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I/O performance studies of analysis workloads on production and dedicated resources at CERN
The recent evolutions of the analysis frameworks and physics data formats of the LHC experiments provide the opportunity of using central analysis facilities with a strong focus on interactivity and short turnaround times, to complement the more common distributed analysis on the Grid. In order to plan for such facilities, it is essential to know in detail the performance of the combination of a given analysis framework, of a specific analysis and of the installed computing and storage resources. This contribution describes performance studies performed at CERN, using the EOS disk-based storage, either directly or through an XCache instance, from both batch resources and highperformance compute nodes which could be used to build an analysis facility. A variety of benchmarks, both synthetic and based on real-world physics analyses and their corresponding input datasets, are utilized. In particular, the RNTuple format from the ROOT project is put to the test and compared to the latest version of the TTree format, and the impact of caches is assessed. In addition, we assessed the difference in performance between the use of storage system specific protocols, like XRootd, and FUSE. The results of this study are intended to be a valuable input in the design of analysis facilities, at CERN and elsewhere.
Lead and Arsenic Bioaccessibility and Speciation as a Function of Soil Particle Size
Bioavailability research of soil metals has advanced considerably from default values to validated in vitro bioaccessibility (IVBA) assays for site‐specific risk assessment. Previously, USEPA determined that the soil‐size fraction representative of dermal adherence and consequent soil ingestion was <250 μm. This size fraction was widely used in testing efforts for both in vivo and in vitro experiments. However, recent studies indicate the <150‐μm size fraction better represents the particle size that adheres to skin for potential ingestion. At issue is the relevance of validated in vivo and in vitro methods developed with <250 μm moving to the <150‐μm fraction. The objectives of this study were to investigate <250‐μm versus <150‐μm particle size and particle size groups for evaluating lead (Pb) and arsenic (As) IVBA and speciation. Soils with different properties were homogenized, oven dried, and sieved: <250 to > 150, <150 to >75, <75 to >38, and <38 μm. Sieved versus ground subsamples of <250‐μm and <150‐μm bulk soils were also used for IVBA and synchrotron‐based Pb and As speciation. Although we observed an increase in total and IVBA‐extractable Pb and As with decreased soil particle size, changes in %IVBA of Pb and As (dependent on the ratio extractable:total) remained consistent in all of the tested soils. No significant changes in Pb and As speciation were observed across the soil fractions. The results suggest that using the more relevant <150‐μm fraction will not undermine currently validated IVBA protocols in future bioavailability studies. Core Ideas Identified critical knowledge gaps regarding the <250‐μm vs. <150‐μm particle size used for IVBA. Wider implementation of the <150‐μm size fraction maintains past validation with <‐250 μm fraction. Regardless of increase in total and extractable Pb and As, %IVBA results remained consistent. Using <150‐μm particle size for IVBA requires much higher volumes/masses of soils. Synchrotron‐based speciation is significant in bioavailability studies to understand the fate and transport of contaminants.
Identification and Evaluation for Fueling of NRIC DOME Reactors Report
The National Reactor Innovation Center (NRIC) has designed a testbed for advanced microreactor experiments that enables and encourages technology developers to bring advanced designs closer to commercial availability. The test bed, Demonstration of Microreactor Experiments (DOME), will be used to facilitate much of the operation experimentation process of the each advanced microreactor including fueling and operational power experiments. This report identifies and evaluates the options for initial fueling the microreactors in DOME. This report also discusses the optional locations that were considered for the initial fueling of microreactor; namely the Transient Reactor Test (TREAT) reactor building, and an unspecified temporary location. But various logistical and construction issues essentially eliminated these other options from further consideration. A brief discussion in this report outlines potential equipment and protocol associated with fueling in DOME.
Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.
SITCOMTN-148: LSST Camera Electro-Optical Test (Run 7) Results
This note collects results from the LSST Camera electro-optical testing prior to installation on the TMA. We describe the focal plane characterization, optimization, and the resulting default settings. Results from eo-pipe are shown for standard runs such as B-protocols, Dense and SuperDense PTCs, gain stability, OpSim runs of Darks, and Darks with variable delays. We also describe features such as e2v Persistence, ITL phosphorescence in coffee stains, remnant charge near Serial register following saturated images, vampire pixels, ITL dips, and other sensor features.
Rapid and high-throughput determination of sorghum ( Sorghum bicolor ) biomass composition using near infrared spectroscopy and chemometrics
Compositional characterization of biomass is vital for the biofuel industry. Traditional wet chemistry-based methods for analyzing biomass composition are laborious, time-consuming, and require extensive use of chemical reagents as well as highly skilled personnel. In this study, near-infrared (NIR) spectroscopy was used to quickly assess the composition of above-ground vegetative biomass from 113 diverse, photoperiod-sensitive, biomass-type sorghum (Sorghum bicolor) accessions cultivated under field conditions in Central Illinois. Biomass samples were analyzed using NIR spectra collected in the spectral range of 867–2536 nm, with their chemical compositions determined following the National Renewable Energy Laboratory (NREL) protocol. Advanced spectral pre-treatment and band selection techniques were utilized to develop calibration models using partial least squares regression (PLSR). The models’ effectiveness was assessed through cross-validation and independent data tests. The predictions for moisture, ash, extractives, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin were accurate and reliable, demonstrating the capability of NIR spectroscopy to provide rapid and precise characterization of sorghum biomass. The results demonstrated that NIR spectroscopy is an efficient tool for rapidly characterizing sorghum biomass, making it a sustainable option for screening desirable feedstock for biofuel or bioproduct production.
Building energy simulation in real time through an open standard interface
Building energy models (BEMs) are typically used for design and code compliance for new buildings and in the renovation of existing buildings to predict energy use. We present the increasing adoption of BEM as standard practice in the building industry presents an opportunity to extend the use of BEMs into construction, commissioning and operation. In 2009, the authors developed a real-time simulation framework to execute an EnergyPlus model in real time to improve building operation. This paper reports an enhancement of that real-time energy simulation framework. The previous version only works with software tools that implement the custom co-simulation interface of the Building Controls Virtual Test Bed (BCVTB), such as EnergyPlus, Dymola and TRNSYS. The new version uses an open standard interface, the Functional Mockup Interface (FMI), to provide a generic interface to any application that supports the FMI protocol. In addition, the new version utilizes the Simple Measurement and Actuation Profile (sMAP) tool as the data acquisition system to acquire, store and present data. Lastly, this paper introduces the updated architecture of the real-time simulation framework using FMI and presents proof-of-concept demonstration results which validate the new framework.
Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations
We present that borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. Lastly, the results shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.
Data for Rapid and High-Throughput Determination of Sorghum ( Sorghum bicolor ) Biomass Composition using Near Infrared Spectroscopy and Chemometrics
Compositional characterization of biomass is vital for the biofuel industry. Traditional wet chemistry-based methods for analyzing biomass composition are laborious, time-consuming, and require extensive use of chemical reagents as well as highly skilled personnel. In this study, near-infrared (NIR) spectroscopy was used to quickly assess the composition of above-ground vegetative biomass from 113 diverse, photoperiod-sensitive, biomass-type sorghum ( Sorghum bicolor ) accessions cultivated under field conditions in Central Illinois. Biomass samples were analyzed using NIR spectra collected in the spectral range of 867–2536 nm, with their chemical compositions determined following the National Renewable Energy Laboratory (NREL) protocol. Advanced spectral pre-treatment and band selection techniques were utilized to develop calibration models using partial least squares regression (PLSR). The models’ effectiveness was assessed through cross-validation and independent data tests. The predictions for moisture, ash, extractives, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin were accurate and reliable, demonstrating the capability of NIR spectroscopy to provide rapid and precise characterization of sorghum biomass. The results demonstrated that NIR spectroscopy is an efficient tool for rapidly characterizing sorghum biomass, making it a sustainable option for screening desirable feedstock for biofuel or bioproduct production.
Stress Relaxation Cracking of Alloys at Temperatures Higher Than 540°C
Type 347H stainless steel (347H SS), used in commercial concentrating solar power (CSP) thermal energy storage to store solar-salt at a temperature of 565°C, has been reported in the literature to be susceptible to stress-relaxation cracking (SRC). The welded heat-affected zone (HAZ) and fusion zone (FZ) of 347H SS, particularly in thick sections, are known to be susceptible to failure during post-weld heat treatment (reheat cracking). SRC could also occur after months or years under an elevated-temperature service environment. Two conditions must be present for failure to occur in the HAZ and/or FZ: 1) a modified or sensitized microstructure and 2) sufficiently high tensile residual stresses present at the elevated service temperature. The overarching goal of this project is to recommend SRC mitigation protocols to avoid susceptibility to fail through SRC at temperatures relevant for CSP. Post weld heat treatment conditions and alternative alloys are investigated as potential mitigation solutions to SRC. We used Gleeble thermomechanical simulation tests and finite element (FE) models to understand the susceptibility of 347H SS to SRC as a function of temperature, stress, and microstructure. We started with a literature review of weldability issues with 347H SS and techniques to mitigate SRC in 347H SS weldments. Next, we used Gleeble experiments to determine reheat cracking susceptibility in the simulated HAZ of 347SS weldments and an alternative alloy, 316L SS (NUCL 167 SPH) with boron added. We also performed Gleeble experiments to compare the reheat cracking susceptibility of 347H cross welded with two different fillers: E347, which is used in some commercial CSP TES tanks, and E16.8.2. We validated the experimental results with FE models of the residual stresses. We found that although the 316L (NUCL 167 SPH) is less susceptible to reheat cracking, it is slightly weaker than 347H and ASME BP&V codes limit its use to a service condition of 565°C. We also found that welds using E16.8.2 as the weld filler are less susceptible to failure than those using E347, likely due to the higher creep ductility of E16.8.2, and that it may be used as an alternative filler for repair welding of 347H welds or as the primary choice of filler for newly developed weld joints. We also found that post weld heat treatment could be a viable solution for mitigating stress in E347-347H SS thick, constrained welds, like those found in CSP tanks, and propose several options for mitigating SRC in existing and future TES tanks.
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g –1 of soil than other methods tested. All method combinations yielded VLPs g –1 of soil on the 10 8 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g –1 of soil among the soil types. In conclusion, this research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.
Nominal Device Support for ATCA Shelf Manager
The ATCA standard specifies a mandatory Shelf Manager (ShM) unit which is a key element for the system operation. It includes the Intelligent Platform Management Controller (IPMC) which monitors the system health, retrieves inventory information and controls the Field Replaceable Units (FRUs). These elements enable the intelligent health monitoring, providing high-availability and safety operation, ensuring the correct system operation. For critical systems like ones of tokamak ITER these features are mandatory to support the long pulse operation. The Nominal Device Support (NDS) was designed and developed for the ITER CODAC Core System (CCS), which will be the responsible for plant Instrumentation and Control (I and C), supervising and monitoring on ITER. It generalizes the Enhanced Physics and Industrial Control System (EPICS) device support interface for Data Acquisition (DAQ) and timing devices. However the support for health management features and ATCA ShM are not yet provided. This paper presents the implementation and test of a NDS for the ATCA ShM, using the ITER Fast Plant System Controller (FPSC) prototype environment. This prototype is fully compatible with the ITER CCS and uses the EPICS Channel Access (CA) protocol as the interface with the Plant Operation Network (PON). The implemented solution running in an EPICS Input / Output Controller (IOC) provides Process Variables (PV) to the PON network with the system information. These PVs can be used for control and monitoring by all CA clients, such as EPICS user interface clients and alarm systems. The results are presented, demonstrating the fully integration and the usability of this solution. (authors)
Combining genome-wide association studies and expression quantitative trait nucleotide mapping with molecular and genetic validations to identify transcriptional networks regulating drought tolerance in Populus
Objectives: (i). To deploy a large-scale experimental drought trial for up to 1000 unique genotypes of Populus equipping the sites with controlled irrigation and drought treatments that are fully automated and monitored. FULLY COMPLETED (ii) To test the hypothesis that a suite of traits identified for drought tolerance in P. nigra can be measured in drought and control treatments in the wide germplasm collection of P. trichocarpa. FULLY COMPLETED (iii) To use established and novel GWAS model approaches to identify gene loci linked to drought tolerance traits on interest in P. trichocarpa. FULLY COMPLETED (iv) To undertake comparative analysis of GWAS results for drought tolerance traits in P. nigra and P. trichocarpa. PARTIALLY COMPLETED – remains active (v) Using RNAseq in P. trichocarpa, in droughted and control treatments to identify cis- and trans-regulated eQTN. FULLY COMPLETED (vi) Validate up to 50 cis-QTNs, from network hubs using transient protoplast assays. FULLY COMPLETED (vii) To establish Agrobacterium-based gene editing protocols in Populus. FULLY COMPLETED (viii) To utilize early leads from previous research to investigate at least 6 candidate genes for drought tolerance in Populus. FULLY COMPLETED (ix) To validate up to 20 candidate genes for drought tolerance in P. trichocarpa refined from the long-list tested in the transient assays for cis-acting hub gene targets. PARTIALLY COMPLETED- remains active.
Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves
The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model pho-tosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosyn-thetic parameters using concurrent gas exchange and chlorophyll fluorescence mea-surements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, Km, that is, Michaelis constant for CO2 by Rubisco, prefixed. Additionally, we show that including detailed low CO2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement proto-cols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided.
Understanding the Stability of Manganese Chromium Antimonate Electrocatalysts through Multimodal In Situ and Operando Measurements
Herein, we utilize an on-line electrochemical flow cell coupled with an inductively coupled plasma-mass spectrometer (ICP-MS) to characterize the impact of composition and reactant gas on the multielement dissolution of Mn(-Cr)-Sb-O electrocatalysts. Compared to Mn 2 O 3 and Cr 2 O 3 oxides, we find that the antimonate framework stabilizes Mn at OER potentials and Cr at both ORR and OER potentials. Furthermore, dissolution of Mn and Cr from Mn(-Cr)-Sb-O is found to be driven by ORR reaction rate, with minimal dissolution under N 2 . We observe preferential dissolution of Cr totaling 13% over 10 minutes at 0.3, 0.6, and 0.9 V vs RHE, with only 1.5% loss of Mn, indicating an enrichment of Mn at the surface of the particles. Despite this asymmetric dissolution, in situ X-ray absorption spectroscopy (XAS) showed no measurable changes in the Mn K-edge at comparable potentials. This lack of change could suggest that modification to the Mn oxidation state in the surface layer is too small or that layer is too thin to be measured with the bulk XAS measurement. Lastly, on-line ICP-MS was used to assess the effects of applied potential, scan rate, and current of Mn-Cr-Sb-O during cyclic voltammetry and accelerated stress tests. With this deeper understanding of the interplay between oxygen reduction and dissolution, testing procedures were identified to maximize both activity and stability. This work highlights the use of multi-modal in situ characterization techniques in tandem to build a more complete model of stability and develop protocols for optimizing catalyst performance.
The combined force field-sampling problem in simulations of disordered amyloid-β peptides
Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field–sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm. The force field and sampling combinations are used to characterize the structural ensembles of the amyloid-beta peptides Aβ42 and Aβ43, which both should be random coils as shown recently by experimental nuclear magnetic resonance (NMR) and 2D Förster resonance energy transfer (FRET) experiments. The results illustrate the key importance of the sampling algorithm: while the standard force field using TREx is in poor agreement with the NMR J-coupling and nuclear Overhauser effect and 2D FRET data, when using the TCW method, the standard and optimized protein-water force field combinations are in very good agreement with the same experimental data since the TCW sampling method produces qualitatively different ensembles than TREx. Lastly, we also discuss the relative merit of the 2D FRET data when validating structural ensembles using the different force fields and sampling protocols investigated in this work for small IDPs such as the Aβ42 and Aβ43 peptides.
A Data Exchange Interface for a Standards Based Data Integration Platform
The modern electrical grid is a complex and a data rich system, requiring several sub-systems to provide the capability and support needed to perform functions such as distributed energy resource management, outage management, and fault location and isolation, to name a few. There is a need to develop software solutions and platforms that provide an integrated infrastructure to allow interoperability between these subsystems, while leveraging the abundant data available from today’s grid. In this paper, we present the development and deployment of an application service to integrate GridAPPS-D which is an open source, standards-based software platform with SurvalentONE, a commonly used DNP3 based ADMS platform that allows operation, monitoring, analysis, restoration, and optimization of network operations. We present details of the integration architecture, including its implementation, and provide results from functional testing of the architecture on a 13 bus IEEE system. The results validate that the integration is successful and is able to provide a two-way exchange of communication and translation between different communication protocols.