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At least 19 records

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing

Quantum reference frames from top-down crossed products

All physical observations are made relative to a reference frame, which is a system in its own right. If the system of interest admits a group symmetry, the reference frame observing it must transform commensurately under the group to ensure the covariance of the combined system. We point out that the crossed product is a way to realize quantum reference frames from the bottom-up; adjoining a quantum reference frame and imposing constraints generates a crossed product algebra. We provide a top-down specification of crossed product algebras and show that one cannot obtain inequivalent quantum reference frames using this approach. As a remedy, we define an abstract algebra associated to the system and symmetry group built out of relational crossed product algebras associated with different choices of quantum reference frames. We term this object the G -framed algebra, and show how potentially inequivalent frames are realized within this object. We comment on this algebra’s analog of the classical Gribov problem in gauge theory, its importance in gravity where we show that it is relevant for semiclassical de Sitter and potentially beyond the semiclassical limit, and its utility for understanding the frame dependence of physical notions like observables, density states, and entropies. Published by the American Physical Society 2024

Astronomy & Astrophysics

Servomotor-driven leveling elements for machine tool frame-to-floor alignment

This paper presents the results of aligning the frame to concrete floor of a large 5-axis machine tool by leveling element adjustments using servomotors instead of manual operation. The machine tool leveling elements used in this study are mechanical devices that attach the machine tool frame to the concrete foundation. These leveling elements are also adjustable so that each location along the machine tool can be uniquely adjusted such that the geometric errors of the frame are minimized, and the accuracy of the machine tool is improved. Off-the-shelf servomotors and connection equipment were installed at each of 12 leveling element locations for a precision 5-axis machine tool at Oak Ridge National Laboratory. The servomotors allow a technician to align the machine tool frame remotely, instead of crawling under the machine tool to iteratively manually adjust each of the 12 leveling elements. The open-loop servomotor-leveling element system design is presented in this paper as well as machine tool frame alignment results. The servomotor system significantly reduces leveling element adjustment time, eliminates the need for under-machine access, reduces technician physical strain, and significantly improves the adjustment repeatability.

Honeycutt, Andrew [ORNL]

ECAR-8823 Rev 0 Structural Evaluation of the MARVEL Support Frame in Dry Critical Configuration

The purpose of this ECAR is to structurally evaluate the MARVEL reactor support frame during the dry critical (DryCrit) start-up testing. The ECAR includes evaluation of the DryCrit configuration for tip-over of the frame during a seismic event, floor loading of the frame on the MFC-720 (TREAT) operating floor, stress analysis of the adapter ring, and stress analysis of the frame itself for gravity and seismic loads.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN

Experimental impact of jet fragmentation reference frames at particle colliders

In collider physics, the properties of hadronic jets are often measured as a function of their lab-frame momenta. However, jet fragmentation must occur in a particular rest frame defined by all color-connected particles. Since this frame may not be the lab frame, the fragmentation of a jet depends on the properties of its sibling objects. This non-factorizability of jets has consequences for experimental jet techniques such as jet tagging, boosted boson measurements, and searches for physics Beyond the Standard Model. In this paper, we will describe the effect and show its impact as predicted by simulation.

Fragmentation into hadrons

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame

Electric-field-assisted chemistry has attracted much attention in recent years, particularly in the context of oriented external electric fields for controlling molecular structure and reactivity. Such fields have been explored in a wide range of applications, including switching materials, nanoparticles, controllable catalysts, medicines, and clinical therapies. However, the determination of fixed fields in the laboratory frame becomes ineffective for flexible molecules, as conformational changes can significantly alter the relative orientation between the applied field and molecular structure. In this work, we propose two molecular reference frames─the principal axis frame and the local reference frame─to define oriented electric fields within the molecular framework. These coordinate systems powerfully eliminate ambiguities in the relative orientation between the applied field and the molecule. Analytic nuclear gradients in the presence of external electric fields are derived and implemented, with an initial application to field-dependent geometry optimizations of cis - and trans -formanilide. Analysis of the resulting field-induced equilibrium structures reveals distinct structural responses, validating the accuracy and robustness of the proposed formalism. The analytic gradient framework enables systematic investigations of molecular properties and reactivity under arbitrarily oriented electric fields, opening new opportunities for computational modeling and rational design in electric-field-controlled chemistry.

electric fields

Competing ionization and dissociation: Extension of the energy-dependent frame transformation to the gerade symmetry of H 2

This article solves two major tasks that frequently arise in the theory of electron collisions with a target molecular cation. First, it extends the energy-dependent frame transformation (EDFT) treatment, which is needed to map fixed-nuclei electron-molecule scattering matrices into an energy-dependent laboratory-frame scattering matrix with vibrational channel indices. The EDFT mapping can now be carried out even when the target molecule possesses multiple low-energy potential curves, significantly transcending previous applications. Second, it implements a method to extract the rest of the full laboratory-frame scattering matrix, i.e., the columns and rows describing input and/or output dissociation channels. The treatment is benchmarked in this article against the essentially exact solution of a refined two-dimensional model of the singlet gerade Σ symmetry of H 2 . Our tests demonstrate that the theory accurately maps fixed-nuclei scattering information, of the type provided by existing electron-molecule computer codes, into a laboratory-frame scattering matrix that includes both ionization and dissociation. Furthermore, this treatment can provide a general framework applicable to a broad class of electron collision processes involving diatomic target ions, suitable for an accurate description of challenging processes such as dissociative recombination.

74 ATOMIC AND MOLECULAR PHYSICS

CAD-based Energy & Cost Models Prove Affordable Net Zero Energy Performance for WonderWindows + 24" On-center Framing

Windows are thermally the “weakest link” in the building envelope. Increasing the thermal resistance of windows can make buildings more energy efficient and reduce the cost of electricity needed for conditioning the building. The proper design and placement of framing can also help to reduce the thermal bridging that occurs near the window frame area. This study investigates the energy performance of multi-pane acrylic windows fitting 24" on-center framing. Initial parametric analysis is done for a single zone accessory dwelling unit (ADU). Then, an energy model was developed for three types of wood-framed buildings: townhomes, stacked flats and hotels. A whole building energy simulation is performed for each of these building types in hot-humid Houston, mixed-humid New York, and cold-humid Minneapolis climates. The results show up to a 39% reduction in heating, ventilation, and air-conditioning (HVAC) related electricity consumption for the cold climate compared to the Base case which has window and wall properties based on ASHRAE standard 90.1 2019. In the hot climate, a modest increase in electricity consumption was seen due to an increase in cooling electricity demand. The ADU achieved Net Zero Energy performance in all 3 Climate Zones despite having the highest exterior surface area-to-floor area ratio: the ADU also had the highest PV kW to floor area ratio compared to the other multi-story building types. The townhomes, hotel and stacked flats respectively met 73, 52 and 57 % of electrical use in Houston, 71, 48 and 56 % in New York, and 63, 40 and 53 % in Minneapolis from energy produced by rooftop solar. If 400 W solar panels are used instead of 320 W panel used for energy simulation, it is estimated that in the townhomes, hotel and stacked flats rooftop solar can meet 91, 65 and 71 % of electrical use in Houston; 89, 60 and 70% in New York, and 79, 50 and 66 % in Minneapolis. A preliminary evaluation of cost shows that such superior performance can potentially be achieved at less first cost with this 24"on-center solution than conventional construction. All the building types at the three locations used for simulation had net energy use intensity under 20 kBtu/sf/year with 320 W solar panel and under 17 kBtu/sf/year with 400 W solar panel. Further tailoring of building envelope R-values and window solar heat gain to particular Climate Zone locations for each building type shows promise in reducing the HVAC electricity use that comprises almost half of building energy use.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Model Development for the ACME Lab Modular Wall and A-Frame Assemblies

The structural frame used for conducting large structural tests was replaced by the ACME (Applied Combined Mechanical Environments) Lab in Building 860 of Sandia National Laboratories in Albuquerque, NM. This new design required simulation and analysis to verify maximum loads and corresponding factors of safety. Two major assemblies which are part of the ACME Lab, the Modular Wall and A-Frame, were designed to operate with a multitude of components in various configurations and with varying loads. Simulations of the Modular Wall and A-Frame structures were performed through explicit analysis to determine safety factors for numerous loading scenarios. The Modular Wall had safety factors of 1.1 for the lateral, diagonal, and gusset loading conditions. The A-Frame had safety factors of 2 for all loading conditions simulated.

42 ENGINEERING

1016516285-AA - Handling Frame Assembly Table Structural and Seismic Analysis

Within the NIF (National Ignition Facility) sustainment project, LLNL is replacing all 1,728 blast shields with new ones. Before the new blast shield glass can be installed on NIF, it must pass through the AMOL (Amplifier Main Optics Loop). The AMOL process involves cleaning and coating the glass, assembling it into a Line Replaceable Unit (LRU), and performing testing and inspection. This work will be conducted in the OPFX cleanroom facility (Building 391, Room 1250) and requires several pieces of custom equipment. One key piece of equipment within the loop is the Handling Frame Assembly Table (see Figure 1.1). Its purpose is to assist operators in installing the blast shield glass into handling frames (1014442709) (see Figure 1.2). The table is also used to store handling frame assembly components. The primary components stored are the L-frames (1015208271), which are kept in a drawer underneath the table (see Figure 1.3). The purpose of this safety note is to ensure that the system does not pose a risk of injury to personnel during a seismic event. The system owner is OMST Engineering & Maintenance.

42 ENGINEERING

A computational investigation of high-flux, plate-and-frame membrane modules for industrial carbon capture

In this work, we study the application of membrane-based separation systems for carbon capture, considering plate-and-frame membrane modules. The successful deployment of membrane CO 2 capture system relies on high-performing membranes as well as effective membrane modules that can fully exploit the developed membranes. A plate-and-frame membrane module is especially attractive for CO 2 capture from industrial flue gas due to its lower pressure drop compared to its counterparts such as spiral wound modules and hollow fiber modules. To design better plate-and-frame modules, we investigate their basic unit - a single membrane stack through a combination of computational modeling and experimental investigations. The modeling approach is based on Computational Fluid Dynamics (CFD) to represent a multiphysics problem, including the fluid flow and diffusion processes within a membrane module. We use experimental data collected under different operating conditions to validate the CFD model. Numerical results suggest a good agreement between experiments and model outputs for the CO 2 recovery, CO 2 mole fraction in the retentate and permeate, and stage-cut. The CFD model is able to predict accurately the flow behavior, providing valuable insights on the effects of fluid dynamics on mass transfer of CO 2 . We also carry out a sensitivity analysis to identify the effect of key parameters on the CO 2 recovery and the CO 2 purity of the outlet streams.

CFD simulation

CFD modeling of high-flux plate-and-frame membrane modules for industrial carbon capture

In this work, we study the application of membrane-based separation systems for carbon capture, considering plate-and-frame membrane modules. The successful deployment of membrane CO2 capture system relies on high-performing membranes as well as effective membrane modules that can fully exploit the developed membranes. A plate-and-frame membrane module is especially attractive for CO2 capture from industrial flue gas due to its lower pressure drop compared to its counterparts such as spiral wound modules and hollow fiber modules. To design better plate-and-frame modules, we investigate their basic unit - a single membrane stack through a combination of computational modeling and experimental investigations. The modeling approach is based on Computational Fluid Dynamics (CFD) to represent a multiphysics problem, including the fluid flow and diffusion processes within a membrane module. We use experimental data collected under different operating conditions to validate the CFD model. Numerical results suggest a good agreement between experiments and model outputs for the CO2 recovery, CO2 mole fraction in the retentate and permeate, and stage-cut. The CFD model is able to predict accurately the flow behavior, providing valuable insights on the effects of fluid dynamics on mass transfer of CO2. We also carry out a sensitivity analysis to identify the effect of key parameters on the CO2 recovery and the CO2 purity of the outlet streams.

Dosso, Cheick

A Material Frame: Hard Recoils from Slow Force Carriers

We modify the Standard Model by making the longitudinal component of the photon physical, propagating with small speed $c_L \ll 1$. This modification breaks gauge invariance and Lorentz symmetry, defining a preferred reference frame. No new fields or scales are introduced, and the photon mass is protected by a Galilean higher-form symmetry. The theory has a smooth $c_L\to0$ limit: the new modes decouple from standard matter and ordinary gauge theory predictions are recovered. Experimental constraints are severe. Charged particles Cherenkov-emit these slow modes, experiencing hard recoils against the preferred frame. The recoil rate decreases with $c_L$, but the momentum transfer remains of the order of the particle's momentum. Dark matter detectors, sensitive to keV-scale nuclear recoils, imply an order-of-magnitude bound $c_L \lesssim 10^{-60}$, tens of orders of magnitude stronger than speed-difference bounds. At such values, $c_L$ is better understood as a recoil-rate factor rather than a physically relevant speed. The slow modes, practically fixed in space, make the reference frame a material medium capable of absorbing momentum from charged particles.

Serra, Francesco [Johns Hopkins U.]

Data reduction for low energy nuclear physics experiments using data frames

Low energy nuclear physics experiments are transitioning towards fully digital data acquisition systems. Realizing the gains in flexibility afforded by these systems relies on equally flexible data reduction techniques. In this paper, methods utilizing data frames and in-memory techniques to work with data, including data from self-triggering, digital data acquisition systems, are discussed within the context of a Python package, sauce. It is shown that data frame operations can encompass common analysis needs and allow interactive data analysis. Two event building techniques, dubbed referenced and referenceless event building, are shown to provide a means to transform raw list mode data into correlated multi-detector events. These techniques are demonstrated in the analysis of two example data sets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Multi-frame x-ray radiography and image tracking for quantification of expansion in laser-driven tin ejecta microjets

One regime of experimental particle-laden flow study involves ejecta microjets—often defined as a stream of micrometer-scale particles generated through shock interaction with a non-uniform surface and generally travel above 1 km/s. In order to capture the change in characteristics as a function of propagation time, we apply a multi-frame x-ray radiography platform to observe and track the jet transport dynamics. A synchrotron x-ray source allows us to perform quantitative analyses and comparisons between the eight images captured by the imaging system. Observation of a single jet through time allows the use of a cross correlation algorithm to independently track various regions within the jet and quantify the jet expansion over time using normalized area and normalized areal density values. Through a comparison with the calculated values of ballistic transport, these findings show less expansion than expected for ballistically transporting particles. In conclusion, this work combines multi-frame synchrotron radiography with image tracking to establish a foundation for future studies on jet transport and particle interaction dynamics.

Sun, Yuchen [Lawrence Livermore National Laborator

The polarized-signal density matrix: A practical way to recover molecular frame information from isotropic samples

We present a novel approach to model ultrafast time-dependent nonlinear optical polarization sensitive signals emitted from randomly oriented molecules. By projecting the laboratory-frame analyzer polarization axis into the molecular-frame and linking that axis with the density matrix through a tensor product, we demonstrate an approach to find a specific molecular orientation that yields a good approximation to simulated four-wave mixing signals produced by the same model but with averaging over molecular orientation.

Thurston, Richard L

Comment on “Nonlocal nucleon matrix elements in the rest frame”

In a recent paper, “Nonlocal nucleon matrix elements in the rest frame” [1], it was observed that the next-to-leading order calculations of the renormalization factor can describe, to a few percent accuracy, the logarithm of the lattice quantum chromodynamics (QCD) rest frame matrix elements with separations up to distances of 0.6 fm on multiple lattice spacings. We argue that perturbative QCD breaks down at such a distance scale after resumming the associated large logarithms, while the Ansatz used in the analysis there is not justified in perturbation theory. Besides, we explain the observation in Ref. [1] and demonstrate that the Ansatz fails to describe the data for 𝑧 > 0.3 fm, showing an opposite trend. Finally, although Ref. [1] proposes multiplying the Ansatz by a Gaussian correction model, which is shown to reduce the discrepancy with the data, this does not legitimize the use of perturbative QCD at such distance scales.

Lattice QCD

Unified and optimal frame choice for generalized parton distributions

Reconstructing the internal three-dimensional quark and gluon structures of hadrons through generalized parton distributions (GPDs) from hard exclusive scattering processes is one of the most challenging tasks in nuclear and particle physics. In this paper, we introduce a new optimized reference frame that, for the first time, enables a unified view of all the reactions sensitive to GPDs and facilitates the interpretation of a variety of phase-space patterns that were previously hardly accessible and interpretable. Similarly to how the heliocentric description advanced our understanding of the solar system and gravitation, our new frame centers around a quasireal state, allows for a consistent separation of physical scales, and reveals a novel quantum interference mechanism. Published by the American Physical Society 2025

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC