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At least 775 records · Page 43

Ginzburg--Landau functionals in the large-graph limit

Ginzburg–Landau (GL) functionals on graphs, which are relaxations of graph-cut functionals on graphs, have yielded a variety of insights in image segmentation and graph clustering. In this paper, we study large-graph limits of GL functionals by taking a functional-analytic view of graphs as nonlocal kernels. For a graph Wn with n nodes, the corresponding graph GL functional GL W n ϵ is an energy for functions on Wn. We minimize GL functionals on sequences of growing graphs that converge to functions called graphons. For such sequences of graphs, we show that the graph GL functional Γ-converges to a continuous and nonlocal functional that we call the graphon GL functional. We investigate the sharp-interface limits of the graph GL and graphon GL functionals, and we relate these limits to a nonlocal total-variation (TV) functional. We express the limiting GL functional in terms of Young measures and thereby obtain a probabilistic interpretation of the minimization problem in the large-graph limit. Finally, to develop intuition about graphon GL functionals, we determine the GL minimizer for several example families of graphons.

Zhang, Edith↗

A search for the binary companion of Polaris

Polaris has a spectroscopic orbit determined from an extensive series of observations as well as a more uncertain astrometric orbit. The determination of its mass and evolutionary state is of considerable interest because it is a low-amplitude classical Cepheid with unusual period and amplitude variations. In this study, IUE spectra are investigated to search for light from the companion. The spectra of Polaris from 1600 A to 3200 A are a good match for nonvariable supergiants of similar spectral type. The lack of any excess flux at the shortest wavelengths implies that a main-sequence companion must be later than A8 V. Although this is the most likely companion, the ultraviolet observations cannot rule out a white dwarf 15,000 K or cooler. Both these companions are consistent with either an evolutionary mass or a smaller pulsation mass for the Cepheid.

Evans, Nancy Remage↗

The soft x ray telescope for Solar-A

The Solar-A satellite being prepared by the Institute for Sapce and Astronautical Sciences (ISAS) in Japan is dedicated to high energy observations of solar flares. The Soft X Ray Telescope (SXT) is being prepared to provide filtered images in the 2 to 60 A interval. The flight model is now undergoing tests in the 1000 foot tunnel at MSFC. Launch will be in September 1991. Earlier resolution and efficiency tests on the grazing incidence mirror have established its performance in soft x rays. The one-piece, two mirror grazing incidence telescope is supported in a strain free mount separated from the focal plane assembly by a carbon-epoxy metering tube whose windings and filler are chosen to minimize thermal and hygroscopic effects. The CCD detector images both the x ray and the concentric visible light aspect telescope. Optical filters provide images at 4308 and 4700 A. The SXT will be capable of producing over 8000 of the smallest partial frame images per day, or fewer but larger images, up to 1024 x 1024 pixel images. Image sequence with two or more of the five x ray analysis filters, with automatic exposure compensation to optimize the charge collection by the CCD detector, will be used to provide plasma diagnostics. Calculations using a differential emission measure code were used to optimize filter selection over the range of emission measure variations and to avoid redundancy, but the filters were chosen primarily to give ratios that are monotonic in plasma temperature.

Brown, W. A.↗

Earth Return Aerocapture for the TransHab/Ellipsled Vehicle

The current architecture being considered by NASA for a human Mars mission involves the use of an aerocapture procedure at Mars arrival and possibly upon Earth return. This technique would be used to decelerate the vehicles and insert them into their desired target orbits, thereby eliminating the need for propulsive orbital insertions. The crew may make the interplanetary journey in a large, inflatable habitat known as the TransHab. It has been proposed that upon Earth return, this habitat be captured into orbit for use on subsequent missions. In this case, the TransHab would be complimented with an aeroshell, which would protect it from heating during the atmospheric entry and provide the vehicle with aerodynamic lift. The aeroshell has been dubbed the "Ellipsled" because of its characteristic shape. This paper reports the results of a preliminary study of the aerocapture of the TransHab/Ellipsled vehicle upon Earth return. Undershoot and overshoot boundaries have been determined for a range of entry velocities, and the effects of variations in the atmospheric density profile, the vehicle deceleration limit, the maximum vehicle roll rate, the target orbit, and the vehicle ballistic coefficient have been examined. A simple, 180 degree roll maneuver was implemented in the undershoot trajectories to target the desired 407 km circular Earth orbit. A three-roll sequence was developed to target not only a specific orbital energy, but also a particular inclination, thereby decreasing propulsive inclination changes and post-aerocapture delta-V requirements. Results show that the TransHab/Ellipsled vehicle has a nominal corridor width of at least 0.7 degrees for entry speeds up to 14.0 km/s. Most trajectories were simulated using continuum flow aerodynamics, but the impact of high-altitude viscous effects was evaluated and found to be minimal. In addition, entry corridor comparisons have been made between the TransHab/Ellipsled and a modified Apollo capsule which is also being considered as the crew return vehicle; because of its slightly higher lift-to-drag ratio, the TransHab has a modest advantage with regard to corridor width. Stagnation-point heating rates and integrated heat loads were determined for a range of vehicle ballistic coefficients and entry velocities.

Muth, W. D.↗

Spatial and Temporal Patterns of Tidal Dissipation in Synchronous Satellites

Tidal heating is an important energy source for several solar system bodies, and there is a wide-spread perception that the pattern of surface heat flow is diagnostic of internal structure. We wish to clarify that situation. Our analysis depends upon two important assumptions: First, that heat transport is dominated by conduction. Second, that the body can be modeled by a sequence of spherically symmetric layers, each with a linear visco-elastic rheology. Under these assumptions, surface heat flow patterns in tidally dominated satellites will reflect radially integrated dissipation patterns. For synchronously rotating satellites with zero obliquity, this pattern depends quite strongly on orbital eccentricity but relatively little on purely radial variations in internal structure. The total amount of heat generated within the body does depend sensitively on internal structure, but the spatial pattern is rather insensitive to structure, especially at low orbital eccentricities.

Bills, Bruce G.↗

Sensitivity of 44 Ti and 56 Ni Production in Core-collapse Supernova Shock-driven Nucleosynthesis to Nuclear Reaction Rate Variations

Recent observational advances have enabled high resolution mapping of 44 Ti in core-collapse supernova (CCSN) remnants. Comparisons between observations and models provide stringent constraints on the CCSN mechanism. However, past work has identified several uncertain nuclear reaction rates that influence 44 Ti and 56 Ni production in postprocessing model calculations. We evolved one-dimensional models of 15 M ⊙ , 18 M ⊙ , 22 M ⊙ , and 25 M ⊙ stars from zero age main sequence through CCSN using Modules for Experiments in Stellar Astrophysics and investigated the previously identified reaction rate sensitivities of 44 Ti and 56 Ni production. In this work, we tested the robustness of our results by making various assumptions about the CCSN explosion energy and mass cut. We found a number of reactions that have a significant impact on the nucleosynthesis of 44 Ti and 56 Ni, particularly for lower progenitor masses. Notably, the reaction rates ${}^{13}{\rm{N}}{(\alpha ,p)}^{16}{\rm{O}}$, ${}^{17}{\rm{F}}{(\alpha ,p)}^{20}\mathrm{Ne}$, ${}^{52}\mathrm{Fe}{(\alpha ,p)}^{55}\mathrm{Co}$, ${}^{56}\mathrm{Ni}{(\alpha ,p)}^{59}\mathrm{Cu}$, ${}^{57}\mathrm{Ni}{(n,p)}^{57}\mathrm{Co}$, ${}^{56}\mathrm{Co}{(p,n)}^{56}\mathrm{Ni}$, ${}^{39}{\rm{K}}{(p,\gamma )}^{40}\mathrm{Ca}$, ${}^{47}{\rm{V}}{(p,\gamma )}^{48}\mathrm{Cr}$, ${}^{52}\mathrm{Mn}{(p,\gamma )}^{53}\mathrm{Fe}$, ${}^{57}\mathrm{Co}{(p,\gamma )}^{58}\mathrm{Ni}$, and ${}^{39}{\rm{K}}{(p,\alpha )}^{36}\mathrm{Ar}$ are influential for a large number of model conditions. Furthermore, we found the list of influential reactions identified by previous postprocessing studies of CCSN shock-driven nucleosynthesis is likely incomplete, motivating future larger-scale sensitivity studies.

79 ASTRONOMY AND ASTROPHYSICS↗

A unified catalog of 204,938 reference genomes from the human gut microbiome

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

Abstract Background Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition. Results We report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales , Thermoleophilia , Geobacter , Spirochaeta , Gaiella , and Defluviicoccus . DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis. Conclusions Our study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.

Microbiology↗

Global MHD Simulation of Mesoscale Structures at the Magnetospheric Boundary

The research carried out for this protocol was focused on the study of mesoscales structures at the magnetospheric boundary. We investigated three areas: (1) the structure of the magnetospheric boundary for steady solar wind conditions; (2) the dynamics of the dayside magnetospheric boundary and (3) the dynamics of the distant tail magnetospheric boundary. Our approach was to use high resolution three-dimensional global magnetohydrodynamic (MHD) simulations of the interaction of the solar wind with the Earth's magnetosphere. We first considered simple variations of the interplanetary conditions to obtain generic cases that helped us in establishing the basic cause and effect relationships for steady solar wind conditions. Subsequently, we used actual solar wind plasma and magnetic field parameters measured by an upstream spacecraft as input to the simulations and compared the simulation results with sequences of events observed by another or several other spacecraft located downstream the bow shock. In particular we compared results with observations made when spacecraft crossed the magnetospheric boundary.

Berchem, Jean↗

Geologic Evolution of Mars' North Polar Layered Deposits and Related Materials from Mars Odyssey THEMIS

The presence of a thick sequence of horizontal layers of ice-rich material at Mars north pole, dissected by troughs and eroding at its margins, is undoubtedly telling us something about the evolution of Mars climate we just don't know what yet. The North Polar Layered Deposits (NPLD) most likely formed as astronomically driven climate variations led to the deposition of conformable, areally extensive layers of ice and dust over the polar region. More recently, the balance seems to have fundamentally shifted to net erosion, as evidenced by the many troughs within the NPLD and the steep, arcuate scarps present near its margins, both of which expose layering.

A R Vasavada↗

Impact of crowding on the diversity of expanding populations

Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population’s range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria–Delbrück fluctuation tests, lineage tracing in a novel microfluidic incubator, cell-based simulations, and theoretical modeling, we find that the majority of mutations arise behind the expanding frontier, giving rise to clones that are mechanically “pushed out” of the growing region by the proliferating cells in front. These excluded-volume interactions result in a clone-size distribution that solely depends on where the mutation first arose relative to the front and is characterized by a simple power law for low-frequency clones. Our model predicts that the distribution depends on a single parameter—the characteristic growth layer thickness—and hence allows estimation of the mutation rate in a variety of crowded cellular populations. Combined with previous studies on high-frequency mutations, our finding provides a unified picture of the genetic diversity in expanding populations over the whole frequency range and suggests a practical method to assess growth dynamics by sequencing populations across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗

Temporal variation in skin microbiota of cohabitating amphibians

Temporal changes and transmission patterns in host-associated microbial communities have important implications for host health. The diversity of amphibian skin microbial communities is associated with disease outcome in amphibians exposed to the fungal pathogen Batrachochytrium dendrobatidis (Bd). To successfully develop conservation strategies against Bd, we need a comprehensive understanding of how skin microbes are maintained and transmitted over time within populations. Here we used 16S rRNA sequence analysis to compare Epipedobates anthonyi frogs housed with one conspecific to frogs housed singly at four time points over the course of 1 year. We found that both α and β diversity of frog skin bacterial communities changed significantly over the course of the experiment. Specifically, we found that bacterial communities of cohabitating frogs became more similar over time. We also observed that some bacterial taxa were differentially abundant between frogs housed singly and frogs housed with a conspecific. These results suggest that conspecific contact may play a role in mediating amphibian skin microbial diversity and that turnover of skin microbial communities can occur across time. Our findings provide rationale for future studies exploring horizontal transmission as a potential mechanism of host-associated microbial maintenance in amphibians.

59 BASIC BIOLOGICAL SCIENCES↗

EStokTP: Electronic Structure to Temperature- and Pressure-Dependent Rate Constants—A Code for Automatically Predicting the Thermal Kinetics of Reactions

A priori rate predictions for gas phase reactions have undergone a gradual but dramatic transformation, with current predictions often rivaling the accuracy of the best available experimental data. The utility of such kinetic predictions would be greatly magnified if they could more readily be implemented for large numbers of systems. Here, we report the development of a new computational environment, namely, EStokTP, that reduces the human effort involved in the rate prediction for single channel reactions essentially to the specification of the methodology to be employed. The code can also be used to obtain all the necessary master equation building blocks for more complex reactions. In general, the prediction of rate constants involves two steps, with the first consisting of a set of electronic structure calculations and the second in the application of some form of kinetic solver, such as a transition state theory (TST)-based master equation solver. EStokTP provides a fully integrated treatment of both steps through calls to external codes to perform first the electronic structure and then the master equation calculations. It focuses on generating, extracting, and organizing the necessary structural properties from a sequence of calls to electronic structure codes, with robust automatic failure recovery options to limit human intervention. The code implements one or multidimensional hindered rotor treatments of internal torsional modes (with automated projection from the Hessian and with optional vibrationally adiabatic corrections), Eckart and multidimensional tunneling models (such as small curvature theory), and variational treatments (based on intrinsic reaction coordinate following). This focus on a robust implementation of high-level TST methods allows the code to be used in high accuracy studies of large sets of reactions, as illustrated here through sample studies of a few hundred reactions. At present, the following reaction types are implemented in EStokTP: abstraction, addition, isomerization, and beta-decomposition. Finally, preliminary protocols for treating barrierless reactions and multiple-well and/or multiple-channel potential energy surfaces are also illustrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗

Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests

Bacteria are one of the most abundant and diverse groups of micro-organisms and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across forests, and the processes that determine these patterns lags significantly behind that of macroorganisms. Here, we evaluated the geographic distributions of bacterial diversity and their driving factors across nine latitudinal forests along a 3,700-km north–south transect in eastern China, using high-throughput 16S rRNA gene sequencing. Four of 32 phyla detected were dominant: Acidobacteria , Actinobacteria , Alphaproteobacteria and Chloroflexi (relative abundance > 5%). Significant increases in bacterial richness and phylogenetic diversity were observed for temperate forests compared with subtropical or tropical forests. The soil organic matter (SOM) mineralisation rate (SOM min , an index of SOM availability) explained the largest significant variations in bacterial richness. Variation partition analysis revealed that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 80.5% of community variation. Among all environmental factors, climatic features (MAT and MAP) were the best predictors of the bacterial community structure, whereas soil pH and SOM min emerged as the most important edaphic drivers of the bacterial community structure. Plant functional traits (community weighted means of litter N content) and diversity resulted in weak but significant correlations with the bacterial community structure. Our findings provide new evidence of bacterial biogeography patterns from tropical to cold temperate forests. Additionally, the results indicated a close linkage among soil bacterial diversity, climate and SOM decomposition, which is critical for predicting continental-scale responses under future climate change scenarios and promoting sustainable forest ecosystem services.

59 BASIC BIOLOGICAL SCIENCES↗

Vortex pairing and organized structures in axisymmetric jets under controlled excitation

A description is given of experiments which have been carried out in a circular air jet facility consisting of two settling chambers in sequence. Sinusoidal perturbations in the exit profile are introduced at controlled frequencies and amplitudes with the aid of a loudspeaker attached to the wall of the first chamber. It was found that vortex pairing in circular jets can occur in two distinct modes, including the shear layer mode and the jet mode. Amplitude variations, the conditions for strong vortex pairing, and the spectral evolution downstream are illustrated with the aid of graphs.

Zaman, K. B. M. Q.↗

Chemical and petrographic constraints on the origin of chondrules and inclusions in carbonaceous chondrites

Bulk chemical compositions of the various petrographic types of chondrules and inclusions in Type 3 carbonaceous chondrites (excluding those affected by metamorphism) have been determined by microprobe defocused-beam analysis. Inclusion compositions follow approximately the theoretical compositional trajectory for equlibrium condensation. Chondrules occurring in the same meteorites have higher silica contents and show only slight overlap with inclusion compositions. Dust fusion is apparently an inadequate mechanism for producing the wide chemical variations observed among chondrules. Impact-melting models require sampling of complex target rocks which are unknown as components of meteorites; this mechanism also demands efficient mechanical processing of chondrules before accretion. A genetic relationship between chondrules and inclusions in carbonaceous chondrites is suggested by the compositional continuum between these objects. A condensation sequence which dips into the liquid stability field at lower temperatures is advocated for the production of both inclusions and chondrules. Textural relationships between intergrown chondrules and inclusions support such a sequence. This model suggests that the assembled components (inclusions and chondrules) of carbonaceous chondrites are related by a common process.

Mcsween, H. Y., Jr.↗

Generalized minimum shift-keying modulation techniques

The simultaneous data demodulation and phase tracking of an MSK signal using the Viterbi algorithm is described and two variations of MSK modulation are studied. The MSK with overlay is a dual rate modulation technique where low-and high-rate data are superimposed on an MSK signal. Here the demodulator uses the Viterbi algorithm to estimate both the low-and high-rate data simultaneously. The MSK with pseudorandom sequence spreading combats intentional or unintentional jamming. A simplified receiver for these spread spectrum MSK signals is found, which takes into consideration the effect of random phase perturbations. The performance of these demodulators is evaluated using transfer function bounds for the bit error probability. It is shown that with a reasonable short overlay period, at a relatively high signal-to-noise ratio (13 dB), there is a small (0.7 dB) loss of performance. For demodulation of the spread spectrum MSK signal, a simplified receiver is derived, and its performance in the presence of continuous jamming is evaluated.

Sadr, Ramin↗