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At least 559 records · Page 31

The Structure of the Young Star Cluster NGC 6231. I. Stellar Population

NGC 6231 is a young cluster (age ∼2–7 Myr) dominating the Sco OB1 association (distance ∼1.59 kpc) with ∼100 O and B stars and a large pre-main-sequence stellar population. We combine a reanalysis of archival Chandra X-ray data with multiepoch near-infrared (NIR) photometry from the VISTA Variables in the Vía Lactéa (VVV) survey and published optical catalogs to obtain a catalog of 2148 probable cluster members. This catalog is 70% larger than previous censuses of probable cluster members in NGC 6231. It includes many low-mass stars detected in the NIR but not in the optical and some B stars without previously noted X-ray counterparts. In addition, we identify 295 NIR variables, about half of which are expected to be pre-main-sequence stars. With the more complete sample, we estimate a total population in the Chandra field of 5700–7500 cluster members down to 0.08 M{sub ⊙} (assuming a universal initial mass function) with a completeness limit at 0.5 M{sub ⊙}. A decrease in stellar X-ray luminosities is noted relative to other younger clusters. However, within the cluster, there is little variation in the distribution of X-ray luminosities for ages less than 5 Myr. The X-ray spectral hardness for B stars may be useful for distinguishing between early-B stars with X-rays generated in stellar winds and B-star systems with X-rays from a pre-main-sequence companion (>35% of B stars). A small fraction of catalog members have unusually high X-ray median energies or reddened NIR colors, which might be explained by absorption from thick or edge-on disks or being background field stars.

79 ASTRONOMY AND ASTROPHYSICS↗

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13 C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13 C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.

54 ENVIRONMENTAL SCIENCES↗

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗

MO-FG-202-07: Real-Time EPID-Based Detection Metric For VMAT Delivery Errors

Purpose: To create and test an accurate EPID-frame-based VMAT QA metric to detect gross dose errors in real-time and to provide information about the source of error. Methods: A Swiss cheese model was created for an EPID-based real-time QA process. The system compares a treatmentplan- based reference set of EPID images with images acquired over each 2° gantry angle interval. The metric utilizes a sequence of independent consecutively executed error detection Methods: a masking technique that verifies infield radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment to quantify rotation, scaling and translation; standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each test were determined. For algorithm testing, twelve different types of errors were selected to modify the original plan. Corresponding predictions for each test case were generated, which included measurement-based noise. Each test case was run multiple times (with different noise per run) to assess the ability to detect introduced errors. Results: Averaged over five test runs, 99.1% of all plan variations that resulted in patient dose errors were detected within 2° and 100% within 4° (∼1% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 91.5% were detected by the system within 2°. Based on the type of method that detected the error, determination of error sources was achieved. Conclusion: An EPID-based during-treatment error detection system for VMAT deliveries was successfully designed and tested. The system utilizes a sequence of methods to identify and prevent gross treatment delivery errors. The system was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of errors in real-time and indicate the error source. J. V. Siebers receives funding support from Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗

Genome sequence of the model rice variety KitaakeX

Abstract Background The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica ), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica ). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

Nipponbare↗

Texture analysis of placental MRI: can it aid in the prenatal diagnosis of placenta accreta spectrum?

Purpose: To determine if texture analysis can differentiate placenta accreta spectrum (PAS) from normal placenta on MRI. Methods: We performed retrospective image analysis of 80 patients, comprised of 46 patients with PAS and 34 patients without PAS. Histopathology was used as the reference standard. Sagittal single shot fast spin echo T2-weighted MRI sequences acquired from a single institution were analyzed. Placental heterogeneity was quantified using in-house software on a Matlab platform, including the standard deviation of pixel intensity, coefficient of variation, gray-level co-occurrence matrices (GLCM), histogram-oriented gradients (HOG), and fractal analysis with box sizes from 2 to 512. Two-tailed unpaired Student’s t test was used with statistical significance of p < 0.05. Results: PAS was associated with higher values for standard deviation of pixel intensity and fractal analysis at every box size. Fractal analysis at box sizes 256 (p = 0.011) and 32 (p = 0.021), and standard deviation of pixel intensity (p = 0.023) were the most statistically significant. Fractal values at box size 256 for PAS was 0.13 versus 0.090 for patients without PAS, while standard deviation of pixel intensity was 3.7 for PAS versus 2.5 for patients without PAS. No statistically significant association between PAS and GLCM, coefficient of variation, and HOG was found. Conclusion: Statistically significant differences were found between normal and abnormal groups using standard deviation of pixel intensity and fractal analysis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

PDB↗

Mid-IR Spectra Herbig Ae/Be Stars

Herbig Ae/Be stars are intermediate mass pre-main sequence stars, the higher mass analogues to the T Tauri stars. Because of their higher mass, they are expected form more rapidly than the T Tauri stars. Whether the Herbig Ae/Be stars accrete only from collapsing infalling envelopes or whether accrete through geometrically flattened viscous accretion disks is of current debate. When the Herbig Ae/Be stars reach the main sequence they form a class called Vega-like stars which are known from their IR excesses to have debris disks, such as the famous beta Pictoris. The evolutionary scenario between the pre-main sequence Herbig Ae/Be stars and the main sequence Vega-like stars is not yet revealed and it bears on the possibility of the presence of Habitable Zone planets around the A stars. Photometric studies of Herbig Ae/Be stars have revealed that most are variable in the optical, and a subset of stars show non-periodic drops of about 2 magnitudes. These drops in visible light are accompanied by changes in their colors: at first the starlight becomes reddened, and then it becomes bluer, the polarization goes from less than 0.1 % to roughly 1% during these minima. The theory postulated by V. Grinnin is that large cometary bodies on highly eccentric orbits occult the star on their way to being sublimed, for systems that are viewed edge-on. This theory is one of several controversial theories about the nature of Herbig Ae/Be stars. A 5 year mid-IR spectrophotometric monitoring campaign was begun by Wooden and Butner in 1992 to look for correlations between the variations in visible photometry and mid-IR dust emission features. Generally the approximately 20 stars that have been observed by the NASA Ames HIFOGS spectrometer have been steady at 10 microns. There are a handful, however, that have shown variable mid-IR spectra, with 2 showing variations in both the continuum and features anti-correlated with visual photometry, and 3 showing variations in the emission features only while the continuum level remained unchanged. The first 2 stars mentioned probably have reprocessing envelopes. The other 3 stars gives important clues to the controversy over the geometry of the gas and dust around these pre-main sequence stars: the steady underlying 10 microns continuum and variable features indicates that an optically thick continuum probably arising from an accretion disk is decoupled from the optically thin emission features which may arise in a disk atmosphere. Bernadette Rodgers has joined this monitoring campaign in the near-IR using GRIMII with the goal of detecting variations in the hot dust continuum and the gas density in the dense accretion region close to these stars.

Wooden, Diane↗

Camelina sativa , an oilseed at the nexus between model system and commercial crop

The rapid assessment of metabolic engineering strategies in plants is aided by crops that provide simple, high throughput transformation systems, a sequenced genome, and the ability to evaluate the resulting plants in field trials. Camelina sativa provides all of these attributes in a robust oilseed platform. The ability to perform field evaluation of Camelina is a useful, and in some studies essential benefit that allows researchers to evaluate how traits perform outside the strictly controlled conditions of a greenhouse. In the field the plants are subjected to higher light intensities, seasonal diurnal variations in temperature and light, competition for nutrients, and watering regimes dictated by natural weather patterns, all which may affect trait performance. There are difficulties associated with the use of Camelina . The current genetic resources available for Camelina pale in comparison to those developed for the model plant Arabidopsis thaliana; however, the sequence similarity of the Arabidopsis and Camelina genomes often allows the use of Arabidopsis as a reference when additional information is needed. Camelina ’s genome, an allohexaploid, is more complex than other model crops, but the diploid inheritance of its three subgenomes is straightforward. The need to navigate three copies of each gene in genome editing or mutagenesis experiments adds some complexity but also provides advantages for gene dosage experiments. In conclusion, the ability to quickly engineer Camelina with novel traits, advance generations, and bulk up homozygous lines for small-scale field tests in less than a year, in our opinion, far outweighs the complexities associated with the crop.

59 BASIC BIOLOGICAL SCIENCES↗

Atmospheric connections with the North Atlantic enhanced the deglacial warming in northeast China

Variations in atmospheric circulation across the last deglaciation in the northernmost monsoon-influenced regions of Asia are not well constrained, highlighting a fundamental gap in our understanding of Asian climate. Here we reconstruct continental air temperatures for northeast China across the last deglaciation (past 16 k.y.), based on the distribution of bacterial branched glycerol dialkyl glycerol tetraethers in a sequence of the Hani peat (Jilin Province, northeast China). Our results indicate large (as much as 10 °C) oscillations in temperature in northeast China across the deglaciation, oscillations significantly larger than observed in other temperature records from low-latitude or same-latitude East Asia, but consistent with climate model simulations. This enhanced magnitude, as well as the timing of temperature variations, provides evidence for atmospheric teleconnections with high latitudes; in particular, we suggest that high-latitude cooling associated with Arctic ice expansion and changes in Atlantic Meridional Overturning Circulation enhanced the intensity and lowered the temperature of Eurasian mid-latitude westerlies and northwesterly winds over East Asia during the last glacial, delivering cold air masses to northeast China. During the deglaciation the westerlies and therefore delivery of cold air masses weakened, amplifying the deglacial warming in this region. We conclude that changes in North Atlantic climate had a particularly strong impact on the northernmost parts of the East Asian monsoon–influenced area.

54 ENVIRONMENTAL SCIENCES↗

Exposing structural variations in SARS-CoV-2 evolution

The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

New Blue and Red Variable Stars in NGC 247

Images recorded with the Gemini Multi-Object Spectrograph (GMOS) on Gemini South are combined with archival images from other facilities to search for variable stars in the southern half of the nearby disk galaxy NGC 247. Fifteen new periodic and nonperiodic variables are identified. These include three Cepheids with periods <25 days, four semiregular variables, one of which shows light variations similar to those of R CrB stars, five variables with intrinsic visible/red brightnesses and colors that are similar to those of luminous blue variables (LBVs), and three fainter blue variables, one of which may be a noneclipsing close binary system. The S Doradus instability strip defines the upper envelope of a distinct sequence of objects on the (i, g-i) color–magnitude diagram (CMD) of NGC 247. The frequency of variability of an amplitude ≥0.1 magnitude in the part of the CMD that contains LBVs over the seven-month period when the GMOS images were recorded is ~0.2. The light curve of the B[e] supergiant J004702.18–204739.9, which is among the brightest stars in NGC 247, is also examined. Low-amplitude variations on day-to-day timescales are found, coupled with a systematic trend in mean brightness over a six-month time interval.

47 OTHER INSTRUMENTATION↗

Uncertainties in νp-process nucleosynthesis from Monte Carlo variation of reaction rates

ABSTRACT It has been suggested that a νp-process can occur when hot, dense, and proton-rich matter is expanding within a strong flux of antineutrinos. In such an environment, proton-rich nuclides can be produced in sequences of proton captures and (n, p) reactions, where the free neutrons are created in situ by $\overline{\nu }_\mathrm{e}+\mathrm{p} {\rightarrow} \mathrm{n}+\mathrm{e}^+$ reactions. The detailed hydrodynamic evolution determines where the nucleosynthesis path turns off from N = Z line and how far up the nuclear chart it runs. In this work, the uncertainties on the final isotopic abundances stemming from uncertainties in the nuclear reaction rates were investigated in a large-scale Monte Carlo approach, simultaneously varying more than 10 000 reactions. A large range of model conditions was investigated because a definitive astrophysical site for the νp-process has not yet been identified. The present parameter study provides, for each model, identification of the key nuclear reactions dominating the uncertainty for a given nuclide abundance. As all rates appearing in the νp-process involve unstable nuclei, and thus only theoretical rates are available, the final abundance uncertainties are larger than those for nucleosynthesis processes closer to stability. Nevertheless, most uncertainties remain below a factor of 3 in trajectories with robust nucleosynthesis. More extreme conditions allow production of heavier nuclides but show larger uncertainties because of the accumulation of the uncertainties in many rates and because the termination of nucleosynthesis is not at equilibrium conditions. It is also found that the solar ratio of the abundances of 92Mo and 94Mo could be reproduced within uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗

Causal interaction in high frequency turbulence at the biosphere–atmosphere interface: Structure–function coupling

At the biosphere–atmosphere interface, nonlinear interdependencies among components of an ecohydrological complex system can be inferred using multivariate high frequency time series observations. Information flow among these interacting variables allows us to represent the causal dependencies in the form of a directed acyclic graph (DAG). Here, we use high frequency multivariate data at 10 Hz from an eddy covariance instrument located at 25 m above agricultural land in the Midwestern US to quantify the evolutionary dynamics of this complex system using a sequence of DAGs by examining the structural dependency of information flow and the associated functional response. We investigate whether functional differences correspond to structural differences or if there are no functional variations despite the structural differences. We base our analysis on the hypothesis that causal dependencies are instigated through information flow, and the resulting interactions sustain the dynamics and its functionality. To test our hypothesis, we build upon causal structure analysis in the companion paper to characterize the information flow in similarly clustered DAGs from 3-min non-overlapping contiguous windows in the observational data. We characterize functionality as the nature of interactions as discerned through redundant, unique, and synergistic components of information flow. Through this analysis, we find that in turbulence at the biosphere–atmosphere interface, the variables that control the dynamic character of the atmosphere as well as the thermodynamics are driven by non-local conditions, while the scalar transport associated with CO and H 2 O is mainly driven by short-term local conditions.

58 GEOSCIENCES↗

Long-read sequencing transcriptome quantification with lr-kallisto

RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. “Long-read” sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.

Loving, Rebekah K. (ORCID:0000000187250376)↗

Confirmation of dust clusters in the coma of Comet Halley

Measurements from the Ducma dust counter and mass analyzer on the Vega spacecraft are compared with those from the SP-1 sensor on the same spacecraft. It is shown that the sequence of pulses recorded by the SP-1 instruments show deviations from a random distribution. Some of the nonrandom sequences observed by SP-1 are in the same time intervals as the clusters observed by the Ducma instrument. The results support the analysis of Ducma data which showed highly structured variations of dust intensity through the coma and large fluxes of low mass particles extending to great distances beyond the coma (Simpson et al., 1986).

Simpson, J. A.↗

Optimal Area Profiles for Ideal Single Nozzle Air-Breathing Pulse Detonation Engines

The effects of cross-sectional area variation on idealized Pulse Detonation Engine performance are examined numerically. A quasi-one-dimensional, reacting, numerical code is used as the kernel of an algorithm that iteratively determines the correct sequencing of inlet air, inlet fuel, detonation initiation, and cycle time to achieve a limit cycle with specified fuel fraction, and volumetric purge fraction. The algorithm is exercised on a tube with a cross sectional area profile containing two degrees of freedom: overall exit-to-inlet area ratio, and the distance along the tube at which continuous transition from inlet to exit area begins. These two parameters are varied over three flight conditions (defined by inlet total temperature, inlet total pressure and ambient static pressure) and the performance is compared to a straight tube. It is shown that compared to straight tubes, increases of 20 to 35 percent in specific impulse and specific thrust are obtained with tubes of relatively modest area change. The iterative algorithm is described, and its limitations are noted and discussed. Optimized results are presented showing performance measurements, wave diagrams, and area profiles. Suggestions for future investigation are also discussed.

Paxson, Daniel E.↗

Photometric Studies of GEO Orbital Debris

The photometric signature of a debris object can be useful in determining what the physical characteristics of a piece of debris are. We report on optical observations in multiple filters of debris at geosynchronous Earth orbit (GEO). Our sample is taken from GEO objects discovered in a survey with the University of Michigan's 0.6-m aperture Schmidt telescope MODEST (for Michigan Orbital DEbris Survey Telescope), and then followed up in real-time with the Cerro Tololo Inter- American Observatory (CTIO) 0.9-m for orbits and photometry. Our goal is to determine 6 parameter orbits and measure colors for all objects fainter than R=15th magnitude that are discovered in the MODEST survey. At this magnitude the distribution of observed angular rates changes significantly from that of brighter objects. There are two objectives: 1. Estimate the orbital distribution of objects selected on the basis of two observational criteria: brightness (magnitude) and angular rates. 2. Obtain magnitudes and colors in standard astronomical filters (BVRI) for comparison with reflectance spectra of likely spacecraft materials. What is the faint debris likely to be? More than 90 calibrated sequences of R-B-V-I-R magnitudes for a sample of 50 objects have been obtained with the CTIO 0.9-m. For objects that do not show large brightness variations, the colors are largely redder than solar in both B-R and R-I. The width of the color distribution may be intrinsic to the nature of the surfaces, but also could be that we are seeing irregularly shaped objects and measuring the colors at different times with just one telescope. For a smaller sample of objects we have observed with synchronized CCD cameras on the two telescopes. The CTIO 0.9-m observes in B, and MODEST in R. The CCD cameras are electronically linked together so that the start time and duration of observations are the same to better than 50 milliseconds. Thus the B-R color is a true measure of the surface of the debris piece facing the telescopes for that observation. Any change in color reflects a real change in the debris surface. We will compare our observations with models and laboratory measurements of selected surfaces.

Seitzer, Patrick↗