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Data for Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum
These data were collected in 2018 and 2019 at the University of Illinois Energy Farm (N 40.063607, W 88.206926). During each growing season, bulk and rhizosphere soil were collected from replicate Sorghum bicolor nitrogen use efficiency trial plots at three separate time points (approximately July 1, August 1, and September 1). We measured soil moisture, pH, soil nitrate and ammonium, potential nitrification, potential denitrification, and extracted and sequenced the V4 region of the 16S rRNA gene for microbial community analysis. All microbial sequence data is archived in the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (accession number SRP326979, project number PRJNA741261).
Physics-Based Constraints in the Forward Modeling Analysis of Time-Correlated Image Data (Long Version)
The forward-model approach has been shown to produce accurate model reconstructions of scientific measurements for single-time image data. Here we extend the approach to a series of images that are correlated in time using the physics-based constraints that are often available with scientific imaging. The constraints are implemented through a representational bias in the model and, owing to the smooth nature of the physics evolution in the specified model, provide an effective temporal regularization. Unlike more general temporal regularization techniques, this restricts the space of solutions to those that are physically realizable. We explore the performance of this approach on a simple radiographic imaging problem of a simulated object evolving in time. We demonstrate that the constrained simultaneous analysis of the image sequence outperforms the independent forward modeling analysis over a range of degrees of freedom in the physics constraints, including when the physics model is under-constrained. Further, this approach outperforms the independent analysis over a large range of signal-to-noise ratios.
A Complete-Sequence Population for Pan-Genome Analysis of Sorghum
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Insight from in-situ analysis of grain boundary character radiation sequence and thermal conditions on defect structure evolution in nickel.
Abstract not provided.
Insight from in-situ analysis of grain boundary character radiation sequence and thermal conditions on defect structure evolution in nickel.
Abstract not provided.
A systematic approach to the analysis of double faults within design basic accident methodology - 14501
Within the UK there is a general trend towards adopting Design Basis Accident (DBA) methodology for the assessment of radiological hazards, including criticality. DBA is a single fault methodology and comprises identifying the initiating event, its frequency and consequence. A fault with a very low initiating event frequency will not require further analysis. A fault sequence that terminates in a sub-critical configuration would also not require further analysis; although the identified passive features ensuring sub-criticality are subjected to engineering substantiation. Where faults do not pass this initial screening, two safety measures are generally required to ensure the fault does not progress to a criticality incident. This methodology provides a robust approach to single faults ensuring that an appropriate level and range of plant measures are identified and subjected to appropriate substantiation. However, a criticality is a cliff-edge effect and is dependent on multiple parameters. It is entirely possible under DBA to evaluate several single fault sequences and conclude that no measures are required because the single faults terminate in a sub-critical configuration. Importantly, for criticality safety, under DBA, there is no requirement to prevent important parameters from deviating from normal or upper bound 'safe' levels leaving the plant at greater risk in the event that further faults initiate. The combination of two faults could lead to a criticality incident but there is no current driver within DBA methodology to analyze these coincident or double faults. There is, therefore, potential to significantly under estimate the risk of criticality. This understanding is embodied within other methodologies such as the Double Contingency Principle. However, within the UK the DBA methodology has so significantly improved the analysis of single faults that, in some instances, consideration of double faults has taken a back seat. This is despite the UK regulator stating that 'criticality safety cases should employ the double contingency approach'. This paper presents a systematic approach to ensure that the potential for double faults or multiple parameter deviations to result in a criticality is effectively evaluated within the wider DBA methodology. The methodology determines which faults may be screened out from double fault analysis on the grounds of being 'unlikely' to initiate and being present for a 'short' duration. For those faults screened into double fault analysis, this guidance sets out the potential means of determining acceptable risk. These means include the specific evaluation of the risk of two criticality control parameters deviating simultaneously, the definition of additional safety measures and the definition of the boundary of safety for multiple parameters and the risk of exceeding this boundary. (authors)
A HIGH-RESOLUTION MULTIBAND SURVEY OF WESTERLUND 2 WITH THE HUBBLE SPACE TELESCOPE. II. MASS ACCRETION IN THE PRE-MAIN-SEQUENCE POPULATION
We present a detailed analysis of the pre-main-sequence (PMS) population of the young star cluster Westerlund 2 (Wd2), the central ionizing cluster of the H ii region RCW 49, using data from a high-resolution multiband survey with the Hubble Space Telescope. The data were acquired with the Advanced Camera for Surveys in the F555W, F814W, and F658N filters and with the Wide Field Camera 3 in the F125W, F160W, and F128N filters. We find a mean age of the region of 1.04 ± 0.72 Myr. The combination of dereddened F555W and F814W photometry in combination with F658N photometry allows us to study and identify stars with Hα excess emission. With a careful selection of 240 bona-fide PMS Hα excess emitters we were able to determine their Hα luminosity, which has a mean value L(Hα)=1.67×10{sup −31} erg s{sup −1}. Using the PARSEC 1.2S isochrones to obtain the stellar parameters of the PMS stars, we determined a mean mass accretion rate M-dot {sub acc}=4.43×10{sup −8} M{sub ⊙} yr{sup −1} per star. A careful analysis of the spatial dependence of the mass accretion rate suggests that this rate is ∼25% lower in the center of the two density peaks of Wd2 in close proximity to the luminous OB stars, compared to the Wd2 average. This rate is higher with increasing distance from the OB stars, indicating that the PMS accretion disks are being rapidly destroyed by the far-ultraviolet radiation emitted by the OB population.
An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types
Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can’t directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.
Top-down analysis of protein samples by de novo sequencing techniques
MOTIVATION: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. RESULTS: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.
Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years
We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.
MemGaze: Rapid and Effective Load-Level Memory Trace Analysis
A major challenge of memory analysis tools is combining high-resolution analysis and low overhead measurement. Currently, hardware/software-based analysis of load-level sequences incurs time slowdowns of O(100×). We present MemGaze, a tool for low-overhead, high-resolution memory analysis. MemGaze uses Intel’s Processor Tracing (PT) instruction ptwrite to collect sampled and compressed memory address traces for load-level, sequence-aware analysis of data reuse. We describe multi-resolution analysis for locations vs. operations, accesses vs. spatio-temporal reuse, and reuse (distance, rate, volume) vs. access patterns. Both trace size and resolution are controllable. We use MemGaze to elucidate the memory effects of different data structures and algorithms. For sampled traces that are ˜1% of a full one, analysis metrics have 1-25% MAPE for histograms of varying dynamic sequence lengths. With current suboptimal kernel support (PT runs continuously), MemGaze’s time overhead is typically 10–95%; 7× at worst. However, when PT runs only during samples, overhead is 10–35% on memory intensive regions and correlates with executed ptwrites.
A survey of the sorghum transcriptome using single-molecule long reads
Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, these results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.
RISK-INFORMED EXTERNAL HAZARDS ANALYSIS BY EEVE TOOLKIT
Introducing risk-informed safety analyses for external events can bring sensible benefits to the nuclear power industry easing the regulatory burden introduced in the aftermath of the Fukushima accident. In the framework of the US-DOE Light-Water Reactor Sustainability program, Risk-Informed Margin Characterization project (LWRS-RISMC), research activities were conducted at INL for developing and applying a toolkit for performing risk-informed external hazards analysis. The “EEVE” (External EVEnts) toolkit, a chain of INL and state-of-the-art codes, was set-up and applied for simulating earthquake-induced transients with internal flooding in a PWR. This was done using methodology set-up for evaluating new data and determining critical areas that would benefit most from advanced analysis methods. The methodology is agnostic and it can be applied to other external hazards than just seismic and flooding (e.g., high winds, intense precipitation, etc.). The first step was the deterministic calculations for evaluating the propagation of a set of earthquakes and for determining the effects on a fire suppression system in an auxiliary building. These deterministic calculations were performed using the LS-DYNA and the OPENSEE structural mechanics codes. Probability failures and event trees of a generic 3-loops Westinghouse PWR were derived from a generic SAPHIRE model. Seismically induced Loss of Offsite Power, Station Blackout, and fire suppression piping failure events were considered. SAPHIRE code allowed a pre-screening of all possible branches of the event tree and a selection of those with the largest Core Damage Frequency increase for further analysis using dynamic PRA methods. INL's EMRALD code performed dynamic PRA calculations of the identified sequences, integrating risk analysis with on-line deterministic safety analysis results (seismically-induced internal flooding calculations by NEUTRINO code and system analysis by RELAP5-3D code). RELAP5-3D Best-Estimate calculations coupled with RAVEN statistical code were used for deriving limit surfaces as function of relevant transient parameters. This data was used by EMRALD for determining the final core status (core damage/core safe). Finally, the coupling of seismic, flooding, system thermal-hydraulic, uncertainty quantification and probabilistic risk analysis for an advanced risk-informed external hazards analysis was demonstrated. Results showed the sensible decrease in the level of conservatism achieved using the developed risk-informed methodology, which allowed also improving the evaluation of the failure modes and failure probabilities of different components.
The metagenomic data life-cycle: standards and best practices
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is still needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.
Ensuring Solution Uniqueness in Three-Phase Power System State Estimation
This paper is concerned with the issue of potential non-unique solutions in three-phase state estimation. Theory of observability analysis for positive sequence power system state estimation is based on certain assumptions that avoid possibility of multiple solutions. Also, it is shown that observability of a positive sequence network remains independent of the network parameters or the operating state. When extending single-phase observability analysis directly to the three-phase case, this paper considers the possibility of converging to multiple solutions, i.e. solution non-uniqueness, even for cases where state estimator successfully converges. The study illustrates via numerical examples the likelihood of converging to entirely different solutions for certain network parameters. It also examines how the operating state, particularly under unbalanced loading, leads to solution non-uniqueness. The paper then describes an alternative approach to ensure a unique solution in three-phase state estimation. This method aims to accurately and uniquely estimate the state of any unbalanced three-phase system, irrespective of load imbalance, network configuration, existence of synchronous generators or transformers.