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At least 253 records · Page 14

Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer

The High Throughput Truthing project aims to develop a dataset for validating artificial intelligence and machine learning models (AI/ML) fit for regulatory purposes. The context of this AI/ML validation dataset is the reporting of stromal tumor-infiltrating lymphocytes (sTILs) density evaluations in hematoxylin and eosin-stained invasive breast cancer biopsy specimens. After completing the pilot study, we found notable variability in the sTILs estimates as well as inconsistencies and gaps in the provided training to pathologists. Using the pilot study data and an expert panel, we created custom training materials to improve pathologist annotation quality for the pivotal study. We categorized regions of interest (ROIs) based on their mean sTILs density and selected ROIs with the highest and lowest sTILs variability. In a series of eight one-hour sessions, the expert panel reviewed each ROI and provided verbal density estimates and comments on features that confounded the sTILs evaluation. We aggregated and shaped the comments to identify pitfalls and instructions to improve our training materials. From these selected ROIs, we created a training set and proficiency test set to improve pathologist training with the goal to improve data collection for the pivotal study. We are not exploring AI/ML performance in this paper. Instead, we are creating materials that will train crowd-sourced pathologists to be the reference standard in a pivotal study to create an AI/ML model validation dataset. The issues discussed here are also important for clinicians to understand about the evaluation of sTILs in clinical practice and can provide insight to developers of AI/ML models.

60 APPLIED LIFE SCIENCES↗

Ammonia in northeast Colorado is increasing, rising most quickly in regions close to confined animal feeding operations

The Colorado Front Range urban corridor and nearby agricultural operations are important source regions of atmospheric ammonia (NH 3 ). Upslope flows periodically transport these emissions into Rocky Mountain National Park (RMNP), located 50 km west of the urban corridor, where wet and dry deposition of excess reactive nitrogen (N) impacts ecosystems. Here, we use a combination of in situ passive NH 3 measurements and NH 3 vertical column density retrievals from the Infrared Atmospheric Sounding Interferometer (IASI) to assess variability and changes in NH 3 across three land use categories in the northeast Colorado source region (agricultural, urban, and remote) during the period 2013-2023. A strong seasonal cycle is present across the region with increased NH 3 during summer months. Elevated NH 3 is spatially correlated with the number of permitted animal units in confined animal feeding operations (CAFOs) within 12 km. Ground-level NH 3 concentrations are strongly positively correlated with monthly gridded IASI satellite column densities. Satellite retrievals reveal an increasing trend in NH 3 column amounts of ∼3% per year in agricultural and ∼2% per year in urban sub-regions. The magnitude of the trend observed in NH 3 columns averaged over the agricultural sub-region is > 3 times larger than observed near and over Denver. The largest increases in NH 3 are closely aligned with the distribution of CAFOs. Reductions in particle sulfate associated with declining sulfur dioxide (SO 2 ) emissions could account for only ∼0.1% per year increase in gaseous NH 3 . Wildfire smoke across the region has increased but appears unlikely to explain the majority of the observed NH 3 increase.

54 ENVIRONMENTAL SCIENCES↗

Density streams in the disc winds of Classical T Tauri stars

ABSTRACT Spectral and photometric variability of the Classical T Tauri stars RY Tau and SU Aur from 2013 to 2022 is analysed. We find that in SU Aur the H α line’s flux at radial velocity RV = −50 ± 7 km s−1 varies with a period P = 255 ± 5 d. A similar effect previously discovered in RY Tau is confirmed with these new data: P = 21.6 d at RV = −95 ± 5 km s. In both stars, the radial velocity of these variations, the period, and the mass of the star turn out to be related by Kepler’s law, suggesting structural features on the disc plane orbiting at radii of 0.2 au in RY Tau and 0.9 au in SU Aur, respectively. Both stars have a large inclination of the accretion disc to the line of sight – so that the line of sight passes through the region of the disc wind. We propose there is an azimuthal asymmetry in the disc wind, presumably in the form of ‘density streams,’ caused by substructures of the accretion disc surface. These streams cannot dissipate until they go beyond the Alfven surface in the disc’s magnetic field. These findings open up the possibility to learn about the structure of the inner accretion disc of CTTS on scales less than 1 au and to reveal the orbital distances related to the planet’s formation.

Petrov, P. P. (ORCID:0000000155514963)↗

Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture

Abstract Background and Aims Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. Methods We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. Key Results Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. Conclusions While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.

59 BASIC BIOLOGICAL SCIENCES↗

Centroidal Voronoi tessellation based methods for optimal rain gauge location prediction

With more satellite and model precipitation data becoming available, new analytical methods are needed that can take advantage of emerging data patterns to make well informed predictions in many hydrological applications. Herein we propose a new strategy where we extract precipitation variability patterns and use correlation map to build the resulting density map that serves as an input to centroidal Voronoi tessellation construction that optimizes placement of precipitation gauges. We provide results of numerical experiments based on the data from the Alto-Adige region in Northern Italy and Oklahoma and compare them against actual gauge locations. This method provides an automated way for choosing new gauge locations and can be generalized to include physical constraints and to tackle other types of resource allocation problems.

54 ENVIRONMENTAL SCIENCES↗

A Kinetic Model-Driven Techno-Economic Analysis of Plastic Pyrolysis: Linking Process Dynamics to Economic Viability

This study employs a kinetic model integrated into Aspen Plus to predict pyrolysis product distribution under various conditions. A techno-economic assessment calculated the minimum selling price (MSP) of pyrolysis oil under different operating conditions for the baseline capacity of 100 kta, and across eight processing capacities ranging from 30 to 150 kta. The lowest MSP under the baseline capacity is estimated at $\$$420/ton, which is 33% lower than the 2023 average US crude oil price ($\$$74.6/bbl, equivalent to $\$$634/ton based on the density of pyrolysis oil). Under Monte Carlo simulation, accounting for variability in key economic and technical parameters, the mean MSP is estimated at $\$$1137/ton. The economic viability depends on feedstock price remaining below $\$$320/ton, defining the break-even feedstock price threshold. Sensitivity analysis further identifies capital investment and transportation cost as key economic drivers. Capacities beyond 90 kta show limited economies of scale benefits. Reducing product storage time cuts capital costs by 7% but raises operational risk. Uncertainty analysis suggests the economic feasibility of pyrolysis oil is unlikely to compete with crude oil without policy incentives.

petrochemicals↗

Revealing Fast Cu-Ion Transport and Enhanced Conductivity at the CuInP 2 S 6 –In 4/3 P 2 S 6 Heterointerface

Van der Waals layered ferroelectrics, such as CuInP 2 S 6 (CIPS), offer a versatile platform for miniaturization of ferroelectric device technologies. Control of the targeted composition and kinetics of CIPS synthesis enables the formation of stable self-assembled heterostructures of ferroelectric CIPS and nonferroelectric In 4/3 P 2 S 6 (IPS). Here, we use quantitative scanning probe microscopy methods combined with density functional theory (DFT) to explore in detail the nanoscale variability in dynamic functional properties of the CIPS-IPS heterostructure. Within, we report evidence of fast ionic transport which mediates an appreciable out-of-plane electromechanical response of the CIPS surface in the paraelectric phase. Further, we map the nanoscale dielectric and ionic conductivity properties as we thermally stimulate the ferroelectric-paraelectric phase transition, recovering the local dielectric behavior during this phase transition. Finally, aided by DFT, we reveal a substantial and tunable conductivity enhancement at the CIPS/IPS interface, indicating the possibility of engineering its interfacial properties for next generation device applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle

Abstract Nowcasting is a term originating from economics, finance, and meteorology. It refers to the process of determining the uncertain state of the economy, markets or the weather at the current time by indirect means. In this paper, we describe a simple two‐parameter data analysis that reveals hidden order in otherwise seemingly chaotic earthquake seismicity. One of these parameters relates to a mechanism of seismic quiescence arising from the physics of strain‐hardening of the crust prior to major events. We observe an earthquake cycle associated with major earthquakes in California, similar to what has long been postulated. An estimate of the earthquake hazard revealed by this state variable time series can be optimized by the use of machine learning in the form of the Receiver Operating Characteristic skill score. The ROC skill is used here as a loss function in a supervised learning mode. Our analysis is conducted in the region of 5° × 5° in latitude‐longitude centered on Los Angeles, a region which we used in previous papers to build similar time series using more involved methods (Rundle & Donnellan, 2020, https://doi.org/10.1029/2020EA001097 ; Rundle, Donnellan et al., 2021, https://doi.org/10.1029/2021EA001757 ; Rundle, Stein et al., 2021, https://doi.org/10.1088/1361-6633/abf893 ). Here we show that not only does the state variable time series have forecast skill, the associated spatial probability densities have skill as well. In addition, use of the standard ROC and Precision (PPV) metrics allow probabilities of current earthquake hazard to be defined in a simple, straightforward, and rigorous way.

58 GEOSCIENCES↗

Initial assessment of second generation of large-area picosecond photodetectors with multi-channel systems-on-a-chip readout

Here, we first briefly describe the history and motivation behind Cherenkov and scintillation light detection. We then discuss the instrumentation needed to detect these photons as it applies to both photodetectors and readout electronics. One of the motivations is future large neutrino detectors that could, in principle, differentiate between Cherenkov and scintillation light if using novel water-based scintillators. In this paper, we present the first measurements utilizing the second generation of Large Area Picosecond Photodetectors (LAPPDs) in conjunction with commercial system-on-a-chip readouts from Nalu Scientific—in particular, the High Density System on Chip (HDSoC) and Advanced ASoC Rapid Digitizer, Variable Adaptive Readout Chip (AARDVARC) platforms. These state-of-the-art full-waveform digitizers feature sampling rates on the order of 1 and 10 samples per nanosecond, respectively. Using a picosecond laser, we measured the timing jitter between a pair of LAPPD channels, demonstrating the potential of this setup for precise timing applications.

Li, V. A. [Lawrence Livermore National Laboratory ↗

Carbon Dioxide Removal Measurement, Reporting, and Verification Simulation toolkit (CDR MRVSim) v0.1

CDR MRVSim is a statistical software toolkit for techno-economic analysis of measurement, reporting, and verification of multiple carbon dioxide removal technologies. The current version applies Monte Carlo simulation to existing datasets estimate the cost and uncertainty of measuring the soil organic carbon (SOC) content of agricultural land, accounting for multiple sources of uncertainty, using data from field measurements. We are planning to incorporate enhanced rock weathering and other technologies into the software. The current model leverages existing data to characterize underlying variability in soil organic carbon and related parameters, including bulk density, in an agricultural field attempting to increase its SOC. We then simulate baseline and post-intervention "measurement campaigns" in which some number of SOC and bulk density measurements are conducted using a selected technology. This enables estimates of the cost and accuracy of measuring changes in SOC in the simulated field. The primary advantages over similar software are: 1) ability to quantify tradeoffs between cost and uncertainty in MRV across a range of possible MRV approaches 2) focus on guiding development of novel sensors by determining desirable sets of characteristics

Sherwin, Evan [Lawrence Berkeley National Laborato↗

Enabling off-highway diesel engine downsizing and performance improvement using electrically assisted turbocharging

Internal combustion engine (ICE) downsizing through various turbocharging configurations is generally known by the powertrain design community as an effective means to reduce frictional losses, increase waste heat recovery, and improve fuel efficiency while increasing engine power density. However, often is the case that turbocharging strategies, including variable geometry turbochargers, and regulated two-stage turbochargers, incur the performance tradeoff between transient response and fuel economy (pumping losses) at high engine speeds. For off-highway vehicles having particularly transient and high-powered duty cycles, efforts to improve this tradeoff and increase operational flexibility have turned to evaluating various electrified air system architectures. In this study, a 4.5 L diesel-ICE configured with an electrically driven compressor (eBooster ® ) is placed in series with a conventional turbocharger and integrated into a 48 V mild-hybrid powertrain architecture. The objective of this powertrain configuration is to enable engine downsizing by 34%, replacing the current 6.8 L ICE platform with the hybridized 4.5 L ICE concept. The commercial 1-D simulation software GT-SUITE is used for powertrain system development and system optimization. Development and validation of the GT-SUITE model and air system controls is concurrently supported through experimental data collection. The simulation model development includes using machine learning methods for optimizing exhaust gas dilution, injection timing, and eBooster ® power to improve steady-state and transient brake-specific fuel consumption while minimizing criteria pollutant emissions. It was found that total specific fluid consumption over the standardized non-road transient engine duty cycle could be reduced by 18% over the current 6.8 L engine by using an optimized eBoosted 4.5 L engine. The hybridized 4.5 L engine concept concurrently showed sufficient transient response capability and nearly an order of magnitude reduction in duty cycle total soot production.

25 ENERGY STORAGE↗

Manipulation and statistical analysis of the fluid flow of polymer semiconductor solutions during meniscus-guided coating

Recent work in structure–processing relationships of polymer semiconductors have demonstrated the versatility and control of thin-film microstructure offered by meniscusguided coating (MGC) techniques. Here, we analyze the qualitative and quantitative aspects of solution shearing, a model MGC method, using coating blades augmented with arrays of pillars. The pillars induce local regions of high strain rates—both shear and extensional—not otherwise possible with unmodified blades, and we use fluid mechanical simulations to model and study a variety of pillar spacings and densities. We then perform a statistical analysis of 130 simulation variables to find correlations with three dependent variables of interest: thin-film degree of crystallinity and transistor field-effect mobilities for charge-transport parallel (Μ para ) and perpendicular (Μ perp ) to the coating direction. Our study suggests that simple fluid mechanical models can reproduce substantive correlations between the induced fluid flow and important performance metrics, providing a methodology for optimizing blade design.

36 MATERIALS SCIENCE↗

Medium-density amorphous ice unveils shear rate as a new dimension in water’s phase diagram

Recent experiments revealed a new amorphous ice phase, medium-density amorphous ice (MDA), formed by ball-milling ice I h at 77 K [Rosu-Finsen et al., Science 379, 474–478 (2023)]. MDA has density between that of low-density amorphous (LDA) and high-density amorphous (HDA) ices, adding to the complexity of water’s phase diagram, known for its glass polyamorphism and two-state thermodynamics. The nature of MDA and its relation to other amorphous ices and liquid water remain unsolved. Here, we use molecular simulations under controlled pressure and shear rate at 77 K to produce and investigate MDA. Here. we find that MDA formed at constant shear rate is a steady-state nonequilibrium shear-driven amorphous ice (SDA), that can be produced by shearing ice I h , LDA, or HDA. Our results suggest that MDA could be obtained by ball-milling water glasses without crystallization interference. Increasing the shear rate at ambient pressure produces SDAs with densities ranging from LDA to HDA, revealing shear rate as a new thermodynamic variable in the nonequilibrium phase diagram of water. Indeed, shearing provides access to amorphous states inaccessible by controlling pressure and temperature alone. SDAs produced with shearing rates as high as 10 6 s −1 sample the same region of the potential energy landscape than hyperquenched glasses with identical density, pressure, and temperature. Intriguingly, SDAs obtained by shearing at ~10 8 s −1 have density, enthalpy, and structure indistinguishable from those of water “instantaneously” quenched from room temperature to 77 K over 10 ps, making them good approximants for the “true glass” of ambient liquid water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High resolution density pedestal measurements during edge localized modes by short-pulse reflectometry in the TCV tokamak

Here, this publication presents high spatio-temporal resolution (mm µs -1 ) density profile measurements of the pedestal top during type I, III, and small edge localized mode (ELM) H-mode plasmas in the tokamak à configuration variable (TCV). These measurements were performed using a novel short-pulse reflectometer. Average inter-ELM density profiles are obtained via conditional averaging using the D α trace as ELM indicator. Changes to the pedestal density profile gradients prior to type-III ELMs reveal unique pedestal dynamics leading to the ELM crash which can provide important experimental data for validation of non-linear MHD ELM simulations. The small-ELM scenario is found to feature a ~25–35 kHz quasi-coherent density fluctuation near the separatrix ρ ψ 0.993–1.05 not observed during a similar type-I ELM discharge. This oscillation is also found in low-field-side magnetic pick-up probes displaying a ballooning character and n = +1 toroidal mode number. This oscillation could help explain the markedly different pedestal dynamics observed in the small-ELM regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High resolution density pedestal measurements during edge localized modes by short-pulse reflectometry in the TCV tokamak

This publication presents high spatio-temporal resolution (mm/μs) density profile measurements of the pedestal top during type I, III, and small edge localized mode (ELM) H-mode plasmas in the Tokamak à Configuration Variable (TCV). These measurements were performed using a novel short-pulse reflectometer. Average inter-ELM density profiles are obtained via conditional averaging using the Dα trace as ELM indicator. Changes to the pedestal density profile gradients prior to type-III ELMs reveal unique pedestal dynamics leading to the ELM crash which can provide important experimental data for validation of non-linear MHD ELM simulations. The small-ELM scenario is found to feature a ∼25-35 kHz quasi-coherent density fluctuation near the separatrix rho_psi ∼0.993-1.05 not observed during a similar type-I ELM discharge. This oscillation is also found in low-field-side magnetic pick- up probes displaying a ballooning character and n=+1 toroidal mode number. This oscillation could help explain the markedly different pedestal dynamics observed in the small-ELM regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Lagrangian and Dirac constraints for the ideal incompressible fluid and magnetohydrodynamics

The incompressibility constraint for fluid flow was imposed by Lagrange in the so-called Lagrangian variable description using his method of multipliers in the Lagrangian (variational) formulation. An alternative is the imposition of incompressibility in the Eulerian variable description by a generalization of Dirac’s constraint method using noncanonical Poisson brackets. Here it is shown how to impose the incompressibility constraint using Dirac’s method in terms of both the canonical Poisson brackets in the Lagrangian variable description and the noncanonical Poisson brackets in the Eulerian description, allowing for the advection of density. Both cases give the dynamics of infinite-dimensional geodesic flow on the group of volume preserving diffeomorphisms and explicit expressions for this dynamics in terms of the constraints and original variables is given. Since Lagrangian and Eulerian conservation laws are not identical, comparison of the various methods is made.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multiplicative noise and the diffusion of conserved densities

Stochastic fluid dynamics governs the long time tails of hydrodynamic correlation functions, and the critical slowing down of relaxation phenomena in the vicinity of a critical point in the phase diagram. In this work we study the role of multiplicative noise in stochastic fluid dynamics. Multiplicative noise arises from the dependence of transport coefficients, such as the diffusion constants for charge and momentum, on fluctuating hydrodynamic variables. We study long time tails and relaxation in the diffusion of a conserved density (model B), and a conserved density coupled to the transverse momentum density (model H). Careful attention is paid to fluctuation-dissipation relations. We observe that multiplicative noise contributes at the same order as non-linear interactions in model B, but is a higher order correction to the relaxation of a scalar density and the tail of the stress tensor correlation function in model H.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Verification and validation of the open-source plasma fluid code: Zapdos

Zapdos is an open-source finite element plasma fluid solver based on the MOOSE multiphysics framework. This paper outlines Zapdos verification, benchmarking, and validation efforts for 1D and 2D RF capacitively coupled plasma discharge models for mid-range pressures (0.1 - 1 Torr). The verification process involved using the method of manufactured solutions to assess Zapdos spatial and temporal error convergence. L2 errors ranged from 10 -2 to 10 -4 , while the convergence’s slope were in agreement with the predicted slopes for the tested variable and time integration orders. The benchmarking process involved comparisons to previously results from the validated finite element code, LSODI. These works included 1D and 2D simulations for a range of plasma parameters (densities, temperatures, voltage, etc.). For the 1D cases, Zapdos and LSODI results were in very good agreement. In the 2D cases, variable behaviors matched, with slight discrepancies in peak values. The validation process involved comparisons to experimental works including electron density measurements by microwave interferometry and metastable density measurements by planar laser-induced fluorescence imaging. Results shown reasonable agreement at higher pressure, with results starting to diverge at low pressures. Furthermore, probable causes for this diverges are the limitation of the fluid assumption for plasmas at low pressure, or the need for more robust boundary conditions. Overall, Zapdos shown reasonable results for the verification, benchmarking, and validation efforts, and Zapdos can be downloaded at https://github.com/shannon-lab/zapdos.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗