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Dual Channel Dual Staging: Hierarchical and Portable Staging for GPU-Based In-Situ Workflow
In-situ workflows have emerged as an attractive approach for addressing data movement challenges at very large scales. Since GPU-based architectures dominate the HPC landscapes, porting these in-situ workflows, and, specifically, the inter-application data exchange, to GPU-based systems can be challenging. Technologies such as GPUDirect RDMA (GDR), which is typically used for I/O in GPU applications as an optimization that circumvents the CPU overhead, can be leveraged to support bulk data exchanges between GPU applications. However, current GDR design often lacks performance portability across HPC clusters built with different hardware configurations. Furthermore, the local CPU may also be effectively used as an auxiliary communication mechanism to offload data exchanges. In this paper, we present a dual channel dual staging approach for efficient, scalable, and performance-portable inter-application data exchange for in-situ workflows. This approach exploits the data access pattern within in-situ workflows along with the inherent execution asynchrony to accelerate data exchanges and, at the same time, improve performance portability. Specifically, the dual channel dual staging method leverages both the local CPU and the remote data staging server to build a hierarchical joint staging area and uses this staging area to transform blocking inter-application bulk data exchanges into best-effort local data movements between GPU and CPU. The dual channel dual staging is implemented as a portability extension of the Dataspaces-GPU staging framework. We present an experimental evaluation of its performance, portability, and scalability using this implementation on three leadership GPU clusters. The evaluation results demonstrate that the dual channel dual staging method saves up to 75% in data-exchange time compared to host-based, GDR, and alternate portable designs, while maintaining scalability (up to 512 GPUs) and performance portability across the three platforms.
Two-stage formation-energy correction (NbZr, TaZr, VZr)
This bundle contains the scripts, the raw and corrected per-structure data, and the manuscript plots for the NbZr / TaZr / VZr BCC binary formation energies and the associated RMSDs. Why a two-stage correction is necessary: The "raw" formation energy of every relaxed VASP configuration is computed in the usual way, FE_raw(c) = E_alloy(c) - sum_i x_i * E_pure_i , where E_pure_i are the per-atom total energies of the pure-element reference structures (Nb, Ta, V, Zr in the same BCC supercell, with identical INCAR / KPOINTS / PAW choices). With perfectly consistent reference runs the raw FE should vanish at the two pure-element endpoints (x = 0 and x = 1) by construction. In practice this does not hold for two reasons that are present in our dataset: 1. Reference-energy inconsistency (composition-dependent bias). Even with identical input parameters, the pure-element runs (stored in `corrected_DFT_pure_element_runs/`) differ slightly from the values that would be implied by the alloy runs at near-pure compositions (a few meV/atom). This bias is approximately linear in concentration, because the residual error in E_pure_Nb (or E_pure_Ta / E_pure_V) propagates into FE_raw(c) as (1 - x) * dE_pure_1, and the corresponding error in E_pure_Zr propagates as x * dE_pure_2. Left uncorrected, this produces a non-physical "tilt" of FE_raw(x) and shifts the entire FE-vs-x cloud away from zero at the endpoints. 2. Endpoint anchoring against the audited true endpoints. The strict endpoint values (FE_x0_meVatom, FE_x1_meVatom in `corrected_fe_strict_endpoints_20260518/strict_endpoint_check_20260518.csv`) were re-derived from an independent cross-check of the pure-element runs. After stage 1 removes the linear bias, the near-pure compositions in the alloy dataset still extrapolate to values that differ slightly from these audited endpoints — because stage 1 is fit from a few near-end alloy bins, not from the audited pure-element references themselves. The README.txt file discusses how these issues are addressed by the two-stage correction, and describes folder layout, pipeline summary, and how to re-run.
Sporophyte Stage Genes Exhibit Stronger Selection Than Gametophyte Stage Genes in Haplodiplontic Giant Kelp
Macrocystis pyrifera (giant kelp), a haplodiplontic brown macroalga that alternates between a macroscopic diploid (sporophyte) and a microscopic haploid (gametophyte) phase, provides an ideal system to investigate how ploidy background affects the evolutionary history of a gene. In M. pyrifera , the same genome is subjected to different selective pressures and environments as it alternates between haploid and diploid life stages. We assembled M. pyrifera gene models using available expression data and validated 8,292 genes models using the model alga Ectocarpus siliculosus . Differential expression analysis identified gene models expressed in either or both the haploid and diploid life stages while functional annotation identified processes enriched in each stage. Genes expressed preferentially or exclusively in the gametophyte stage were found to have higher nucleotide diversity (π = 2.3 × 10 –3 and 2.8 × 10 –3 , respectively) than those for sporophytes (π = 1.1 × 10 –3 and 1 × 10 –3 , respectively). While gametophyte-biased genes show faster sequence evolution, the sequence evolution exhibits less signatures of adaptations when compared to sporophyte-biased genes. Our findings contrast the standing masking hypothesis, which predicts higher standing genetic variation at the sporophyte stage, and support the strength of expression theory, which posits that genes expressed more strongly are expected to evolve slower. We argue that the sporophyte stage undergoes more stringent selection compared with the gametophyte stage, which carries a heavy genetic load associated with broadcast spawning. Furthermore, using whole-genome sequencing, we confirm the strong population structure in wild M. pyrifera populations previously established using microsatellite markers, and estimate population genetic parameters, such as pairwise genetic diversity and Tajima’s D , important for conservation and domestication of M. pyrifera .
A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data
This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. Furthermore, the results demonstrate the advantage of the algorithm in finding high-precision solutions.
Nitrogen increases early‐stage and slows late‐stage decomposition across diverse grasslands
1. To evaluate how increased anthropogenic nutrient inputs alter carbon cycling in grasslands, we conducted a litter decomposition study across 20 temperate grasslands on three continents within the Nutrient Network, a globally distributed nutrient enrichment experiment 2. We determined the effects of addition of experimental nitrogen (N), phosphorus (P) and potassium plus micronutrient (K μ ) on decomposition of a common tree leaf litter in a long-term study (maximum of 7 years; exact deployment period varied across sites). The use of higher order decomposition models allowed us to distinguish between the effects of nutrients on early- versus late-stage decomposition. 3. Across continents, the addition of N (but not other nutrients) accelerated early-stage decomposition and slowed late-stage decomposition, increasing the slowly decomposing fraction by 28% and the overall litter mean residence time by 58%. 4. Synthesis. Using a novel, long-term cross-site experiment, we found widespread evidence that N enhances the early stages of above-ground plant litter decomposition across diverse and widespread temperate grassland sites but slows late-stage decomposition. These findings were corroborated by fitting the data to multiple decomposition models and have implications for N effects on soil organic matter formation. For example, following N enrichment, increased microbial processing of litter substrates early in decomposition could promote the production and transfer of low molecular weight compounds to soils and potentially enhance the stabilization of mineral-associated organic matter. By contrast, by slowing late-stage decomposition, N enrichment could promote particulate organic matter (POM) accumulation. Such hypotheses deserve further testing.
Validation of Stage N3 of the Eighth Edition AJCC Staging System for Nasopharyngeal Carcinoma
Objectives To validate stage nodal (N)3 of the 8th edition American Joint Committee on Cancer (AJCC) staging system for nasopharyngeal carcinoma (NPC). Methods This retrospective cohort study extracted NPC patients from the Surveillance, Epidemiology, and End Results database between 2004 and 2016. Pathologically confirmed patients with complete data of level IV, N3a, and N3b lymph node metastasis were investigated. The included patients were divided into level IV, N3a, and N3b groups. Five‐year overall survival (OS) and cancer‐specific survival (CSS) were compared among the three groups. Results A total of 693 patients were included: 285 (41.13%) patients in the level IV group, 124 (17.89%) patients in the N3a group, and 284 (40.98%) patients in the N3b group. The 5‐year OS (57.1%, 55.0%, and 55.2%) and CSS (64.4%, 63.5%, and 64.4%) were not different among the level IV, N3a, and N3b groups. Multivariate regression analysis revealed that N stage was not an independent prognostic factor for OS (hazard ratio [HR] = 1.03, 95% confidence interval [CI]: 0.91–1.17; P = .65) or CSS (HR = 1.03, 95% CI: 0.89–1.19; P = .70). Conclusion Stage N3 of the 8th edition AJCC staging system for NPC is reasonable. Level of Evidence III Laryngoscope , 131:535–540, 2021
Transitioning from Stage-III to Stage-IV: cosmology from galaxy×CMB lensing and shear×CMB lensing
ABSTRACT We examine the cosmological constraining power from two cross-correlation probes between galaxy and cosmic microwave background (CMB) surveys: the cross-correlation of lens galaxy density with CMB lensing convergence 〈δgκCMB〉, and source galaxy weak lensing shear with CMB lensing convergence 〈γκCMB〉. These two cross-correlation probes provide an independent cross-check of other large-scale structure constraints and are insensitive to galaxy-only or CMB-only systematic effects. In addition, when combined with other large-scale structure probes, the cross-correlations can break degeneracies in cosmological and nuisance parameters, improving both the precision and robustness of the analysis. In this work, we study how the constraining power of 〈δgκCMB〉 + 〈γκCMB〉 changes from Stage-III (ongoing) to Stage-IV (future) surveys. Given the flexibility in selecting the lens galaxy sample, we also explore systematically the impact on cosmological constraints when we vary the redshift range and magnitude limit of the lens galaxies using mock galaxy catalogs. We find that in our setup, the contribution to cosmological constraints from 〈δgκCMB〉 and 〈γκCMB〉 are comparable in the Stage-III data sets; but in Stage-IV surveys, the noise in 〈δgκCMB〉 becomes subdominant to cosmic variance, preventing 〈δgκCMB〉 to further improve the constraints. This implies that to maximize the cosmological constraints from future 〈δgκCMB〉 + 〈γκCMB〉 analyses, we should focus more on the requirements on 〈γκCMB〉 instead of 〈δgκCMB〉. Furthermore, the selection of the lens sample should be optimized in terms of our ability to characterize its redshift or galaxy bias instead of its number density.
Electrolyte Role in SEI Evolution at Si in the Pre-lithiation Stage vs the Post-lithiation Stage
The formation and evolution of the dynamic solid electrolyte interphase (SEI) at the Si anode/electrolyte interface are yet to be completely understood to solve irreversible capacity loss and increase battery cycle life. Herein, the evolution of SEI and its dynamic properties at the Si anode/electrolyte interface are investigated in two electrolyte systems, a 1.2 M LiPF6 in EC: EMC 3:7 (wt%) electrolyte (referred to as Gen2) and a 1.2 M LiTFSI in EC: EMC 3:7 (wt%) electrolyte (referred to as LiTFSI). Two lithiation stages are studied: the pre-lithiation (pre-Li) SEI stage and the post-lithiation (post-Li) stage. Findings reveal at the pre-Li, SEI formation starts at an early potential and contributes to the greater mass gain in the Si/Gen2, and it is dominated by the formation of a non-uniform F- and P-rich layer in Si/Gen2, in contrast to a homogeneous F- and C-containing layer at the Si/LiTFSI interphase. The initially formed SEI in LiTFSI further benefits the charge transfer kinetics. At the post-Li stage, a more substantial SEI evolution is observed at Si/LiTFSI. This paper offers a foundational understanding of the SEI dynamic evolution with electrolyte dependence. Findings from this report offer important insights into solving the complex SEI stability issues on Si.
Transitioning from Stage-III to Stage-IV: Cosmology from galaxy×CMB lensing and shear×CMB lensing (Final Report for Grant SC0021429 "Cosomology with Galaxy and CMB Surveys: Mitigating Systematic Effects Through Combining Datasets")
We examine the cosmological constraining power from two cross-correlation probes between galaxy and cosmic microwave background (CMB) surveys: the cross-correlation of lens galaxy density with CMB lensing convergence $\langle δ_g$$^κ\text{CMB}\rangle$, and source galaxy weak lensing shear with CMB lensing convergence $\langle^{γκ}$$_{\text{CMB}}\rangle$. These two cross-correlation probes provide an independent cross-check of other large-scale structure constraints and are insensitive to galaxy-only or CMB-only systematic effects. In addition, when combined with other large-scale structure probes, the cross-correlations can break degeneracies in cosmological and nuisance parameters, improving both the precision and robustness of the analysis. In this work, we study how the constraining power of $\langle δ_g$$^κ\text{CMB}\rangle + \langle^{γκ}$$_{\text{CMB}}\rangle$ changes from Stage-III (ongoing) to Stage-IV (future) surveys. Given the flexibility in selecting the lens galaxy sample, we also explore systematically the impact on cosmological constraints when we vary the redshift range and magnitude limit of the lens galaxies using mock galaxy catalogs. We find that in our setup, the contribution to cosmological constraints from $\langle δ_g$$^κ\text{CMB}\rangle$ and $\langle^{γκ}$$_{\text{CMB}}\rangle$ are comparable in the Stage-III data sets; but in Stage-IV surveys, the noise in$\langle δ_g$$^κ\text{CMB}\rangle$ becomes subdominant to cosmic variance, preventing $\langle δ_g$$^κ\text{CMB}\rangle$ to further improve the constraints. This implies that to maximize the cosmological constraints from future $\langle δ_g$$^κ\text{CMB}\rangle$ + $\langle^{γκ}$$_{\text{CMB}}\rangle$ analyses, we should focus more on the requirements on$^{γκ}$$_{\text{CMB}}\rangle$ instead of$\langle δ_g$$^κ\text{CMB}\rangle$. Furthermore, the selection of the lens sample should be optimized in terms of our ability to characterize its redshift or galaxy bias instead of its number density.
Comprehensive Analysis of the Relative Dispersion of Droplet-Size Distributions and Their Relationships to Key Physical Fog Processes Under Different Aerosol Conditions and Evolutionary Stages
The relative dispersion of cloud and fog droplets has significant impacts on aerosol indirect effects, radiative transfer, and microphysical processes. However, previous studies have been mostly concerned with clouds, with limited studies on fog, particularly those that examine the combined influences of all key physical processes and their roles during fog evolution. As such, this study aims to conduct a comprehensive investigation by examining the relationships between relative dispersion and other microphysical variables, as well as the underlying microphysical and dynamic processes, based on field fog campaigns in polluted and clean conditions. In polluted fog, droplet concentrations are higher, leading to smaller droplets and increased dispersion. The correlation between dispersion and droplet volume-mean radius is positive in the polluted fog, but shifts to negative in clean fog. Here, we attribute the difference to various microphysical processes like aerosol activation, condensation, collision-coalescence, and entrainment-mixing. In polluted fog, high aerosol concentrations, low supersaturations, and strong turbulence (entrainment-mixing) provide suitable conditions for the simultaneous occurrence of droplet condensation and aerosol activation, resulting in a positive correlation between dispersion and volume-mean radius, especially during the fog formation stage. In contrast, during the mature stage in clean fog, condensation is dominant with weak aerosol activation leading to a negative correlation between relative dispersion and volume-mean radius. The collision-coalescence process is more active in the mature stage, increasing radii and leading to the negative correlation between dispersion and volume-mean radius. This result sheds new light on understanding the relative dispersion and mechanisms in fog under different aerosol backgrounds.
Polyethylene glycol as a robust, biocompatible encapsulant for two-stage treatment of food and beverage wastewater
Polyethylene glycol beads encapsulating anaerobic microbes developed for on-site food and beverage wastewater treatment.
NNSS 3013 Staging and Enhanced Staging Program (ESP) Update
Explore the source record for details and available documents.
Nucleation and early stage crystallization in barium disilicate glass
Abstract not provided
Energy innovation in the US buildings sector: Setting the stage and mapping the future
Jared Langevin is a staff scientist at Lawrence Berkeley National Laboratory, where he leads modeling of US buildings sector innovation and its implications for energy demand, consumer costs, and the power grid. Eric Wilson is a senior research engineer in the Building Technologies and Sciences Center at the National Renewable Energy Laboratory (NREL). Much of his 15-year career at NREL has revolved around modeling and analysis of the US building stock. Jared and Eric co-led the development of a National Blueprint for buildings sector innovation while serving as advisors to the US Department of Energy’s Deputy Assistant Secretary for Buildings and Industry.
Evaluation of a smart activatable MRI nanoprobe to target matrix metalloproteinases in the early-stages of abdominal aortic aneurysms
Not provided.
Element redistributions during early stages of oxidation in a Ni38Cr22Fe20Mn10Co10 multi-principal element alloy
Element redistributions after initial gaseous oxidation of a Ni38Cr22Fe20Mn10Co10 (at%) multi-principle element alloy at 120°C and 300°C is captured via psuedo in situ atom probe tomography. All cations contribute to the oxide in both conditions, consisting of a Cr-rich inner oxide and Fe, Mn, Co and Ni-rich outer oxide. At the lower temperature, Ni tends to be trapped at the outer/inner oxide interface, while Ni enriches at the oxide/metal interface at higher temperature in tandem with Cr metal depletion. These observations confirm oxidation of complex alloys involves the formation of metastable, multi-layered oxide films, with a distinct tendency for solute trapping.