Target highlights in CASP14: Analysis of models by structure providers
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Alexander, Leila T.↗
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OpenMP Target Task: Tasking and Target Offloading on Heterogeneous Systems
This work evaluated the use of OpenMP tasking with target GPU offloading as a potential solution for programming productivity and performance on heterogeneous systems. Also, it is proposed a new OpenMP specification to make the implementation of heterogeneous codes simpler by using OpenMP target task, which integrates both OpenMP tasking and target GPU offloading in a single OpenMP pragma. As a test case, the authors used one of the most popular and widely used Basic Linear Algebra Subprogram Level-3 routines: triangular solver (TRSM). To benefit from the heterogeneity of the current high-performance computing systems, the authors propose a different parallelization of the algorithm by using a nonuniform decomposition of the problem. This work used target GPU offloading inside OpenMP tasks to address the heterogeneity found in the hardware. This new approach can outperform the state-of-the-art algorithms, which use a uniform decomposition of the data, on both the CPU-only and hybrid CPU-GPU systems, reaching speedups of up to one order of magnitude. The performance that this approach achieves is faster than the IBM ESSL math library on CPU and competitive relative to a highly optimized heterogeneous CUDA version. One node of Oak Ridge National Laboratory’s supercomputer, Summit, was used for performance analysis.
Valero Lara, Pedro↗
Multiple-Targeted Graphene-based Nanocarrier for Intracellular Imaging of mRNAs
Simultaneous detection and imaging of multiple intracellular messenger RNA (mRNAs) hold great significant for early cancer diagnostics and preventive medicine development. Herein, we propose a multiple-targeted graphene oxide (GO) nanocarrier that can simultaneously detect and image different type mRNAs in living cells. First of all, in vitro detection of multiple targets have been realized successfully based on the multiple-targeted GO nanocarrier with linear relationship ranging from 3 nM to 200 nM, as well as sensitive detection limit of 1.84 nM for manganese superoxide dismutase (Mn-SOD) mRNA and 2.45 nM for β-actin mRNA. Additionally, this nanosensing platform composed of fluorescent labeled single strand DNA probes and GO nanocarrier can identify Mn-SOD mRNA and endogenous mRNA of β-actin in living cancer cells, showing rapid response, high specificity, nuclease stability, and good biocompatibility during the cell imaging. Thirdly, changes of the expression levels of mRNA in living cells before or after the drug treatment can be monitored successfully. By using multiple ssDNA as probes and GO nanocarrier as the cellular delivery cargo, the proposed simultaneous multiple-targeted sensing platform will be of great potential as a powerful tool for intracellular trafficking process from basic research to clinical diagnosis.
59 BASIC BIOLOGICAL SCIENCES↗
An Interbacterial NAD(P)+ Glycohydrolase Toxin Requires Elongation Factor Tu for Delivery to Target Cells
Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD + and NADP + . Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.
59 BASIC BIOLOGICAL SCIENCES↗
Tandem column isolation of zirconium-89 from cyclotron bombarded yttrium targets using an automated fluidic platform: Anion exchange to hydroxamate resin columns
The development of a tandem column purification method for the production of high-purity 89Zr is presented. The primary column was a macroporous strongly basic anion exchange resin on styrene divinylbenzene co-polymer. The secondary column, with an internal volume of ~27 µL, was packed with hydroxamate resin. A condition of inverted selectivity was developed, whereby the 89Zr eluent from the primary column is synonymous with the load condition on the secondary column. The ability to transfer 89Zr from one column to the next allows two sequential column clean-up methods to be performed prior to the final elution of the 89Zr. This approach assures delivery of high purity 89Zr product and assures a 89Zr product that is eluted in a substantially smaller volume than is possible when using the traditionally-employed single hydroxamate resin column method. The tandem column purification process has been implemented into a prototype automated fluidic system. The system is configured with on-line gamma detection so column effluents can be monitored in near-real time. The automated method was tested using seven cyclotron bombarded Y foil targets. It was found that 95.1±1.3% of the 89Zr present in the foils was recovered in the secondary column elution fraction. Furthermore, elution peak analysis of several 89Zr elution profile radiochromatograms made possible the determination of 89Zr recovery as a function of volume; a 89Zr product volume that contains 90% of the mean secondary column elution peak can be obtained in 0.29±0.06 mL (representing 86±5% of the 89Zr activity in the target). This product volume represents a significant increase in isotope product concentration over the predominant method used in the field. In addition to the reduced 89Zr product elution volume, titrations of the 89Zr product with deferoxamine mesylate salt across two preparatory methods resulted in mean effective specific activity (ESA) values of 279 and 340 TBq·mmole-1 and mean bindable metals concentrations ([MB]) of 13.5 and 16.7 nmole·g-1. These ESA and [MB] values infer that the 89Zr product resulting from this tandem column isolation method has the highest purity reported to date.
immunoPET, zirconium-89, laboratory automation, de↗
Improved production of 76Br, 77Br and 80mBr via CoSe cyclotron targets and vertical dry distillation
Not provided.
Radiology, Nuclear Medicine & Medical Imaging↗
Semi-inclusive π 0 target and beam-target asymmetries from 6 GeV electron scattering with CLAS
Here, we present precision measurements of the target and beam-target spin asymmetries from neutral pion electroproduction in deep-inelastic scattering (DIS) using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. We scattered 6-GeV, longitudinally polarized electrons off longitudinally polarized protons in a cryogenic 14 NH 3 target, and extracted double and single target spin asymmetries for ep → e'π 0 X in multidimensional bins in fourmomentum transfer (1.0 < Q 2 < 3.2 GeV 2 ), Bjorken-x (0.12 < x < 0.48), hadron energy fraction (0.4 < z < 0.7), transverse pion momentum (0 < P T < 1.0 GeV), and azimuthal angle Φh between the lepton scattering and hadron production planes. We extracted asymmetries as a function of both x and P T , which provide access to transverse-momentum distributions of longitudinally polarized quarks. The double spin asymmetries depend weakly on P T . The sin 2Φ h moments are zero within uncertainties, which is consistent with the expected suppression of the Collins fragmentation function. The observed sin Φ h moments suggest that quark gluon correlations are significant at large x.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Synthesis of a biofuel target through conventional organic chemistry
In this work, the biofuel target compound 2-ethyl-5,5-dimethylcyclopenta-1,3-diene (1) and its exo isomers (9a and 9b), were successfully synthesized via two different pathways from the common intermediate 4,4-dimethylcyclopent-2-ene-1-one (2). The first pathway produced the endocyclic product as a pure isomer via a triflate intermediate obtained from the ketone 2 in 60% yield, followed by copper catalyzed coupling with ethyl magnesium bromide in 63% yield. The second pathway employed a Grignard reaction with ketone 2, which generated an alcohol that was immediately subjected to mild acid catalyzed elimination upon workup of the previous step to yield a primarily a mixture of exo diastereomers 9a and 9b in 77% yield. These targets had their fuel properties characterized in a separate study.
Biofuel↗
Adenovirus E1A TRRAP-targeting domain-mediated enhancement of MYC association with the NuA4 complex activates a panel of MYC target genes enriched for gene expression and ribosome biogenesis
Cellular transformation by adenovirus E1A requires targeting TRRAP, a scaffold protein which helps assemble histone acetyltransferase complexes, including the NuA4 complex. We recently reported that E1A and E1A 1–80 (N-terminal 80 aa) promote association of the proto-oncogene product MYC with the NuA4 complex. The E1A N-terminal TRRAP-targeting (ET) domain is required for E1A 1–80 to interact with the NuA4 complex. We demonstrate that an ET-MYC fusion associates with the NuA4 complex more efficiently than does MYC alone. Because MYC regulates genes for multiple cellular pathways, we performed global RNA-sequence analysis of cells expressing MYC or ET-MYC, and identified a panel of genes (262) preferentially activated by ET-MYC and significantly enriched in genes involved in gene expression and ribosome biogenesis, suggesting that E1A enhances MYC association with the NuA4 complex to activate a set of MYC target genes likely involved in cellular proliferation and cellular transformation by E1A and by MYC. - Highlights: • E1A N-terminal-MYC chimeric protein associates with the NuA4 complex efficiently. • A panel of MYC-target genes is preferentially activated by E1A N-terminal-MYC fusion. • This panel of genes may be activated by MYC association with NuA4 complex. • This panel of genes may be involved in E1A and MYC-mediated transformation.
60 APPLIED LIFE SCIENCES↗
Beyond conventional batteries: a review on semi-solid and redox targeting flow batteries-LiFePO{sub 4} as a case study.
Clean and sustainable energy is becoming increasingly crucial to tackle the current energy crisis. However, the intermittent nature of renewable energy sources presents a challenge for their effective implementation. Redox flow batteries (RFBs) have emerged as a promising solution to this problem, as they can help enhance the stability of grid networks and promote the use of renewable energy sources. RFBs are highly modular and scalable systems that can be customized to meet the power and energy requirements of different renewable energy plants. Moreover, they offer several advantages over conventional battery technologies, including cost and safety concerns. However, conventional RFBs have limited energy densities due to the low solubility of their active species in electrolyte. To overcome this limitation, semi-solid (SSRFBs) and redox targeting (RTFBs) flow batteries have been proposed. These systems feature high concentrations of active species and impressive energy densities, making them highly attractive for renewable energy applications. LiFePO4 (LFP) is a highly promising active material for semi-solid and targeting flow batteries. One of the key advantages of LFP is its low raw materials cost, as it is composed of Earth-abundant elements such as iron and phosphorus. This makes it an attractive option for large-scale battery production. The recent developments in SSRFBs and RTFBs using LFP as catholyte hold great promise for the future of sustainable energy storage. The combination of LFP's low cost, safety, durability, and high energy density with the modularity and scalability of flow battery systems make for a compelling solution to the challenges of intermittent renewable energy sources. Ongoing research and development in this area will likely yield even further improvements in the performance and efficiency of LFP-based flow batteries, opening exciting new possibilities for sustainable energy storage.
El Halya, Nabil↗
Pulsed-coil magnet systems for applying uniform 10–30 T fields to centimeter-scale targets on Sandia's Z facility
Sandia has successfully integrated the capability to apply uniform, high magnetic fields (10–30 T) to high energy density experiments on the Z facility. This system uses an 8-mF, 15-kV capacitor bank to drive large-bore (5 cm diameter), high-inductance (1–3 mH) multi-turn, multi-layer electromagnets that slowly magnetize the conductive targets used on Z over several milliseconds (time to peak field of 2–7 ms). This system was commissioned in February 2013 and has been used successfully to magnetize more than 30 experiments up to 10 T that have produced exciting and surprising physics results. These experiments used split-magnet topologies to maintain diagnostic lines of sight to the target. We describe the design, integration, and operation of the pulsed coil system into the challenging and harsh environment of the Z Machine. We also describe our plans and designs for achieving fields up to 20 T with a reduced-gap split-magnet configuration, and up to 30 T with a solid magnet configuration in pursuit of the Magnetized Liner Inertial Fusion concept.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Early-time radiation flux symmetry optimization and its effect on gas-filled hohlraum ignition targets on the National Ignition Facility
Achieving ignition on the National Ignition Facility (NIF) is tied to our ability to control and minimize deviations from sphericity of the capsule implosion. Low-mode asymmetries of the hot spot result from the combined effect of radiation drive asymmetries throughout the laser pulse and initial roughness on the capsule surface. In this paper, we report on simulations and experiments designed to assess, measure, and correct the drive asymmetries produced by the early-time (≈first 2 ns or “picket”) period of the laser pulse. The drive asymmetry during the picket is commonly thought to introduce distortions in the hot-spot shape at ignition time. However, a more subtle effect not previously considered is that it also leads to an asymmetry in shock velocity and timing, thereby increasing the fuel adiabat and reducing the margin for ignition. It is shown via hydrodynamic simulations that minimizing this effect requires that the early-time asymmetry be kept below 7.5% in the second Legendre mode (P{sub 2}), thus keeping the loss of performance margin below ≈10% for a layered implosion. Asymmetries during the picket of the laser pulse are measured using the instantaneous self-emission of a high-Z re-emission sphere in place of an ignition capsule in a hohlraum with large azimuthal diagnostic windows. Three dimensional simulations using the code HYDRA (to capture the effect of non-azimuthal hohlraum features) coupled to a cross-beam energy transfer model [Michel et al., Phys. Plasmas 17, 056305 (2010)] are used to establish the surrogacy of the re-emit target and to assess the early-time drive symmetry. Calculations using this model exhibit the same sensitivity to variations in the relative input powers between the different cones of NIF beams as measured for the “Rev5” CH target [Haan et al., Phys Plasmas 18, 051001 (2011)] and reported by Dewald et al. [Phys. Rev. Lett. 111, 235001 (2013)]. The same methodology applied to recently improved implosions using different hohlraum geometries and picket powers show good agreement with experimental data.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
The importance of laser wavelength for driving inertial confinement fusion targets. II. Target design
We describe details of radiation-hydrodynamics simulations of directly driven targets for inertial confinement fusion using laser drivers with different laser wavelengths. Of particular interest here are comparisons of frequency-tripled glass (laser wavelength 351 nm) lasers with the argon fluoride (193 nm) and krypton fluoride (248 nm) excimer lasers and the effects that these laser wavelengths have on the target designs. We explore the effect these drivers have on the compromise involved between lowering laser plasma instabilities (LPIs) or hydrodynamic instabilities while providing high gains and seek to quantify this trade-off. Short-wavelength drivers have significant advantages, primarily in using less power and energy to drive targets. Additionally, they expand the allowed operating regime that is constrained by LPI avoidance and the production of higher pressures needed for more hydrodynamically stable targets. Potential disadvantages to shorter drive wavelengths, such as increased imprint, are examined and found to be unimportant.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi
Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein–encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain ?cre-1, while glucose repression was still mostly functional in ?exo-1. Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in ?exo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in ?exo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.
Gabriel, Raphael↗
The SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Quasar target selection
As part of the Sloan Digital Sky Survey (SDSS) IV the extended Baryon Oscillation Spectroscopic Survey (eBOSS) will improve measurements of the cosmological distance scale by applying the Baryon Acoustic Oscillation (BAO) method to quasar samples. eBOSS will adopt two approaches to target quasars over 7500 deg{sup 2}. First, a “CORE” quasar sample will combine the optical selection in ugriz using a likelihood-based routine called XDQSOz, with a mid-IR-optical color cut. eBOSS CORE selection (to g < 22 or r < 22) should return ∼70 deg{sup −2} quasars at redshifts 0.9 < z < 2.2 and ∼7 deg{sup −2}z > 2.1 quasars. Second, a selection based on variability in multi-epoch imaging from the Palomar Transient Factory should recover an additional ∼3–4 deg{sup −2}z > 2.1 quasars to g < 22.5. A linear model of how imaging systematics affect target density recovers the angular distribution of eBOSS CORE quasars over 96.7% (76.7%) of the SDSS north (south) Galactic Cap area. The eBOSS CORE quasar sample should thus be sufficiently dense and homogeneous over 0.9 < z < 2.2 to yield the first few-percent-level BAO constraint near z-bar ∼1.5.eBOSS quasars at z > 2.1 will be used to improve BAO measurements in the Lyα Forest. Beyond its key cosmological goals, eBOSS should be the next-generation quasar survey, comprising >500,000 new quasars and >500,000 uniformly selected spectroscopically confirmed 0.9 < z < 2.2 quasars. At the conclusion of eBOSS, the SDSS will have provided unique spectra for more than 800,000 quasars.
79 ASTRONOMY AND ASTROPHYSICS↗
Measurement of the Target-Normal Single-Spin Asymmetry in Deep-Inelastic Scattering from the Reaction He 3 ↑ ( e , e ' ) X
We report here the first measurement of the target-normal single-spin asymmetry in deep-inelastic scattering from the inclusive reaction He 3 ↑ ( e , e ' ) X on a polarized He 3 gas target. Assuming time-reversal invariance, this asymmetry is strictly zero in the Born approximation but can be nonzero if two-photon-exchange contributions are included. The experiment, conducted at Jefferson Lab using a 5.89 GeV electron beam, covers a range of 1.7 < W < 2.9 GeV , 1.0 < Q 2 < 4.0 GeV 2 and 0.16 < x < 0.65 . Neutron asymmetries were extracted using the effective nucleon polarization and measured proton-to- He 3 cross-section ratios. The measured neutron asymmetries shown are negative with an average value of ( - 1.09 ± 0.38 ) × 1 0 - 2 for invariant mass W > 2 GeV , which is nonzero at the 2.89 σ level. Our measured asymmetry agrees both in sign and magnitude with a two-photon-exchange model prediction that uses input from the Sivers transverse momentum distribution obtained from semi-inclusive deep-inelastic scattering.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry
PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).
Parris, D. Joshua↗