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At least 451 records · Page 25

Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model

The most common kind of cancer among women is breast cancer. Understanding the tumor microenvironment and the interactions between individual cells and cytokines assists us in arriving at more effective treatments. Here, we develop a data-driven mathematical model to investigate the dynamics of key cell types and cytokines involved in breast cancer development. We use time-course gene expression profiles of a mouse model to estimate the relative abundance of cells and cytokines. We then employ a least-squares optimization method to evaluate the model’s parameters based on the mice data. The resulting dynamics of the cells and cytokines obtained from the optimal set of parameters exhibit a decent agreement between the data and predictions. We perform a sensitivity analysis to identify the crucial parameters of the model and then perform a local bifurcation on them. The results reveal a strong connection between adipocytes, IL6, and the cancer population, suggesting them as potential targets for therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica

Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.

54 ENVIRONMENTAL SCIENCES↗

Fracture Description of the HFTS-2 Slant Core, Delaware Basin, West Texas

Previous work in the Midland Basin Hydraulic Fracture Test Site project (HFTS1) has shown the value of core recovered from a stimulated volume in providing information on the geometry and extent of hydraulic fractures. This project (HFTS2) is in the Wolfcamp Formation of the Delaware Basin. A slant core through the stimulated volume was acquired above and below a stimulated well and the results of the fracture description are presented here. Here, nine, 3-inch-diameter whole cores from the slant well were examined for fractures prior to slabbing, together with a CT scan of the core. We used criteria developed during the HFTS1 project to identify hydraulic, natural, drilling-induced and core-handling fractures. Material collected from a few fracture faces was cleaned, sieved, and examined under a microscope to look for proppant. A total of 1261 fractures, including 500 hydraulic fractures, were described in 948 feet of core. Hydraulic fractures are not evenly distributed through the cores; they tend to occur in clusters. Many are remarkably planar, smooth, and featureless, while others have twist hackles, steps, plumose, and kinks. Natural, subvertical fractures, mostly less than 1 mm in width, sealed with blocky calcite, are oriented NE-SW (Set 1) and WNW-ESE (Set 2). Two Set 1 fractures have drusy cement on parted faces and were possibly open prior to drilling. A few subvertical sealed fractures with different orientations are also present. Bed-parallel natural fractures, most having fibrous cement (beef), and some showing top-to-north bed-parallel shear are present. Faults with normal/oblique movement were found in one part of the core. Drilling induced and core-handling breaks were identified in all cores, and were also noted to have reactivated some natural fractures. The results from this work will allow hydraulic fracture distribution relative to the stimulated well to be assessed. The number of fractures is generally greater than the number of perforations, but these can be compared for different stages and perforation clusters. Surface features provide information about the direction of hydraulic fracture propagation and about segmentation and bifurcation that might increase the number of fracture strands. Reactivation of natural fractures, including bedding-parallel fractures, occurs although the mechanism of parting is mostly unknown. The wider HFTS2 project will make use of this fracture description to improve hydraulic fracture modeling (geomechanics and engineering), to help explain pressure depletion and fiber optics observations (reservoir depletion and frac geometry), to help verify indirect fracture diagnostic techniques such as microseismic monitoring (geophysics), and to help calibrate horizontal well image logs.

58 GEOSCIENCES↗

Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSCquartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study.

Bjorner, Marianne B.↗

Construction Support for New Slab Creek Powerhouse Project (Final Technical Report)

The Sacramento Municipal Utility District (SMUD) has constructed a new powerhouse and Boating Flow Release Facility (BFRF) ¼ mile downstream of the existing Slab Creek Dam with the assistance of grant funding from the Department of Energy in the amount of $1.5 million. Slab Creek Dam impounds 16,600 acre-feet of storage and has a normal full pool elevation of 1850ft. Water is conveyed from Slab Creek Reservoir through a 4.9 mile power tunnel to the 224 MW White Rock Powerhouse which discharges into Chili Bar Reservoir. A small 450 kW powerhouse located at Slab Creek Dam utilizes the original license in-stream flow requirement. The new license (FERC Project No. 2101-084) requires significantly more instream flows immediately below the dam for aquatic preservation and recreational flows over the original license. The terms of the new license allow the Slab Creek Powerhouse to utilize the original required dam releases, while the new South Fork Powerhouse will use the new instream flow requirements above the original license requirement. The South Fork Powerhouse routes flows back to the South Fork of the American River via a new penstock that is tied into the White Rock Tunnel at Adit #3. This new penstock bifurcates at the Adit #3 portal with one leg going to the BFRF and the other to the new powerhouse. The South Fork Powerhouse is a single generating unit with a capacity of 2.98 kVA. The BFRF is valve house with an energy dissipation chamber for a 60” fixed cone valve capable of passing 1,300 cfs for meeting the recreational flow requirements of the license.

power tunnel↗

Overcoming the Technical Challenges of Coordinating Distributed Load Resources at Scale (Final Report)

Significant recent research has investigated the potential for loads to provide balancing services to the grid. However, this research has not addressed key issues that may arise when such schemes are applied at scale including: 1. Distribution Network Issues. Coordination of large numbers of loads could result in power flows that violate distribution network constraints; 2. Stability Issues. Certain strategies to control loads can exhibit nonlinearity in the form of period-adding bifurcations and chaos. Other control strategies can potentially synchronize the behavior of large numbers of loads. In both cases, the outcome can be power oscillations and instability; 3. Communication Network Issues. Bidirectional low-latency communication channels between a central controller (or several distributed controllers) and each resource are expensive and likely not necessary for effective coordination. Our research questions were: What network, stability, and communication issues might arise in practice when we coordinate large aggregations of loads? How can we coordinate loads to achieve performance objectives in a cost effective manner while avoiding these issues? The ultimate technical goal of the project was the development of network-aware, communication-constrained, non-disruptive load control strategies with stability guarantees that achieve the performance requirements of typical balancing services at a sufficiently low cost to enable the load aggregator and customer to profit. The overall goal was to establish credibility for load control at scale and contribute to U.S. energy security and environmental goals. The team succeeded in answering these research questions and developing these control strategies. The overall approach was based on the development of three testing environments: a simulation testbed, an experimental testbed (20 physical model houses with window-box air conditioners) coupled with the simulation testbed, and a field testbed (100 actual homes in Austin, TX) coupled with the simulation testbed, which enabled controller testing, identification of issues, controller development, and controller validation. The resulting controller was used to demonstrate fast timescale grid balancing (frequency regulation) by aggregations of physical and virtual air conditioners, with sufficient quality to participate in the electricity market. Cost benefit analysis showed overall benefits to the participating households, load aggregators, and the grid, especially if the control technology was integrated directly into existing programmable communicating thermostats. The project provides a variety of wider benefits. Our technology transfer and outreach activities lead us to choose an open-source licensing commercialization pathway, enabling the project results to be available to researchers, industry, and the public. Furthermore, new grid balancing technologies will increase grid flexibility and will enable higher penetrations of intermittent renewable energy resources, such as wind and solar, to be connected to the grid, reducing its environmental impact, and mitigating climate change to the benefit of society.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Biological Electron Transfer and Catalysis EFRC

The focus of the Biological Electron Transfer and Catalysis (BETCy) EFRC research is elucidating mechanisms of conversion of electrochemical potential into chemical bond energy and is organized into two integrated Thrusts: Electron Bifurcation Catalysis and Electron Transfer Kinetics. We are developing a collective knowledge of metalloenzymes as models for redox reactions by applying physical science and computational tools to characterize biochemical reactions catalyzed by multi- subunit enzymes harboring arrays of iron-sulfur clusters and flavin cofactors. Understanding these mechanisms is central to overcoming the thermodynamic barriers that currently limit production of reduced products and fuels. Biological systems have elegant strategies for converting electrochemical potential energy into chemical bond energy (e.g., C-H, H-H, and N-H) stored in reduced compounds that can serve as advanced biofuels. One significant limitation for the production of highly reduced compounds is that their production in natural and industrial processes relies on low oxidation-reduction potential chemicals as feedstocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Supporting Risk-informed Decision-making During Reactor Accidents

Uncertainty in severe accident evolution and outcome is driven by event bifurcations that represent distinctive challenges to defensive layers and tend to promote the emergence of discrete classes of core damage and accident risk. This discrete set of "attractor" states arise from the complex networks of competing physical phenomena and conditional event cascades occurring as the overall system degrades – a process that yields increasing degrees of freedom and accident progression pathways. Characterization of these event spaces has proven elusive to more traditional data interrogation methods, but proves tractable by application of more advanced data collection and machine learning approaches. Through application of these approaches we demonstrate a conceptual framework that enables real-time/robust, risk-informed decision-making support to improve accident mitigation and encourage “graceful exits” during low probability, extreme events limiting accident consequences. In this analysis, we simulated over 8,000 short-term station blackout (STSBO) accidents with the state-of-the-art integral severe accident code, MELCOR, and demonstrate the potential for ML approaches to predict simulation outcomes. We chose to pair ML tools with interpretable and mechanistic event trees for the considered STSBO accident space to predict the likelihood of future event paths along the tree. In addition to the current state of the system, we use information from recent trajectories of temperature, pressure, and other physical features, combining both the current state and past trajectories to forecast future event paths. Finally, we simulate the random injection of variable amounts of water to quantify the efficacy of available actions at reducing risks along the many branches in the event tree. We identify scenarios and windows of opportunity to mitigate risk as well as scenarios in which such actions are unlikely to alter the accident end-state.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Sensitivity Analysis Comparisons on Geologic Case Studies: An International Collaboration, Volume 2

Over the past six years, an informal working group has developed to investigate existing sensitivity analysis methods, examine new methods, and identify best practices. The focus is on the use of sensitivity analysis in case studies involving geologic disposal of spent nuclear fuel or nuclear waste. Three additional case studies are presented in this Volume 2 report, including more nonlinear behavior, outputs which exhibit bifurcation, regime changes, and nested sampling.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Breaking C-C Bonds via Electrochemically Mediated Hydrogen Atom Transfer Reactions

Cleaving inert SP3-SP3 carbon-carbon (C-C) bonds selectively remains a major challenge in organic chemistry and a main bottleneck in the chemical upcycling of recalcitrant polyolefin waste. Here, we present an electrochemical strategy using redox mediators to activate and break C-C bonds at room temperature and ambient pressure. Specifically, we use N-hydroxyphthalimide (NHPI) as a redox mediator that undergoes electrochemical oxidation to form the phthalimide-N-oxyl (PINO) radical to initiate hydrogen atom transfer (HAT) reactions with benzylic C-H bonds. The resulting benzylic carbon radical is readily captured by molecular oxygen to form a peroxy radical that decomposes into oxygenated C-C bond-scission fragments. This indirect, mediated approach for Csp3-Csp3 bond cleavage reduces the oxidation potential by > 1.2 V compared to the direct oxidation of the substrate, thereby eliminating deleterious side reactions, such as solvent oxidation, that may occur at high potentials. Studies with a bibenzyl model compound revealed a bifurcated reaction pathway following the initial HAT step. At a bibenzyl conversion of 61.0%, the C-C bond cleavage pathway generates benzaldehyde and benzoic acid products at 38.4% selectivity, and the C-H bond oxygenation pathway leads to 1,2-diphenylethanone and benzil products at 39.2% selectivity. Changes in reaction selectivity were investigated with various model compounds, including bibenzyl, 1,3-diphe-nylpropane, 1,4-diphenylbutane, and their derivatives. Product selectivity is correlated with the C-C bond strength of the reactant, with weaker C-C bonds favoring the C-C bond cleavage pathway. We also evaluated the mediated oxidation of oligo-meric styrene (Mn= 510 Da, OS510) which were converted into oxygenated products. Lastly, proof-of-concept depolymeriza-tion of polystyrene (PS, ~10,000 Da) into oxygenated monomers, dimers, and oligomers was demonstrated using NHPI-mediated oxidation.

benzoic acid↗

Nonlinear Anti-(Parity-Time) Symmetric Dimer

In the present work we propose a nonlinear anti- P T -symmetric dimer, that at the linear level has been experimentally created in the realm of electric circuit resonators. We find four families of solutions, the so-called upper and lower branches, both in a symmetric and in an asymmetric (symmetry-broken) form. We unveil analytically and confirm numerically the critical thresholds for the existence of such branches and explore the bifurcations (such as saddle-node ones) that delimit their existence, as well as transcritical ones that lead to their potential exchange of stability. We find that out of the four relevant branches, only one, the upper symmetric branch, corresponds to a spectrally and dynamically robust solution. We subsequently leverage detailed direct numerical computations in order to explore the dynamics of the different states, corroborating our spectral analysis results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Impact of Erbium Doping in the Structural and Magnetic Properties of the Anisotropic and Frustrated SrYb 2 O 4 Antiferromagnet

We present a systematic study of the structural and magnetic properties of a series of powder samples of SrYb 2-x Er x O 4 with different Yb/Er concentrations. Magnetometry and neutron diffraction have been used to study the magnetic ground states of the compound series, while inelastic neutron scattering was used to investigate the crystal field excitations for a chosen concentration. These results show that the crystal structure remains the same for all compositions, while the lattice parameters increase linearly with the Er content. All compounds showed some type of magnetic transition below 1 K, however, both the magnetic structure and nature of the phase transition vary throughout the series. The samples present a non-collinear magnetic structure with the moments lying on the ab plane for low Er content. For high Er content, the magnetic structure is collinear with the moments aligned along the c-axis. A critical concentration is found where there is a bifurcation between zero-field and field-cooled magnetic susceptibility. This irreversible process could be due to the random mixture of single-ion magnetic anisotropies.

36 MATERIALS SCIENCE↗

Two Views of the Radius Gap and the Role of Light Curve Fitting

Recently, several groups have resolved a gap that bifurcates planets between the size of Earth and Neptune into two populations. The location and depth of this feature is an important signature of the physical processes that form and sculpt planets. In particular, planets residing in the radius gap are valuable probes of these processes as they may be undergoing the final stages of envelope loss. Here, we discuss two views of the radius gap by Fulton & Petigura (F18) and Van Eylen et al. (V18). In V18, the gap is wider and more devoid of planets. This is due, in part, to V18's more precise measurements of planet radius R{sub p}. Thanks to Gaia, uncertainties in stellar radii R{sub ⋆} are no longer the limiting uncertainties in determining R{sub p} for the majority of Kepler planets; instead, errors in R{sub p}/R{sub ⋆} dominate. V18's analysis incorporated short-cadence photometry along with constraints on mean stellar density that enabled more accurate determinations of R{sub p}/R{sub ⋆}. In the F18 analysis, less accurate R{sub p}/R{sub ⋆} blurs the boundary the radius gap. The differences in R{sub p}/R{sub ⋆} are largest at high impact parameter (b≳0.8) and often exceed 10%. This motivates excluding high-b planets from demographic studies, but identifying such planets from long-cadence photometry alone is challenging. We show that transit duration can serve as an effective proxy, and we leverage this information to enhance the contrast between the super-Earth and sub-Neptune populations.

79 ASTRONOMY AND ASTROPHYSICS↗

DESI Mg II Absorbers: Extinction Characteristics and Quasar Redshift Accuracy

In this paper, we study how absorption-line systems affect the spectra and redshifts of quasi-stellar objects (QSOs), using catalogs of Mg II absorbers from the early data release and first data release of the Dark Energy Spectroscopic Instrument. We determine the reddening effect of an absorption system by fitting an unreddened template spectrum to a sample of 50,674 QSO spectra that contain Mg II absorbers. We find that reddening caused by intervening absorbers (v off > 3500 km s −1 ) has an average color excess of $\overline{E(B-V)}$ = 0.04 mag. We find that the E(B − V) tends to be greater for absorbers at low redshifts, or those having Mg II absorption lines with higher equivalent widths, but shows no clear trend with v off for intervening systems. However, the $\overline{E(B-V)}$ of associated absorbers, those at v off < 3500 km s −1 , shows a strong trend with v off , increasing rapidly with decreasing v off and peaking (∼0.15 mag) around v off = 0 km s −1 . We demonstrate that Mg II absorbers impact redshift estimation for QSOs by investigating the distributions of v off for associated absorbers. We find that at z > 1.5, these distributions broaden and bifurcate in a nonphysical manner. In an effort to mitigate this effect, we mask pixels associated with the Mg II absorption lines and recalculate the QSO redshifts. We find that we can recover voff populations in better agreement with those for z < 1.5 absorbers and in doing so typically shift background QSO redshifts by Δz ≈ ± 0.005.

79 ASTRONOMY AND ASTROPHYSICS↗

On the Spectral Evolution of Hot White Dwarf Stars. II. Time-dependent Simulations of Element Transport in Evolving White Dwarfs with STELUM

White dwarf stars are subject to various element transport mechanisms that can cause their surface composition to change radically as they cool, a phenomenon known as spectral evolution. In this paper, we undertake a comprehensive theoretical investigation of the spectral evolution of white dwarfs. First, we introduce STELUM, a new implementation of the stellar evolutionary code developed at the Université de Montréal. We provide a thorough description of the physical content and numerical techniques of the code, covering the treatment of both stellar evolution and chemical transport. Then, we present two state-of-the-art numerical simulations of element transport in evolving white dwarfs. Atomic diffusion, convective mixing, and mass loss are considered simultaneously as time-dependent diffusive processes and are fully coupled to the cooling. We first model the PG 1159-DO-DB-DQ evolutionary channel: a helium-, carbon-, and oxygen-rich PG 1159 star transforms into a pure-helium DB white dwarf due to gravitational settling and then into a helium-dominated, carbon-polluted DQ white dwarf through convective dredge-up. We also compute for the first time the full DO-DA-DC evolutionary channel: a helium-rich DO white dwarf harboring residual hydrogen becomes a pure-hydrogen DA star through the float-up process and then a helium-dominated, hydrogen-bearing DC star due to convective mixing. We demonstrate that our results are in excellent agreement with available empirical constraints. In particular, our DO-DA-DC simulation perfectly reproduces the lower branch of the bifurcation observed in the Gaia color–magnitude diagram, which can therefore be interpreted as a signature of spectral evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

High fusion performance in Super H-mode experiments on Alcator C-Mod and DIII-D

The ‘Super H-Mode’ regime is predicted to enable pedestal height and fusion performance substantially higher than standard H-Mode operation. This regime exists due to a bifurcation of the pedestal pressure, as a function of density, that is predicted by the EPED model to occur in strongly shaped plasmas above a critical pedestal density. Experiments on Alcator C-Mod and DIII-D have achieved access to the Super H-Mode (and Near Super H) regime, and obtained very high pedestal pressure, including the highest achieved on a tokamak (pped ~ 80 kPa) in C-Mod experiments operating near the ITER magnetic field. DIII-D Super H experiments have demonstrated strong performance, including the highest stored energy in the present configuration of DIII-D (W ~ 2.2–3.2 MJ), while utilizing only about half of the available heating power (Pheat ~ 7–12 MW). These DIII-D experiments have obtained the highest value of peak fusion gain, QDT,equiv ~ 0.5, achieved on a medium scale (R < 2 m) tokamak. Sustained high performance operation (βN ~ 2.9, H98 ~ 1.6) has been achieved utilizing n = 3 magnetic perturbations for density and impurity control. Pedestal and global confinement has been maintained in the presence of deuterium and nitrogen gas puffing, which enables a more radiative divertor condition. A pair of simple performance metrics is developed to assess and compare regimes. Super H-Mode access is predicted for ITER and expected, based on both theoretical prediction and observed normalized performance, to allow ITER to achieve its goals (Q = 10) at Ip < 15 MA, and to potentially enable more compact, cost effective pilot plant and reactor designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Axisymmetric Snap Buckling of Conical Shells

The authors give a brief account of some of their recent analytical and numerical studies of cone buckling. limiting the discussion to axisymmetric deformations. Pertinent numerical results for the relaxation buckling of full cones subjected to uniform external pressure and Belleville springs deformed by axial edge loads are presented. In addition. bifurcation buckling problems are discussed. For a specific case. the existence of Friedrichs' intermediate buckling load, P(m). as applied to cones. is established. Upper and lower bounds for its value are given.

LOADING↗