$/MWh during their normal operations, while $\$ 7-16$/MWh would incentivize using onsite, compressed natural gas storage. We estimate that the capital expenses associated with the fuel storage options would be less expensive than installing battery backup for resource adequacy at current battery prices.
03 NATURAL GAS↗
A modeling pipeline to relate municipal wastewater surveillance and regional public health data
As COVID-19 becomes endemic, public health departments require improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging. We have developed a generalized methodology to improve the predictive power of wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but all model estimates of prevalence significantly improved correlation compared to doing no correction. We also investigate the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We do this in a rolling manner for corrected wastewater data and for other prevalence indicators, and statistically compare the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We find that wastewater trends often lead other COVID-19 indicators in predicting new surges.
60 APPLIED LIFE SCIENCES↗
Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Toward High-Voltage Cathodes for Zinc-Ion Batteries: Discovery Pipeline and Material Design Rules
Efficient energy storage systems are crucial to address the intermittency of renewable energy sources. As multivalent batteries, Zn-ion batteries (ZIBs), while inherently low voltage, offer a promising low-cost alternative to Li-ion batteries due to the viable use of zinc as the anode. However, to maximize the potential impact of ZIBs, rechargeable cathodes with improved Zn diffusion are needed. To better understand the chemical and structural factors influencing Zn-ion mobility within battery electrode materials, we employ a high-throughput computational screening approach to systematically evaluate candidate intercalation hosts for ZIB cathodes, expanding the chemical search space on empty intercalation hosts that do not contain Zn. We leverage a high-throughput screening funnel to identify promising cathodes in ZIBs, integrating screening criteria with density functional theory (DFT)-based calculations of Zn2+ intercalation and diffusion inside the host materials. Using these data, we identify the design principles that favor Zn-ion mobility in candidate cathode materials. Building on previous work on divalent-ion cathodes, this study broadens the chemical space for next-generation multivalent energy storage systems.
electrodes↗
High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin–Iron Complexes: Novel Pipeline and Complex Structures
Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools. The protocol was used for investigating the Fe complexes formed by model compounds of lignin-derived organic ligands, namely, caffeic acid (CA), p-coumaric acid (CMA), vanillin (VNL), and cinnamic acid (CNA). Isotopologue analysis of 54/56 Fe was used to screen out the potential UHPLC-HRMS (m/z) features for complexes formed between organic ligands and Fe, with multiple features captured for CA, CMA, VNL, and CNA when 35/37 Cl isotopologue analysis was used as supplementary evidence for the complexes with Cl. MS/MS spectra, fragment analysis, and structure prediction with SIRIUS were used to annotate the structures of mono/bidentate mono/biligand complexes. The analysis determined the structures of monodentate and bidentate complexes of FeL x Cl y (L: organic ligand, x = 1–4, y = 0–3) formed by model compounds. The protocol developed in this study can be used to identify unknown organic ligands occurring in complex environmental samples and shed light on the molecular-level processes governing the stability of the SOC.
54 ENVIRONMENTAL SCIENCES↗
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Bridging microscopy with molecular dynamics and quantum simulations: an atomAI based pipeline
Recent advances in (scanning) transmission electron microscopy have enabled a routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for atomistic simulations. In this fashion, the theory will address experimentally emerging structures, as opposed to the full range of theoretically possible atomic configurations. However, this challenge is highly nontrivial due to the extreme disparity between intrinsic timescales accessible to modern simulations and microscopy, as well as latencies of microscopy and simulations per se. Addressing this issue requires as a first step bridging the instrumental data flow and physics-based simulation environment, to enable the selection of regions of interest and exploring them using physical simulations. Here we report the development of the machine learning workflow that directly bridges the instrument data stream into Python-based molecular dynamics and density functional theory environments using pre-trained neural networks to convert imaging data to physical descriptors. Additionally, the pathways to ensure structural stability and compensate for the observational biases universally present in the data are identified in the workflow. This approach is used for a graphene system to reconstruct optimized geometry and simulate temperature-dependent dynamics including adsorption of Cr as an ad-atom and graphene healing effects. However, it is universal and can be used for other material systems.
36 MATERIALS SCIENCE↗
The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data
Correction to: Scientific Data https://doi.org/10.1038/s41597-020-0534-3, published online 09 July 2020
54 ENVIRONMENTAL SCIENCES↗
A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs
Tuberculosis (TB) is the deadliest infectious disease worldwide. The design of new treatments for TB is hindered by the large number of candidate drugs, drug combinations, dosing choices, and complex pharmaco-kinetics/dynamics (PK/PD). Here we study the interplay of these factors in designing combination therapies by linking a machine-learning model, INDIGO-MTB, which predicts in vitro drug interactions using drug transcriptomics, with a multi-scale model of drug PK/PD and pathogen-immune interactions called GranSim. We calculate an in vivo drug interaction score (iDIS) from dynamics of drug diffusion, spatial distribution, and activity within lesions against various pathogen sub-populations. The iDIS of drug regimens evaluated against non-replicating bacteria significantly correlates with efficacy metrics from clinical trials. Our approach identifies mechanisms that can amplify synergistic or mitigate antagonistic drug interactions in vivo by modulating the relative distribution of drugs. Our mechanistic framework enables efficient evaluation of in vivo drug interactions and optimization of combination therapies.
59 BASIC BIOLOGICAL SCIENCES↗
A Practical Flake Segmentation and Indexing Pipeline for Automated 2D Material Stacking
Explore the source record for details and available documents.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Simple and Scalable Streaming: The GRETA Data Pipeline
The Gamma Ray Energy Tracking Array (GRETA) is a state of the art gamma-ray spectrometer being built at Lawrence Berkeley National Laboratory to be first sited at the Facility for Rare Isotope Beams (FRIB) at Michigan State University. A key design requirement for the spectrometer is to perform gamma-ray tracking in near real time. To meet this requirement we have used an inline, streaming approach to signal processing in the GRETA data acquisition system, using a GPU-equipped computing cluster. The data stream will reach 480 thousand events per second at an aggregate data rate of 4 gigabytes per second at full design capacity. We have been able to simplify the architecture of the streaming system greatly by interfacing the FPGA-based detector electronics with the computing cluster using standard network technology. A set of highperformance software components to implement queuing, flow control, event processing and event building have been developed, all in a streaming environment which matches detector performance. Prototypes of all high-performance components have been completed and meet design specifications.
Cromaz, Mario↗
A path to intelligent watersheds: coordinating the data to decision pipeline
Operations of multi-reservoir systems are challenged in-part by the interplay of complex physical processes functioning within the watershed. The employment of intelligent systems can be of aid by linking environmental sensing, information technology, data analytics, simulation and decision support to achieve a data-to-decision flow of information. A further challenge is that watershed resources are managed for multiple purposes requiring some level of coordination among numerous resource managers, asset operators and users. System intelligence in this context relies on shared community platforms (data portals, community models), and coordinated communication between decision makers. Opportunities to enrich watershed intelligence has been the subject of a roadmapping exercise for the Department of Energy’s Water Power Technologies Office which has relied on broad stakeholder engagement. Initial phases of engagement involved personal interviews and a series of virtual group meetings, which focused on identifying opportunities to improve the intelligence of the physical infrastructure within our watersheds—examples of feedback include improved sensing of snowpack and runoff, data standards for facilitated data sharing, and better forecasting tools. The latter phase of engagement involved the conduct of a case study in the Upper Colorado River basin where key stakeholders were interviewed to map how their decisions are informed by intelligence from other basin stakeholders. Our presentation will highlight the interdisciplinary flow of information in complex watershed systems and identify physical and institutional opportunities toward the strategic operation of water infrastructure.
Colorado River↗
Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding
Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.
59 BASIC BIOLOGICAL SCIENCES↗