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At least 757 records · Page 42

The Dark Energy Survey Year 3 and eBOSS: constraining galaxy intrinsic alignments across luminosity and colour space

ABSTRACT We present direct constraints on galaxy intrinsic alignments (IAs) using the Dark Energy Survey Year 3 (DES Y3), the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and its precursor, the Baryon Oscillation Spectroscopic Survey (BOSS). Our measurements incorporate photometric red sequence (redMaGiC) galaxies from DES with median redshift z ∼ 0.2–1.0, luminous red galaxies from eBOSS at z ∼ 0.8, and also an SDSS-III BOSS CMASS sample at z ∼ 0.5. We measure two-point IA correlations, which we fit using a model that includes lensing, magnification, and photometric redshift error. Fitting on scales 6 Mpc h−1 < rp < 70 Mpc h−1, we make a detection of IAs in each sample, at 5σ–22σ (assuming a simple one-parameter model for IAs). Using these red samples, we measure the IA–luminosity relation. Our results are statistically consistent with previous results, but offer a significant improvement in constraining power, particularly at low luminosity. With this improved precision, we see detectable dependence on colour between broadly defined red samples. It is likely that a more sophisticated approach than a binary red/blue split, which jointly considers colour and luminosity dependence in the IA signal, will be needed in future. We also compare the various signal components at the best-fitting point in parameter space for each sample, and find that magnification and lensing contribute $\sim 2\!-\!18~{{\ \rm per\ cent}}$ of the total signal. As precision continues to improve, it will certainly be necessary to account for these effects in future direct IA measurements. Finally, we make equivalent measurements on a sample of emission-line galaxies from eBOSS at z ∼ 0.8. We constrain the non-linear alignment amplitude to be $A_1=0.07^{+0.32}_{-0.42}$ (|A1| < 0.78 at 95 per cent CL).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Abstract Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Results Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp 614 Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro 323 Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. Conclusions These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

Controlled Parametric Forcing During Directional Solidification of a Bulk Organic Alloy Under Microgravity

The response of dendritic microstructures to step-like pulling velocity conditions is investigated using microgravity directional solidification experiments conducted on DECLIC-DSI combined with phase-field simulations. Under a constant pulling velocity of 1.5 µm/s, the evolution toward steady-state growth is characterized in terms of primary spacing, dendrite drift, and tip dynamics. For the first time, side-view observations enabled direct measurement of tip radius and sidebranching frequency. When step-like oscillations of the pulling velocity are imposed, the dendritic array exhibits a strongly period-dependent response: short periods lead to rapid tip adaptation, whereas longer periods induce a phase lag between tip position and morphology, resulting in progressive tip flattening and, above a critical period, interface destabilization and dendrite splitting. Quantitative phase-field simulations, including a realistic thermal field and stochastic noise, reproduce the experimental observations and provide insight into the governing mechanisms, highlighting the role of characteristic relaxation times, sequence-dependent effects, and the irreversible reorganization of the microstructure following splitting.

Microgravity↗

A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies

HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency.

59 BASIC BIOLOGICAL SCIENCES↗

Equatorial X-rays and their effect on the lower mesosphere

On the night of May 23/24, 1975, a sequence of rocket and balloon experiments was launched from Chilca Base, Peru (12.5 deg S, 76.8 deg W, magnetic dip = - 0.7 deg). Detailed analysis and comparisons of the data yielded the first direct measurement of lower mesospheric response to a galactic X-ray source. This result could only have been determined at the equator, where cosmic ray background effects are minimal. The objective of the experiments was to seek out the equatorial energetic electron belt, sporadically reported to contain fluxes near auroral levels, measure the bremsstrahlung radiation produced by this particle belt, and determine the influence of this radiation on the middle atmosphere. High altitude rocket payloads (Nike Tomahawk 18.170 and 18.171) were launched to probe the thermosphere during and following the anticipated downward drift period. Each carried an on-axis X-ray scintillation detector and Geiger Mueller energetic electron detectors. Magnetometers and lunar sensors were used to determine payload aspect.

Goldberg, R. A.↗

Modelling the IRAS colors of galaxies

A physical interpretation is proposed for the color-color diagram of galaxies which are powered only by star formation. The colors of each galaxy result from the combination of two components: cirrus-like emission from the neutral disk, and warmer emission from regions directly involved in on-going star formation. This approach to modelling the emission is based on dust properties, but independent evidence for it is found in the relation between the color sequence and the luminosity sequence. Implications of data and interpretations are discussed and possible tests mentioned for the model.

Helou, George↗

Laboratory testing of candidate robotic applications for space

Robots have potential for increasing the value of man's presence in space. Some categories with potential benefit are: (1) performing extravehicular tasks like satellite and station servicing, (2) supporting the science mission of the station by manipulating experiment tasks, and (3) performing intravehicular activities which would be boring, tedious, exacting, or otherwise unpleasant for astronauts. An important issue in space robotics is selection of an appropriate level of autonomy. In broad terms three levels of autonomy can be defined: (1) teleoperated - an operator explicitly controls robot movement; (2) telerobotic - an operator controls the robot directly, but by high-level commands, without, for example, detailed control of trajectories; and (3) autonomous - an operator supplies a single high-level command, the robot does all necessary task sequencing and planning to satisfy the command. Researchers chose three projects for their exploration of technology and implementation issues in space robots, one each of the three application areas, each with a different level of autonomy. The projects were: (1) satellite servicing - teleoperated; (2) laboratory assistant - telerobotic; and (3) on-orbit inventory manager - autonomous. These projects are described and some results of testing are summarized.

Purves, R. B.↗

Numerical studies of asymmetric adiabatic accretion flow - The effect of velocity gradients

A numerical study of the time variation of the angular momentum and mass capture rates for a central object accreting from a uniform medium with a velocity gradient transverse to the direction of the mean flow is presented, covering a range of velocity asymmetries and Mach numbers in the incident flow. It is found that the mass accretion rate in a given evolutionary sequence varies in an irregular manner, with the matter accreting onto the central object from either a continuously moving accretion wake or from an accretion disk. The implications of the results from the study of short-term fluctuations observed in the pulse period and luminosity of X-ray pulsars are discussed.

Taam, Ronald E.↗

Morphology, near-infrared luminosity, and mass of the Galactic bulge from COBE DIRBE observations

Near-infrared images of the Galactic bulge at 1.25, 2.2, 3.5, and 4.9 microns obtained by the Diffuse Infrared Background Experiment (DIRBE) onboard the Cosmic Background Explorer (COBE) satellite are used to characterize its morphology and to determine its infrared luminosity and mass. Earlier analysis of the DIRBE observations (Weiland et al. 1994) provided supporting evidence for the claim made by Blitz & Spergel (1991) that the bulge is bar-shaped with its near end in the first Galactic quadrant. Adopting various triaxial analytical functions to represent the volume emissivity of the source, we confirm the barlike nature of the bulge and show that triaxial Gaussian-type functions provide a better fit to the data than other classes of functions, including an axisymmetric spheroid. The introduction of a `boxy' geometry, such as the one used by Kent, Dame, & Fazio (1991) improves the fit to the data. Our results show that the bar is rotated in the plane with its near side in the first Galactic quadrant creating an angle of 20 deg +/- 10 deg between its major axis and the line of sight to the Galactic center. Typical axis ratios of the bar are (1:0.33 +/- 0.11:0.23 +/- 0.08), resembling the geometry of prolate spheroids. There is no statistically significant evidence for an out-of-plane tilt of the bar at 2.2 microns, and marginal evidence for a tilt of approximately equal 2 deg at 4.9 microns. The introduction of a roll around the intrinsic major axis of the bulge improves the `boxy' appearance of some functions. A simple integration of the observed projected intensity of the bulge gives a bulge luminosity of 1.2 x 10(exp 9), 4.1 x 10(exp 8), 2.3 x 10(exp 8), and 4.3 x 10(exp 7) solar luminosity, respectively, at 1.25, 2.2, 3.5, and 4.9 microns wavelength for a Galactocentric distance of 8.5 kpc. The 2.2 microns luminosity function of the bulge population in the direction of Baade's window yields a bolometric luminosity of L(sub bol) = 5.3 x 10(exp 9) solar luminosity. Stellar evolutionary models relate this luminosity to the number of main-sequence progenitor stars that currently populate the red giant branch. Combined with the recent determination of the main-sequence turnoff mass for the bulge by the Hubble Space Telescope (Holtzman et al. 1993) we derive a photometrically determined bulge mass of approximately equal to 1.3 x 10(exp 10) solar mass for a Salpeter initial mass function extended down to 0.1 solar mass.

Dwek, E.↗

A Kepler Mission, A Search for Habitable Planets: Concept, Capabilities and Strengths

The detection of extrasolar terrestrial planets orbiting main-sequence stars is of great interest and importance. Current ground-based methods are only capable of detecting objects about the size or mass of Jupiter or larger. The technological challenges of direct imaging of Earth-size planets from space are expected to be resolved over the next twenty years. Spacebased photometry of planetary transits is currently the only viable method for detection of terrestrial planets (30-600 times less massive than Jupiter). The method searches the extended solar neighborhood, providing a statistically large sample and the detailed characteristics of each individual case. A robust concept has been developed and proposed as a Discovery-class mission. The concept, its capabilities and strengths are presented.

Koch, David↗

The Kepler Mission: Search for Habitable Planets

Detecting extrasolar terrestrial planets orbiting main-sequence stars is of great interest and importance. Current ground-based methods are only capable of detecting objects about the size or mass of Jupiter or larger. The difficulties encountered with direct imaging of Earth-size planets from space are expected to be resolved in the next twenty years. Spacebased photometry of planetary transits is currently the only viable method for detection of terrestrial planets (30-600 times less massive than Jupiter). This method searches the extended solar neighborhood, providing a statistically large sample and the detailed characteristics of each individual case. A robust concept has been developed and proposed as a Discovery-class mission. Its capabilities and strengths are presented.

Borucki, William↗

Determination of human DNA polymerase utilization for the repair of a model ionizing radiation-induced DNA strand break lesion in a defined vector substrate

Human DNA polymerase and DNA ligase utilization for the repair of a major class of ionizing radiation-induced DNA lesion [DNA single-strand breaks containing 3'-phosphoglycolate (3'-PG)] was examined using a novel, chemically defined vector substrate containing a single, site-specific 3'-PG single-strand break lesion. In addition, the major human AP endonuclease, HAP1 (also known as APE1, APEX, Ref-1), was tested to determine if it was involved in initiating repair of 3'-PG-containing single-strand break lesions. DNA polymerase beta was found to be the primary polymerase responsible for nucleotide incorporation at the lesion site following excision of the 3'-PG blocking group. However, DNA polymerase delta/straightepsilon was also capable of nucleotide incorporation at the lesion site following 3'-PG excision. In addition, repair reactions catalyzed by DNA polymerase beta were found to be most effective in the presence of DNA ligase III, while those catalyzed by DNA polymerase delta/straightepsilon appeared to be more effective in the presence of DNA ligase I. Also, it was demonstrated that the repair initiating 3'-PG excision reaction was not dependent upon HAP1 activity, as judged by inhibition of HAP1 with neutralizing HAP1-specific polyclonal antibody.

Non-NASA Center↗

Co- and/or post-translational modifications are critical for TCH4 XET activity

TCH4 encodes a xyloglucan endotransglycosylase (XET) of Arabidopsis thaliana. XETs endolytically cleave and religate xyloglucan polymers; xyloglucan is one of the primary structural components of the plant cell wall. Therefore, XET function may affect cell shape and plant morphogenesis. To gain insight into the biochemical function of TCH4, we defined structural requirements for optimal XET activity. Recombinant baculoviruses were designed to produce distinct forms of TCH4. TCH4 protein engineered to be synthesized in the cytosol and thus lack normal co- and post-translational modifications is virtually inactive. TCH4 proteins, with and without a polyhistidine tag, that harbor an intact N-terminus are directed to the secretory pathway. Thus, as predicted, the N-terminal region of TCH4 functions as a signal peptide. TCH4 is shown to have at least one disulfide bond as monitored by a mobility shift in SDS-PAGE in the presence of dithiothreitol (DTT). This disulfide bond(s) is essential for full XET activity. TCH4 is glycosylated in vivo; glycosidases that remove N-linked glycosylation eliminated 98% of the XET activity. Thus, co- and/or post-translational modifications are critical for optimal TCH4 XET activity. Furthermore, using site-specific mutagenesis, we demonstrated that the first glutamate residue of the conserved DEIDFEFL motif (E97) is essential for activity. A change to glutamine at this position resulted in an inactive protein; a change to aspartic acid caused protein mislocalization. These data support the hypothesis that, in analogy to Bacillus beta-glucanases, this region may be the active site of XET enzymes.

NASA Discipline Cell Biology↗

COMETBOARDS Can Optimize the Performance of a Wave-Rotor-Topped Gas Turbine Engine

A wave rotor, which acts as a high-technology topping spool in gas turbine engines, can increase the effective pressure ratio as well as the turbine inlet temperature in such engines. The wave rotor topping, in other words, may significantly enhance engine performance by increasing shaft horse power while reducing specific fuel consumption. This performance enhancement requires optimum selection of the wave rotor's adjustable parameters for speed, surge margin, and temperature constraints specified on different engine components. To examine the benefit of the wave rotor concept in engine design, researchers soft coupled NASA Lewis Research Center's multidisciplinary optimization tool COMETBOARDS and the NASA Engine Performance Program (NEPP) analyzer. The COMETBOARDS-NEPP combined design tool has been successfully used to optimize wave-rotor-topped engines. For illustration, the design of a subsonic gas turbine wave-rotor-enhanced engine with four ports for 47 mission points (which are specified by Mach number, altitude, and power-setting combinations) is considered. The engine performance analysis, constraints, and objective formulations were carried out through NEPP, and COMETBOARDS was used for the design optimization. So that the benefits that accrue from wave rotor enhancement could be examined, most baseline variables and constraints were declared to be passive, whereas important parameters directly associated with the wave rotor were considered to be active for the design optimization. The engine thrust was considered as the merit function. The wave rotor engine design, which became a sequence of 47 optimization subproblems, was solved successfully by using a cascade strategy available in COMETBOARDS. The graph depicts the optimum COMETBOARDS solutions for the 47 mission points, which were normalized with respect to standard results. As shown, the combined tool produced higher thrust for all mission points than did the other solution, with maximum benefits around mission points 11, 25, and 31. Such improvements can become critical, especially when engines are sized for these specific mission points.

Patnaik, Surya N.↗

Fast Plasma Instrument for MMS: Simulation Results

Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. The Dual Electron Spectrometer (DES) of the Fast Plasma Instrument (FPI) for MMS meets these demanding requirements by acquiring the electron velocity distribution functions (VDFs) for the full sky with high-resolution angular measurements every 30 ms. This will provide unprecedented access to electron scale dynamics within the reconnection diffusion region. The DES consists of eight half-top-hat energy analyzers. Each analyzer has a 6 deg. x 11.25 deg. Full-sky coverage is achieved by electrostatically stepping the FOV of each of the eight sensors through four discrete deflection look directions. Data compression and burst memory management will provide approximately 30 minutes of high time resolution data during each orbit of the four MMS spacecraft. Each spacecraft will intelligently downlink the data sequences that contain the greatest amount of temporal structure. Here we present the results of a simulation of the DES analyzer measurements, data compression and decompression, as well as ground-based analysis using as a seed re-processed Cluster/PEACE electron measurements. The Cluster/PEACE electron measurements have been reprocessed through virtual DES analyzers with their proper geometrical, energy, and timing scale factors and re-mapped via interpolation to the DES angular and energy phase-space sampling measurements. The results of the simulated DES measurements are analyzed and the full moments of the simulated VDFs are compared with those obtained from the Cluster/PEACE spectrometer using a standard quadrature moment, a newly implemented spectral spherical harmonic method, and a singular value decomposition method. Our preliminary moment calculations show a remarkable agreement within the uncertainties of the measurements, with the results obtained by the Cluster/PEACE electron spectrometers. The data analyzed was selected because it represented a potential reconnection event as currently published.

Figueroa-Vinas, Adolfo↗

Seasonally Active Slipface Avalanches in the North Polar Sand Sea of Mars: Evidence for a Wind-Related Origin

Meter-scale MRO/HiRISE camera images of dune slipfaces in the north polar sand sea of Mars reveal the presence of deep alcoves above depositional fans. These features are apparently active under current climatic conditions, because they form between observations taken in subsequent Mars years. Recently, other workers have hypothesized that the alcoves form due to destabilization and mass-wasting during sublimation of CO2 frost in the spring. While there is evidence for springtime modification of these features, our analysis of early springtime images reveals that over 80% of the new alcoves are visible underneath the CO2 frost. Thus, we present an alternative hypothesis that formation of new alcoves and fans occurs prior to CO2 deposition. We propose that fans and alcoves form primarily by aeolian processes in the mid- to late summer, through a sequence of aeolian deposition on the slipface, over-steepening, failure, and dry granular flow. An aeolian origin is supported by the orientations of the alcoves, which are consistent with recent wind directions. Furthermore, morphologically similar but much smaller alcoves form on terrestrial dune slipfaces, and the size differences between the terrestrial and Martian features may reflect cohesion in the near-subsurface of the Martian features. The size and preservation of the largest alcoves on the Martian slipfaces also support the presence of an indurated surface layer; thus, new alcoves might be sites of early spring CO2 sublimation and secondary mass-wasting because they act as a window to looser, less indurated materials that warm up more quickly in the spring.

Horgan, Briony H. N.↗

Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement

Abstract Wild emmer wheat (Triticum turgidumsubsp.dicoccoides) is the tetraploid progenitor of hexaploid bread wheat (Triticum aestivumL.) and is known to be a valuable source of genetic variation for wheat improvement. However, direct evaluation of wild emmer diversity for agronomic potential has limited value unless performed in the backgrounds of adapted cultivars. Here, we present a genetic characterization of a population of 1601 backcross recombinant inbred lines, with an average genome composition of 75% bread wheat and 25% wild emmer. Low‐coverage whole‐genome sequencing allowed introgressions and aneuploidies to be identified at a relatively low cost per sample. We identified a relatively large proportion of small introgressions (median length 38 Mb), and we found introgressions to be distributed across all chromosomes. Approximately 44% of genotyped progeny carried at least one aneuploidy, with monosomies being by far the most common. This population, which we have denoted as the Great Plains Wild Emmer/Hard Winter Wheat introgression population (GPWEW‐IP), is, to our knowledge, the first introgression population developed through the direct hybridization of wild emmer wheat and US‐adapted hard winter wheat. We believe that this population represents a valuable resource for wheat breeders and will accelerate the discovery and integration of useful variation from wild emmer wheat.

Genetics & Heredity↗

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↗