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At least 1,531 records · Page 85

Cognitive analysis of metabolomics data for systems biology

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.

59 BASIC BIOLOGICAL SCIENCES↗

Fracture-matrix fluid exchange in oil-bearing unconventional mudstones

The poromechanical properties of unconventional reservoir materials are in large part dictated by their mineralogy. Since these properties govern the response to stress experienced during hydraulic fracturing, fluid production, and fluid injection, they play a central role in the formation of microcracks or bedding delaminations which ultimately dominate mass transport. In this work we study access to the porosity of end member unconventional reservoir materials, where the end members are predominantly dictated by carbonate content. Access to the porosity is quantified using state of the art 3D x-ray computed tomography coupled with physics informed data analytics. Xenon gas, which attenuates x-rays, provides a spatiotemporal map of access to the porosity. The accessible porosity is quantified over a range of net confining stress relevant to the manmade disturbances listed above. These experiments demonstrate that heavily carbonated mudstones are nearly impermeable at the core (~ cm) scale, while carbonate free analogues afford better access to the microstructure. Consistent with previous qualitative 2D radiographs, access to the interior of the clastic mudstones is first observed along planar microcracks, followed by slow penetration into the surrounding matrix. Physics informed data analytics of the 3D tomography measurements presented here show that these microcracks do not permit uniform access to the adjacent rock matrix. In addition, variation of the effective pressure elucidates the mechanisms that govern fracture/matrix fluid exchange. Under conditions consistent with hydrocarbon production fluid accumulates in the immediate vicinity of the nearest microcrack. While there is clear evidence that, as intended, part of this accumulation is from the more distant matrix, fluid is also squeezed out of the microcrack. The fluid build-up at the microcrack indicates that migration out of the rock is hindered by the coupled poroelastic response of the microcrack and adjacent rock matrix. We show that these mechanisms ultimately account for the meager oil recovery factors realized in practice. These insights have implications for making reservoir scale predictions based on core scale observations, and provide a basis for devising new asset development techniques to access more porosity, and enhance fluid extraction. Finally, these findings shed light on key features and mechanisms that govern shale storage capacity, with relevance to other important industrial processes, such as geologic CO 2 storage.

58 GEOSCIENCES↗

High-resolution multicontrast tomography with an X-ray microarray anode–structured target source

Multicontrast X-ray imaging with high resolution and sensitivity using Talbot–Lau interferometry (TLI) offers unique imaging capabilities that are important to a wide range of applications, including the study of morphological features with different physical properties in biological specimens. The conventional X-ray TLI approach relies on an absorption grating to create an array of micrometer-sized X-ray sources, posing numerous limitations, including technical challenges associated with grating fabrication for high-energy operations. We overcome these limitations by developing a TLI system with a microarray anode–structured target (MAAST) source. The MAAST features an array of precisely controlled microstructured metal inserts embedded in a diamond substrate. Using this TLI system, tomography of a Drum fish tooth with high resolution and tri-contrast (absorption, phase, and scattering) reveals useful complementary structural information that is inaccessible otherwise. The results highlight the exceptional capability of high-resolution multicontrast X-ray tomography empowered by the MAAST-based TLI method in biomedical applications.

47 OTHER INSTRUMENTATION↗

Generative adversarial networks for scintillation signal simulation in EXO-200

Generative Adversarial Networks trained on samples of simulated or actual events have been proposed as a way of generating large simulated datasets at a reduced computational cost. In this work, a novel approach to perform the simulation of photodetector signals from the time projection chamber of the EXO-200 experiment is demonstrated. The method is based on a Wasserstein Generative Adversarial Network — a deep learning technique allowing for implicit non-parametric estimation of the population distribution for a given set of objects. Our network is trained on real calibration data using raw scintillation waveforms as input. We find that it is able to produce high-quality simulated waveforms an order of magnitude faster than the traditional simulation approach and, importantly, generalize from the training sample and discern salient high-level features of the data. In particular, the network correctly deduces position dependency of scintillation light response in the detector and correctly recognizes dead photodetector channels. Furthermore, the network output is then integrated into the EXO-200 analysis framework to show that the standard EXO-200 reconstruction routine processes the simulated waveforms to produce energy distributions comparable to that of real waveforms. Finally, the remaining discrepancies and potential ways to improve the approach further are highlighted.

47 OTHER INSTRUMENTATION↗

Beyond fragmented dopant dynamics in quantum spin lattices: Robust localization and non-Gaussian diffusion

The motion of dopants in magnetic spin lattices has received tremendous attention for at least four decades due to its connection to high-temperature superconductivity. Despite these efforts, we lack a complete understanding of their behavior, especially out of the equilibrium and at nonzero temperatures. In this paper, we take a significant step towards a much deeper understanding based on state-of-the-art matrix-product-state calculations. In particular, we investigate the nonequilibrium dynamics of a dopant in two-leg 𝑡−𝐽 ladders with antiferromagnetic XXZ spin interactions. In the Ising limit, we find that the dopant is localized for all investigated nonzero temperatures due to an emergent disordered potential, with a localization length controlled by the underlying correlation length of the spin lattice, which increases exponentially with decreasing temperature. The dopant, hereby, only delocalizes asymptotically in the zero temperature limit. This greatly generalizes the localization effect discovered recently in Hilbert space fragmented models [Phys. Rev. Res. 6, 023325 (2024), SciPost Phys. Core 7, 054 (2024)]. In the presence of spin-exchange processes at rate 𝛼, the dopant diffuses with a diffusion coefficient, 𝐷 ℎ , depending nonmonotonically on 𝛼. It initially increases linearly as 𝐷 ℎ ∝ 𝛼 for 𝛼 ≪ 1 before dropping off as 𝛼 −1 for 𝛼 > 1. Moreover, we show that the underlying spin dynamics at infinite temperature behaves qualitatively the same, albeit with important quantitative differences. We substantiate these findings by showing that the dynamics features self-similar scaling behavior, which strongly deviates from the Gaussian behavior of regular diffusion, especially for weak spin exchange. Finally, we show that the diffusion coefficient 𝐷 ℎ follows an Arrhenius relation at high temperatures, whereby it is exponentially suppressed upon cooling.

Anomalous diffusion↗

Fundamental aspects of Spacetime and Quantum Fields

The proposal contained two goals: firstly, placing fundamental bound on thermalization in Quantum Field Theories (QFTs) and, secondly, developing our understanding of emergent spacetime from matrices through concrete models. Since the previous reporting period, in collaboration with Sean Hartnoll we have continued our study of entanglement edge modes in matrix quantum mechanics (MQM). This has resulted in two papers. The first applies our construction for the Matrix Quantum Hall system first to fuzzy sphere states known to correspond to stringy M2-branes in MQM. Entanglement in these states using machine learning methods have also been studied by Sean Hartnoll and Xizhi Han in previous work done under this grant. Our construction builds on this work, and further demonstrates how area laws on fuzzy geometries emerge from strongly coupled systems. The second paper generalizes this construction to all noncommutative geometries with curvature much larger than the noncommutativity parameter. We demonstrate that despite UV/IR mixing effects, the structure of entanglement edge mode irreducible representations is determined by the boundary area of subsystems. On manifolds without global symmetries, we have demonstrated that nonlocal effects inherent to noncommutative geometries resum into a change of frame of the metric structure, similar to the change from string frame to Einstein frame for entanglement entropies calculated in string theory. These advancements lay the groundwork for future progress in the understanding of emergent geometry from large-N theories. Using these techniques, we are currently working on applying our methods to noncom mutative geometries whose construction is not so well understood, such as the fuzzy 5-sphere. Despite their opacity these objects are quite important, as string physics in the bulk of holographic systems bears many features of noncommutative geometry. We have also laid the groundwork of applying our methods to tensor networks, one of the most powerful models for understanding how geometry emerges from entanglement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Large-scale Structure of the Heliospheric Current Sheets within the Heliosheath Inferred from Voyager 2 Observations

In this paper, we conducted an analysis of the heliospheric current sheets (HCSs) in the heliosheath (HS), utilizing observations by Voyager 2 between 2008 and 2018. Employing rigorous criteria, we identified a total of 34 HCSs that indicate significant changes in magnetic polarity. These occurrences were more prevalent during solar maximum periods when the HCS expanded to higher latitudes, coinciding with the spacecraft positioned at an average latitude of –31° from the solar equator. We determined certain features of the large-scale structures of the identified HCSs. Most importantly, employing two distinct methods indicates that the thickness of the HCSs within the HS ranges from ~0.003 to ~0.4 au with an average thickness of ~0.03 to ~0.1 au, depending on methods of event selection and fitting techniques. This thickness surpasses that known near 1 au or other heliospheric distances. It is also notably thicker than the typical proton inertial length, implying unfavorable conditions for magnetic reconnection. Additionally, our analysis reveals a frequent tilt of HCS planes relative to the solar equatorial plane by a varying angle up to several tens of degrees, likely implying a common occurrence of a warped structure of the HCS within the HS. Longitudinally, the HCS planes closely align with the Parker spiral field direction expected in the HS. Finally, for a large fraction of the identified HCS events, the HCS planes are likely characterized by a rotational discontinuity. These findings are valid within the limits of the 1 hr resolution data used in this study.

79 ASTRONOMY AND ASTROPHYSICS↗

Nimbus 3 and 4 Observations of Snow Cover and Other Hydrological Features in the Western Himalayas

Photographs from the Nimbus 3 and 4 image dissector camera systems and high resolution infrared radiometers illustrate and demonstrate their applicability in observing snow cover and other hydrological features. This collection of imagery shows the relative merits of daily observations of these features in the visible, near infrared, and far infrared portions of the electromagnetic spectrum with sensors having nominal spatial resolutions between 4 and 8 kilometers. Particular emphasis has been placed on observing features associated with the Indus River because of the economic and social importance of this in the lives of millions of people. The overall results clearly indicate that it is feasible to monitor quantitatively the extent of the snow cover over the Indus River watershed during a given year and from one year to another using meteorological satellite imagery.

Salomonson, V. V.↗

Modes of emplacement of basalt terrains and an analysis of mare volcanism in the Orientale Basin

Three distinctive types of basalt terrains can be recognized on earth on the basis of surface morphology: flood basalts, shield basalts, and plains basalts, each of which reflects unique styles of eruption and modes of emplacement. Two of these, flood basalts and plains basalts, appear to be important in the emplacement of mare basalts on the moon. Using surface features as identifying criteria, mare units in the Orientale Basin were examined and the following emplacement sequence was derived: (1) initial emplacement of impact melt in the basin center, (2) eruption of flood-type basalts in the basin center and approximately concurrent emplacement of plains type basalts in Lacus Veris, and (3) emplacement of plains type basalts in Lacus Autumni

Greeley, R.↗

Observations of the 51.8 micron (O III) emission line in Orion

The 51.8 micron fine structure transition P2:3P2 3P1 for doubly ionized oxygen was observed in the Orion nebula. The observed line strength is of 5 plus or minus 3 times 10 to the minus 15th power watt/sq cm is in good agreement with theoretical predictions. Observations are consistent with the newly predicted 51.8 micron line position. The line lies close to an atmospheric water vapor feature at 51.7 micron, but is sufficiently distant so that corrections for this feature are straightforward. Observations of the 51.8 (O III) line are particularly important since the previously discovered 88 micron line from the same ion also is strong. This pair of lines should, therefore, yield new data about densities in observed H II regions; or else, if density data already are available from radio or other observations, the lines can be used to determine the differential dust absorption between 52 and 88 micron in front of heavily obscured regions.

Melnick, G.↗

Airglow from the inner comas of comets

The intensities of radiation from the inner comas of comets which are composed primarily of water and carbon monoxide have been calculated. Only 'airglow' emissions initiated by the absorption of EUV radiation have been considered. The photoionizations of H2O, CO, CO2, and N2 are the most important emission sources, although photoelectron excitation is also considered. Among the emission features for which intensities were calculated are H2O(+), CO(+) (first negative), CO (fourth positive), CO (Cameron), CO2(+), N2 (Vegard-Kaplan), N2(+) (first negative), and O I (1304 A). In the inner coma (collision region) these airglow mechanisms are shown to be possible competitors with the usually assumed resonance-scattering and fluorescence-excitation mechanisms appropriate for the outer coma and tail.

Cravens, T. E.↗

A comparative study on synthetic aperture radar and optical imagery of ocean waves

The ocean imaging capability of synthetic aperture radar (SAR) is examined in terms of an intercomparison between simultaneous, spatially collocated images of a coastal ocean scene, as recorded by aerial photography and aircraft-borne SAR. Based on a detailed study of these images, this paper examines various local features of oceanographic interest as they are imaged by the two methods. This provides information not available in the usual comparisons of normalized SAR and single point buoy spectra. In addition, aspects of the intensity wavenumber spectra of the two images are examined and discussed. An interesting and surprising conclusion arising from the comparison study is the ability of the SAR to image accurately non-uniform (possibly nonlinear) wave features which are imaged by the aerial photography. This result should have important implications on the development of SAR imaging models and the interpretation of the effect of ocean surface motion on the SAR images.

Banner, M. L.↗

X-ray emission from cataclysmic variables

X-ray observations of cataclysmic variables and theoretical work on X-ray emission from them are reviewed, emphasizing recent developments. Observations of luminosities and space densities, X-ray spectra and temporal behavior, and X-ray emitting cataclysmic variables in globular clusters are addressed. The relationship of disk and radial accretion to X-ray emission is qualitatively considered, and the spectra and correlation between spectral temperature and luminosity are examined for magnetic and nonmagnetic stars. The relationship between ionization structure and line features is summarized, and nuclear burning and electron conduction are briefly addressed. Important issues concerning X-ray emission from cataclysmic variables are discussed, including magnetic fields, the origin of hard and soft X-rays, the soft X-ray puzzle in AM Her stars, nuclear burning, long-period pulsing sources, cyclotron-dominated sources, high-luminosity sources, and the stability of accretion flow.

Lamb, D. Q.↗

Phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5S ribosomal RNA sequences

The complete nucleotide sequences of 5S ribosomal RNAs from Rhodocyclus gelatinosa, Rhodobacter sphaeroides, and Pseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains. Rhodobacter sphaeroides is specifically related to Paracoccus denitrificans and Rc. gelatinosa is related to Ps. cepacia. These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found in P. denitrificans are present also in the 5S RNA of Rb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of obtaining these new sequences is that it is possible to clarify the phylogenetic origins of the plant mitochondrion. In particular, a close phylogenetic relationship is found between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely, Rb. sphaeroides, P. denitrificans, and Rhodospirillum rubrum.

Villanueva, E.↗

Weight and power savings shaft encoder interfacing techniques for aerospace applications

Many aerospace applications for shaft angle digitizers such as optical shaft encoders require special features that are not usually required on commercial products. Among the most important user considerations are the lowest possible weight and power consumption. A variety of mechanical and electrical interface techniques that have large potential weight and power savings are described. The principles to be presented apply to a wide variety of encoders, ranging from 16 to 22 bit resolution and with diameters from 152 to 380 mm (6 to 15 in.).

Breslow, Donald H.↗

Measuring and modeling the backscattering cross section of a leaf

Leaves are a significant feature of any vegetation canopy, and for remote sensing purposes it is important to develop an effective model for predicting the scattering from a leaf. From measurements of the X band backscattering cross section of a coleus leaf in varying stages of dryness, it is shown that a uniform resistive sheet constitutes such a model for a planar leaf. The scattering is determined by the (complex) resistivity which is, in turn, entirely specified by the gravimetric moisture content of the leaf. Using an available asymptotic expression for the scattering from a rectangular resistive plate which includes, as a special case, a metallic plate whose resistivity is zero, the computed backscattering cross sections for both principal polarizations are found to be in excellent agreement with data measured for rectangular sections of leaves with different moisture contents. If the resistivity is sufficiently large, the asymptotic expressions do not differ significantly from the physical optics ones, and for naturally shaped leaves as well as rectangular sections, the physical optics approximation in conjunction with the resistive sheet model faithfully reproduces the dominant feataures of the scattering patterns under all moisture conditions.

Senior, T. B. A.↗

Run-time implementation issues for real-time embedded Ada

A motivating factor in the development of Ada as the department of defense standard language was the high cost of embedded system software development. It was with embedded system requirements in mind that many of the features of the language were incorporated. Yet it is the designers of embedded systems that seem to comprise the majority of the Ada community dissatisfied with the language. There are a variety of reasons for this dissatisfaction, but many seem to be related in some way to the Ada run-time support system. Some of the areas in which the inconsistencies were found to have the greatest impact on performance from the standpoint of real-time systems are presented. In particular, a large part of the duties of the tasking supervisor are subject to the design decisions of the implementer. These include scheduling, rendezvous, delay processing, and task activation and termination. Some of the more general issues presented include time and space efficiencies, generic expansions, memory management, pragmas, and tracing features. As validated compilers become available for bare computer targets, it is important for a designer to be aware that, at least for many real-time issues, all validated Ada compilers are not created equal.

Maule, Ruth A.↗

Enhancement Of Penetrant-Inspection Images

Proposed computerized video system processes images of fluorescent dyes absorbed in flaws in welds. Video camera, held by operator or by remote manipulator, views weld illuminated by visible white and ultraviolet light. Images of penetrating dye in cracks and voids in weld joint appear on video monitor. Fluorescent features enhanced by software to facilitate identification of true flaws and record important data.

Wilson, Rhonda C.↗