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At least 19 records

Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics

Sinapis alba is a wild member of the Brassicaceae family reported to possess genetic resistance against major biotic and abiotic stresses of oilseed brassicas. However, the resistance nature of S. alba was not exploited generously due to the unavailability of usable genome sequences in public databases. Therefore, the present study was conducted to assemble the first draft genome from raw whole genome shotgun sequences with annotation and develop simple sequence repeat markers for molecular genetics and marker-assisted breeding. Results The raw genome sequences had 96x coverage on the Illumina platform with 170 Gbp data. The developed assembly by SOAPdenovo2 has ~459 Mbp genome size covered in 403,423 contigs with an average size of 1138.04 bp. The assembly was BLASTX with Arabidopsis thaliana which showed 32.9% positive hits between both plants. The top hit species distribution analysis showed the highest similarity with A. thaliana. A total of 809,597 GO level annotations were recorded after BLASTX results, and 34,012 sequences were annotated with different enzyme codes grouped under seven classes. The gene prediction tool AUGUSTUS identified 113,107 probable genes with an average size of 684 bp. The biochemical pathway annotation assigned 16,119 potential genes to 152 KEGG maps and 1751 enzyme codes. The development of potential SSRs from the de-novo assembly yielded 70731 unique primer pairs. Out of 159 randomly selected SSR markers for validation, 149 successfully amplified in S. alba. However, 10 SSR markers did not amplify during the validation experiment. Conclusion The annotated genome assembly with a large number of SSRs was developed in the present study. To the best of our knowledge, this is the first report of S. alba genome assembly development, annotation, and SSRs mining to date. The data presented here will be a very important resource for future crop improvement programs, especially for resistant breeding.

59 BASIC BIOLOGICAL SCIENCES↗

N-point correlation functions in the CfA and SSRS redshift distribution of galaxies

Using counts in cells, we estimate the volume-average N-point galaxy correlation functions for N = 2, 3, and 4, in redshift samples of the CfA and SSRS catalogs. Volume-limited samples of different sizes are used to study the uncertainties at different scales, the shot noise, and the problem with the boundaries. The hierarchical constants S3 and S4 agree well in all samples in CfA and SSRS, with average S3 = 194 +/- 0.07 and S4 = 4.56 +/- 0.53. We compare these results with estimates obtained from angular catalogs and recent analysis over IRAS samples. The amplitudes SJ seem larger in real space than in redshift space, although the values from the angular analysis correspond to smaller scales, where we might expect larger nonperturbative effects. It is also found that S3 and S4 are smaller for IRAS than for optical galaxies. This, together with the fact that IRAS galaxies have smaller amplitude for the above correlation functions, indicates that the density fluctuations of IRAS galaxies cannot be simply proportional to the density fluctuations of optical galaxies, i.e., biasing has to be nonlinear between them.

Gaztanaga, Enrique↗

SSRS (Stochastic Soaring Raptor Simulator)

SSRS (Stochastic Soaring Raptor Simulator) is a generalizable, probabilistic, and predictive tool for wind energy developers, ecologists, wildlife managers and industry consultants to estimate the potential for soaring raptors to interact with operating wind turbines, without the need for site-specific data collection. Rapid expansion of wind energy development across the world has exposed the risk of turbine collisions for birds and bats. The risk to obligate soaring raptors such as golden eagles is of particular concern due to their small population and influence on ecological balance. Golden eagles rely heavily on updrafts to subsidize their flight, putting them in direct conflict with operational wind turbines that utilize the same wind resource. Understanding the behavior of soaring raptors with varying atmospheric conditions is crucial for predicting and mitigating the risk of turbine collision. This software contains a predictive movement model that simulates individual flight paths of golden eagles during updraft-subsidized long-distance flight, including migration. For a given set of atmospheric conditions, the model simulates thousands of eagles at turbine-scale spatial resolution (50m) to produce a relative presence density map. The simulated eagles rely on updrafts to pursue uninterrupted directional flight with minimal energy expenditure, following fluid-flow principles. The simulator includes a stochastic model of eagle behavior and a systematic method of accounting for spatiotemporal variations in atmospheric conditions. This framework only requires publicly available atmospheric data to estimate orographic and thermal updrafts, ensuring general usability.

Sandhu, Rimple↗

Kmer-SSR: a fast and exhaustive SSR search algorithm

Motivation: One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a ‘good enough’ solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a ‘good enough’ solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions. Results: We present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm. Availability and implementation: The source code is freely available on GitHub at https://github. com/ridgelab/Kmer-SSR.

59 BASIC BIOLOGICAL SCIENCES↗

32 species validation of a new Illumina paired-end approach for the development of microsatellites

Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs) remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485), with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.

54 ENVIRONMENTAL SCIENCES↗

Reconstructed Parachute System Performance During the Second LDSD Supersonic Flight Dynamics Test

NASA’s Low-Density Supersonic Decelerators project (LDSD) has developed and tested four new aerodynamic decelerator technologies for future Mars missions: two attached toroidal inflatable decelerators, a ballute, and a large supersonic parachute. On June 8, 2015, the project conducted a high-altitude, supersonic flight test of a 30.5-meter supersonic Ringsail (SSRS) canopy at the US Navy’s Pacific Missile Range Facility (PMRF) on Kauai, HI. This test, the second in a series of Supersonic Flight Dynamics Tests (SFDT-2), allowed the LDSD project to test the deployment and performance of its parachute decelerator system in the wake of a representative test vehicle (a 4.7-meter aeroshell and 6-meter toroidal inflatable aerodynamic decelerator) at conditions relevant to Mars entry for the second time. The parachute decelerator system consisted of the SSRS main parachute and a 4.4-meter ballute (called the parachute deployment device, or PDD) for its extraction. The ballute was mortar-deployed at a Mach number of 2.78 and a dynamic pressure of 493 Pa, and inflated with the aid of a water-methanol based gas generator. After flying in the wake of the test vehicle for ten seconds, the PDD was released and allowed to extract the main parachute pack. The SSRS reached line-stretch at a Mach number of 2.37 and dynamic pressure of 602 Pa. Following full inflation, the propagation of a tear in the canopy led to the failure of the parachute skirt band and to the subsequent failure of the vent band. The test vehicle was instrumented with load sensors, inertial sensors, and high-speed and high resolution cameras that provided data on the performance of the PDD and SSRS through deployment, inflation, and flight. This paper describes the resulting reconstructed behavior of the PDD and SSRS during deployment and inflation, their aerodynamic performance on SFDT-2, the failure of the SSRS shortly after full inflation, and the LDSD project’s investigation into its underlying causes.

O'Farrell, Clara↗

Enforcing central processing unit quality of service guarantees when servicing accelerator requests

Systems, apparatuses, and methods for enforcing processor quality of service guarantees when servicing system service requests (SSRs) are disclosed. A system includes a first processor executing an operating system and a second processor executing an application which generates SSRs for the first processor to service. The first processor monitors the number of cycles spent servicing SSRs over a previous time interval, and if this number of cycles is above a threshold, the first processor starts delaying the servicing of subsequent SSRs. In one implementation, if the previous delay was non-zero, the first processor increases the delay used in the servicing of subsequent SSRs. If the number of cycles is less than or equal to the threshold, then the first processor services SSRs without delay. As the delay is increased, the second processor begins to stall and its SSR generation rate falls, reducing the load on the first processor.

Basu, Arkaprava↗

Creation of a Prognostic Index for Spine Metastasis to Stratify Survival in Patients Treated With Spinal Stereotactic Radiosurgery: Secondary Analysis of Mature Prospective Trials

Purpose: There exists uncertainty in the prognosis of patients following spinal metastasis treatment. We sought to create a scoring system that stratifies patients based on overall survival. Methods and Materials: Patients enrolled in 2 prospective trials investigating stereotactic spine radiation surgery (SSRS) for spinal metastasis with ≥3-year follow-up were analyzed. A multivariate Cox regression model was used to create a survival model. Pretreatment variables included were race, sex, age, performance status, tumor histology, extent of vertebrae involvement, previous therapy at the SSRS site, disease burden, and timing of diagnosis and metastasis. Four survival groups were generated based on the model-derived survival score. Results: Median follow-up in the 206 patients included in this analysis was 70 months (range: 37-133 months). Seven variables were selected: female sex (hazard ratio [HR] = 0.7, P=.02), Karnofsky performance score (HR = 0.8 per 10-point increase above 60, P=.007), previous surgery at the SSRS site (HR = 0.7, P=.02), previous radiation at the SSRS site (HR = 1.8, P=.001), the SSRS site as the only site of metastatic disease (HR = 0.5, P=.01), number of organ systems involved outside of bone (HR = 1.4 per involved system, P<.001), and >5 year interval from initial diagnosis to detection of spine metastasis (HR = 0.5, P<.001). The median survival among all patients was 25.5 months and was significantly different among survival groups (in group 1 [excellent prognosis], median survival was not reached; group 2 reached 32.4 months; group 3 reached 22.2 months; and group 4 [poor prognosis] reached 9.1 months; P<.001). Pretreatment symptom burden was significantly higher in the patient group with poor survival than in the group with excellent survival (all metrics, P<.05). Conclusions: We developed the prognostic index for spinal metastases (PRISM) model, a new model that identified patient subgroups with poor and excellent prognoses.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Cogeneration of hot electrons from multiple laser-plasma instabilities

Interactions of two plasmon decay (TPD) and side stimulated Raman scattering (SSRS) were studied using 3-D particle-in-cell simulations under ICF-relevant conditions for linearly and circularly polarized lasers. In the linear stage, SSRS took place under n e = 0.235n c and TPD dominated near the quarter-critical density surface and their growth rates agreed with theory. In the nonlinear stage, SSRS reduced TPD through pump depletion. Hot electrons were found to be first accelerated by the SSRS plasma waves and then by TPD plasma waves through a co-generation mechanism. Compared to the linearly polarized case with the same laser intensity, both SSRS and TPD were reduced due to the lower laser amplitude in the circularly-polarized case. As a result, a 30 percent decrease in hot electron flux was observed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Transcriptome Analysis in Sheepgrass (Leymus chinensis). A Dominant Perennial Grass of the Eurasian Steppe

BACKGROUND: Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. RESULTS: The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. CONCLUSIONS: This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.

59 BASIC BIOLOGICAL SCIENCES↗

High Altitude Supersonic Decelerator Test Vehicle

The Low Density Supersonic Decelerator (LDSD) project is tasked by NASA's Office of the Chief Technologist (OCT) to advance the state of the art in Mars entry and descent technology in order to allow for larger payloads to be delivered to Mars at higher altitudes with better accuracy. The project will develop a 33.5 m Do Supersonic Ringsail (SSRS) parachute, 6m attached torus, robotic class Supersonic Inflatable Aerodynamic Decelerator (SIAD-R), and an 8 m attached isotensoid, exploration class Supersonic Inflatable Aerodynamic Decelerator (SIAD-E). The SSRS and SIAD-R should be brought to TRL-6, while the SIAD-E should be brought to TRL-5. As part of the qualification and development program, LDSD must perform a Mach-scaled Supersonic Flight Dynamics Test (SFDT) in order to demonstrate successful free flight dynamic deployments at Mars equivalent altitude, of all three technologies. In order to perform these tests, LDSD must design and build a test vehicle to deliver all technologies to approximately 180,000 ft and Mach 4, deploy a SIAD, free fly to approximately Mach 2, deploy the SSRS, record high-speed and high-resolution imagery of both deployments, as well as record data from an instrumentation suite capable of characterizing the technology induced vehicle dynamics. The vehicle must also be recoverable after splashdown into the ocean under a nominal flight, while guaranteeing forensic data protection in an off nominal catastrophic failure of a test article that could result in a terminal velocity, tumbling water impact.

Cook, Brant T.↗

Progress Towards a Predictive Eagle Behavior and Risk Modeling Framework: Overview and Recent Validation Efforts

This presentation summarizes progress to date of the U.S. Department of Energy project, "Development of a computational framework for modeling golden eagles (Aquila chrysaetos) near wind farms," which focuses on stochastic behavioral modeling of soaring raptors across landscape, facility, and turbine spatiotemporal scales. This publicly available, open-source modeling framework includes behavioral models based on three different underlying principles: energy minimization at landscape scale, behavioral heuristics at landscape-facility scale, and data-driven behaviors at the facility-micro-scale. We will briefly overview the key advancements in the behavioral modeling state of the art, which leverages multiple high-resolution telemetry data sources combined with high-fidelity atmospheric flow modeling insights. We then present preliminary results from a validation study in Altamont, California. This new study involves a novel application of the Stochastic Soaring Raptor Simulator (SSRS), in a new geographic locale, to understand facility scale eagle movement patterns over time scales representative of a wind project's lifetime. For this desktop analysis (that does not depend on any high-performance computing resources), SSRS simultaneously considers a variety of wind conditions and eagle approach vectors toward a project site of interest. This work demonstrates the integration of publicly available landscape-scale atmospheric datasets, our recently improved engineering updraft models (see presentation from Thedin et al.), and our energy minimization behavioral models within the SSRS framework. While we only present results from a single behavioral model, the integration of these three modeling components forms the foundation for our more sophisticated behavioral models (see presentations from Brandes et al., Sandhu et al.) that are under active development. Results are presented in the form of presence maps, which may be applied to estimate risk to wildlife, augment ground survey data, inform wind-plant operations, or incorporated into wind-plant designs.

agent-based modeling↗

Stable perovskite-fluorite dual-phase composites synthesized by one-pot solid-state reactive sintering for protonic ceramic fuel cells

We report that this work synthesized a series of oxide composites with nominal compositions of BaCe 05 Zr 0.4 Y 0.1 O 3-δ (BCZY)-Ce 0.5 Y 0.5 O 2-δ (YDC) based on the BCZY/YDC molar ratios of 0.5:1, 1:1, 2:1, and 4:1 (BCZY-YDC-0.5–1, BCZY-YDC-1-1, BCZY-YDC-2-1, and BCZY-YDC-4-1) using a one-pot solid state reactive sintering (SSRS) method. The X-ray diffraction (XRD) patterns and refinement proved that the one-pot SSRS at 1450 °C for 12 h could achieve the perovskite-fluorite dual-phase composites (DPCs) with the desired structure compositions. The scanning electron microscopy (SEM) images showed that the two DPCs of BCZY-YDC-1-1 and BCZY-YDC-2-1 formed excellent percolation for perovskite and fluorite phases. The conductivity measurement by electrochemical impedance spectroscopy (EIS) and the transference number measurement by the electromotive force (EMF) test proved that changing the BCZY/YDC molar ratio and operating condition could adjust the DPC's conduction property to make them suitable for electrolytes and electrode scaffolds for protonic ceramic fuel cells (PCFCs). The long-term conductivity testing and the crystal structure analysis after EMF testing under versatile conditions indicated that the DPCs of BCZY-YDC-2-1 and BCZY-YDC-1-1 were durable PCFC component materials. The PCFC button cells with the as-discovered BCZY-YDC-2-1 and BCZY-YDC-1-1 as an electrolyte and an anode scaffold, respectively, and the reported Ba–Ce–Fe–Co–O perovskite-perovskite composite as a cathode showed promising performance under H 2 /air gradient.

08 HYDROGEN↗

The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions

Here, bacterial outer membrane vesicles (OMVs), as well as OMV-associated small RNAs, have been demonstrated to play a role in host–pathogen interactions. The presence of larger RNA transcripts in OMVs has been less studied and their potential role in host–pathogen interactions remains largely unknown. Here we analyze RNA from OMVs secreted by Salmonella enterica serovar Typhimurium ( S . Typhimurium) cultured under different conditions, which mimic host–pathogen interactions. S . Typhimurium was grown to exponential and stationary growth phases in minimal growth control medium (phosphate-carbon-nitrogen, PCN), as well as in acidic and phosphate-depleted PCN, comparable to the macrophage environment and inducing therefore the expression of Salmonella pathogenicity island 2 (SPI-2) genes. Moreover, Salmonella pathogenicity island 1 (SPI-1), which is required for virulence during the intestinal phase of infection, was induced by culturing S. Typhimurium to the stationary phase in Lysogeny Broth (LB). For each condition, we identified OMV-associated RNAs that are enriched in the extracellular environment relative to the intracellular space. All RNA classes could be observed, but a vast majority of rRNA was exported in all conditions in variable proportions with a notable decrease in LB SPI-1 inducing media. Several mRNAs and ncRNAs were specifically enriched in/on OMVs dependent on the growth conditions. Important to note is that some RNAs showed identical read coverage profiles intracellularly and extracellularly, whereas distinct coverage patterns were observed for other transcripts, suggesting a specific processing or degradation. Moreover, PCR experiments confirmed that distinct RNAs were present in or on OMVs as full-length transcripts ( IsrB-1/2; IsrA; ffs; SsrS; CsrC; pSLT035; 10Sa; rnpB; STM0277; sseB; STM0972; STM2606 ), whereas others seemed to be rather present in a processed or degraded form. Finally, we show by a digestion protection assay that OMVs are able to prevent enzymatic degradation of given full-length transcripts ( SsrS, CsrC,10Sa, and rnpB ). In summary, we show that OMV-associated RNA is clearly different in distinct culture conditions and that at least a fraction of the extracellular RNA is associated as a full-length transcripts with OMVs, indicating that some RNAs are protected by OMVs and thereby leaving open the possibility that those might be functionally active.

59 BASIC BIOLOGICAL SCIENCES↗

On the derivation of selection functions from redshift survey data

A previously unrecognized effect is described in the derivation of luminosity functions and selection functions from existing redshift survey data, due to binning of quoted magnitudes and diameters. Corrections are made for this effect in the Center for Astrophysics (CfA) and Southern Sky (SSRS) Redshift Surveys. The correction makes subtle but systematic changes in the derived density fields of the CfA survey, especially within 2000 km/s of the Local Group. The effect on the density field of the SSRS survey is negligible.

Strauss, Michael A.↗

Redshift distortions of galaxy correlation functions

To examine how peculiar velocities can affect the two-, three-, and four-point redshift correlation functions, we evaluate volume-average correlations for configurations that emphasize and minimize redshift distortions for four different volume-limited samples from each of the CfA, SSRS, and IRAS redshift catalogs. We present the results as the correlation length r(sub 0) and power index gamma of the two-point correlations, bar-xi(sub 0) = (r(sub 0)/r)(exp gamma), and as the hierarchical amplitudes of the three- and four-point functions, S(sub 3) = bar-xi(sub 3)/bar-xi(exp 2)(sub 2) and S(sub 4) = bar-xi(sub 4)/bar-xi(exp 3)(sub 2). We find a characteristic distortion for bar-xi(sub 2), the slope gamma is flatter and the correlation length is larger in redshift space than in real space; that is, redshift distortions 'move' correlations from small to large scales. At the largest scales (up to 12 Mpc), the extra power in the redshift distribution is compatible with Omega(exp 4/7)/b approximately equal to 1. We estimate Omega(exp 4/7)/b to be 0.53 +/- 0.15, 1.10 +/- 0.16, and 0.84 +/- 0.45 for the CfA, SSRS, and IRAS catalogs. Higher order correlations bar-xi(sub 3) and bar-xi(sub 4) suffer similar redshift distortions but in such a way that, within the accuracy of our ananlysis, the normalized amplitudes S(sub 3) and S(sub 4) are insensitive to this effect. The hierarchical amplitudes S(sub 3) and S(sub 4) are constant as a function of scale between 1 and 12 Mpc and have similar values in all samples and catalogs, S(sub 3) approximately equal to 2 and S(sub 4) approximately equal to 6, despite the fact that bar-xi(sub 2), bar-xi(sub 3), and bar-xi(sub 4) differ from one sample to another by large factors (up to a factor of 4 in bar-xi(sub 2), 8 for bar-xi(sub 3), and 12 for bar-xi(sub 4)). The agreement between the independent estimations of S(sub 3) and S(sub 4) is remarkable given the different criteria in the selection of galaxies and also the difference in the resulting range of densities, luminosities, and locations between samples.

Fry, J. N.↗

Analytic Confusion Matrix Bounds for Fault Detection and Isolation Using a Sum-of-Squared- Residuals Approach

Given a system which can fail in 1 or n different ways, a fault detection and isolation (FDI) algorithm uses sensor data in order to determine which fault is the most likely to have occurred. The effectiveness of an FDI algorithm can be quantified by a confusion matrix, which i ndicates the probability that each fault is isolated given that each fault has occurred. Confusion matrices are often generated with simulation data, particularly for complex systems. In this paper we perform FDI using sums of squares of sensor residuals (SSRs). We assume that the sensor residuals are Gaussian, which gives the SSRs a chi-squared distribution. We then generate analytic lower and upper bounds on the confusion matrix elements. This allows for the generation of optimal sensor sets without numerical simulations. The confusion matrix bound s are verified with simulated aircraft engine data.

Simon, Dan↗