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tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1

Here we present the genome sequence of Rhodotorula graminis WP1, a pink-pigmented, encapsulated yeast strain belonging to the Basidiomycota phylum that was isolated from within stems of Populus trichocarpa growing in its native riparian environment alongside the Snoqualmie River in Western Washington state(Xin et al., 2009). Although numerous bacterial endophytes, the microorganisms living fully within plants, have been characterized, relatively few endophytic yeast strains have been studied (Doty, 2011). The genome of strain WP1 was the first endophytic yeast to be sequenced, and has been included in several genomic analyses (Spatafora et al., 2013; Nagy et al., 2014; Pendleton et al., 2014). Although originally isolated from poplar, WP1 has a broad host range, providing growth benefits not only to poplar (Knoth et al., 2014; Khan et al. in review) but also to grasses and agricultural crop species (Khan et al., 2012; Knoth et al., 2013). Strain WP1 improves plant vigor and has useful biochemical properties (Doty, 2014) including the ability to ferment both pentoses and hexoses and to degrade fermentation inhibitors (Xu et al., 2011). Genomic analysis of bacterial endophytes has revealed certain features in common including genes for phytohormone synthesis, adhesion, colonization, stress reduction, and iron and phosphate acquisition (Fouts et al., 2008; Taghavi et al., 2010; Sessitsch et al., 2012; Witzel et al., 2012). We analyzed the genome of WP1 with a focus on genes potentially involved in plant-microbe interactions.

microbiome↗

An assessment of the crustal remelting hypothesis for volcanism in the Freyja Montes deformation zone

The linear mountain belts of Ishtar Terra on Venus are notable for their topographic relief and slope and for the intensity of surface deformation. The mountains surround the highland plain Lakshmi Planum, the site of two major paterae and numerous other volcanic features and deposits, and evidence is widespread for volcanism within the mountains and in terrain immediately outward of the mountain belt units. While two hypotheses for magmatism can be distinguished on the basis of the chemistry of the melts, chemical data are presently lacking for the Ishtar region. The competing hypotheses for magmatism in Western Ishtar Terra can also be tested with thermal models, given a kinematic or dynamic model for the evolution of the region. The crustal remelting hypothesis is assessed, using the kinematic scenario of Head for the evolution of Freyja Montes. In that scenario, Freyja Montes formed by a sequence of large scale underthrusts of the lithosphere of the North Polar Plains beneath Ishtar Terra, with successive blocks of underthrust crust sutured in imbricate fashion onto the thickened crust of Lakshmi Planum and the mantle portion of underthrusting lithosphere episodically detached. The numerical experiments thus show that volcanic activity associated with the formation of the Frejya Montes deformation zone can be explained by crustal melting, due either to direct contact of crustal material with the hot asthenosphere or to heat generation in a thickened crustal layer.

Namiki, Noriyuki↗

A Summary of Airframe Results from a Fokker F28 Full-Scale Crash Test

On June 20, 2019, a full-scale crash test was conducted on a Fokker F28 MK1000 aircraft as a part of a joint NASA / Federal Aviation Administration (FAA) research effort to investigate the crashworthiness characteristics of a Transport Category Aircraft (TCA), as defined by 14 Code of Federal Regulations, Part 25. The test was conducted at NASA Langley Research Center’s Landing and Impact Research Facility and was the third in a test series to further understand TCA crashworthiness characteristics. The test article featured 24 Anthropomorphic Test Devices (ATDs, a.k.a. crash test dummies), and over 700 channels of instrumentation covering major aircraft structures such as the wings, tail, nose, cockpit and cabin, along with recording seat, overhead bin and ATD accelerations. Five different U.S. Government agencies collaborated on the test including: NASA, the FAA, the U.S. Army Research Laboratory, the National Transportation Safety Board (NTSB) and the National Highway Traffic Safety Administration (NHTSA). This report will covertest article build up, which includes weight and balance measurements and pre-test laser scans. It will also cover the events of the test, which includes the test sequence of events and post-test damage inspections. Finally, it will show airframe level accelerations at all positions measured, with discussion on correlation to the airframe damage witnessed. The test build up consisted of outfitting the main cabin section of the aircraft with 24 ATDs seated in 12 rows of seats, overhead mass and the under floor cargo area with foam representing the luggage. The main cabin also included all of the onboard data system pallets, which recorded711 channels of data from the test. All major portions of the aircraft were instrumented, including locations at the floor / frame junction locations in the cabin where the ATDs were located along with other major exterior components such as the nose, the tail, each engine cowling, and at overhead hat rack ballast locations. The aircraft impacted a soil surface at65.3 ft/s horizontal and 31.8 ft/s vertical velocities. The aircraft plowed through the soil and slid a distance of 32.5 feet from the initial impact location. There was a secondary impact occurring 0.9 s due to the “slap down” of the nose during the post-impact response. The duration of the event from impact to rest was1.62 seconds. There was major structural damage in the lower fuselage areas around the Wingbox and Aft Fuselage sections. The Aft Fuselage section deformation caused some cabin intrusion from the keel beams pushing the aft cabin floor into the cabin. Other structural deformations occurred around the tail and at transition regions in the aircraft structure; mainly in locations of differing overall stiffness. The data obtained showed average vertical accelerations between 12 and 16 g with spikes reaching almost 40 g at certain floor locations. Average horizontal accelerations were approximately 10 g for all floor locations measured with spikes reaching approximately 25 g in some locations. The report includes a full set of results on aircraft deformation and accelerations along with discussions as to the effect on the aircraft structure.

Justin D Littell↗

Pulsar-wind-nebula-powered Galactice center X-ray filament G0.13-0.11

We report the discovery of X-ray polarization from the X-ray-bright filament G0.13−0.11 in the Galactic center (GC) region. This filament features a bright, hard X-ray source that is most plausibly a pulsar wind nebula (PWN) and an extended and structured diffuse component. Combining the polarization signal from IXPE with the imaging/spectroscopic data fromChandra, we find that X-ray emission of G0.13−0.11 is highly polarized PD=57(±18)% in the 3−6 keV band, while the polarization angle is PA=21◦(±9◦). This high degree of polarization proves the synchrotron origin of the X-ray emission from G0.13−0.11. In turn, the measured polarization angle implies that the X-ray emission is polarized approximately perpendicular to a sequence of nonthermal radio filaments that may be part of the GC Radio Arc. The magnetic field on the order of 100μGappears to be preferentially ordered along the filaments. The above field strength is the fiducial value that makes our model self-consistent, while the other conclusions are largely model independent

magnetic fields↗

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

59 BASIC BIOLOGICAL SCIENCES↗

Estimation of conditional cumulative incidence functions under generalized semiparametric regression models with missing covariates, with application to analysis of biomarker correlates in vaccine trials

Herein, this article presents generalized semiparametric regression models for conditional cumulative incidence functions with competing risks data when covariates are missing by sampling design or happenstance. A doubly robust augmented inverse probability weighted (AIPW) complete-case approach to estimation and inference is investigated. This approach modifies IPW complete-case estimating equations by exploiting the key features in the relationship between the missing covariates and the phase-one data to improve efficiency. An iterative numerical procedure is derived to solve the nonlinear estimating equations. The asymptotic properties of the proposed estimators are established. A simulation study examining the finite-sample performances of the proposed estimators shows that the AIPW estimators are more efficient than the IPW estimators. The developed method is applied to the RV144 HIV-1 vaccine efficacy trial to investigate vaccine-induced IgG binding antibodies to HIV-1 as correlates of acquisition of HIV-1 infection while taking account of whether the HIV-1 sequences are near or far from the HIV-1 sequences represented in the vaccine construct.

97 MATHEMATICS AND COMPUTING↗

Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the bdelloid rotifer Adineta vaga

Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemimethylated intermediates and eventually fully methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle–regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle–regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis–dependent methylation following DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗

A universal and constant rate of gene content change traces pangenome flux to LUCA

Abstract Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome—the proportion of the genome harboring gene content difference for genome pairs—varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%–33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.

Microbiology↗

Palomar observations of the collision of comet Shoemaker-Levy 9 with Jupiter

We present two papers of the near-infrared observations from Palomar observatory of the impact of fragment R of comet Shoemaker-Levy 9 with Jupiter on July 21, 1994. The first paper is concerned with the lightcurves found from these observations: Two instruments were used to image the event at 3.2 and 4.5 microns simultaneously. The lightcurves from these image sequences both show two faint precursor flashes, a bright main peak, and several oscillations over the following hour. We identify the precursor flashes with the entry of the bolide into Jupiter's upper atmosphere, and with the post-impact ejecta plume rising above the planet's limb. The main peak is due to the re-entry of the collapsing plume in Jupiter's atmosphere and the resultant shock heating. The second paper is concerned with the low-resolution spectra from the lightcurves: Low-resolution 8-13 micron spectra taken near the peak of the lightcurve show a broad emission feature that resembles the delicate silicate feature commonly seen in comets and the interstellar medium. We use this feature to estimate the dust content of the impact plume. The overall infrared spectral energy distribution at the time of peak brightness is consistent with emission from an optically-thin layer of small particles at approximately 600 K. Integrating over the spectrum and the lightcurve, we obtain a total radiated energy from the R impact of greater than or equal to 10(exp 25) ergs and a plume mass of greater than or equal to 3 x 10(exp 13) g.

Neugebauer, G.↗

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi

Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. We establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of bond line discontinuities in a high-Mn TWIP steel pipe welded by HF-ERW

In this work, the microstructure and defects in a high-frequency electrical resistance welded (HF-ERW) pipe of high-Mn twinning-induced plasticity (TWIP) steel were characterized. The microstructure of the base metal and the bond line were examined using both optical microscopy and scanning electron microscopy. The features of the bond line were similar to those of conventional steel. Simultaneously, the circumferential ductility was evaluated via a flaring test. It was concluded that the deterioration of the circumferential ductility in a high-Mn TWIP steel pipe was caused by irregular shaped oxide defects and a penetrator that had been formed during welding. Specifically, the penetrator, which is composed of MnO and Mn{sub 2}SiO{sub 4}, was found to be the most influential on the circumferential ductility of the welded pipe. The penetrator was analyzed using both an electron probe micro analyzer and transmission electron microscopy, and the formation sequence of the penetrator was evaluated. - Highlights: •This study focused on applying the HF-ERW process to the seam welding of expandable pipe using TWIP steels. •For improvement of the circumferential ductility, deterioration factors were characterized. •Penetrator which would mainly deteriorate the circumferential ductility consisted of round MnO and Mn{sub 2}SiO{sub 4}. •Metallurgical evidence of existing theory regarding the mechanism of defect formation during the HF-ERW was characterized.

36 MATERIALS SCIENCE↗

Voyager Encounter Highlights

The following are presented: computer animation of trajectories for both Voyagers 1 and 2; view of Jupiter during one orbit of Ganymede; computer animation of Voyager 2's encounter with Jupiter and its satellites; time lapse of the planet's rotation and its satellites; stroboscopic sequence of selected frames; cloud motion; Jupiter's Great Red Spot (4/25 - 5/24, 1979) through a violet filter; and the Great Red Spot through a blue filter by Voyager 1. The dynamics of Jupiter's clouds are shown - the whole planet is shown first, then two closer looks are repeated several times. Also included are pans of stills of Jupiter's satellites and a computer simulation tour of Saturn system from POV just behind Voyager, made of 116 images of Saturn through a green filter and of 516 images taken by Voyager 1 (9/12 - 9/14, 1980). Frames are enhanced to show the motion of features in Saturn's rings. Pans of stills of Saturn's satellites are shown. There is computer animation of the planet's system, rings, and Sigma Sagittari. Images on January 14, 1986 are through an orange filter. Uranus's satellites are shown as is computer animation of an August 1989 encounter.

Source record↗

Overview of IMPACT Data Acquisition System and Data Reduction Process

This report documents the development of the data acquisition system (DAS) and data reduction methodologies for the Irradiated Material Property Accelerated Characterization Test (IMPACT) experiment at the Advanced Test Reactor (ATR). The IMPACT experiment is designed to enable in-pile measurement of thermal conductivity in metallic nuclear fuels, specifically U-10Zr, using an instrumented thermal conductivity probe. The DAS supports both passive temperature monitoring and active thermal interrogation of the probe through controlled AC and DC excitation. Significant modifications to laboratory-scale systems were required to accommodate the higher resistance paths associated with the in-pile application. Custom electronics and relay-controlled measurement sequencing were developed to enable the measurement and sufficient power delivery to the sensing region. A reduced-order, axisymmetric thermal model based on the thermal quadrupoles method is presented to support data interpretation. This model enables efficient evaluation of transient heat transfer behavior and facilitates solution of the inverse problem required to extract thermal properties from measured signals. Multiple boundary condition formulations are discussed to address varying experimental time scales and geometries. Additionally, machine learning techniques are introduced to support data reduction and improve confidence in inverse solutions. Convolutional neural networks are applied to identify the presence of gas gaps and other evolving geometric features that significantly impact thermal response during irradiation. These efforts contribute to the broader integration of digital twin frameworks and real-time modeling capabilities within the Advanced Fuels Campaign.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

Mars - Evidence for dynamic processes from Mariners 6 and 7.

Detailed study of the evolution of the Martian surface on the basis of an analysis of Mariner 6 and 7 photographs of certain features of the equatorial region of Mars. It is concluded that the planet Mars is characterized by an internal dynamic activity on the scale of the interior of the African plate. Cited as evidence are scarps resembling fault scarps in Meridiani Sinus and on the Hellas-Hellespontus border. Ridges associated with craters on the boundary of Hellas and Hellespontus are most easily explained by volcanic activity, and at least some of the associated craters may themselves be of volcanic origin. Ridges on the Hellas-Hellespontus border and part of the wall of Edom seem to bulge out into cratered swellings or domes. A sequence of events is worked out for different parts of Mars, and an attempt is made to develop a crude threefold geologic time scale. The sequence suggests that dynamic activity was confined neither to the earliest nor the latest periods of Martian history.

Elston, W. E.↗

Constraints on the origin of the ultraviolet upturn in elliptical galaxies from Hopkins Ultraviolet Telescope observations of NGC 1399

Results are presented of observations of the giant elliptical galaxy NGC 1399 in December 1990, which provide measurements of the spectral energy distribution of the elliptical galaxy and allow detection of absorption features in the sub-2000-A UV. The spectrum shows no emission features other than well-known geocoronal lines. Strong Lyman series absorption is evident at the galaxy redshift. Other absorption features attributable to the hot stellar population are detected, but there is no evidence of C IV 1548, 1551 absorption. Thse data are used to set constraints on the origin of the UV upturn in elliptical galaxies. The lack of detectable C IV absorption and the shape of the continuum spectrum exclude star formation with a standard IMF as the sole contributor to the 1550-A flux. The observed continuum flux decreases from 1050 A to the Lyman limit, indicating that the light is dominated by stars with temperatures less than 25,000 K. For star-formation models, this temperature puts the main-sequence turnoff near B0, implying either that star formation ended about 2 x 10 exp 7 yr ago, or that stars are currently forming with a truncated IMF.

Ferguson, Henry C.↗

Sequential deformation of plains along Tessera boundaries on Venus: Evidence from Alpha Regio

Tesserae are regions of elevated terrain characterized by two or more sets of ridges and grooves that intersect orthogonally. Tesserae comprise 15-20 percent of the surface of Venus, but the nature of their formation and evolution is not well understood; processes proposed to account for their characteristics are many and varied. Two types of tessera boundaries have been described: type 1 are generally embayed by plains; and type 2 boundaries are characterized by being linear at the 100-km scale and often associated with steep scarps or tectonic features. Margins such as the western edge of Alpha have been described as type 2. Some of the tessera have boundaries that display deformation of both the edge of the tessera and the adjoining plains. This study focuses on the western edge of Alpha Regio in an effort to characterize on occurrence of this type of boundary and assess the implications of the style in general. Using Magellan SAR imagery, lineament lengths, orientations, and spacing were measured for ten 50 x 60 km areas spanning 500 km of the western boundary. Structural characteristics and orientations were compared to stratigraphic units in order to assess the sequence and style of deformation.

Gilmore, M. S.↗

A Day in the Life of an Industrial Hearing Conservationist: A Template for Successful Career Education and Outreach Presentations

Whether in a classroom setting or at a local community meeting, opportunities for providing descriptive and positive information about our professions to an audience unfamiliar with acoustics, noise control or hearing conservation often call for alternatives to technical demonstrations that illustrate principles of acoustics or noise control. More importantly, successful outreach presentations must convey images of our day-to-day activities and the challenges we address, many of which are non-technical. One successful approach to career outreach presentations makes use of a collection of photo slides featuring the speaker, his colleagues, customers and workplaces to vividly illustrate the specific job tasks, people and environment of the speaker's job or career. Against this fluid and multi-dimensional visual backdrop, an accompanying script addresses the main theme. A comprehensive photo slide collection may be established gradually, often by making use of and adding to technical and personal slides already in the speaker's possession. Slide collections are portable, easily and quickly reconfigured for back-to-back or spontaneous engagements, and they are well suited to speaking opportunities where technical presentations or demonstrations are not practical or appropriate. A carefully chosen sequence of photo slides minimizes the need for speaker's notes, as each photo itself provides a visual prompt. Although photo slide presentations are appropriate to a variety of outreach and professional settings, the specific illustrative and explanatory material presented here illustrates their application in career education outreach activities, using industrial hearing conservation as an example.

Cooper, Beth A.↗