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DOE OSTI2021

Impact of improved energy resolution on DUNE sensitivity to neutrino non-standard interactions

The full physics potential of the next-generation Deep Underground Neutrino Experiment (DUNE) is still being explored. In particular, there have been some recent studies on the possibility of improving DUNE’s neutrino energy reconstruction. The main motivation is that a better determination of the neutrino energy in an event-by-event basis will translate into an improved measurement of the Dirac C P phase and other neutrino oscillation parameters. To further motivate studies and improvements on the neutrino energy reconstruction, we evaluate the impact of energy resolution at DUNE on an illustrative new physics scenario, viz. non-standard interactions (NSI) of neutrinos with matter. We show that a better energy resolution in comparison to the ones given in the DUNE conceptual and technical design reports may significantly enhance the experimental sensitivity to NSI, particularly when degeneracies are present. While a better reconstruction of the first oscillation peak helps disentangling standard C P effects from those coming from NSIs, we find that the second oscillation peak also plays a nontrivial role in improving DUNE’s sensitivity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Keeping it simple: simplified frameworks for long-lived particles at neutrino facilities

Modern-day accelerator neutrino facilities are excellent venues for searches for new-physics particles. Many distinct new-physics models predict overlapping signatures and phenomenology in these experiments. In this work, we advocate for the adoption of simplified frameworks when studying these types of new-physics signatures, which are characterized by a small number of primary variables, including particle masses, lifetimes, and production and decay modes/rates that most directly control signal event rates and kinematics. In particular, taking the example of long-lived particles that decay inside a neutrino detector as a test case, we study formulate and study simplified frameworks in the context of light scalars/fermions produced in kaon decays which then decay into final states containing an electron-positron pair. We show that using these simplified frameworks can allow for individual experimental analyses to be applicable to a wide variety of specific model scenarios. As a side benefit, we demonstrate that using this approach can allow for the T2K collaboration, by reinterpreting its search for Heavy Neutral Leptons, to be capable of setting world-leading limits on the Higgs-Portal Scalar model. Furthermore, we argue the simplified framework interpretation can serve as a bridge to model identification in the hopeful detection of a new-physics signal. As an illustration, we perform a first determination of the likelihood that, in the presence of a new-physics signal in a detector like the DUNE ND-GAr, multiple different new-physics hypotheses (such as the Higgs-Portal Scalar and Heavy Neutral Lepton ones) can be disentangled. We demonstrate that this model discrimination is favorable for some portions of detectable new-physics parameter space but for others, it is more challenging.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Imprints of a supercooled phase transition in the gravitational wave spectrum from a cosmic string network

A network of cosmic strings (CS), if present, would continue emitting gravitational waves (GW) as it evolves throughout the history of the Universe. This results in a characteristic broad spectrum making it a perfect source to infer the expansion history. In particular, a short inflationary period caused by a supercooled phase transition would cause a drop in the spectrum at frequencies corresponding to that event. However, the impact on the spectrum is similar to the ones caused by an early matter-dominated era or from particle production, making it difficult to disentangle these different physical origins. We point out that, in the case of a short inflationary period, the GW spectrum receives an additional contribution from the phase transition itself. This leads to a characteristic imprint of a peak on top of a wide plateau both visible at future GW observatories.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

The role of charm and unflavored mesons in prompt atmospheric lepton fluxes

The all-sky very-high-energy (10 4 − 10 6 GeV) atmospheric muon flux measured by IceCube shows a spectral hardening at the highest energies, indicating the presence of a prompt component. IceCube has also measured the atmospheric muon neutrino flux at high energy. However, since this flux is dominated by astrophysical neutrinos, only an upper bound can be placed on the prompt atmospheric ν μ + $\overline{ν}$ μ contribution. In this work, we provide a new evaluation of the prompt atmospheric muon flux including an intrinsic charm component in the cosmic ray-air interactions. The latter enhances the forward production of $\overline{D}$ 0 , D – and Λc, which subsequently decay into final states containing muons and muon neutrinos. We show how the increase in the prompt muon flux due to intrinsic charm is accompanied by a corresponding enhancement in the prompt muon neutrino flux. We implement different intrinsic charm production models in MCEq to calculate the resulting lepton fluxes. We discuss the challenges of achieving predictions that are simultaneously consistent with both IceCube’s high-energy atmospheric muon flux measurements and IceCube upper bounds on the prompt muon neutrino flux, and we quantify the resulting discrepancies. As possible solutions, we explore scaling of the unflavored meson contributions to the prompt atmospheric muon flux to assess how such adjustments can reconcile these differences. The tensions emphasized in our work call for a refinement of the hadronic interaction models, especially the production of unflavored mesons, and for new experimental data sensitive to unflavored meson and heavy flavor production with reliable estimates of the associated uncertainties. We suggest that the energy and zenith angle dependence of muon and neutrino flux ratios from future neutrino telescope measurements may help to disentangle different scenarios.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The Observed and Projected Changes of Global Monsoons: Current Status and Future Perspectives

The global monsoon system, encompassing the Asian-Australian, African, and American monsoons, sustains two-thirds of the world’s population by regulating water resources and agriculture. Monsoon anomalies pose severe risks, including floods and droughts. Recent research associated with the implementation of the Global Monsoons Model Intercomparison Project under the umbrella of CMIP6 has advanced our understanding of its historical variability and driving mechanisms. Observational data reveal a 20th-century shift: increased rainfall pre-1950s, followed by aridification and partial recovery post-1980s, driven by both internal variability (e.g., Atlantic Multidecadal Oscillation) and external forcings (greenhouse gases, aerosols), while ENSO drives interannual variability through ocean-atmosphere interactions. Future projections under greenhouse forcing suggest long-term monsoon intensification, though regional disparities and model uncertainties persist. Models indicate robust trends but struggle to quantify extremes, where thermodynamic effects (warming-induced moisture rise) uniformly boost heavy rainfall, while dynamical shifts (circulation changes) create spatial heterogeneity. Volcanic eruptions and proposed solar radiation modification (SRM) further complicate predictions: tropical eruptions suppress monsoons, whereas high-latitude events alter cross-equatorial flows, highlighting unresolved feedbacks. The emergent constraint approach is booming in terms of correcting future projections and reducing uncertainty with respect to the global monsoons. Critical challenges remain. Model biases and sparse 20th-century observational data hinder accurate attribution. The interplay between natural variability and anthropogenic forcings, along with nonlinear extreme precipitation risks under warming, demands deeper mechanistic insights. Additionally, SRM’s regional impacts and hemispheric monsoon interactions require systematic evaluation. Addressing these gaps necessitates enhanced observational networks, refined climate models, and interdisciplinary efforts to disentangle multiscale drivers, ultimately improving resilience strategies for monsoon-dependent regions.

climate extreme events↗

DOE OSTI2021

Divergent controls of soil organic carbon between observations and process-based models

Abstract The storage and cycling of soil organic carbon (SOC) are governed by multiple co-varying factors, including climate, plant productivity, edaphic properties, and disturbance history. Yet, it remains unclear which of these factors are the dominant predictors of observed SOC stocks, globally and within biomes, and how the role of these predictors varies between observations and process-based models. Here we use global observations and an ensemble of soil biogeochemical models to quantify the emergent importance of key state factors – namely, mean annual temperature, net primary productivity, and soil mineralogy – in explaining biome- to global-scale variation in SOC stocks. We use a machine-learning approach to disentangle the role of covariates and elucidate individual relationships with SOC, without imposing expected relationships a priori . While we observe qualitatively similar relationships between SOC and covariates in observations and models, the magnitude and degree of non-linearity vary substantially among the models and observations. Models appear to overemphasize the importance of temperature and primary productivity (especially in forests and herbaceous biomes, respectively), while observations suggest a greater relative importance of soil minerals. This mismatch is also evident globally. However, we observe agreement between observations and model outputs in select individual biomes – namely, temperate deciduous forests and grasslands, which both show stronger relationships of SOC stocks with temperature and productivity, respectively. This approach highlights biomes with the largest uncertainty and mismatch with observations for targeted model improvements. Understanding the role of dominant SOC controls, and the discrepancies between models and observations, globally and across biomes, is essential for improving and validating process representations in soil and ecosystem models for projections under novel future conditions.

58 GEOSCIENCES↗

DOE OSTI2026

Evaluating ecosystem water use efficiency under drought stress: a case study of the Helan Mountain region, northwest China

Context Water use efficiency (WUE) is a fundamental ecological indicator links carbon assimilation and water loss in terrestrial ecosystems. Understanding its responses to drought stress is essential for adaptive ecosystem management, particularly in climate-sensitive mountain landscapes. Objectives This study aimed to investigate drought-driven variations in WUE across major vegetation types in the Helan Mountain region of Northwest China. Specifically, we sought to identify dominant ecological drivers of WUE variability and to disentangle their relative importance and causal pathways. Methods We quantified WUE using the Moderate Resolution Imaging Spectroradiometer (MODIS) products and the Drought Severity Index (DSI) data from 2001 to 2020. To examine WUE – drought relationships across contrasting vegetation types, we employed a spatially explicit analytical framework integrating Random Forest (RF) modeling, partial correlation analysis, and structural equation modeling (SEM). Results Regional WUE exhibited relatively stable interannual dynamics, yet pronounced spatial heterogeneity that was strongly modulated by drought conditions. Vegetation properties, particularly Leaf Area Index (LAI) and Normalized Difference Vegetation Index (NDVI), emerged as the dominant determinants of WUE, with NDVI alone explaining over 20% of its spatial variance in forest and grassland during non-drought periods. SEM analyses revealed that climate forcing influenced WUE mainly through indirect pathways mediated by soil moisture availability and vegetation structural dynamics, rather than through direct climatic controls. Among all regulating factors, LAI acted as the central control node governing ecosystem carbon–water coupling. In contrast, short-term climatic stress, especially atmospheric demand and drought duration, exerted weak or negative direct effects on WUE. Ecosystem-specific responses were observed, with croplands mainly regulated by soil water availability, whereas forests and grasslands showed more sensitive to atmospheric drought stress. Together, these results reveal a hierarchical control framework where soil–vegetation interactions mediate climate impacts on WUE, driving strong spatial heterogeneity in drought responses across mountain landscapes. Conclusions Our findings highlight the pivotal role of indirect drought effects mediated by vegetation and soil processes in shaping ecosystem WUE. The identified soil–vegetation–climate regulatory hierarchy provides mechanistic insight into landscape–scale drought sensitivity and supports integrated modeling approaches for evaluating ecosystem resilience and sustainable management in arid mountain regions.

China↗

DOE OSTI2022

Ending the Energy-Poverty Nexus: An Ethical Imperative for Just Transitions

Arguments for a just transition are integral to debates about climate change and the drive to create a carbon-neutral economy. There are currently two broad approaches rooted in ethics and justice for framing just energy transitions. The first can be described as internal to the transition and emphasizes the anticipation, assessment, and redressing of harms created by the transition itself and the inclusion in transition governance of groups or communities potentially harmed by its disruptions. In this article, we propose a second approach to ethics and justice in an energy transition, which we describe as systemic or societal in scope. This approach complements attention to the proximate dynamics and impacts of the transition process with a focus on the distant societal and economic outcomes the transition brings into being and how they compare to conditions prior to the transition. It poses the question: do the transformative social, economic, and technological changes wrought by energy systems create more just societies and economies, or do they instead reinforce or recreate long-standing injustices and inequalities? We illustrate this approach with an assessment of one of the most significant existing forms of energy injustice: the energy-poverty nexus. We argue that the energy-poverty nexus reflects configurations of socio-energy systems that create complex, extractive feedbacks between energy insecurity and economic insecurity and, over time, reinforce or exacerbate poverty. We further argue that just energy transitions should work to disentangle these configurations and re-design them so as to create generative rather than extractive feedbacks, thus ending the energy-poverty nexus and creating long-term outcomes that are more just, equitable, and fair.

14 SOLAR ENERGY↗

DOE OSTI2023

Natural gas odorants: A scoping review of health effects

Organosulfur compounds are intentionally added to natural gas as malodorants with the intent of short-term nasal inhalation to aid in leak detection. Regulatory exposure limits have not been established for all commonly used natural gas odorants, and recent community-level exposure events and growing evidence of indoor natural gas leakage have raised concerns associated with natural gas odorant exposures. We conducted a scoping review of peer-reviewed scientific publications on human exposures and animal toxicological studies of natural gas odorants to assess toxicological profiles, exposure potential, health effects and regulatory guidelines associated with commonly used natural gas odorants. We identified only 22 studies which met inclusion criteria for full review. Overall, there is limited evidence of both transient nonspecific health symptoms and clinically diagnosed causative neurotoxic effects associated with prolonged odorant exposures. Across seven community-level exposure events and two occupational case reports, consistent symptom patterns included: headache, ocular irritation, nose and throat irritation, respiratory complaints such as shortness of breath and asthma attacks, and skin irritation and rash. Of these, respiratory inflammation and asthma exacerbations are the most debilitating, whereas the high prevalence of ocular and dermatologic symptoms suggest a non-inhalation route of exposure. The limited evidence available raises the possibility that organosulfur odorants may pose health risks at exposures much lower than presently understood, though additional dose-response studies are needed to disentangle specific toxicologic effects from nonspecific responses to noxious organosulfur odors. Numerous recommendations are provided including more transparent and prescriptive natural gas odorant use practices.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2024

Imaging the initial condition of heavy-ion collisions and nuclear structure across the nuclide chart

High-energy nuclear collisions encompass three key stages: the structure of the colliding nuclei, informed by low-energy nuclear physics, the initial condition , leading to the formation of quark–gluon plasma (QGP), and the hydrodynamic expansion and hadronization of the QGP, leading to final-state hadron distributions that are observed experimentally. Recent advances in both experimental and theoretical methods have ushered in a precision era of heavy-ion collisions, enabling an increasingly accurate understanding of these stages. However, most approaches involve simultaneously determining both QGP properties and initial conditions from a single collision system, creating complexity due to the coupled contributions of these stages to the final-state observables. To avoid this, we propose leveraging established knowledge of low-energy nuclear structures and hydrodynamic observables to independently constrain the QGP’s initial condition. By conducting comparative studies of collisions involving isobar-like nuclei—species with similar mass numbers but different ground-state geometries—we can disentangle the initial condition’s impacts from the QGP properties. This approach not only refines our understanding of the initial stages of the collisions but also turns high-energy nuclear experiments into a precision tool for imaging nuclear structures, offering insights that complement traditional low-energy approaches. Opportunities for carrying out such comparative experiments at the Large Hadron Collider and other facilities could significantly advance both high-energy and low-energy nuclear physics. Additionally, this approach has implications for the future electron-ion collider. While the possibilities are extensive, we focus on selected proposals that could benefit both the high-energy and low-energy nuclear physics communities. Originally prepared as input for the long-range plan of U.S. nuclear physics, this white paper reflects the status as of September 2022, with a brief update on developments since then.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Shear strain gradient in Cu/Nb nanolaminates: Strain accommodation and chemical mixing

Disentangling the intragranular and interfacial plasticity contribution to the overall strain accommodation is crucial to understanding the microstructural evolution and mass transport upon deformation in materials with the nanoscale feature size. In this study, we devise a new approach to tackle the issue by introducing shear strain gradients into Cu/Nb nanolaminates of different layer thicknesses with the shear perpendicular to the laminate interfaces. The measurement of the strain gradient and the resultant lattice disorientation enables a quantitative understanding of the intragranular and interfacial plasticity contribution. We found that intragranular slip entirely governs the deformation in the 300 nm-layer laminate and, unexpectedly, contributes ~80% of the total plasticity in the 30 nm-layer laminate. The high intragranular plasticity in the thin laminate is attributed to the large width of confined slip planes and their remnant potential for storing dislocations. In addition, substantial forced chemical mixing is observed in the top region of the 30 nm-layer laminate where the effective layer thickness is reduced below 8 nm. The transition of deformation mechanism from confined layer slip to dislocation transmission is largely responsible for the initiation of substantial mixing. Our method and findings shed light on the deformation mechanism and deformation-induced mass transport behavior in nanostructured materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Landscape composition and configuration have scale-dependent effects on agricultural pest suppression

Increasing landscape heterogeneity (composition and configuration) can enhance natural enemy populations and support pest suppression in agricultural landscapes. Using a network-based data mining approach, we examined independent gradients of landscape composition and configuration at six spatial scales that were associated with pest suppression services measured at 32 sites in Michigan and Wisconsin, USA. We compared the relative effects of landscape composition and configuration across scales with those of local crop type (corn or grassland). We found that multiple gradients of configurational heterogeneity were independent of composition and strongly associated with pest suppression, with different configuration metrics being predictive of pest suppression depending on the spatial scales and regions considered. Landscapes that were more configurationally heterogeneous at smaller spatial scales consistently supported higher pest suppression. In Michigan, pest suppression increased in landscapes with high edge contrast between annual crops and surrounding habitats and high edge density of grassland within 250-500 m radii. In Wisconsin, pest suppression increased with large core area of grassland and high field density within a 250 m radius. The main compositional effect we found was a positive relationship between grassland cover and pest suppression occurring at larger spatial scales (1000-1500 m) and occurring in Wisconsin but not in Michigan. Our findings demonstrate that effects of landscape composition and configuration on pest suppression differ across spatial scales and vary regionally. The network-based data mining techniques used here could be useful for disentangling intercorrelated landscape metrics in a variety of other contexts in landscape ecology.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Hourly water-carbon interactions modulate decadal water-use efficiency trends inferred from ecosystem-scale measurements

Plant stomatal conductance regulates photosynthesis and transpiration. This physiological link affects ecosystem responses to microclimate and harmonizes carbon, energy, and water exchanges between the biosphere and atmosphere. The relationship between water losses via transpiration and carbon gains via photosynthesis can be quantified by plant water-use efficiency (WUE). While leaf- and ecosystem-scale observations both suggest rising WUE in recent decades, WUE trends inferred from the ecosystem scale are much larger than those inferred from the leaf scale or implied by theory. The unexpectedly large ecosystem-scale WUE trends complicate interpretation of ecophysiological responses to changing environmental conditions. Here, we analyze ecosystem-scale WUE inferred from 40 FLUXNET sites, each with at least 10 years of measurements. Furthermore, our results demonstrate that observed ecosystem-scale WUE trends are more sensitive to hourly weather conditions than longer-term changes in atmospheric carbon dioxide or vapor pressure deficit. Our analysis shows that Earth System Models participating in CMIP6 did not capture the observed WUE sensitivity to inter-site variability and microclimatic conditions. Collectively, our findings suggest that ecosystem-scale WUE trends reflect water-carbon interactions across multiple temporal scales, and disentangling factors contributing to emergent ecosystem responses is needed to infer ecophysiological relationships and model structures from observations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii

This work demonstrates an approach to produce and select hybrid algal strains exhibiting increased photosynthetic productivity under multiple environmental conditions. This simultaneously addresses two major impediments to improving algal bioenergy production: 1) generating new genetic variants with improved performance; and 2) disentangling complex interactions between genetic and physiological factors contributing to these improvements. We pooled progeny generated from mating two environmental isolates of the green alga Chlamydomonas reinhardtii and cultured the pools under multiple environmental conditions. Strains from the outcompeting populations showed substantial (in some cases over 3 fold) increases in productivity over the parental lines under certain environments related to biomass production, including laboratory conditions as well as hyperoxia, fluctuating light, high salinity and high temperature. The results indicate that C. reinhardtii has remarkable, untapped, directed evolution capacity that may be harnessed using breeding and competition approaches. The populations were deep sequenced at multiple time points to identify “Selection-Enriched Genomic Loci” (SEGL) that accumulated in the populations, and thus likely confer increased fitness under the respective environmental conditions. With improved resolution, SEGL mapping can identify allelic combinations used for targeted breeding approaches, generating elite algal lines with multiple desirable traits, as well as to further understand the genetic and mechanistic bases of photosynthetic productivity. Increasing the photosynthetic efficiency of algae during biomass production is perhaps the most critical hurdle for economically sustainable algal based biofuels. This presents unique challenges because modifications designed to increase photosynthesis often result in decreased fitness, due to production of toxic reactive oxygen species when photosynthesis is not adequately regulated. These problems are exacerbated under natural and outdoor production environments because of the complex nature of photosynthesis and the multifaceted interactions between genetic, environmental and physiological factors. Here, we demonstrate a high throughput biotechnological screening approach that simultaneously produces algal strains with highly increased autotrophic productivity and identifies genomic loci contributing to these improvements. Our results demonstrate that Chlamydomonas reinhardtii exhibits high directed evolutionary capacity readily accessed through breeding and selection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Observable measurement-induced transitions

One of the main postulates of quantum mechanics is that measurements destroy quantum coherence (wave function collapse). Recently it was discovered that in a many-body system dilute local measurements still preserve some coherence across the entire system. As the measurement density is increased, a phase transition occurs that is characterized by the disentanglement of different parts of the system. Unfortunately, this transition is impossible to observe experimentally for macroscopic systems because it requires an exponentially costly full tomography of the many-body wave function or a comparison with the simulation on an oracle classical computer. In this work we report the discovery of another measurement-induced phase transition that can be observed experimentally if quantum dynamics can be reversed. On one side of this phase transition the quantum information encoded in some part of the Hilbert space is fully recovered after the time inversion. On the other side, all quantum information is corrupted. This transition also manifests itself as the change in the behavior of the probability to observe the same measurement outcome in the process that consists of identical blocks repeated many times. In each block the unitary evolution is followed by the measurement. On one side of the transition the probability decreases exponentially with the number of repetitions, on the other it tends to a constant as the number of repetitions is increased. We confirm the existence of the proposed phase transition through numerical simulations of realistic quantum circuits and analytical calculations using an effective random-matrix theory model.

Measurement-induced phase transitions↗

DOE OSTI2021

Adoption of perennial energy crops in the US Midwest: Causal and heterogeneous determinants

The success of a bioenergy policy relies largely on the wide adoption of perennial energy crops at the farm-scale. This study uses survey data to examine potential adoption decisions by farmers in the US Midwest and the causal effects of various direct and indirect influencing factors, especially heterogeneous preferences of farmers. A Bayesian network (BN) model is developed to delineate the causal-relationship between farmers adoption decisions and the influencing factors. Here, we find a dominating role of economic factors and a non-negligible impact of non-economic factors, such as the perceived environmental benefits and the extent of familiarity with perennial energy crops. To examine the effect of heterogeneity in farmer preferences, we classify the surveyed farmers into four categories based on their attitudes toward the economic, social, and environmental dimensions of perennial energy crops. We identify statistically significant between-group differences in the responses of the four types of farmers to the various influencing factors. Our findings contribute to disentangling the complicated motivations that will influence perennial energy crop adoption decisions and provide implications for more targeted policy development that need to consider the heterogeneous drivers of farmer decisions about land use.

09 BIOMASS FUELS↗

DOE OSTI2022

Kinetics-Informed Neural Networks

Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize feed-forward artificial neural networks as basis functions to solve ordinary differential equations (ODEs) constrained by differential algebraic equations (DAEs) that describe microkinetic models (MKMs). We present an algebraic framework for the mathematical description and classification of reaction networks, types of elementary reaction, and chemical species. Under this framework, we demonstrate that the simultaneous training of neural nets and kinetic model parameters in a regularized multi-objective optimization setting leads to the solution of the inverse problem through the estimation of kinetic parameters from synthetic experimental data. We analyze a set of scenarios to establish the extent to which kinetic parameters can be retrieved from transient kinetic data, and assess the robustness of the methodology with respect to statistical noise. Furthermore, this approach to inverse kinetic ODEs can assist in the elucidation of reaction mechanisms based on transient data.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution

Tumor deconvolution is a reliable way to disentangle the diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor samples, and the gold standard datasets used to assess the algorithms are geared toward the analysis of gene expression (e.g., RNA-seq) rather than protein levels in tumor cells. While gene expression is less expensive to measure, protein levels provide a more accurate view of immune markers. To facilitate the development as well as improve the reproducibility and reusability of multi-omic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages containerization to compare tumor deconvolution algorithms across multiomic data sets. Decomprolute incorporates the large-scale multiomic data sets produced by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomic data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteogenomic tumor deconvolution benchmarking platform. The platform consists of modular architecture and it comes with well-defined input and output formats at each module. As a result, it is robust and extendable easily with additional algorithms or analyses. The platform is available for access and use at http://pnnl-compbio.github.io/decomprolute.

60 APPLIED LIFE SCIENCES↗