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At least 559 records · Page 31

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗

A CRISPR-Cas9–integrase complex generates precise DNA fragments for genome integration

CRISPR-Cas9 is an RNA-guided DNA endonuclease involved in bacterial adaptive immunity and widely repurposed for genome editing in human cells, animals and plants. In bacteria, RNA molecules that guide Cas9 s activity derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-Cas2 CRISPR integrase. How cells generate the specific lengths of DNA required for integrase capture is a central unanswered question of type II-A CRISPR-based adaptive immunity. Here, we show that an integrase supercomplex comprising guide RNA and the proteins Cas1, Cas2, Csn2 and Cas9 generates precisely trimmed 30-base pair DNA molecules required for genome integration. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming by a mechanism that is independent of the guide RNA sequence. These results show that Cas9 possesses a distinct catalytic capacity for generating immunological memory in prokaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

The MVM imaging system and its spacecraft interactions

The present work describes the main considerations and steps taken in determining the functional design of the imaging system of the Mariner Venus/Mercury (MVM) spacecraft and gives examples of some of the interactions between the spacecraft and the imaging instrument during the design and testing phases. Stringent cost and scheduling constraints dictated the use of the previous Mariner 9 dual-camera TV system. The TV parameters laid the groundwork for the imaging definition. Based on the flyby distances from Venus and Mercury and the goal of surface resolution better than 500 meters per sample pair, calculation was performed on focal length, format size, planetary coverage, and data rates. Some problems encountered in initial mechanical operation and as a result of spacecraft drift during the mission are also discussed.

Vescelus, F. E.↗

Ion-Pair Reorganization Regulates Reactivity in Photoredox Catalysts

Cyclometalated and polypyridyl complexes of d6 metals are promising photoredox catalysts, using light to drive reactions with high kinetic or thermodynamic barriers via the generation of reactive radical intermediates. However, while tuning of their redox potentials, absorption energy, excited-state lifetime and quantum yield are well-known criteria for modifying activity, other factors could be important. Here we show that dynamic ion-pair reorganization controls the reactivity of a photoredox catalyst, [Ir[dF(CF3)ppy]2(dtbpy)]X. Time-resolved dielectric-loss experiments show how counter-ion identity influences excited-state charge distribution, evincing large differences in both the ground- and excited-state dipole moment depending on whether X is a small associating anion (PF6-) that forms a contact-ion pair versus a large one that either dissociates or forms a solvent-separated pair (BArF4-). These differences correlate with the reactivity of the photocatalyst toward both reductive and oxidative electron transfer, amounting to a 4-fold change in selectivity toward oxidation versus reduction. These results suggest that ion pairing could be an underappreciated factor that modulates reactivity in ionic photoredox catalysts.

catalysis↗

Impact of the adhesion-force lever-arm “a” on the Rock ‘n’ Roll resuspension model and how to compute it from contact mechanics

The paper proposes a methodology to fill a gap in the context of mechanistic particle resuspension models related to the adhesion and lift force lever arms ( a ): to date, only one experimental observation exists from a centrifuge experiment with a specific particle/surface pair which found r P / a = 100 and assumed that the contact points were symmetric with respect to the particle center. However, the Reeks and Hall’s (2001) model is highly sensitive to this parameter, which therefore cannot be used as-is for different particle diameters or materials. This paper proposes a methodology to compute the adhesion and lift force lever arms ( a A and a L , respectively) based on Atomic Force Microcopy (AFM) surface roughness measurements and contact mechanics arguments. In practice, a spherical, perfectly smooth particle is brought in contact (computationally) with the measured surface roughness and is then rotated by the point of contact to determine the two or more asperities over which the particle would sit on the surface. A method to compute the asperity radius of curvature is devised to compute the asperity deformation and the correct partitioning of the total deformation between the particle and the asperity is presented. For the glass surface under consideration, the asperity deformation was negligible, i.e., it was below the van der Waals radius, which is the limit of applicability of contact mechanics. The Reeks and Hall’s (2001) model is then extended to account for the joint probability of a A and a L . Significant differences in particle resuspended after a day in common atmospheric conditions are found between the approach that uses the lever-arm distributions or their mean values. Also, important differences are found when comparing the lever-arm distribution and r P / a = 100. Hence, one should be cautious of using r P / a = 100 for surface/particle pairs differing from those in the original study. Finally, limits of applicability of the theories used are presented together with considerations regarding how to extend the method to non-spherical particles and different materials.

42 ENGINEERING↗

Reactive force fields for aqueous and interfacial magnesium carbonate formation

Here we develop Mg/C/O/H ReaxFF parameter sets for two environments: an aqueous force field for magnesium ions in solution and an interfacial force field for minerals and mineral–water interfaces. Since magnesium is highly ionic, we choose to fix the magnesium charge and model its interaction with C/O/H through Coulomb, Lennard-Jones, and Buckingham potentials. We parameterize the forcefields against several crystal structures, including brucite, magnesite, magnesia, magnesium hydride, and magnesium carbide, as well as Mg 2+ water binding energies for the aqueous forcefield. Then, we test the forcefield for other magnesium-containing crystals, solvent separated and contact ion-pairs and single-molecule/multilayer water adsorption energies on mineral surfaces. We also apply the forcefield to the forsterite–water and brucite–water interface that contains a bicarbonate ion. We observe that a long-range proton transfer mechanism deprotonates the bicarbonate ion to carbonate at the interface. Free energy calculations show that carbonate can attach to the magnesium surface with an energy barrier of about 0.22 eV, consistent with the free energy required for aqueous Mg–CO 3 ion pairing. Also, the diffusion constant of the hydroxide ions in the water layers formed on the forsterite surface are shown to be anisotropic and heterogeneous. These findings can help explain the experimentally observed fast nucleation and growth of magnesite at low temperature at the mineral–water–CO 2 interface in water-poor conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superconductivity in multiorbital systems with repulsive interactions: Hund's pairing versus spin-fluctuation pairing

Hund's pairing refers to Cooper pairing generated by onsite interactions that become attractive due to large Hund's exchange J. This is possible in multiorbital systems even when all local bare interactions are repulsive, since attractions in specific channels are given by certain linear combinations of interaction parameters. On the other hand, pairing processes such as the exchange of spin fluctuations are also present. We compare mean-field Hund's pairing and spin-fluctuation-mediated pairing using electronic bands appropriate for different classes of multiorbital systems over a wide range of interaction parameters. We find that, for systems without clear nesting features, the superconducting state generated by the Hund's mechanism agrees well with that from the full fluctuation exchange vertex when Hund's exchange and spin-orbit coupling are sufficiently large. On the other hand, for systems characterized by a peaked finite-momentum particle-hole susceptibility, spin-fluctuation pairing generally dominates over Hund's pairing. From this perspective Hund's pairing states appear unlikely to be realized in systems like Sr 2 RuO 4 and generic iron-based superconductors.

36 MATERIALS SCIENCE↗

Entanglement structures in quantum field theories. II. Distortions of vacuum correlations through the lens of local observers

When observing a quantum field via detectors with access to only the mixed states of spatially separated, local regions—a ubiquitous experimental design—the capacity to access the full extent of distributed entanglement can be limited, shrouded by classical correlations. By performing projective measurements of the field external to two detection patches and classically communicating the results, underlying pure states may be identified for which entanglement quantification is clear. In the Gaussian continuous-variable states of the free scalar field vacuum, this protocol uncovers a disparity between the spacelike entanglement established within the field and that which is locally detectable. Further, this discrepancy is found to grow exponentially with the separation between observation regions. The protocol developed herein offers insight and practical guidance for clarifying the unavoidable distortion of quantum field correlations when viewed from the vantage of a pair of local observers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Initiation of Long-Wave Instability of Vortex Pairs at Cruise Altitudes

Previous studies have usually attributed the initiation of the long-wave instability of a vortex pair to turbulence in the atmosphere or in the wake of the aircraft. The purpose here is to show by use of observations and photographs of condensation trails shed by aircraft at cruise altitudes that another initiating mechanism is not only possible but is usually the mechanism that initiates the long-wave instability at cruise altitudes. The alternate initiating mechanism comes about when engine thrust is robust enough to form an array of circumferential vortices around each jet-engine-exhaust stream. In those cases, initiation begins when the vortex sheet shed by the wing has rolled up into a vortex pair and descended to the vicinity of the inside bottom of the combined shear-layer vortex arrays. It is the in-and-out (up and down) velocity field between sequential circumferential vortices near the bottom of the array that then impresses disturbance waves on the lift-generated vortex pair that initiate the long-wave instability. A time adjustment to the Crow and Bate estimate for vortex linking is then derived for cases when thrust-based linking occurs.

Rossow, Vernon J.↗

Experimental evidence of hole injection through V-defects in long wavelength GaN-based LEDs

Hole injection through V-defect sidewalls into all quantum wells (QWs) of long wavelength GaN light emitting diodes had previously been proposed as means to increase efficiency of these devices. In this work, we directly tested the viability of this injection mechanism by electroluminescence and time-resolved photoluminescence measurements on a device in which QW furthest away from the p-side of the structure was deeper, thus serving as an optical detector for presence of injected electron–hole pairs. Emission from the detector well confirmed that, indeed, the holes were injected into this QW, which could only take place through the {$10\bar{1}1$} V-defect sidewalls. Unlike direct interwell transport by thermionic emission, this transport mechanism allows populating all QWs of a multiple QW structure despite the high potential barriers in the long wavelength InGaN/GaN QWs.

Atomic force microscopy↗

First-principles insights into chromium-induced oxide phases in NiO

The high-temperature oxidation of Ni–Cr alloys leads to complex oxide scales comprising Ni(Cr)O solid solutions, NiCr 2 O 4 spinel, and Cr 2 O 3 corundum within the NiO matrix. Understanding the atomic-scale mechanisms of Cr segregation and precipitate formation is crucial for enhancing oxidation resistance. Here, we employ density functional theory calculations to investigate Cr behavior on NiO(100), (110), and (111) surfaces and in the bulk. Our results reveal that isolated Cr atoms preferentially segregate to the surfaces, stabilizing Ni(Cr)O solid solutions via strong Cr–O bonding, whereas Cr pairs and clusters favor subsurface migration and bulk aggregation, promoting nucleation of NiCr 2 O 4 and Cr 2 O 3 phases. These findings elucidate a size-dependent segregation mechanism linking Cr coordination environments to oxide phase evolution. This atomic-scale insight informs strategies to tailor oxide microstructures and enhance the high-temperature oxidation resistance of Ni–Cr alloys.

Chromium Segregation↗

Actuator mechanism

An actuator mechanism is described, having a frame with a rotatable shaft supported in the frame, a positioning mechanism coupled to the shaft for rotating the shaft in two rotary positions, disposed approximately 180 degrees apart, and a pair of plungers coupled to the shaft. Each plunger is responsive to a control signal for applying bi-directional rotation to the shaft.

Stange, W. C.↗

A mobile work station concept for mechanically aided astronaut assembly of large space trusses

This report presents results of a series of truss assembly tests conducted to evaluate a mobile work station concept intended to mechanically assist astronaut manual assembly of erectable space trusses. The tests involved assembly of a tetrahedral truss beam by a pair of test subjects with and without pressure (space) suits, both in Earth gravity and in simulated zero gravity (neutral buoyancy in water). The beam was assembled from 38 identical graphite-epoxy nestable struts, 5.4 m in length with aluminum quick-attachment structural joints. Struts and joints were designed to closely simulate flight hardware. The assembled beam was approximately 16.5 m long and 4.5 m on each of the four sides of its diamond-shaped cross section. The results show that average in-space assembly rates of approximately 38 seconds per strut can be expected for struts of comparable size. This result is virtually independent of the overall size of the structure being assembled. The mobile work station concept would improve astronaut efficiency for on-orbit manual assembly of truss structures, and also this assembly-line method is highly competitive with other construction methods being considered for large space structures.

Heard, W. L., Jr.↗

Antipodal hotspot pairs on the earth

The results of statistical analyses performed on three published hotspot distributions suggest that significantly more hotspots occur as nearly antipodal pairs than is anticipated from a random distribution, or from their association with geoid highs and divergent plate margins. The observed number of antipodal hotspot pairs depends on the maximum allowable deviation from exact antipodality. At a maximum deviation of not greater than 700 km, 26 to 37 percent of hotspots form antipodal pairs in the published lists examined here, significantly more than would be expected from the general hotspot distribution. Two possible mechanisms that might create such a distribution include: (1) symmetry in the generation of mantle plumes, and (2) melting related to antipodal focusing of seismic energy from large-body impacts.

Rampino, Michael R.↗

The source of the relativistic particles in the galactic center arc

Three fields in the molecular cloud M0.20-0.033, located near the midpoint of the filamentary 'Galactic center arc,' have been imaged in the CS J = 2-1 line with the OVRO millimeter interferometer. Several molecular clumps have been found to coincide with the endpoints of a number of the arc's nonthermal filaments (NTFs), suggesting that the relativistic particles present along the filaments originate in these molecular cloudlets. The most striking correlation involves a clump that is elongated along the direction of a pair of NTFs, and that approximately coincides with both their endpoints. These observations thus provide clues to the particle acceleration mechanism operative in the Galactic center arc: magnetic energy is likely liberated as the ambient field, tangled by the clumps' motions, reconnects in the advancing clumps' leading, externally ionized, surface layers.

Serabyn, E.↗

High-Energy Emission From Millisecond Pulsars

The X-ray and gamma-ray spectrum of rotation-powered millisecond pulsars is investigated in a model for acceleration and pair cascades on open field lines above the polar caps. Although these pulsars have low surface magnetic fields, their short periods allow them to have large magnetospheric potential drops, but the majority do not produce sufficient pairs to completely screen the accelerating electric field. In these sources, the primary and secondary electrons continue to accelerate to high altitude and their Lorentz factors are limited by curvature and synchrotron radiation reaction. The accelerating particles maintain high Lorentz factors and undergo cyclotron resonant absorption of radio emission, that produces and maintains a large pitch angle, resulting in a strong synchrotron component. The resulting spectra consist of several distinct components: curvature radiation from primary electrons dominating from 1 - 100 GeV, synchrotron radiation from primary and secondary electrons dominating up to about 100 MeV, and much weaker inverse-Compton radiation from primary electrons a t 0.1 - 1 TeV. We find that the relative size of these components depends on pulsar period, period derivative, and neutron star mass and radius with the level of the synchrotron component also depending sensitively on the radio emission properties. This model is successful in describing the observed X-ray and gamma-ray spectrum of PSR J0218+4232 as synchrotron radiation, peaking around 100 MeV and extending up to a turnover around several GeV. The predicted curvature radiation components from a number of millisecond pulsars, as well as the collective emission from the millisecond pulsars in globular clusters, should be detectable with AGILE and GLAST. We also discuss a hidden population of X-ray-quiet and radio-quiet millisecond pulsars which have evolved below the pair death line, some of which may be detectable by telescopes sensitive above 1 GeV. Subject headings: pulsars: general - radiation mechanisms: nonthermal - stars: neutron - gamma rays: theory

Harding, Alice K.↗

NASA Tech Briefs, July 2011

Topics covered include: 1) Collaborative Clustering for Sensor Networks; 2) Teleoperated Marsupial Mobile Sensor Platform Pair for Telepresence Insertion Into Challenging Structures; 3) Automated Verification of Spatial Resolution in Remotely Sensed Imagery; 4) Electrical Connector Mechanical Seating Sensor; 5) In Situ Aerosol Detector; 6) Multi-Parameter Aerosol Scattering Sensor; 7) MOSFET Switching Circuit Protects Shape Memory Alloy Actuators; 8) Optimized FPGA Implementation of Multi-Rate FIR Filters Through Thread Decomposition; 9) Circuit for Communication Over Power Lines; 10) High-Efficiency Ka-Band Waveguide Two-Way Asymmetric Power Combiner; 11) 10-100 Gbps Offload NIC for WAN, NLR, and Grid Computing; 12) Pulsed Laser System to Simulate Effects of Cosmic Rays in Semiconductor Devices; 13) Flight Planning in the Cloud; 14) MPS Editor; 15) Object-Oriented Multi Disciplinary Design, Analysis, and Optimization Tool; 16) Cryogenic-Compatible Winchester Connector Mount and Retaining System for Composite Tubes; 17) Development of Position-Sensitive Magnetic Calorimeters for X-Ray Astronomy; 18) Planar Rotary Piezoelectric Motor Using Ultrasonic Horns; 19) Self-Rupturing Hermetic Valve; 20) Explosive Bolt Dual-Initiated from One Side; 21) Dampers for Stationary Labyrinth Seals; 22) Two-Arm Flexible Thermal Strap; 23) Carbon Dioxide Removal via Passive Thermal Approaches; 24) Polymer Electrolyte-Based Ambient Temperature Oxygen Microsensors for Environmental Monitoring; 25) Pressure Shell Approach to Integrated Environmental Protection; 26) Image Quality Indicator for Infrared Inspections; 27) Micro-Slit Collimators for X-Ray/Gamma-Ray Imaging; 28) Scatterometer-Calibrated Stability Verification Method; 29) Test Port for Fiber-Optic-Coupled Laser Altimeter; 30) Phase Retrieval System for Assessing Diamond Turning and Optical Surface Defects; 31) Laser Oscillator Incorporating a Wedged Polarization Rotator and a Porro Prism as Cavity Mirror; 32) Generic, Extensible, Configurable Push-Pull Framework for Large-Scale Science Missions; 33) Dynamic Loads Generation for Multi-Point Vibration Excitation Problems; 34) Optimal Control via Self-Generated Stochasticity; 35) Space-Time Localization of Plasma Turbulence Using Multiple Spacecraft Radio Links; 36) Surface Contact Model for Comets and Asteroids; 37) Dust Mitigation Vehicle; 38) Optical Coating Performance for Heat Reflectors of the JWST-ISIM Electronic Component; 39) SpaceCube Demonstration Platform; 40) Aperture Mask for Unambiguous Parity Determination in Long Wavelength Imagers; 41) Spaceflight Ka-Band High-Rate Radiation-Hard Modulator; 42) Enabling Disabled Persons to Gain Access to Digital Media; 43) Cytometer on a Chip; 44) Principles, Techniques, and Applications of Tissue Microfluidics; and 45) Two-Stage Winch for Kites and Tethered Balloons or Blimps.

Source record↗

Search for Non-resonant Higgs Boson Pair Production in the Four Bottom Quark Decay Channel With the CMS Experiment

This dissertation presents a search for non-resonant Higgs boson pair production, focusing on the four bottom quark decay channel. It explores the gluon fusion and vector boson fusion production mechanisms. The analysis is performed with a dataset of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the CMS detector at the LHC, corresponding to an integrated luminosity of around 138 inverse femtobarns. Innovative techniques in the areas of object identification, event categorization, signal identification, and background modeling are used to maximize the analysis sensitivity. No excess of signal events are observed relative to the background-only expectation, and 95% CL upper limits on the production cross section are set. The observed upper limit on the standard model production cross section is set at 3.6 times the theoretical expectation. At the time of writing this dissertation, it is the most stringent constraint at the LHC from an individual channel. Furthermore, the observed constraint on the coupling modifier of the Higgs boson self-interaction is set between -2.3 and 9.4. The observed constraint on the coupling modifier of the di-vector-boson-di-Higgs-boson interaction is set between -0.1 and 2.2.

Guerrero Ibarra, Guerrero Fernando↗