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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Baryon fraction from the BAO amplitude: a consistent approach to parameterizing perturbation growth

Galaxy clustering constrains the baryon fraction Omega_b/Omega_m through the amplitude of baryon acoustic oscillations and the suppression of perturbations entering the horizon before recombination. This produces a different pre-recombination distribution of baryons and dark matter. After recombination, the gravitational potential responds to both components in proportion to their mass, allowing robust measurement of the baryon fraction. This is independent of new-physics scenarios altering the recombination background (e.g. Early Dark Energy). The accuracy of such measurements does, however, depend on how baryons and CDM are modeled in the power spectrum. Previous template-based splitting relied on approximate transfer functions that neglected part of information. We present a new method that embeds an extra parameter controlling the balance between baryons and dark matter in the growth terms of the perturbation equations in the CAMB Boltzmann solver. This approach captures the baryonic suppression of CDM prior to recombination, avoids inconsistencies, and yields a clean parametrization of the baryon fraction in the linear power spectrum, separating out the simple physics of growth due to the combined matter potential. We implement this framework in an analysis pipeline using Effective Field Theory of Large-Scale Structure with HOD-informed priors and validate it against noiseless LCDM and EDE cosmologies with DESI-like errors. The new scheme achieves comparable precision to previous splitting while reducing systematic biases, providing a more robust way to baryon-fraction measurements. In combination with BBN constraints on the baryon density and Alcock-Paczynski estimates of the matter density, these results strengthen the use of baryon fraction measurements to derive a Hubble constant from energy densities, with future DESI and Euclid data expected to deliver competitive constraints.

Crespi, Andrea [U. Waterloo (main); Waterloo U., I↗
DOE OSTI2026

Dark Energy Survey Year 6 Results: Weak Lensing and Galaxy Clustering Cosmological Analysis Framework

We present the methodology for the weak lensing and galaxy clustering analyses of the Dark Energy Survey (DES) Year 6 data set. In this work, we design and validate the analysis pipeline for the cosmic shear, galaxy clustering plus galaxy$-$galaxy lensing ($2 \times 2$pt), and the joint analysis in the $3 \times 2$pt. Our framework accounts for key theoretical uncertainties, such as baryonic feedback and galaxy bias, incorporating both linear and non-linear models. We apply scale cuts in regimes where theoretical modeling becomes unreliable. The robustness of the pipeline is validated using mock data and simulations, confirming unbiased cosmological constraints and highlighting the importance of posterior projection effects in the validation process. As a result, we deliver robust and validated analysis pipelines for cosmic shear, $2 \times 2$pt, and $3 \times 2$pt in $Λ$CDM and $w$CDM scenarios, including a well-defined set of scales suitable for real data analysis, a robust prescription for theoretical systematics, and the theoretical covariance of the signal. This comprehensive methodology also lays the groundwork for future galaxy surveys such as the Vera C. Rubin Observatory Legacy Survey of Space and Time.

Sanchez-Cid, D. [Zurich U.; Madrid, CIEMAT; Madrid↗
DOE OSTI2021

Clogging, dynamics, and reentrant fluid for active matter on periodic substrates

Here, we examine the collective states of run-and-tumble active matter disks driven over a periodic obstacle array. When the drive is applied along a symmetry direction of the array, we find a clog-free uniform liquid state for low activity, while at higher activity, the density becomes increasingly heterogeneous and an active clogged state emerges in which the mobility is strongly reduced. For driving along nonsymmetry or incommensurate directions, there are two different clogging behaviors consisting of a drive-dependent clogged state in the low activity thermal limit and a drive-independent clogged state at high activity. These regimes are separated by a uniform flowing liquid at intermediate activity. There is a critical activity level above which the thermal clogged state does not occur, as well as an optimal activity level that maximizes the disk mobility. Thermal clogged states are dependent on the driving direction while active clogged states are not. In the low activity regime, diluting the obstacles produces a monotonic increase in the mobility; however, for large activities, the mobility is more robust against obstacle dilution. We also examine the velocity-force curves for driving along nonsymmetry directions and find that they are linear when the activity is low or intermediate but become nonlinear at high activity and show behavior similar to that found for the plastic depinning of solids. At higher drives, the active clustering is lost. For low activity, we also find a reentrant fluid phase, where the system transitions from a high mobility fluid at low drives to a clogged state at higher drives and then back into another fluid phase at very high drives. We map the regions in which the thermally clogged, partially clogged, active uniform fluid, clustered fluid, active clogged, and directionally locked states occur as a function of disk density, drift force, and activity.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Application of Machine Learning and Data Augmentation Algorithms in the Discovery of Metal Hydrides for Hydrogen Storage

The development of efficient and sustainable hydrogen storage materials is a key challenge for realizing hydrogen as a clean and flexible energy carrier. Among various options, metal hydrides offer high volumetric storage density and operational safety, yet their application is limited by thermodynamic, kinetic, and compositional constraints. In this work, we investigate the potential of machine learning (ML) to predict key thermodynamic properties—equilibrium plateau pressure, enthalpy, and entropy of hydride formation—based solely on alloy composition using Magpie-generated descriptors. We significantly expand an existing experimental dataset from ~400 to 806 entries and assess the impact of dataset size and data augmentation, using the PADRE algorithm, on model performance. Models including Support Vector Machines and Gradient Boosted Random Forests were trained and optimized via grid search and cross-validation. Results show a marked improvement in predictive accuracy with increased dataset size, while data augmentation benefits are limited to smaller datasets and do not improve accuracy in underrepresented pressure regimes. Furthermore, clustering and cross-validation analyses highlight the limited generalizability of models across different material classes, though high accuracy is achieved when training and testing within a single hydride family (e.g., AB2). The study demonstrates the viability and limitations of ML for accelerating hydride discovery, emphasizing the importance of dataset diversity and representation for robust property prediction.

augmentation↗
DOE OSTI2026

Creating a Training Dataset for Semantic Segmentation of Canal Networks for Irrigation Modernization

Canal infrastructure has provided critical irrigation water to the western United States for over a century. To continue providing vital water resources to the semi-arid West, irrigation systems must undergo maintenance and modernization. Many canal companies are resource-constrained, and because funding opportunities often require detailed knowledge of existing infrastructure, they can struggle to secure financial capital. We address this problem by creating training data for a semantic segmentation deep learning model to map canal networks throughout the western United States. To create a diverse and robust training dataset, we labelled 1-m NAIP imagery with the locations of no canals, wet canals, and dry/vegetated canals. Since creating these datasets is time consuming, we first developed a preprocessing methodology to identify canals within our four study areas. We used NAIP imagery and provided canal centerline data to buffer, standardize, and cluster the imagery, automating the labeling process as much as possible. However, this still required manual cleaning and manual classification of canal type. Challenges arose when canals were interrupted (e.g., road culverts or piped sections) or when nearby features shared similar characteristics (e.g., irrigated fields, trees, and shadows). Combining automated preprocessing with manual refinement produced four detailed canal masks to be used in the semantic segmentation model developed by Richard Tapia.

13 - HYDRO ENERGY↗
DOE OSTI2025

The z ∼ 1.03 Merging Cluster SPT-CL J0356–5337: New Strong Lensing Analysis with HST and MUSE

We present a strong lensing analysis and reconstruct the mass distribution of SPT-CL J0356−5337, a galaxy cluster at redshift z = 1.034. Our model supersedes previous models by making use of new multiband Hubble Space Telescope data and Multi-Unit Spectroscopic Explorer (MUSE) spectroscopy. We identify two additional lensed galaxies to inform a more well-constrained model using 12 sets of multiple images in five separate lensed sources. The three previously known sources were spectroscopically confirmed by G. Mahler et al. at redshifts of z = 2.363, z = 2.364, and z = 3.048. We measured the spectroscopic redshifts of two of the newly discovered arcs using MUSE data, at z = 3.0205 and z = 5.3288. We increase the number of cluster member galaxies by a factor of 3 compared to previous work. We also report the detection of extended Lyα emission from several background galaxies. We measure the total projected mass density of the two major subcluster components, one dominated by the brightest cluster galaxy and the other by a compact group of luminous red galaxies. We find ${M}_{{\rm{B}}{\rm{C}}{\rm{G}}}(\lt 80\,\rm{kpc})=3.9{3}_{-0.14}^{+0.21}\times 1{0}^{13}$ M⊙ and ${M}_{{\rm{LRG}}}(\lt 80\,\rm{kpc})=2.9{2}_{-0.23}^{+0.16}\times 1{0}^{13}$ M⊙, yielding a mass ratio of $1.3{5}_{-0.08}^{+0.16}$ . The strong lensing constraints offer a robust estimate of the projected mass density regardless of modeling assumptions; allowing more substructure in this line of sight does not change the results or conclusions. Our results corroborate the conclusion that SPT-CL J0356−5337 is dominated by two mass components and is likely undergoing a major merger on the plane of the sky.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Uncertainty in Synthetic Tropical Cyclone Hazard and Risk Estimates: Insights from RAFT, CHAZ, MIT, STORM, and CLIMADA

We synthesize five complementary tropical cyclone (TC) hazard frameworks—RAFT (physics-based machine learning), CHAZ and MIT (statistical–dynamical), STORM (fully statistical), and CLIMADA (observation-driven resampling)—to characterize uncertainty in wind-related TC metrics relevant to energy applications. All datasets and the IBTrACS observational record are harmonized to a common 6-hourly, 2.5° grid. We compare basin-wide and coastal properties using consistent definitions for TC frequency, mean and maximum intensity, 24-hour intensification, and 6-hour translation speed, and quantify agreement with Pearson r, RMSE, and Kling–Gupta efficiency (KGE) alongside resampling-based confidence intervals. CLIMADA is included for basin context but excluded from coastal skill scoring because it resamples historical IBTrACS; if supplied with projected future tracks from an external hazard model, CLIMADA can be used to simulate future TC scenarios. Results show robust, cross-model signals: (i) a corridor of activity from the tropical Atlantic through the Caribbean into the Bahamas and western subtropical Atlantic; (ii) a meridional dipole in 24-hour intensification (low-latitude strengthening, subtropical weakening); and (iii) a transition from slower tropical motion to faster midlatitude translation. Coastal winds (mean and maximum) consistently cluster from the eastern Gulf into the Bahamas–western Atlantic transition. The largest structural spread occurs in the amplitude and footprint of lifetime maximum intensity and, secondarily, in translation speed; intensification exhibits similar central behavior across frameworks with variability in extremes. Translation speed shows the most uniform coastal agreement. These findings provide a decision envelope for wind-focused risk screening and clarify where uncertainty should be carried forward; wind-only results represent a lower bound on total hazard, motivating integration of surge and rainfall modules and a companion, asset-level damage analysis.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

The SDSS-Gaia View of the Color–Magnitude Relation for Blue Horizontal-branch Stars

We present an updated sample of blue horizontal-branch (BHB) stars selected from the photometric and spectroscopic data from Sloan Digital Sky Survey and its associated project Sloan Extension for Galactic Understanding and Exploration (SEGUE). With these data, we selected candidates for A-type stars in the color–color space and then a mixture modeling technique was implemented in order to distinguish between BHB and main-sequence/blue-straggler stars based on their surface gravity values (log g) estimated by the SEGUE Stellar Parameter Pipeline. Our robust approach allows us to attribute individual probabilities of each star truly being in the BHB stage. Hence, our method is advantageous in comparison to previous SEGUE BHB selections that adopted simple log g cuts. We also revisit the color–magnitude relation for these stars and propose two calibrations, based on updated distances for Galactic globular clusters, to estimate absolute magnitudes with (g – r) 0 and (u – r) 0 colors.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1990

Knowledge base rule partitioning design for CLIPS

This describes a knowledge base (KB) partitioning approach to solve the problem of real-time performance using the CLIPS AI shell when containing large numbers of rules and facts. This work is funded under the joint USAF/NASA Advanced Launch System (ALS) Program as applied research in expert systems to perform vehicle checkout for real-time controller and diagnostic monitoring tasks. The Expert System advanced development project (ADP-2302) main objective is to provide robust systems responding to new data frames of 0.1 to 1.0 second intervals. The intelligent system control must be performed within the specified real-time window, in order to meet the demands of the given application. Partitioning the KB reduces the complexity of the inferencing Rete net at any given time. This reduced complexity improves performance but without undo impacts during load and unload cycles. The second objective is to produce highly reliable intelligent systems. This requires simple and automated approaches to the KB verification & validation task. Partitioning the KB reduces rule interaction complexity overall. Reduced interaction simplifies the V&V testing necessary by focusing attention only on individual areas of interest. Many systems require a robustness that involves a large number of rules, most of which are mutually exclusive under different phases or conditions. The ideal solution is to control the knowledge base by loading rules that directly apply for that condition, while stripping out all rules and facts that are not used during that cycle. The practical approach is to cluster rules and facts into associated 'blocks'. A simple approach has been designed to control the addition and deletion of 'blocks' of rules and facts, while allowing real-time operations to run freely. Timing tests for real-time performance for specific machines under R/T operating systems have not been completed but are planned as part of the analysis process to validate the design.

Mainardi, Joseph D.↗
DOE OSTI2024

Magnetic phase diagram of a two-orbital model for bilayer nickelates with varying doping

Motivated by the recently discovered high-T c bilayer nickelate superconductor La 3⁢ Ni 2 ⁢O 7 , we comprehensively research a bilayer 2×2×2 cluster for different electronic densities n by using the Lanczos method. We also employ the random-phase approximation to quantify the first magnetic instability with increasing Hubbard coupling strength, also varying n. Based on the spin structure factor S(q), we have obtained a rich magnetic phase diagram in the plane defined by n and U/W, at fixed Hund coupling, where U is the Hubbard strength and W the bandwidth. We have observed numerous states, such as A-AFM, Stripes, G-AFM, and C-AFM. At half-filling, n=2 (two electrons per Ni site, corresponding to N=16 electrons), the canonical superexchange interaction leads to a robust G-AFM state (π,π,π) with antiferromagnetic couplings both in-plane and between layers. By increasing or decreasing electronic densities, ferromagnetic tendencies emerge from the “half-empty” and “half-full” mechanisms, leading to many other interesting magnetic tendencies. In addition, the spin-spin correlations become weaker both in the hole or electron doping regions compared with half-filling. At n=1.5 (or N=12), density corresponding to La 3 ⁢Ni 2 ⁢O 7 , we obtained the “Stripe 2” ground state (antiferromagnetic coupling in one in-plane direction, ferromagnetic coupling in the other, and antiferromagnetic coupling along the z axis) in the 2×2×2 cluster. In addition, we obtained a much stronger AFM coupling along the z axis than the magnetic coupling in the xy plane. The random-phase approximation calculations with varying n give very similar results as Lanczos, even though both techniques are based on quite different procedures. Additionally, a state with q/π=(0.6,0.6,1) close to the E-phase wavevector is found in our RPA calculations by slightly reducing the filling to n=1.25, possibly responsible for the E-phase SDW recently observed in experiments. In conclusion, our predictions can be tested by chemically doping La 3 ⁢Ni 2 ⁢O 7 .

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structure-activity relationship of Pt catalyst on engineered ceria-alumina support for CO oxidation

In heterogeneous catalysis, the promotion of low temperature activity and enhancement of thermal stability simultaneously especially for precious metal catalysts is always highly demanded but very challenging. In this work, we report a novel Pt catalyst on ceria-alumina (CeO 2 /Al 2 O 3 ) support (Pt/CA-T) engineered by a two-step ceria deposition strategy, exhibiting superior thermal stability and low-temperature carbon monoxide (CO) oxidation activity after activation. Pt single sites anchored to engineered CeO 2 edge sites are much more stable than that to CeO 2 (111) surface, and such stable single sites can be transformed into highly active Pt clusters for efficient low-temperature CO oxidation. Active site identification indicates that the CO oxidation activity of different Pt sites follows such sequence: Pt cluster step sites ≈ Pt cluster terrace sites > Pt cluster corner sites $\gg$ Pt single sites on CeO 2 . The excellent low temperature activity of activated Pt/CA-T catalyst for CO oxidation is associated with its abundant Pt cluster step and terrace sites as well as rich Pt-CeO 2 interfaces, which facilitate the adsorption of active CO species and superior oxygen activation/transfer ability. The present study provides new insights into the structure–activity relationship of Pt-CeO 2 -Al 2 O 3 catalyst, which can also guide the preparation of other highly robust supported catalysts for important industrial applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Solution-Processable High-Modulus Crystalline Artificial Solid Electrolyte Interphase for Practical Lithium Metal Batteries

The solid electrolyte interphase (SEI) has been identified as a key challenge for Li metal anodes. The brittle and inhomogeneous native SEI generated by parasitic reactions between Li and liquid electrolytes can devastate battery performance; therefore, artificial SEIs (ASEIs) have been proposed as an effective strategy to replace native SEIs. Herein, as a collaboration between academia and industrial R&D teams, a multifunctional (crystalline, high modulus, and robust, Li + ion conductive, electrolyte-blocking, and solution processable) ASEI material, LiAl-FBD (where “FBD” refers to 2,2,3,3-tetra-fluoro-1,4-butanediol), for improving Li metal battery performance is designed and synthesized. The LiAl-FBD crystal structure consists of Al 3+ ions bridged by FBD 2– ligands to form anion clusters while Li + ions are loosely bound at the periphery, enabling an Li + ion conductivity of 9.4 × 10 –6 S cm –1 . Further, the fluorinated, short ligands endow LiAl-FBD with electrolyte phobicity and high modulus. The ASEI is found to prevent side reactions and extend the cycle life of Li metal electrodes. Specifically, pairing LiAl-FBD coated 50 μm thick Li with industrial 3.5 mAh cm –2 NMC811 cathode and 2.8 μL mAh –1 lean elec-trolyte, the Li metal full cells show superior cycle life compared to bare ones, achieving 250 cycles at 1 mA cm –2 .

25 ENERGY STORAGE↗
DOE OSTI2022

A Hydro-particle-mesh Code for Efficient and Rapid Simulations of the Intracluster Medium

We introduce the cosmological HYPER code based on an innovative hydro-particle-mesh (HPM) algorithm for efficient and rapid simulations of gas and dark matter. For the HPM algorithm, we update the approach of Gnedin & Hui to expand the scope of its application from the lower-density intergalactic medium (IGM) to the higher-density intracluster medium (ICM). While the original algorithm tracks only one effective particle species, the updated version separately tracks the gas and dark matter particles, as they do not exactly trace each other on small scales. For the approximate hydrodynamics solver, the pressure term in the gas equations of motion is calculated using robust physical models. In particular, we use a dark matter halo model, ICM pressure profile, and IGM temperature–density relation, all of which can be systematically varied for parameter-space studies. We show that the HYPER simulation results are in good agreement with the halo model expectations for the density, temperature, and pressure radial profiles. Simulated galaxy cluster scaling relations for Sunyaev–Zel’dovich (SZ) and X-ray observables are also in good agreement with mean predictions, with scatter comparable to that found in hydrodynamic simulations. HYPER also produces lightcone catalogs of dark matter halos and full-sky tomographic maps of the lensing convergence, SZ effect, and X-ray emission. These simulation products are useful for testing data analysis pipelines, generating training data for machine learning, understanding selection and systematic effects, and for interpreting astrophysical and cosmological constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2002

Machine Learning for Biological Trajectory Classification Applications

Machine-learning techniques, including clustering algorithms, support vector machines and hidden Markov models, are applied to the task of classifying trajectories of moving keratocyte cells. The different algorithms axe compared to each other as well as to expert and non-expert test persons, using concepts from signal-detection theory. The algorithms performed very well as compared to humans, suggesting a robust tool for trajectory classification in biological applications.

Sbalzarini, Ivo F.↗
DOE OSTI2025

In-situ L-TEM observations of dynamics of nanometric skyrmions and antiskyrmions

Nanometer-scale magnetic skyrmions and antiskyrmions exhibit unique dynamical behaviors in response to external stimuli, which are critical for their applications in low-power-consumption spintronic devices. This review discusses recent advancements in in-situ Lorentz transmission electron microscopy (L-TEM) observations of skyrmion and antiskyrmion dynamics, and demonstrates the manipulation and evolution of these textures in various magnetic materials under electric, magnetic, and thermal stimuli. Specifically, the motion tracking of single skyrmions and their clusters, and the deformation and transformation of skyrmions has been demonstrated in chiral helimagnets FeGe, Co 9 Zn 9 Mn 2 , and Co 10 Zn 10 with precise application of electric currents. Skyrmions can undergo dynamic transitions in current-driven skyrmion motions, from pinned states to linear flows, and even exhibit deformation into elliptical shapes, underscoring their topological robustness and dynamic flexibility. In addition, the manipulation of single antiskyrmions and antiskyrmion-lattice phases in (Fe 0.63 Ni 0.3 Pd 0.07 ) 3 P with S 4 symmetry is discussed, highlighting their high mobility and unique sliding capabilities along stripe domains at room temperature, facilitated by nanosecond pulsed electric currents. Finally, the temperature gradient-driven motion and topological transformation of elliptical skyrmions and antiskyrmions in this same material are investigated. In conclusion, the comprehensive insights gained from the L-TEM imaging technique are pivotal in advancing the design and functionality of next-generation skyrmion/antiskyrmion-based spintronic devices.

(Anti)skyrmion↗
DOE OSTI2022

Revisiting the Definition of Rapid Intensification of Tropical Cyclones by Clustering the Initial Intensity and Inner‐Core Size

Abstract Rapid intensification (RI) of tropical cyclones (TCs) provides a great challenge in operational forecasting and contributes significantly to the development of major TCs. RI is commonly defined as an increase in the maximum sustained surface wind speed of at least a certain threshold within 24 hr. The most widely used threshold is 30 kt (15.4 m/s), which was determined statistically. Here we propose a new definition for RI by objectively clustering TCs using the intensification rate, initial intensity, and radius of the maximum wind speed (RMW). A group of 770 samples is separated at a threshold of 45 kt (23.2 m/s). The threshold is 40 kt (20.6 m/s) for the western North Atlantic, where TC size measurements are more reliable. Monte Carlo experiments demonstrate that the proposed threshold is robust even considering the uncertainty in RMW of as high as 30 km. We show that, when a TC undergoes RI, its maximum wind speed is approximately 60 ± 15 kt (30.9 ± 7.7 m/s) and the RMW is 45 ± 20 km. The new threshold outperforms the conventional threshold of 30 kt/24 hr in describing the bimodal distribution of lifetime maximum intensity and explaining the annual count of Category 5 TCs. This new definition provides a more physically based threshold and describes a more reliable representation of extreme events. Although more comparisons are needed for operational application, it is likely to be desirable for case‐based process studies and could provide a more valuable metric for TC intensification classification and research.

Li, Yi↗
DOE OSTI2025

Gravothermal collapse and the diversity of galactic rotation curves

The rotation curves of spiral galaxies exhibit a great diversity that challenges our understanding of galaxy formation and the nature of dark matter. Previous studies showed that in self-interacting dark matter (SIDM) models with a cross section per unit mass of σ/m ≈ $\mathscr{O}$(1) cm 2 /g, the predicted dark matter central densities are a good match to the observed densities in galaxies. Here, in this work, we explore a regime with a larger cross section of σ/m ≈ 20−40 cm 2 /g in dwarf galactic halos. We will show that such strong dark matter self-interactions can further amplify the diversity of halo densities inherited from their assembly history. High concentration halos can enter the gravothermal collapse phase within 10 Gyr, resulting in a high density, while low concentration ones remain in the expansion phase and have a low density. We fit the rotation curves of 14 representative low surface brightness galaxies and demonstrate how the large range of observed central densities is naturally accommodated in the strong SIDM regime of σ/m ≈ 20 – 40 cm 2 /g. Galaxies that are outliers in the previous studies, due to their high halo central densities, are no longer outliers in this SIDM regime as their halos would be in the collapse phase. For galaxies with a low density, the SIDM fits are robust to the variation of the cross section. Our findings open up a new window for testing gravothermal collapse, the unique signature of strong dark matter self-interactions, and exploring a broader SIDM model space. As an example, we illustrate how the larger cross sections favored by our fits, together with upper limits from strong lensing observations in clusters, pick out the preferred SIDM model space for a dark matter particle coupled to a light gauge boson in the Born regime.

dark matter↗
DOE OSTI2024

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗