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At least 217 records · Page 12

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Prior studies have indicated that the transcription factor Creb5 is expressed in the joint interzone, which contains the progenitors for all synovial joint tissues in both mouse and human embryos. In the absence of Creb5 function, most synovial joint interzones fail to form and the cartilage templates in the long bones remain fused. This earlier work did not clarify whether Creb5 initiates a cascade of signaling molecules, such as growth and differentiation factor 5 (Gdf5) and Wnt-family members, that in turn induce the formation of the joint interzone, or instead directly activates the expression of joint interzone markers. In the present study, an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-occupancy in joint progenitors revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of Gdf5 and Sfrp2, each of whose expression in the joint interzone is Creb5-dependent. Functional enhancer analysis indicated that Creb5 binding sites in either the two Creb5 promoters, or in Gdf5 and Sfrp2 regulatory elements are necessary for these sequences to drive transgene expression in the developing synovial joints. While Creb5 directly drives Gdf5 and Sfrp2 expression in the inner joint interzone, Creb5 activates Barx1 expression specifically in the outer joint interzone. Our findings indicate that Creb5 initiates a regulatory network that both promotes the formation of synovial joints, and subsequently activates distinct transcriptional targets in the inner versus the outer regions of the joint interzone, thus regionalizing gene expression in the developing joint.

Zhang, Cheng-Hai↗

Refining the GENEVA method for Higgs boson production via gluon fusion

We describe a number of improvements to the Geneva method for matching NNLO calculations to parton shower programs. In particular, we detail changes to the resummed calculation used in the matching procedure, including disentangling the cross section dependence on factorisation and beam scales, and an improved treatment of timelike logarithms. We also discuss modifications in the implementation of the splitting functions which serve to make the resummed calculation differential in the higher multiplicity phase space. These changes improve the stability of the numerical cancellation of the nonsingular term at small values of the resolution parameter. As a case study, we consider the gluon-initiated Higgs boson production process gg → H. We validate the NNLO accuracy of our predictions against independent calculations, and compare our showered and hadronised results with recent data taken at the ATLAS and CMS experiments in the diphoton decay channel, finding good agreement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulating low-energy neutrino interactions with MARLEY

Monte Carlo event generators are a critical tool for the interpretation of data obtained by neutrino experiments. Several modern event generators are available which are well-suited to the GeV energy scale used in studies of accelerator neutrinos. However, theoretical modeling differences make their immediate application to lower energies difficult. In this paper, I present a new event generator, MARLEY, which is designed to better address the simulation needs of the low-energy (tens of MeV and below) neutrino community. The code is written in C++14 with an optional interface to the popular ROOT data analysis framework. The current release of MARLEY (version 1.2.0) emphasizes simulations of the reaction 40 Ar ( ν e , e − ) 40 K ⁎ but is extensible to other channels with suitable user input. This paper provides detailed documentation of MARLEY's implementation and usage, including guidance on how generated events may be analyzed and how MARLEY may be interfaced with external codes such as Geant4. Further information about MARLEY is available on the official website at http://www.marleygen.org. Program title:MARLEY 1.2.0 CPC Library link to program files:https://doi.org/10.17632/4v7zxnc8j3.1 Developer's respository link:http://github.com/MARLEY-MC/marley Code Ocean capsule:https://codeocean.com/capsule/9868179 Licensing provisions: GNU General Public License 3.0 Programming language: C++14 External routines/libraries used: GNU Scientific Library [1,2] (required), ROOT [3,4] (optional) Nature of problem: Simulation of neutrino-nucleus scattering events at energies of tens-of-MeV and below Solution method: Initial two-to-two scattering kinematics are sampled using the allowed approximation differential cross section and tables of precomputed nuclear matrix elements. Subsequent de-excitations of the remnant nucleus are simulated using a Monte Carlo implementation of the Hauser-Feshbach statistical model and tabulated γ-ray decay schemes for discrete nuclear levels. Additional comments including restrictions and unusual features: Input data are provided with the code that are suitable for producing simulations of the charged-current reaction 40 Ar ( ν e , e − ) 40 K ⁎ , coherent elastic neutrino-nucleus scattering on spin-zero target nuclei, and neutrino-electron elastic scattering on any atomic target. Preparation of new reaction input files (whose format is documented in Appendix B) would enable other reaction channels and nuclear targets to be handled by the existing code framework. Although there is no maximum neutrino energy enforced by the code itself, realistic neutrino-nucleus scattering events may be generated up to roughly 50 MeV. Above this energy, the effects of forbidden nuclear transitions, which are neglected in the current treatment of the cross sections (see section 2.1), become increasingly important.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Loss of Vacuum Condition for IER 479 [Slides]

Conservative thermal transient calculations and simulations show that a loss of vacuum condition would lead to a small (~6 °C) temperature differential across the Jemima Plates. Jemima plates would experience very low thermal stresses, well below the temperature differences of concern (>40 °C).

42 ENGINEERING↗

Kinetic Model of HoxEFU reduction by NADH [SWR-26-087]

This repository is used to release code generated for manuscripts on the Photosynthetic Energy Transduction core program. This code simulates the reduction of HoxEFU by NADH. The electro transfer rate constants for the simulation are specified in the .csv files. The two .csv files correspond tot he two models described in Dawson et al. Cell. Rep. Phys. Sci. 2026. The code utilizes a chemical master equation, a set of differential equations, defining the time evolution of the oxidation and reduction kinetics of NAD+, NADH, a FMN flavin, and a set of iron sulfur clusters. The kinetics of HoxEFU reduction by NADH are evaluated by numerical integration of the chemical master equation using a variable-time-step Runge-Kutta algorithm.

Dahl, Peter [National Laboratory of the Rockies (N↗

Thermal Effects on Far-Field Distributed Acoustic Strain-Rate Sensors

Summary Fiber-optic cables cemented outside of the casing of an unconventional well measure crosswell strain changes during fracturing of neighboring wells with low-frequency distributed acoustic sensing (LF-DAS). As a hydraulic fracture intersects an observation well instrumented with fiber-optic cables, the fracture fluid injected at ambient temperatures can cool a section of the sensing fiber. Often, LF-DAS and distributed temperature sensing (DTS) cables are run in tandem, enabling the detection of such cooling events. The increasing use of LF-DAS for characterizing unconventional hydraulic fracture completions demands an investigation of the effects of temperature on the measured strain response by LF-DAS. Researchers have demonstrated that LF-DAS can be used to extract the temporal derivative of temperature for use as a differential-temperature-gradient sensor. However, differential-temperature-gradient sensing is predicated on the ability to filter strain components out of the optical signal. In this work, beginning with an equation for optical phase shift of LF-DAS signals, a model relating strain, temperature, and optical phase shift is explicitly developed. The formula provides insights into the relative strength of strain and temperature effects on the phase shift. The uncertainty in the strain-rate measurements due to thermal effects is estimated. The relationship can also be used to quantify uncertainties in differential-temperature-gradient sensors due to strain perturbations. Additionally, a workflow is presented to simulate the LF-DAS response accounting for both strain and temperature effects. Hydraulic fracture geometries are generated with a 3D fracture simulator for a multistage unconventional completion. The fracture width distributions are imported by a displacement discontinuity method (DDM) program to compute the strain rates along an observation well. An analytic model is used to approximate the temperature in the fracture. Using the derived formulae for optical phase shift, the model outputs are then used to compute the LF-DAS response at a fiber-optic cable, enabling the generation of waterfall plots including both strain and thermal effects. The model results suggest that before, during, and immediately following a fracture intersecting a well instrumented with fiber, the strain on the fiber drives the LF-DAS signal. However, at later times, as completion fluid cools the observation well, the temperature component of the LF-DAS signal can be equal to or exceed the strain component. The modeled results are compared to a published field case in an attempt to enhance the interpretation of LF-DAS waterfall plots. Finally, we propose a sensing configuration to identify the events when “wet fractures” (fractures with fluids) intersect the observation well.

Engineering↗

Drought adaptation index (DAI) based on BLUP as a selection approach for drought-resilient switchgrass germplasm

This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019–2022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.

BLUP↗

Low Cost Glass-Ceramic Matrix Composite Heat Exchanger

As part of ARPA-E’s High Intensity Thermal Exchange through Materials and Manufacturing Processes (HITEMMP) program, this project sought to develop novel heat exchanger (HX) capabilities to enable efficient and power dense power generation cycles. This class of HX comes under the category of ceramic/composite materials with the higher temperature goal in the program of ≥1100 °C inlet temperature operation. The enabling capability of this effort is the use of glass-ceramic matrix composite (GCMC) material which provides the high temperature durability of a ceramic, the flaw tolerance of a composite, a significantly faster and lower cost manufacturing process than conventional matrix CMCs and very low porosity levels < 0.5%. For thin-walled HX structures and the need to minimize leakage, the low porosity differentiator is particularly important. RTRC has prior experience with this material system and in the current project advanced the component design and manufacturing methods into new territory to produce features required for effective heat exchange under high pressures. In this approach, silicon carbide fiber is fabricated into a fiber preform using various textile processes. Graphite tooling is used both during the build-up of the fiber preform (interior tooling) and after the fiber preform has been completed (exterior tooling). This tooling assembly is heated to high temperature in an environment that has been evacuated and backfilled with inert gas. A reservoir of specialty glass is present and once the desired temperature has been reached to achieve the desired glass viscosity, an actuator distributes the glass throughout the fiber preform using passageways which are part of the tooling design in a process known as glass transfer molding. After the tooling has been removed, the composite is heat treated to convert the amorphous glass to a crystalline ceramic, providing improved properties. The project was divided into three phases focusing on the following: 1) 10 kW HX design and coupon-level tube sheet fabrication, 2) 10 kW HX fabrication, 3) 50 kW HX fabrication. During Budget Period 1 (BP1), additional risks were encountered and the need for additional funds was agreed upon by ARPA-E program leadership. Due to a variety of factors, the contract modification required nominally 18 months to execute at which time the HITEMMP program was effectively concluding. Because of this and the time that would be required to perform BP2 tasks, it was decided to conclude the project at the end of BP1. During the design of the 10 kW HX, manufacturing constraints were learned and incorporated, leading to a revised configuration for the fiber preform and HX. Heat exchange and pressure drop predictions also played a role in modifying the original design concept to be a higher aspect ratio shell-and-tube HX, simplifying the manufacturing process and improving the heat exchanger performance. Good gravimetric and volumetric thermal power densities of 11.2 kW/kg and 10,200 kW/m3 for the entire HX were projected that involved thermo-structural Finite Element Analysis to determine the structural mass needed for the high operation pressures of 250 bar cold inlet and 80 bar hot inlet. Fiber preforms using textile processes were produced for multiple headered tube sheets. Additional challenges were encountered during the glass transfer molding step for which solutions were identified, but programmatics did not allow them to be implemented in BP1. While complete HX test articles were not fabricated, the benefits of this GCMC material for a variety of high temperature applications remain.

30 DIRECT ENERGY CONVERSION↗

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

59 BASIC BIOLOGICAL SCIENCES↗

The soybean β‐expansin gene GmINS1 contributes to nodule development in response to phosphate starvation

Abstract Legume biological nitrogen fixation (BNF) is the most important N source in agricultural ecosystems. Nodule organogenesis from the primordia to the development of mature nodules with the ability to fix N 2 largely determines BNF capacity. However, nodule growth is often limited by low phosphorus (P) availability, while the mechanisms underlying nodule development responses to P deficiency remain largely unknown. In this study, we found that nodule enlargement is severely inhibited by P deficiency, as reflected by the smaller individual nodule size from a soybean core collection in the field. Wide‐ranging natural diversity in nodule size was further identified in soybeans reared in low P soils, with the FC‐1 genotype outperforming FC‐2 in assessments of nodulation under low P conditions. Among β‐expansin members, GmINS1 expression is most abundantly enhanced by P deficiency in FC‐1 nodules, and its transcript level is further displayed to be tightly associated with nodule enlargement. Four single nucleotide polymorphisms discovered in the GmINS1 promoter distinguished the FC‐1 and FC‐2 genotypes and accounted for the differential expression levels of GmINS1 responses to P deficiency. GmINS1 overexpression led to increases in nodule size, infected cell abundance, and N 2 fixation capacity and subsequently promoted increases in N and P content, soybean biomass, and yield. Our findings provide a candidate gene for optimizing BNF capacity responses to low P stress in soybean molecular breeding programs.

Yang, Zhaojun↗

Adsorption of CO on gold: effect of coverage and surface deformations

Recent insights into the nature of catalysts under reactive conditions have motivated investigating heterogeneously catalyzed reactions with non-rigid surfaces. As an example system to revisit, CO interactions with gold have been a longstanding system of interest due to its structure sensitivity. In this work, we investigate coverage-dependent CO adsorption trends on terraces, steps, and kinks. Calculating differential binding energy and mean absolute displacement of the atomic structures as a function of CO coverage, we propose a deformation quenching mechanism that partially determines CO saturation coverage. Extending this analysis to consider CO partial pressure, we show a phase change in CO step occupation, which we highlight as a possible explanation for previously reported temperature-programmed desorption and Fourier-transform infrared reflection-absorption spectroscopy measurements. Furthermore, this work shows how adopting a non-rigid surface model can lead to additional insights which may be applied to other heterogeneously catalyzed systems.

Kavalsky, Lance [University of Wisconsin-Madison, ↗

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES↗

Resolved resonance region evaluations of n+ 206,207,208 Pb for fast spectrum applications

Resolved resonance region evaluations of the major isotopes of natural lead, 206 Pb, 207 Pb, 208 Pb, have been per formed to support the development of Generation IV reactors. In this study, validation of nuclear data for lead fast reactors was performed with simulations of shielding benchmarks, integral critical benchmarks, and quasi-differential scattering measurements. Sensitivity analyses of these systems showed that elastic scattering reactions above 100 keV were the dominant reactions driving system performance. The resolved resonance regions (RRRs) of the lead isotopes extend past 100 keV, making the RRR an ideal starting point to evaluate lead cross sections. Since the R-matrix requires knowledge of bound, distant, and observed resonances, it was necessary to evaluate from 10 -5 eV up to the respective limit of the RRR. The 208 Pb RRR evaluation was extended to 1.5 MeV in order to obtain resonance parameters used to calculate new elastic scattering angular distributions up to 1.5 MeV. Resonance parameter uncertainties and covariance were generated using the R-matrix code SAMMY. The new RRR parameters show a direct improvement to the scattering kernel below 1.5 MeV which in turn greatly improves fast critical experiments over ENDF/B-VIII.0.

206Pb↗

Impact of LHC vector boson production in heavy ion collisions on strange PDFs

Abstract The extraction of the strange quark parton distribution function (PDF) poses a long-standing puzzle. Measurements from neutrino-nucleus deep inelastic scattering (DIS) experiments suggest the strange quark is suppressed compared to the light sea quarks, while recent studies of $$W^\pm /Z$$ W ± / Z boson production at the LHC imply a larger strange component at small x values. As the parton flavor determination in the proton depends on nuclear corrections, e.g. from heavy-target DIS, LHC heavy ion measurements can provide a distinct perspective to help clarify this situation. In this investigation we extend the nCTEQ15 nPDFs to study the impact of the LHC proton-lead $$W^\pm /Z$$ W ± / Z production data on both the flavor differentiation and nuclear corrections. This complementary data set provides new insights on both the LHC $$W^\pm /Z$$ W ± / Z proton analyses and the neutrino-nucleus DIS data. We identify these new nPDFs as nCTEQ15WZ . Our calculations are performed using a new implementation of the nCTEQ code ( nCTEQ++ ) based on C++ which enables us to easily interface to external programs such as HOPPET, APPLgrid and MCFM. Our results indicate that, as suggested by the proton data, the small x nuclear strange sea appears larger than previously expected, even when the normalization of the $$W^{\pm }/Z$$ W ± / Z data is accommodated in the fit. Extending the nCTEQ15 analysis to include LHC $$W^\pm /Z$$ W ± / Z data represents an important step as we advance toward the next generation of nPDFs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

TChem v2.0 - A Software Toolkit for the Analysis of Complex Kinetic Models

TChem is an open source software library for solving complex computational chemistry problems and analyzing detailed chemical kinetic models. The software provides support for: complex kinetic models for gas-phase and surface chemistry; thermodynamic properties based on NASA polynomials; species production/consumption rates; stable time integrator for solving stiff time ordinary differential equations; and, reactor models such as homogenous gas-phase ignition (with analytical Jacobian matrices), continuously stirred tank reactor, plug-flow reactor. This toolkit builds upon earlier versions that were written in C and featured tools for gas-phase chemistry only. The current version of the software was completely refactored in C++, uses an object-oriented programming model, and adopts Kokkos as its portability layer to make it ready for the next generation computing architectures i.e., multi/many core computing platforms with GPU accelerators. We have expanded the range of kinetic models to include surface chemistry and have added examples pertaining to Continuously Stirred Tank Reactors (CSTR) and Plug Flow Reactor (PFR) models to complement the homogenous ignition examples present in the earlier versions. To exploit the massive parallelism available from modern computing platforms, the current software interface is designed to evaluate samples in parallel, which enables large scale parametric studies, e.g. for sensitivity analysis and model calibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ORNL Neutron Cross Section Measurements of 90 Zr NCSP ND-1 Task [Slides]

Luiz Leal's idea to integrate the experimental uncertainties, covariances, and sensitivities in this workflow and centralize the process at one location led to the creation of a cohesive tool for data testing. It has been practiced for more than two decades by the NCS and ND groups at ORNL. The development and use of the ORNL codes TSUNAMI and TSURFER within SCALE made it possible. Today, it has been extended to SAMINT which enables the coupling of differential and integral data evaluation in a continuous-energy framework.

43 PARTICLE ACCELERATORS↗

Spin Diagnostics Using Mott Polarimeter for the EIC Pre-Injector

Polarization measurement and front-end commissioning are critical steps in the EIC preinjector program. We designed a spin-diagnostics beamline at around 4 MeV for front-end commissioning. This paper describes a high-energy Mott polarimeter, including Mott scattering, the Sherman function, and extrapolation toward single elastic scattering in finite-thickness foils. We summarize the key equations used to calculate essential design parameters, including detection time, effective Sherman function, differential cross section, and Mott polarimeter figure of merit. We also present the diagnostics beamline lattice design and kicker design for continuous spin-polarization monitoring. These notes provide concepts, formulas, and methods for diagnostic-beamline design and commissioning measurements.

43 PARTICLE ACCELERATORS↗