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At least 73 records · Page 4

Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models

There is increasing interest in the use of mechanism-based multi-scale computational models (such as agent-based models (ABMs)) to generate simulated clinical populations in order to discover and evaluate potential diagnostic and therapeutic modalities. The description of the environment in which a biomedical simulation operates (model context) and parameterization of internal model rules (model content) requires the optimization of a large number of free parameters. In this work, we utilize a nested active learning (AL) workflow to efficiently parameterize and contextualize an ABM of systemic inflammation used to examine sepsis. Contextual parameter space was examined using four parameters external to the model’s rule set. The model’s internal parameterization, which represents gene expression and associated cellular behaviors, was explored through the augmentation or inhibition of signaling pathways for 12 signaling mediators associated with inflammation and wound healing. We have implemented a nested AL approach in which the clinically relevant (CR) model environment space for a given internal model parameterization is mapped using a small Artificial Neural Network (ANN). The outer AL level workflow is a larger ANN that uses AL to efficiently regress the volume and centroid location of the CR space given by a single internal parameterization. We have reduced the number of simulations required to efficiently map the CR parameter space of this model by approximately 99%. In addition, we have shown that more complex models with a larger number of variables may expect further improvements in efficiency.

97 MATHEMATICS AND COMPUTING↗

Data and scripts associated with “Riverine dissolved organic matter transformations increase with watershed area, water residence time, and Damköhler numbers in nested watersheds” (v2)

This data package is associated with the publication “Riverine dissolved organic matter transformations increase with watershed area, water residence time, and Damköhler numbers in nested watersheds” submitted to Biogeochemistry by Ryan et al., 2024 (DOI: https://doi.org/10.1007/s10533-024-01169-5). This study aims to investigate fundamental and transferable drivers of dissolved organic matter (DOM) diversity across five nested watersheds within the contiguous United States. DOM diversity was explored using ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The samples and the unprocessed FTICR-MS data used in this study are publicly available on the Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) data repository (see DOIs below). The data for the Willamette, Gunnison, Connecticut, and Deschutes basins were collected as part of a collaboration between the Watershed Rules of Life (WROL) project and Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS). The data for the Yakima River basin (YRB) was collected by the PNNL River Corridor SFA. The raw, unprocessed FTICR-MS data with additional (meta)data can be found at doi:10.15485/1895159 for WROL samples and doi:10.15485/1898912 for YRB samples. This data package contains the processed data used in the associated manuscript. This package also contains ancillary geospatial, hydrological, and geochemical information that supports the interpretation of the FTICR-MS data within Ryan et al., 2024. This data package is associated with the GitHub repository found at https://github.com/WHONDRS-Hub/rcsfa-RC4-WROL-YRB_DOM_Diversity. This data package was originally published August 2024. It was updated January 2025 (modified files). See the change history in the readme more details. At the directory level, the data package is comprised of three folders: (1) data, (2) output, and (3) src; and five additional files including the data dictionary (file ending in "_dd.csv”) and file-level metadata (file ending in “_flmd.csv”). The “src” folder contains the scripts used to process the FTICR data, conduct the analyses, and produce the manuscript figures. The inputs for these scripts are in the “data” folder and the returned outputs in the “output” folder. Inputs include temporal and spatial metadata associated with the sampling efforts, processed FTICR data, and total and normalized putative biochemical transformations per sample. Outputs include cleaned and combined data presented as tables, descriptive statistics, and plots. The file-level metadata file lists all files contained in this data package and descriptions for each. The data dictionary describes the units and definitions for each tabular data column or row header.

54 ENVIRONMENTAL SCIENCES↗

Nested Pebble Bed Blanket (NesPeB)

Recent advances in magnetic confinement fusion technology have attracted billions of dollars of investments in startups from venture capitals and corporations, resulting in the development of devices aiming to demonstrate net energy gain in a self-heated burning plasma, such as SPARC (under construction) and others. However, future fusion power plants must operate in regimes that will require technologies far beyond current experience. According to a National Academies of Science, Engineering, and Medicine report, to have nuclear fusion power plants contributing in a timely manner to the planned reduction of atmospheric carbon dioxide, a pilot plant should be built by 2035, and it should demonstrate fusion power production and the performance of the tritium fuel system (requiring a high enough tritium breeding) by 2040. A recognized key technology gap by [26] is the fusion first wall and blanket since no current blanket concept is considered satisfactory or has been built and proven. The first wall and blanket in magnetic fusion reactors form a vital and complex system, as it must satisfy different functions such as power extraction, tritium breeding, plasma containment, radiation shielding, and safety. The list of design requirements is even longer: high enough tritium production for fusion self-sufficiency, low material activation, decay heat and shutdown dose rates, high thermal efficiency, high-capacity factor, high magnets-divertor-vacuum vessel-first wall life, low corrosion, low cost, and intrinsically safe (requiring minimal licensing). Despite fifty-plus years of research, the first wall and blanket concepts proposed suffer from fundamental technical problems and immaturity (TRL=2-3) that jeopardize the timely delivery of a commercial fusion power plant. A fusion first-wall blanket has never been built nor tested, and a "winning", practical functioning design requires enough engineering margins (high enough tritium breeding considering the uncertainty, etc.), manufacturing simplicity, ease of continuous operation, maintenance, and low cost. A new, groundbreaking blanket concept called "Nested Pebble Bed Blanket" (NesPeB) was developed at ORNL under the successful ARPA-E GAMOW FERMI project (patent application allowed by the USPTO). The NesPeB blanket concept addresses current blanket concepts' shortcomings and technical immaturity, paving the way for accelerated delivery of fusion power plants. NesPeB is based on nested pebbles, which are binary-sized lithium-ceramic pebbles enclosed in "Beryllide" perforated and coated spherical shells, which are also binary-sized, stacked on top of each other, forming a "bed" and cooled by Nitrogen gas also "sweeping" the Helium and Tritium generated by the neutron irradiation of Lithium; the vacuum vessel plasma facing material is Molybdenum-96 and -97 with the first wall cooled by Helium while the divertor armor is made of Tungsten. The simulations of the NesPeB blanket using Fusion Reactors Models Integrator (FERMI) are encouraging as they estimate a tritium breeding ratio (TBR) greater than 1.2 using natural Lithium, acceptable pressure drop, and excellent heat transfer properties. Furthermore, the NesPeB blanket is not limited by magneto-hydro-dynamics (MHD) effects, is designed for online refueling, relies on existing tritium extraction technologies, has a simple construction, and limits the corrosion and chemical reactivity problems. NesPeB has the potential to be transformational and disruptive since it can solve all the main, challenging technical problems of fusion device blankets and accelerate a pilot plant delivery for 10 or more years.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Space station Ada runtime support for nested atomic transactions

The Space Station Data Management System (DMS), associated computing subsystems, and applications have varying degrees of reliability associated with their operation. A model has been developed (McKay '86) which allows the DMS runtime environment to appear as an Ada virtual machine to applications executing within it. This model is modular, flexible, and dynamically configurable to allow for evolution and growth over time. Support for Fault-tolerant computing is included within this model. The basic primitive involved in this support is based on atomic actions (Grey '78). An atomic action possesses two fundamental properties: (1) it is indivisible with respect to concurrent actions, and (2) it is indivisible with respect to failure. A transaction is a collection of atomic actions which collectively appear to be one action. Transactions may be nested, providing even more powerful support for reliability. A proposed approach is described for providing support for nested atomic transactions within the Ada runtime model developed for the Space Station environment. The level of support is modular, flexible and dynamically configurable just like the overall runtime support environment.

Monteiro, Edward J.↗

Nested Neural Networks

Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

Baram, Yoram↗

Nested ocean models: Work in progress

The ongoing work of combining three existing software programs into a nested grid oceanography model is detailed. The HYPER domain decomposition program, the SPEM ocean modeling program, and a quasi-geostrophic model written in England are being combined into a general ocean modeling facility. This facility will be used to test the viability and the capability of two-way nested grids in the North Atlantic.

Perkins, A. Louise↗

Mission and Safety Critical (MASC): An EVACS simulation with nested transactions

The Extra-Vehicular Activity Control System (EVACS) Simulation with Nested Transactions, a recent effort of the MISSION Kernel Team, is documented. The EVACS simulation is a simulation of some aspects of the Extra-Vehicular Activity Control System, in particular, just the selection of communication frequencies. The simulation is a tool to explore mission and safety critical (MASC) applications. For the purpose of this effort, its current definition is quite narrow serving only as a starting point for prototyping purposes. (Note that EVACS itself has been supplanted in a larger scenario of a lunar outpost with astronauts and a lunar rover). The frequency selection scenario was modified to embed its processing in nested transactions. Again as a first step, only two aspects of transaction support were implemented in this prototype: architecture and state recovery. Issues of concurrency and distribution are yet to be addressed.

Auty, David↗

Nested-hierarchical scene models and image segmentation

An improved model of scenes for image analysis purposes, a nested-hierarchical approach which explicitly acknowledges multiple scales of objects or categories of objects, is presented. A multiple-pass, region-based segmentation algorithm improves the segmentation of images from scenes better modeled as a nested hierarchy. A multiple-pass approach allows slow and careful growth of regions while interregion distances are below a global threshold. Past the global threshold, a minimum region size parameter forces development of regions in areas of high local variance. Maximum and viable region size parameters limit the development of undesirably large regions. Application of the segmentation algorithm for forest stand delineation in TM imagery yields regions corresponding to identifiable features in the landscape. The use of a local variance, adaptive-window texture channel in conjunction with spectral bands improves the ability to define regions corresponding to sparsely stocked forest stands which have high internal variance.

Woodcock, C.↗

Towards a fast implementation of spectral nested dissection

We describe the spectral nested dissection (SND) algorithm, a new algorithm for computing orderings appropriate for parallel factorization of sparse, symmetric matrices. The algorithm makes use of spectral properties of the Laplacian matrix associated with the given matrix to compute separators. We evaluate the quality of the spectral orderings with respect to several measures: fill, elimination tree height, height and weight balances of elimination trees, and clique tree heights. We use some very large structural analysis problems as test cases and demonstrate on these real applications (such as the Space Shuttle Solid Rocket Booster) that spectral orderings compare quite favorably with commonly used orderings, outperforming them by a wide margin for some of these measures. The only disadvantage of SND is its relatively long execution time. We will present some recent efforts to improve the execution time using both a multilevel and a hybrid approach. We use SND in computing a multifrontal numerical factorization with the different orderings on an eight processor Cray Y-MP and show its effectiveness. We believe that spectral nested dissection is a major breakthrough in terms of generating efficient sparse orderings for parallel machines.

Pothen, Alex↗

Interactions between nested sunspots. 1: The formation and breakup of a delta-type sunspot

We investigate a nest of sunspots in which three ordinary bipolar pairs of sunspots are aligned collinearly. The usual spreading action of the growing regions brings two spots of leading polarity together (p-p collision) and forces the leading and trailing spots of the two interior regions to overlap inot a single penumbra (p-f collision), thus forming a delta-spot. We examine digitally processed images from the Ottawa River Solar Observatory of two related events inside the delta-spot 5 days after the p-f collision begins: the violent disruption of the f-umbra, and the formation in less than a day of an hydrogen-alpha filament. The evolutionary changes in shape, area, relative motions, and brightness that we measure for each spot in the elongated nest are more compatible with Parker's (1979a) hypothesis of a sunspot as a cluster of flux tubes held together by downdrafts than with the notion of a sunspot as a monolithic plug of magnetic flux. From chromospheric developments over the delta-spot, we show that a shearing motion along a polarity inversion is more effective than convergence for creating a chromospheric filament. We invoke the release of an instability, triggered by a sequence of processes lasting 1 day or more, to explain the disruption of the f-umbra in this delta-spot. We show that the sequence is initiated when the colliding p-f umbrae reach a critical separation around 3200 +/- 200 km. We present a descriptive model in which the reconnected magnetic fields block vertical transport of convective heat flux just beneath the photosphere. We observe the formation of an unusual type of penumbra adjacent to the f-polarity portion of this delta-spot just before its disruption. A tangential penumbral band grows out of disordered matter connected to the f-umbra. We present this as evidence for the extrusion of umbral magnetic flux by thermal plumes rising through a loosely bound umbra.

Gaizauskas, V.↗

Interference Lattice-based Loop Nest Tilings for Stencil Computations

A common method for improving performance of stencil operations on structured multi-dimensional discretization grids is loop tiling. Tile shapes and sizes are usually determined heuristically, based on the size of the primary data cache. We provide a lower bound on the numbers of cache misses that must be incurred by any tiling, and a close achievable bound using a particular tiling based on the grid interference lattice. The latter tiling is used to derive highly efficient loop orderings. The total number of cache misses of a code is the sum of (necessary) cold misses and misses caused by elements being dropped from the cache between successive loads (replacement misses). Maximizing temporal locality is equivalent to minimizing replacement misses. Temporal locality of loop nests implementing stencil operations is optimized by tilings that avoid data conflicts. We divide the loop nest iteration space into conflict-free tiles, derived from the cache miss equation. The tiling involves the definition of the grid interference lattice an equivalence class of grid points whose images in main memory map to the same location in the cache-and the construction of a special basis for the lattice. Conflicts only occur on the boundaries of the tiles, unless the tiles are too thin. We show that the surface area of the tiles is bounded for grids of any dimensionality, and for caches of any associativity, provided the eccentricity of the fundamental parallelepiped (the tile spanned by the basis) of the lattice is bounded. Eccentricity is determined by two factors, aspect ratio and skewness. The aspect ratio of the parallelepiped can be bounded by appropriate array padding. The skewness can be bounded by the choice of a proper basis. Combining these two strategies ensures that pathologically thin tiles are avoided. They do not, however, minimize replacement misses per se. The reason is that tile visitation order influences the number of data conflicts on the tile boundaries. If two adjacent tiles are visited successively, there will be no replacement misses on the shared boundary. The iteration space may be covered with pencils larger than the size of the cache while avoiding data conflicts if the pencils are traversed by a scanning-face method. Replacement misses are incurred only on the boundaries of the pencils, and the number of misses is minimized by maximizing the volume of the scanning face, not the volume of the tile. We present an algorithm for constructing the most efficient scanning face for a given grid and stencil operator. In two dimensions it is based on a continued fraction algorithm. In three dimensions it follows Voronoi's successive minima algorithm. We show experimental results of using the scanning face, and compare with canonical loop orderings.

VanderWijngaart, Rob F.↗

More Far-Side Deep Moonquake Nests Discovered

As reported last year, we started to reanalyze the seismic data acquired from 1969 to 1977 with a network of stations established on the Moon during the Apollo mission. The reason for the reanalysis was because recent advances in computer technology make it possible to employ much more sophisticated analysis techniques than was possible previously. The primary objective of the reanalysis was to search for deep moonquakes on the far side of the Moon and, if found, to use them to infer the structure of the Moon's deep interior, including a possible central core. The first step was to identify any new deep moonquakes that escaped our earlier search by applying a combination of waveform cross-correlation and single-link cluster analysis, and then to see if any of them are from previously unknown nests of deep moonquakes. We positively identified 7245 deep moonquakes, more than a five-fold increase from the previous 1360. We also found at least 88 previously unknown deep-moonquake nests. The question was whether any of these newly discovered nets were on the far side of the Moon, and we now report that our analysis of the data indicates that some of them are indeed on the far side.

Nakamura, Y.↗

Spatial Extent of a Deep Moonquake Nest: A Preliminary Report of Reexamination

Deep moonquakes, occurring at depths about halfway to the center of the Moon, were discovered during the Apollo lunar landing missions, 1969-1972. Their near-monthly occurrence with nearly identical waveforms at any given seismic station suggests that they are strongly influenced by tides, caused by the Earth and the Sun, acting on certain limited regions of the deep lunar interior. However, much about them is unknown, why they are restricted to certain depths and to limited source regions (nests), and what they tell us about the nature of the material and dynamics of the interior of the Moon. A piece of information helpful to decipher their true nature is the spatial extent and distribution of their hypocenters. The occurrence of nearly identical waveforms suggests groups of hypocenters appear in close proximity to one another, but can we tell how closely they are located and how they are distributed? The Apollo PSE (Passive Seismic Experiment) data from all stations of the seismic network were received in real time at a common receiving station on Earth in digital form. This provided extremely high inter-station timing accuracy not achievable for most earthquake data on Earth at that time. We took advantage of this to compute relative locations of waveform-matched events, and concluded that deep moonquake foci in the A1 moonquake nest were concentrated on a nearly horizontal plane of less than 1 km in diameter. This earlier study was based on deep moonquake events visually identified on seismograms. A recent reanalysis of earlier unidentified seismic events fully utilizing the high capability of present-day computers expanded the list of positively identified deep moonquakes by more than a factor of five. The new list contains many events that are not visually matched in waveforms, yet correlated at a significant level when cross-correlated with a computer. Thus it became imperative to reexamine the spatial distribution of deep moonquake hypocenters including the newly identified events. Additional information is included in the original extended abstract.

Nakamura, Yosio↗

High-Power Performance of a 100-kW Class Nested Hall Thruster

Operations of a three-channel 100-kW class nested Hall thruster at total power levels from 5 to 102 kW and discharge currents from 16 to 247 A were successful. The thruster was operated in all seven available channel combinations at discharge voltages of 300, 400, and 500 V and at current densities that were 0.60 and 0.95 of the nominal value. Additional test points were also collected at 1.20 the nominal current density. The thruster was throttled through a total of forty-six unique operating conditions. At each condition, thruster performance was measured using a high-power thrust stand designed to measure up to 8 N of thrust. From these thrust measurements, specific impulse and efficiency were calculated. All seven channel combinations showed similar performance at a given discharge voltage and current density. The largest thrust recorded was 5.42 N at 99 kW, 400 V discharge voltage. Total efficiency values 0.54 to 0.67, and total specific impulse ranged from 1800 seconds to 2650 seconds. Discharge current oscillations were also measured. Generally these oscillations increased on the inner and middle channels during multi-channel mode but stayed roughly a constant fraction of the channel discharge current for the outer channel in both single- and multi-channel operation. We also found that the thrust of the three channels firing together was not significantly higher than the sum of each channel _ring individually, a result that differs from what was found previously for nested Hall thrusters.

Hall, Scott J.↗

NECTURUS MACULOSUS (Common Mudpuppy). NESTING

Common Mudpuppies (Necturus maculosus maculosus) are the most widespread and wellstudied of the Proteidae, ranging from northern Georgia into eastern Canada and west to the Great Plains. Despite this extensive range, most of our knowledge of life history traits for mudpuppies is based on studies occurring in the northern half of its range, specifically the Great Lakes region. Little is known regarding life history traits in the southern portion of its range. In Tennessee, N. maculosus is thought to occur statewide in permanent streams, rivers, and likely in reservoirs and lakes. Literature suggests that parturition and nest-guarding in N. maculosus maculosus occurs in late winter through spring, but there are no published observations to verify this in Tennessee (Pasachnik and Niemiller 2011. In Niemiller and Reynolds [eds.], The Amphibians of Tennessee, pp. 231-233. University of Tennessee Press, Knoxville, Tennessee). Here, we report four observations of N. maculosus maculosus nests that were discovered while conducting snorkel surveys and lifting cover objects opportunistically for aquatic salamanders from 2011 to 2017, and approximate timing of laying in three river tributaries to the Tennessee River.

Nelson, Stephen K.↗

Modeling household-level party composition behavior for multiparty activities: a random parameter nested logit modeling approach

This study presents findings of a household-level party composition model for multiparty activities. It exploits data from a comprehensive Household Travel Survey conducted by Chicago Metropolitan Agency of Planning. The study estimates a random parameter nested logit model to capture households’ unobserved preference heterogeneity and non-proportional substitution patterns in terms of activity party composition for multiparty activities. A wide variety of household demographics, activity attributes and residential neighborhood characteristics are examined in this paper. The magnitude of the impacts of the determinants are tested in this study by analyzing the elasticity of the variables, which suggests that household demographics and attributes of the multiparty activities have significant effects on the household-level activity party composition. Residential neighborhood characteristics, although somewhat less impactful, still play a meaningful role. This model will be implemented within the POLARIS transportation systems simulator to improve the activity generation modeling workflow, and the prediction accuracy of various activity-travel components.

activity party composition↗

Capacitated p -hub approach for park-and-ride facility location problem under nested logit demand function: polyhedral approaches

By generalizing the unconstrained p-hub approach for the park-and-ride (P&R) facility location problem under the multinomial logit demand function, the capacitated p-hub approach for the problem under the nested logit demand function captures a broader range of real-world cases. To solve this problem optimally, we introduce a mixed-integer linear program and accelerate its solution by enhancing the branch-and-cut procedure. To address the problem at a large scale, we introduce two other polyhedral approaches: variable neighborhood search (VNS) and adaptive randomized rounding (ARR). Downtown areas in Seoul have a high modal share of public transportation and congested road traffic, yet P&R has not been widely implemented. Therefore, we apply the ARR procedure to solve a real-world problem using traffic and geographic data from the Seoul metropolitan area. ARR performs better than VNS and addresses real-world cases. The solutions obtained by ARR present a phased expansion plan that encourages policymakers to start installing a small number of P&Rs immediately.

Capacitated p-hub approach↗

Nested Fullerenes on Graphite

A novel method of forming nested fullerenes by irradiation of carbon soot using the high energy beam in a 300-kV electron microscope.

fullerenes↗