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At least 505 records · Page 28

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DOE OSTI2024

Insights into posttranslational regulation of skeletal muscle contractile function by the acetyltransferases, p300 and CBP

Here, mice with skeletal muscle-specific and inducible double knockout of the lysine acetyltransferases, p300 (E1A binding protein p300) and CBP (cAMP-response element-binding protein binding protein), referred to as i-mPCKO, demonstrate a dramatic loss of contractile function in skeletal muscle and ultimately die within 7 days. Given that many proteins involved in ATP generation and cross-bridge cycling are acetylated, we investigated whether these processes are dysregulated in skeletal muscle from i-mPCKO mice and, thus, whether they could underlie the rapid loss of muscle contractile function. Just 4–5 days after inducing knockout of p300 and CBP in skeletal muscle from adult i-mPCKO mice, there was ~90% reduction in ex vivo contractile function in the extensor digitorum longus (EDL) and a ~65% reduction in in vivo ankle dorsiflexion torque, as compared with wild type (WT; i.e., Cre negative) littermates. Despite this profound loss of contractile force in i-mPCKO mice, there were no genotype-driven differences in fatigability during repeated contractions, nor were there genotype differences in mitochondrial-specific pathway enrichment of the proteome, intermyofibrillar mitochondrial volume, or mitochondrial respiratory function. As it relates to cross-bridge cycling, remarkably, the overt loss of contractile function in i-mPCKO muscle was reversed in permeabilized fibers supplied with exogenous Ca 2+ and ATP, with active tension being similar between i-mPCKO and WT mice, regardless of Ca 2+ concentration. Actin-myosin motility was also similar in skeletal muscle from i-mPCKO and WT mice. In conclusion, neither mitochondrial abundance/function, nor actomyosin cross-bridge cycling, are the underlying driver of contractile dysfunction in i-mPCKO mice.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Logical Activation Functions v.1.1

SAND2024-01501O Logical Activation Functions software is a PyTorch implementation from the paper, "Logical Activation Functions for Training Arbitrary Probabilistic Boolean Logic." The activation functions approximate logit-space marginalization of probabilistic truth tables from probabilistic interpretations of inputs. They also provide a general methodology to approximate logical relationships between abstract antecedents and consequents for machine learning architectures. They do not target any specific application or use-case. By training probabilistic truth tables, these activation functions can capture more expressive relationships in a neural network than typical elementwise activation functions. This code is only designed for a single compute node with a GPU and is limited to machine learning architectures than can fit within the memory of a single GPU. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Duersch, Jed↗

DOE OSTI2024

Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"

This data package is associated with the publication “A functional microbiome catalog crowdsourced from North American rivers” submitted to Nature (Borton et al., 2024); (https://www.biorxiv.org/content/10.1101/2023.07.22.550117v1). Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices. This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. The Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data were one of many different data types used in establishing the ecological dimensions along which different microbes were detected .This data package only contains the processed FTICR-MS data associated with this manuscript; all other data is accessible via Zenodo (https://zenodo.org/records/8173287), GitHub (https://github.com/jmikayla1991/Genome-Resolved-Open-Watersheds-database-GROWdb), KBase (https://doi.org/10.25982/109073.30/1895615), and NCBI via Bioproject PRJNA946291.This dataset consists of (1) a file-level metadata (flmd) file; (2) a data dictionary (dd) file; (3) a readme; (4) three Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) processed data files (a ‘data’ file containing peak-by-sample observations, a ‘mol’ file containing peak metadata, and a transformation profile containing transformation-by-sample observations). All files are .csv or .pdf.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Refinements to the Graves–Pitarka Kinematic Rupture Generator, Including a Dynamically Consistent Slip-Rate Function, Applied to the 2019 Mw 7.1 Ridgecrest Earthquake

The main objective of this study is to develop physics–based constraints on the spatiotemporal variation of the slip–rate function using a simplified dynamic rupture model. First, we performed dynamic rupture modeling of the 2019 M w 7.1 Ridgecrest, California, earthquake, to analyze the effects of depth–dependent stress and material friction on slip rate. Then, we used our modeling results to guide refinements to the slip–rate function that were implemented in the Graves–Pitarka kinematic rupture generation technique. The dynamic ruptures were computed on a surface–rupturing, planar strike–slip fault that includes a weak (negative to low–stress–drop) zone in the upper 4 km of the crust. Below the weak zone, we placed high–stress–drop patches designed to mirror the large–slip areas seen in various rupture model inversions of the event. The locations of the high–stress–drop patches and the hypocenter were varied in multiple realizations to investigate how changing the dynamic conditions affected the resulting rupture kinematics, in particular, the slip rate. From these simulations, we observed a systematic change in the shape of the slip–rate function from Kostrov type below the weak zone to a predominantly symmetric shape within the weak zone, along with a depth–dependent reduction of peak slip rate. We generalized these shallow rupture features into a depth–dependent parametric variation of the slip–rate function and implemented it in the Graves–Pitarka kinematic rupture model generator. The performance of the updated kinematic approach was then verified in 0–4 Hz simulations of the M w 7.1 Ridgecrest earthquake, which showed that incorporating the depth–dependent variation in the shape of the slip–rate function improves the fit to the observed near–fault ground motions in the 0.5–3 s period range.

58 GEOSCIENCES↗

DOE OSTI2020

Normal modes in thermal AdS via the Selberg zeta function

The heat kernel and quasinormal mode methods of computing 1-loop partition functions of spin s s fields on hyperbolic quotient spacetimes \mathbb{H}^{3}/\mathbb{Z} ℍ 3 / ℤ are related via the Selberg zeta function. We extend that analysis to thermal \text{AdS}_{2n+1} AdS 2 n + 1 backgrounds, with quotient structure \mathbb{H}^{2n+1}/\mathbb{Z} ℍ 2 n + 1 / ℤ . Specifically, we demonstrate the zeros of the Selberg function encode the normal mode frequencies of spin fields upon removal of non-square-integrable modes. With this information we construct the 1-loop partition functions for symmetric transverse traceless tensors in terms of the Selberg zeta function and find exact agreement with the heat kernel method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

ORNL Progress Report on Microreactor Functional Containment Economics

A summary of Oak Ridge National Laboratory’s (ORNL’s) initial contributions to the economic and functional containment evaluation approach for microreactors is presented. A final report will be completed at the end of 2022. This initial progress report does not represent a final product or an expression of a complete technical analysis. Initial contributions from ORNL can be categorized into two parts: (1) description of functional containment as a design optimization tool, and (2) summary of high level technology concepts for an evaluation of economic and functional containment analysis. Additionally, the initial portion of a functional containment evaluation is presented for a generic high temperature gas reactor technology. Remaining tasks include completing the functional containment evaluation by connecting economic and consequence metrics, as well as performing the same effort for other select reactor technologies.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Deep Green: Structural and Functional Genomic Characterization of Conserved Unannotated Green Lineage Proteins

Our overall objective is to improve and increase functional and structural predictions for a growing number of plant proteins of unknown structure and function (the Deep Green proteins), and to make our predictive data useful and accessible to the larger research community. The project is divided into five major objectives which include 1) Assembly and curation of Deep Green candidate protein sets; 2) in silico structural and functional predictions and network analyses; 3) assembly and validation of reverse genetic resources in Chlamydomonas reinhardtii (Chlamydomonas); 4) high throughput functional genomics characterization and prioritization in Chlamydomonas; and 5) structural validation of selected candidates and functional validation in two important reference plant species, Arabidopsis thaliana (Arabidopsis) and Setaria viridis (Setaria).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Stand and environmental conditions drive functional shifts associated with mesophication in eastern US forests

There is a growing body of evidence that mesic tree species are increasing in importance across much of the eastern US. This increase is often observed in tandem with a decrease in the abundance and importance of species considered to be better adapted to disturbance and drier conditions (e.g., Quercus species). Concern over this transition is related to several factors, including the potential that this transition is self-reinforcing (termed “mesophication”), will result in decreased resiliency of forests to a variety of disturbances, and may negatively impact ecosystem functioning, timber value, and wildlife habitat. Evidence for shifts in composition provide broad-scale support for mesophication, but we lack information on the fine-scale factors that drive the associated functional changes. Understanding this variability is particularly important as managers work to develop site-and condition-specific management practices to target stands or portions of the landscape where this transition is occurring or is likely to occur in the future. To address this knowledge gap and identify forests that are most susceptible to mesophication (which we evaluate as a functional shift to less drought or fire tolerant, or more shade tolerant, forests), we used data from the USDA Forest Service Forest Inventory and Analysis program to determine what fine-scale factors impact the rate (change through time) and degree (difference between the overstory and midstory) of change in eastern US forests. We found that mesophication varies along stand and environmental gradients, but this relationship depended on the functional trait examined. For example, shade and drought tolerance suggest mesophication is greatest at sites with more acidic soils, while fire tolerance suggests mesophication increases with soil pH. Mesophication was also generally more pronounced in older stands, stands with more variable diameters, and in wetter sites, but plots categorized as “hydric” were often highly variable. Our results provide evidence that stand-scale conditions impact current and potential future changes in trait conditions and composition across eastern US forests. We provide a starting point for managers looking to prioritize portions of the landscape most at risk and developing treatments to address the compositional and functional changes associated with mesophication.

Woodbridge, Margaret↗

DOE OSTI2024

Structural and functional characterization of IgG- and non-IgG-based T-cell-engaging bispecific antibodies

Bispecific T-cell-engaging antibodies are a growing class of therapeutics with numerous molecules being tested in clinical trials and, currently, seven of them have received market approval. They are structurally complex and function as adaptors to redirect the cytotoxicity of T cells to kill tumor cells. T-cell-engaging bispecific antibodies can be generally divided into two categories: IgG/IgG-like and non-IgG-like formats. Different formats may have different intrinsic potencies and physiochemical properties, and comprehensive studies are needed to gain a better understanding of how the differences in formats impact on structural and functional characteristics. In this study, we designed and generated bispecific T-cell-engaging antibodies with IgG-like (DVD-Ig) and non-IgG (BiTE) formats. Both target the same pair of antigens (EGFR and CD3) to minimize the possible influence of targets on functional characterization. We performed a side-by-side comparison to assess differences in the physiochemical and biological properties of these two bispecific T-cell-engaging antibodies using a variety of breast and ovarian cancer cell-based functional assays to delineate the structural–functional relationships and anti-tumor activities/potency. We found that the Fc portion of T-cell-engaging bispecific antibodies can significantly impact antigen binding activity, potency, and stability in addition to eliciting different mechanisms of action that contribute the killing of cancer cells.

cluster of differentiation 3 (CD3)↗

DOE OSTI2023

The comparison between effects of Taichi and conventional exercise on functional mobility and balance in healthy older adults: a systematic literature review and meta-analysis

Background Taichi is beneficial for functional mobility and balance in older adults. However, such benefits of Taichi when comparing to conventional exercise (CE) are not well understood due to large variance in study protocols and observations. Methods We reviewed publications in five databases. Eligible studies that examined the effects of Taichi on the outcomes of functional mobility and balance in healthy older adults as compared to CE were included. Subgroup analyses compared the effects of different types of CE (e.g., single and multiple-type exercise) and different intervention designs (e.g., Taichi types) on those outcomes (Registration number: CRD42022331956). Results Twelve studies consisting of 2,901 participants were included. Generally, compared to CE, Taichi induced greater improvements in the performance of Timed-Up-and-Go (SMD = −0.18, [−0.33 to −0.03], p = 0.040, I 2 = 59.57%), 50-foot walking (MD = −1.84 s, [−2.62 to −1.07], p < 0.001, I 2 = 0%), one-leg stance with eyes open (MD = 6.00s, [2.97 to 9.02], p < 0.001, I 2 = 83.19%), one-leg stance with eyes closed (MD = 1.65 s, [1.35 to 1.96], p < 0.001, I 2 = 36.2%), and functional reach (SMD = 0.7, [0.32 to 1.08], p < 0.001, I 2 = 86.79%) tests. Subgroup analyses revealed that Taichi with relatively short duration (<20 weeks), low total time (≤24 h), and/or using Yang-style, can induce significantly greater benefits for functional mobility and balance as compared to CE. Uniquely, Taichi only induced significantly greater improvements in Timed-Up-and-Go compared to single- (SMD = −0.40, [−0.55 to −0.24], p < 0.001, I 2 = 6.14%), but not multiple-type exercise. A significant difference between the effects of Taichi was observed on the performance of one-leg stance with eyes open when compared to CE without balance (MD = 3.63 s, [1.02 to 6.24], p = 0.006, I 2 = 74.93%) and CE with balance (MD = 13.90s, [10.32 to 17.48], p < 0.001, I 2 = 6.1%). No other significant difference was shown between the influences of different CE types on the observations. Conclusion Taichi can induce greater improvement in functional mobility and balance in older adults compared to CE in a more efficient fashion, especially compared to single-type CE. Future studies with more rigorous design are needed to confirm the observations here.

Li, Yiting↗

DOE OSTI2021

Recent Trends and Innovation in Additive Manufacturing of Soft Functional Materials

The growing demand for wearable devices, soft robotics, and tissue engineering in recent years has led to an increased effort in the field of soft materials. With the advent of personalized devices, the one-shape-fits-all manufacturing methods may soon no longer be the standard for the rapidly increasing market of soft devices. Recent findings have pushed technology and materials in the area of additive manufacturing (AM) as an alternative fabrication method for soft functional devices, taking geometrical designs and functionality to greater heights. For this reason, this review aims to highlights recent development and advances in AM processable soft materials with self-healing, shape memory, electronic, chromic or any combination of these functional properties. Furthermore, the influence of AM on the mechanical and physical properties on the functionality of these materials is expanded upon. Additionally, advances in soft devices in the fields of soft robotics, biomaterials, sensors, energy harvesters, and optoelectronics are discussed. Lastly, current challenges in AM for soft functional materials and future trends are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Minkowski Functionals of SDSS-III BOSS: Hints of Possible Anisotropy in the Density Field?

We present measurements of the Minkowski functionals extracted from the SDSS-III BOSS catalogs. After defining the Minkowski functionals, we describe how an unbiased reconstruction of these statistics can be obtained from a field with masked regions and survey boundaries, validating our methodology with Gaussian random fields and mock galaxy snapshot data. From the BOSS galaxy data, we generate a set of four density fields in three dimensions corresponding to the northern and southern skies of LOWZ and CMASS catalogs, smoothing over large scales (Gaussian smoothing scale of 35 Mpc) such that the field is perturbatively non-Gaussian. We extract the Minkowski functionals from each data set separately, and measure their shapes and amplitudes by fitting a Hermite polynomial expansion. For the shape parameter of the Minkowski functional curves a0, that is related to the bispectrum of the field, we find that the LOWZ-South data presents a systematically lower value of a 0 = –0.080 ± 0.040 than its northern sky counterpart a 0 = 0.032 ± 0.024. Although the significance of this discrepancy is not very high, it potentially indicates some systematics in the data or that the matter density field exhibits anisotropy at low redshift. By assuming a standard isotropic flat ΛCDM cosmology, the amplitudes of the Minkowski functionals from the combination of northern and southern sky data give the constraints Ω c h 2 n s = 0.110 ± 0.006 and 0.111 ± 0.008 for CMASS and LOWZ, respectively, which is in agreement with the Planck ΛCDM best-fit Ω c h 2 n s = 0.116 ± 0.001.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

On the Stability Analysis of Astrophysical Cooling Functions

To model the temperature evolution of optically thin astrophysical environments at MHD scales, radiative and collisional cooling rates are typically either pretabulated or fit into a functional form and then input into MHD codes as a radiative loss function. Thermal balance requires estimates of the analogous heating rates, which are harder to calculate, and due to uncertainties in the underlying dissipative heating processes these rates are often simply parameterized. The resulting net cooling function defines an equilibrium curve that varies with density and temperature. Such cooling functions can make the gas prone to thermal instability (TI), which will cause departures from equilibrium. There has been no systematic study of thermally unstable parameter space for nonequilibrium states. Motivated by our recent finding that there is a related linear instability, catastrophic cooling instability, that can dominate over TI, here we carry out such a study. We show that Balbus instability criteria for TI can be used to define a critical cooling rate, Λ c , that permits a nonequilibrium analysis of cooling functions through the mapping of TI zones. We furthermore illustrate how thermal conduction modifies the shape of TI zones. Upon applying a Λ c -based stability analysis to coronal loop simulations, we find that loops undergoing periodic episodes of coronal rain formation are linearly unstable to catastrophic cooling instability, while TI is stabilized by thermal conduction.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Weak Form Scientific Machine Learning: Test Function Construction for System Identification

Weak form Scientific Machine Learning (WSciML) is a recently developed framework for data-driven modeling and scientific discovery. It leverages the weak form of equation error residuals to provide enhanced noise robustness in system identification via convolving model equations with test functions, reformulating the problem to avoid direct differentiation of data. The performance, however, relies on wisely choosing a set of compactly supported test functions. In this work, we mathematically motivate a novel data-driven method for constructing Single-scale-Local reference functions for creating the set of test functions. Our approach numerically approximates the integration error introduced by the quadrature and identifies the support size for which the error is minimal, without requiring access to the model parameter values. Through numerical experiments across various models, noise levels, and temporal resolutions, we demonstrate that the selected supports consistently align with regions of minimal parameter estimation error. We also compare the proposed method against the strategy for constructing Multi-scale-Global (and orthogonal) test functions introduced in our prior work, demonstrating the improved computational efficiency.

FOS: Computer and information sciences↗

DOE OSTI2020

Methodology for deriving the telescope focus function and its uncertainty for a heterodyne pulsed Doppler lidar

Doppler lidars provide two measured parameters, radial velocity and signal-to-noise ratio, from which winds and turbulent properties are routinely derived. Attenuated backscatter, which gives quantitative information on aerosols, clouds, and precipitation in the atmosphere, can be used in conjunction with the winds and turbulent properties to create a sophisticated classification of the state of the atmospheric boundary layer. Calculating attenuated backscatter from the signal-to-noise ratio requires accurate knowledge of the telescope focus function, which is usually unavailable. Inaccurate assumptions of the telescope focus function can significantly deform attenuated backscatter profiles, even if the instrument is focused at infinity. Here, we present a methodology for deriving the telescope focus function using a co-located ceilometer for pulsed heterodyne Doppler lidars. The method was tested with Halo Photonics StreamLine and StreamLine XR Doppler lidars but should also be applicable to other pulsed heterodyne Doppler lidar systems. The method derives two parameters of the telescope focus function, the effective beam diameter and the effective focal length of the telescope. Additionally, the method provides uncertainty estimates for the retrieved attenuated backscatter profile arising from uncertainties in deriving the telescope function, together with standard measurement uncertainties from the signal-to-noise ratio. The method is best suited for locations where the absolute difference in aerosol extinction at the ceilometer and Doppler lidar wavelengths is small.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Amidoxime-functionalized materials and their use in extracting metal ions from liquid solutions

A method of producing a functionalized material that extracts metal ions from solution, the method comprising: (i) providing a precursor material having nitrile groups appended to its surface; and (ii) reacting said nitrile groups with hydroxylamine or a derivative thereof in the presence of a polar aprotic solvent at a temperature of 60-80° C. for at least 1 hour, to convert at least a portion of said nitrile groups to amidoxime and imide dioxime groups, followed by reaction with a base capable of hydrolyzing any remaining nitrile groups to carboxylic acid groups; wherein said functionalized material has a higher uranium absorption capacity than a functionalized material produced under same conditions except that the nitrile groups are reacted with hydroxylamine in only a protic solvent. The invention is also directed to functionalized materials produced by the above-described method, and methods for using the functionalized material for extracting metal ions from metal-containing solutions.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Click-chemistry compatible structures, click-chemistry functionalized structures, and materials and methods for making the same

According to various embodiments, systems, methods, and computer program products for click-chemistry compatible structures, additive manufacturing resins for forming the same, and method of formation of such structures and resins, as well as techniques for functionalizing click-chemistry compatible structures are disclosed. The inventive structures generally include a plurality of photo polymerized molecules structurally arranged according to a three-dimensional pattern, while surfaces of the structure are functionalized with one or more click-chemistry compatible molecules each having one or more click-chemistry compatible functional groups. The structures may be formed from single- or dual-component resins, each having unique synthetic pathways. The resulting structures may be functionalized for utility in a wide range of applications by leveraging click chemistry to further functionalize the structure with organic additives also compatible with click-chemistry reaction schemes.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Density functional based methods for light harvesting molecules

The goal of the proposal was to computationally study the photoinduced charge transfer excited states of organic molecules. The systems of interest are the large organic supramolecules that have potential for photovoltaic applications. The simulation of the charge transfer excited states in large supramolecular assemblies require quantum mechanical methods that can be applied to systems with hundreds of atoms. Through this project we have implemented a perturbative delta-self-consistent field method that can easily describe the charge transfer excited states with regular density functionals without range separation. The cost of the calculations of an excited state is similar to that of the ground state. The method also allows for calculation of the energy gradients of the excited state. The developed method was applied to study a number of different supramolecular systems containing hundreds of atoms with excellent agreement with experiment. The absorption characteristics and the influence of density functional approximations were also examined. These led to several studies on the variety of organic electron donor and acceptor molecules. Apart from these developments through this project we also improved the code capabilities by implementing new meta-GGA functionals. This was a major step since the code is purely density functional and earlier the functional capabilities were limited only to generalized gradient approximations. A total of 23 peer-reviewed publications in top chemical physics journals resulted from this grant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗