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At least 415 records · Page 23

Unraveling the mechanism of recognition of the 3’ splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60

Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML3’). We found that the PUF60–AdML3’ dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60’s two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML3’ revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF60 2 :AdML3’) stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3’ splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3’ splice sites.

59 BASIC BIOLOGICAL SCIENCES↗

Non-routine adjustments – towards standardizing M&V approach for quantifying the effects of static factors

The success of an energy management program relies on ensuring that the energy savings can be verified with an adequate level of certainty. Energy savings cannot be directly measured and hence have to be deduced by comparing the pre-retrofit energy consumption with post-retrofit energy consumption data adjusted to account for differences in conditions. These adjustments are needed, since conditions that influence energy consumption may not stay the same between pre- and postinstallation phase of the project. These adjustments can often be routine when accounting for factors like production volume and weather that are expected to change and are included in the energy consumption adjustment model. Existing measurement and verification (M&V) resources and guidance mostly concentrate on developing models for routine adjustment of one or more factors that normally change. On the other hand, there are factors (static) like product mix, operating hours, gross square area, etc. that are assumed to stay constant during normal conditions. However, in order to adapt to dynamic market conditions, the industries are forced to react thereby leading to changes to these static factors. Identifying these static factors that warrant adjustment, called non-routine event, along with quantifying their effect on energy consumption can be complex and lack of proper guidance can exacerbate this issue. This paper reviews some of the current work in terms of how non-routine events are defined, characterized, detected and quantified based on a review of existing M&V guidelines, protocols and other relevant literature. This work also reviewed some of the existing non-routine events and adjustment practices to understand how these different aspects are addressed along with a discussion on some of the key challenges and gaps in the current guidance.

Earni, Shankar↗

The Nucleon Axial Form Factor and Staggered Lattice QCD

The study of neutrino oscillation physics is a major research goal of the worldwide particle physics program over the upcoming decade. Many new experiments are being built to study the properties of neutrinos and to answer questions about the phenomenon of neutrino oscillation. These experiments need precise theoretical cross sections in order to access fundamental neutrino properties. Neutrino oscillation experiments often use large atomic nuclei as scattering targets, which are challenging for theorists to model. Nuclear models rely on free-nucleon amplitudes as inputs. These amplitudes are constrained by scattering experiments with large nuclear targets that rely on the very same nuclear models. The work in this dissertation is the rst step of a new initiative to isolate and compute elementary amplitudes with theoretical calculations to support the neutrino oscillation experimental program. Here, the eort focuses on computing the axial form factor, which is the largest contributor of systematic error in the primary signal measurement process for neutrino oscillation studies, quasielastic scattering. Two approaches are taken. First, neutrino scattering data on a deuterium target are reanalyzed with a model-independent parametrization of the axial form factor to quantify the present uncertainty in the free-nucleon amplitudes. The uncertainties on the free-nucleon cross section are found to be underestimated by about an order of magnitude compared to the ubiquitous dipole model parametrization. The second approach uses lattice QCD to perform a rst-principles computation of the nucleon axial form factor. The Highly Improved Staggered Quark (HISQ) action is employed for both valence and sea quarks. The results presented in this dissertation are computed at physical pion mass for one lattice spacing. This work presents a computation of the axial form factor at zero momentum transfer, and forms the basis for a computation of the axial form factor momentum dependence with an extrapolation to the continuum limit and a full systematic error budget.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Wake loss and energy spread factor of the LEReC Booster cavity caused by short range wake field

LEReC project uses a DC photoemission gun with multi-alkali (CsK 2 Sb or NaK 2 Sb) cathode [1]. To get 24 mm “flat-top” distribution, 32 Gaussian laser bunches with 0.6 mm rms length are stacked together with 0.75 mm distance [2]. In this case one cannot simply use a 1 cm rms length Gaussian/step/delta bunch for short range wake field simulation since a 0.6 mm bunch contains frequency much higher than the 1 cm bunch. A short range wake field simulation was done using CST Particle Studio™ with 0.6 mm rms Gaussian bunch at the speed of light, and this result was compared with the result for 1 cm rms Gaussian bunch in Figure 1, from where one notice that the wake potential for the 0.6 mm bunch is ~10 times higher than that of the 1 cm bunch. The wake potential of the 0.6 mm bunch, as well as the charge distribution, was then “shift and stack” every 0.75 mm, the normalized results are shown in Figure 2. The wake loss factor (WLF) is the integration of the product of wake potential and normalized bunch charge, and the energy spread factor (ESF) is the rms deviation from the average energy loss. It is calculated by summing the weighted squares of the differences and taking the square root of the sum. These two factors were then divided by β 2 for 1.6 MV beam energy. The wake loss factor is at 0.86 V/pC and energy spread factor is at 0.54 V/pC rms. With 100 pC electron bunch, the energy spread inter-bunch is 54 V rms.

43 PARTICLE ACCELERATORS↗

Analysis Report for Determination of pH Correction Factors for Brines under AP-157 Rev.1

This Analysis Report (AR) documents the determination of pH correction factors for the observed pH readings. The correction factor converts the observed pH reading recorded from the brines used in geochemical studies in support of the Waste Isolation Pilot Plant (WIPP) to a corrected pH value. The data analysis in this AR falls under AP-157 Rev. 1 Analysis Plan for Determination of pH Correction Factors in Brines (Kirkes et al, 2021). Measurement of pH in some solutions can be challenging due to numerous factors such as high ionic strength, elevated or lowered temperature, complex matrix composition, etc. (Knauss et al., 1990; and Rai et al., 1995). The measured pH can be corrected by applying the correction factor, empirically obtained from a specific test solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of National New Construction Weighting Factors for the Commercial Building Prototype Analyses (2008-2022)

The U.S. Department of Energy (DOE) tasked Pacific Northwest National Laboratory (PNNL) with updating commercial building construction weights for the purpose of estimating national and state-by-state energy savings impacts of changes made to various commercial energy codes and standards. A similar activity was last completed by PNNL in 2020 using disaggregate construction volume data acquired from the Dodge Data & Analytics database (formerly McGraw Hill) for the years 2003-2018 (Lei et al, 2020). As time passes, changes in economic and social demand reshape construction volume trends. For the current update, PNNL reviewed the same data source with the latest construction data for the years 2008-2022. For commercial building analyses, PNNL typically uses a suite of 16 prototype buildings simulated in the 19 ASHRAE climate zones with 16 of them present in the United States. The 2008-2022 commercial building weighting factors were derived using the same approach employed to develop the 2003-2018 set (Lei et al, 2020). Applying the construction volume data from the database to the prototypes and climate zones resulted in the following new construction area-based weighting factors. Table ES.1 shows the weighting factors including all building categories found in the database, and Table ES.2 shows the weighting factors normalized to include only buildings represented by the 16 prototypes. Section 3.0 also includes national- and state-level weighting factors by area and building count.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Hydropower Capacity Factor Trends & Analytics for the United States

This data repository contains all code, input data, and data generated for Turner et al. (2024)—“Hydropower capacity factors trending down in the United States”. File descriptions: – hydro-cf-trends-inputs.zip: Full set of input data used in this study, organized for direct entry into “/data” directory of hydro-cf-trends data processing pipeline. – hydro-cf-trends.zip: Full data processing pipeline, coded using the R {targets} framework. This is a snapshot release (v1.0) of the code repository stored at https://code.ornl.gov/turnersw/hydro-cf-trends/. – hydro-cf-trends-results.zip: Provides all dam level results required to reproduce results and graphics in Turner et al. (2024). Dams are identified by the “complxID” (root of the hydropower plant ID in the Existing Hydropower Assets Database, inherited from HILARRI). Results include: • dam_CF_trends.csv: Table of long-term trends in annualized capacity factors for 610 dams and modeled annualized capacity factors for 362 modeled dams (naturalized and assimilated flows). • dam_annualized_CF_gen.csv: Annualized time series of the following variables for each of 610 hydropower dams with nameplate > 5MW – Reported nameplate capacity (MW) – Implied maximum annual generation (MWh) – Reported net generation (MWh) – Computed annual capacity factor – Modeled annual capacity factor (362 modeled plants only)

13 HYDRO ENERGY↗

Evaluating the Bulk Lorentz Factors of Outflow Material: Lessons Learned from the Extremely Energetic Outburst GRB 160625B

GRB 160625B is an extremely bright outburst with well-monitored afterglow emission. The geometry-corrected energy is high, up to ∼5.2 × 10{sup 52} erg or even ∼8 × 10{sup 52} erg, rendering it the most energetic GRB prompt emission recorded so far. We analyzed the time-resolved spectra of the prompt emission and found that in some intervals there were likely thermal-radiation components and the high energy emission was characterized by significant cutoff. The bulk Lorentz factors of the outflow material are estimated accordingly. We found out that the Lorentz factors derived in the thermal-radiation model are consistent with the luminosity-Lorentz factor correlation found in other bursts, as well as in GRB 090902B for the time-resolved thermal-radiation components, while the spectral cutoff model yields much lower Lorentz factors that are in tension with the constraints set by the electron pair Compton scattering process. We then suggest that these spectral cutoffs are more likely related to the particle acceleration process and that one should be careful in estimating the Lorentz factors if the spectrum cuts at a rather low energy (e.g., ∼tens of MeV). The nature of the central engine has also been discussed, and a stellar-mass black hole is favored.

79 ASTRONOMY AND ASTROPHYSICS↗

Downwinding for preserving strong stability in explicit integrating factor Runge-Kutta methods

Here strong stability preserving (SSP) Runge-Kutta methods are desirable when evolving in time problems that have discontinuities or sharp gradients and require nonlinear non-inner-product stability properties to be satisfied. Unlike the case for L 2 linear stability, implicit methods do not significantly alleviate the time-step restriction when the SSP property is needed. For this reason, when handling problems with a linear component that is stiff and a nonlinear component that is not, SSP integrating factor Runge-Kutta methods may offer an attractive alternative to traditional time-stepping methods. The strong stability properties of integrating factor Runge-Kutta methods where the transformed problem is evolved with an explicit SSP Runge-Kutta method with non-decreasing abscissas was recently established. However, these methods typically have smaller SSP coefficients (and therefore a smaller allowable time-step) than the optimal SSP Runge-Kutta methods, which often have some decreasing abscissas. In this work, we consider the use of downwinded spatial operators to preserve the strong stability properties of integrating factor Runge-Kutta methods where the Runge-Kutta method has some decreasing abscissas. We present the SSP theory for this approach and present numerical evidence to show that such an approach is feasible and performs as expected. However, we also show that in some cases the integrating factor approach with explicit SSP Runge-Kutta methods with non-decreasing abscissas performs nearly as well, if not better, than with explicit SSP Runge-Kutta methods with downwinding. In conclusion, while the downwinding approach can be rigorously shown to guarantee the SSP property for a larger timestep, in practice using the integrating factor approach by including downwinding as needed with optimal explicit SSP Runge-Kutta methods does not necessarily provide significant benefit over using explicit SSP Runge-Kutta methods with non-decreasing abscissas.

97 MATHEMATICS AND COMPUTING↗

A New Measurement of the Neutron Electric Form Factor with the Super Bigbite Spectrometer Apparatus

Protons and neutrons, collectively known as nucleons, make up the nuclei at the core of atoms which form our world. The nucleon has been under intensive study for over 100 years, and yet we still do not fully understand the internal dynamics which govern properties like its spin or its mass-which contributes to almost all of the visible mass in the universe. These dynamics are governed by quantum chromodynamics(QCD), the predictions of which are experimentally tested at high energy accelerator facilities such as Jefferson Lab. TheGEN-II experiment (E12-09-016) is one such experiment. GEN-II is part of the Super Bigbite Spectrometer (SBS) experimental form factor pro gramme taking place in Hall A at Jefferson Lab, which aims to make precision measurements of the nucleon electromagnetic form factors(EMFFs)at record high values of squared four momentum transfer ¿2. EMFFs describe the electric and magnetic moment distributions within the nucleon. They can be measured through elastic electron scattering off the nucleon, and describe the recoil response of the target nucleon at a given energy scale. GEN-II is a double polarized semi-exclusive beam target asymmetry (BTA) experiment, seeking to measure the electric form factor of the neutron,¿¿ ¿,at three new values of squared four-momentum transfer¿2 =2.92,6.74and9.82GeV². The latter two points being at record high ¿2. The form factor is determined through measuring the BTA of quasielliptical scattering of a neutron from a polarized nuclear target. The experiment utilized the CEBAF accelerator to produce longitudinally polarized electrons up to ~85% polarization, which were scattered off neutrons within a novel polarized helium-3 (³He) target. This new polarized ³He target was employed by building on the technology of its precursors which existed in similar preceding experiments. This target was designed to operate at the high luminosities typical of Hall A, and reached a record breaking combination of polarization and beam intensity known as figure of merit, three times larger than those predecessors. The SBS collaboration designed and constructed two brand new high acceptance spectrometers for these experiments, an electron arm named Bigbite (BB) and a hadron arm named Super Bigbite. Both spectrometers featured a large acceptance EM dipole magnet, and complementary detector systems. The electron arm contained gaseous electronmultipliers(GEMs) which were used for high precision tracking of the scattered electrons, a heavy gas cherenkov (GRINCH) which was used for PID between electrons and pions, a plastic i ii scintillator timing hodoscope to provide high resolution timing of the start of events, and a pair of EM calorimeters (BBCal) which provided energy measurements of detected particles, and provided the experimental trigger. The hadron arm also contained a system of GEMs which will be utilized for future SBS experiments, and a hadron calorimeter designed to provide position, timing and energy measurements of the recoiling nucleon. The calibration of all detector subsystems, beam and target data is discussed, with a focus on novel timing calibrations to the hodoscope and hadron calorimeter. An analysis of selecting quasielliptical events and suppressing background contributions from a number of sources which contaminate the final event sample is given. The largest irreducible backgrounds are found to be from misidentified protons, timing accidentals and inelastic events. The physical asymmetry is measured and used to extract a value for the form factor ratio ¿¿ ¿/¿¿ ¿. High precision ¿2 data for ¿¿ ¿ is used to then extract ¿¿ ¿. This work finds at ¿2 = 2.92 GeV2 that ¿¿ ¿ = 0.0129+0.0019 -0.0020. This result is in statistical agreement with existing fits to world data, and predictions from the constituent quark model and Dyson–Schwinger equations, in this region of ¿2.

Penman, Gary [Univ. of Glasgow, Scotland (United K↗

Race-Specific Risk Factors for Homeownership Disparity in the Continental United States

The United States has a racial homeownership gap due to a legacy of historic inequality and discriminatory policies, but factors that contribute to the racial disparity in homeownership rates between White Americans and people of color have not been fully characterized. In order to alleviate this issue, policymakers need a better understanding of how risk factors affect the homeownership rates of racial and ethnic groups differently. In this study, data from several publicly available surveys, including the American Community Survey and United States Census, were leveraged in combination with statistical learning models to investigate potential factors related to homeownership rates across racial and ethnic categories, with a focus on how risk factors vary by race or ethnicity. Our models indicated that job availability for specific demographics, and specific regions of the United States were factors that affect homeownership rates in Black, Hispanic, and Asian populations in different ways. Based on the results of this study, it is recommended policymakers promote strategies to increase access to jobs for people of color (POC), such as vocational training and programs to reduce implicit bias in hiring practices. These interventions could ultimately increase homeownership rates for POC and be a step toward reducing the racial wealth gap.

99 GENERAL AND MISCELLANEOUS↗

VIEW: A modification of the RAVFAC view factor program for use with the NASTRAN thermal analyzer

The NASTRAN thermal analyzer will include the capability to perform complete thermal analyses on structures. One of the inputs to NASTRAN required to simulate radiative heat transfer between surfaces will be the view factors (also called shape factors, form factors, configuration factors) between those surfaces. The purpose of the VIEW program is to compute these view factors and produce appropriate RADMTX and RADLST output to be used as NASTRAN bulk data.

Puccinelli, E. F.↗

Collocated interfacial stress intensity factors for finite bi-material plates.

This paper deals with elastic stress intensity factors associated with stress fields near partially debonded interfaces in finite, bi-material plates. Bi-material stress intensity factors K1 and K2 are not associated, respectively, with symmetric and skew-symmetric loading and are functions of an arbitrary length parameter. Any fracture condition involving bi-material stress intensity factors must be independent of the arbitrary length parameter and must be consistent with experiment. We define a new parameter called the interfacial stress intensity factor which satisfies the former condition. A truncated Williams power series stress function for stresses in a cracked bi-material plate, as modified by Sih and Rice, is used with a modified boundary collocation procedure to generate interfacial stress intensity factors for finite bi-material plates.

Sawyer, S. G.↗

Preserving sparseness in multivariate polynominal factorization

Attempts were made to factor these ten polynomials on MACSYMA. However it did not get very far with any of the larger polynomials. At that time, MACSYMA used an algorithm created by Wang and Rothschild. This factoring algorithm was also implemented for the symbolic manipulation system, SCRATCHPAD of IBM. A closer look at this old factoring algorithm revealed three problem areas, each of which contribute to losing sparseness and intermediate expression growth. This study led to effective ways of avoiding these problems and actually to a new factoring algorithm. The three problems are known as the extraneous factor problem, the leading coefficient problem, and the bad zero problem. These problems are examined separately. Their causes and effects are set forth in detail; the ways to avoid or lessen these problems are described.

Wang, P. S.↗

The equatorial total electron content and shape factor

The diurnal variations of electron content and shape factor observed at an equatorial station during sunspot minimum are shown to be consistent with the electron density profiles observed at Jicamarca during sunspot minimum. The rapid increase in electron content and the shape factor at sunrise results from the EUV production of ionization in the E and F regions. Day-to-day variations in daytime electron content are observed to be quite small at the equator. The evening decrease in the shape factor results from an upward drift of the F region at sunset and the evening decay of the E and bottomside F regions. The nighttime peak or plateau in the shape factor is produced by the slow downward drift of the electron density profile. The deep predawn dip in the shape factor is caused by the main peak of the F layer reaching low altitudes where high loss rates cause a large reduction in ionization below 300 km and very flat electron density profile.

Donnelly, R. F.↗

Motor power factor controller with a reduced voltage starter

A power factor type motor controller is disclosed in which the conventional power factor constant voltage command signal is replaced during a starting interval with a graduated control voltage. This continuation-impart of a pending patent application (Serial No. 199, 765: Three Phase Factor Controller) provides a means for modifying the operation of the system for a motor start-up interval of 5 to 30 second. Using a ramp generators, an initial ramp-like signal replaces a constant power factor signal supplied by a potentiometer. The ramp-like signal is applied to a 15 terminal where it is summed with an operating power factor signal from phase detectors in order to obtain a control signal for ultimately controlling SCR devices. The SCR devices are turned on at an advancing rate with time responsive to the combination signal described rather than simply a function of a ramp-like signal alone.

Nola, F. J.↗

ERBS Human Factors Analysis: A Case Study

The incorporation of human factors into the system development process and the benefits derived are discussed. The human factors analysis task for the Earth radiation budget satellite (ERBS) payload operations control center (POCC) is a pathfinder in the new applications approach to this discipline within the mission and data operations directorate. The topics covered include: discussions of the motivation for human factors analysis; the involvement of the human factors research group (HFRG) with project and system developers, and some examples of human factors issues addressed in the ERBS analysis task.

Karen L Moe↗

Dipole-field sums and Lorentz factors for orthorhombic lattices, and implications for polarizable molecules

A method for computing the Lorentz tensor components in single crystals via rapidly convergent sums of Bessels functions is developed using the relationship between dipole-field sums and the tensor components. The Lorentz factors for simple, body-centered, and base-centered orthorhombic lattices are computed using this method, and the derivative Lorentz factors for simple orthorhombic lattices are also determined. Both the Lorentz factors and their derivatives are shown to be very sensitive to a lattice structure. The equivalent of the Clausius-Mossotti relation for general orthorhombic lattices is derived using the Lorentz-factor formalism, and the permanent molecular dipole moment is related to crystal polarization for the case of a ferroelectric of polarizable point dipoles. It is concluded that the polarization enhancement due to self-polarization familiar from classical theory may actually be a reduction in consequences of negative Lorentz factors in one or two lattice directions for noncubic crystals.

Purvis, C. K.↗