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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS1995

Neurofilament protein defines regional patterns of cortical organization in the macaque monkey visual system: a quantitative immunohistochemical analysis

Visual function in monkeys is subserved at the cortical level by a large number of areas defined by their specific physiological properties and connectivity patterns. For most of these cortical fields, a precise index of their degree of anatomical specialization has not yet been defined, although many regional patterns have been described using Nissl or myelin stains. In the present study, an attempt has been made to elucidate the regional characteristics, and to varying degrees boundaries, of several visual cortical areas in the macaque monkey using an antibody to neurofilament protein (SMI32). This antibody labels a subset of pyramidal neurons with highly specific regional and laminar distribution patterns in the cerebral cortex. Based on the staining patterns and regional quantitative analysis, as many as 28 cortical fields were reliably identified. Each field had a homogeneous distribution of labeled neurons, except area V1, where increases in layer IVB cell and in Meynert cell counts paralleled the increase in the degree of eccentricity in the visual field representation. Within the occipitotemporal pathway, areas V3 and V4 and fields in the inferior temporal cortex were characterized by a distinct population of neurofilament-rich neurons in layers II-IIIa, whereas areas located in the parietal cortex and part of the occipitoparietal pathway had a consistent population of large labeled neurons in layer Va. The mediotemporal areas MT and MST displayed a distinct population of densely labeled neurons in layer VI. Quantitative analysis of the laminar distribution of the labeled neurons demonstrated that the visual cortical areas could be grouped in four hierarchical levels based on the ratio of neuron counts between infragranular and supragranular layers, with the first (areas V1, V2, V3, and V3A) and third (temporal and parietal regions) levels characterized by low ratios and the second (areas MT, MST, and V4) and fourth (frontal regions) levels characterized by high to very high ratios. Such density trends may correspond to differential representation of corticocortically (and corticosubcortically) projecting neurons at several functional steps in the integration of the visual stimuli. In this context, it is possible that neurofilament protein is crucial for the unique capacity of certain subsets of neurons to perform the highly precise mapping functions of the monkey visual system.

Non-NASA Center↗
NASA NTRS2012

The Algorithm Theoretical Basis Document for the Atmospheric Delay Correction to GLAS Laser Altimeter Ranges

NASA s Ice, Cloud, and Land Elevation Satellite (ICESat) mission will be launched late 2001. It s primary instrument is the Geoscience Laser Altimeter System (GLAS) instrument. The main purpose of this instrument is to measure elevation changes of the Greenland and Antarctic icesheets. To accurately measure the ranges it is necessary to correct for the atmospheric delay of the laser pulses. The atmospheric delay depends on the integral of the refractive index along the path that the laser pulse travels through the atmosphere. The refractive index of air at optical wavelengths is a function of density and molecular composition. For ray paths near zenith and closed form equations for the refractivity, the atmospheric delay can be shown to be directly related to surface pressure and total column precipitable water vapor. For ray paths off zenith a mapping function relates the delay to the zenith delay. The closed form equations for refractivity recommended by the International Union of Geodesy and Geophysics (IUGG) are optimized for ground based geodesy techniques and in the next section we will consider whether these equations are suitable for satellite laser altimetry.

Herring, Thomas A.↗
DOE OSTI2024

Maps of plant functional type (PFT), PFT fractional cover, and uncertainty derived from AVIRIS-NG data, 2019, Seward Peninsula

Remote sensing maps of plant functional type (PFT), PFT fractional cover (fCover), and fCover uncertainty maps derived from NASA’s Airborne Visible / Infrared Imaging Spectrometer – Next Generation (AVIRIS-NG). The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA’s Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE’s Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for flights over Teller, Kougarok, and Council watersheds created using eight AVIRIS-NG imagery collected in July, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as GIS *.kml files. Detailed description of the methods for each map are provided in Yang et al., (2023). These datasets are provided in support of Yang et al., (In revision) “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1995

Aerodynamic shape optimization of wing and wing-body configurations using control theory

This paper describes the implementation of optimization techniques based on control theory for wing and wing-body design. In previous studies it was shown that control theory could be used to devise an effective optimization procedure for airfoils and wings in which the shape and the surrounding body-fitted mesh are both generated analytically, and the control is the mapping function. Recently, the method has been implemented for both potential flows and flows governed by the Euler equations using an alternative formulation which employs numerically generated grids, so that it can more easily be extended to treat general configurations. Here results are presented both for the optimization of a swept wing using an analytic mapping, and for the optimization of wing and wing-body configurations using a general mesh.

Reuther, James↗
NASA NTRS1977

Serotonin involvement in pituitary-adrenal function

Experiments clarifying the effects of serotonin (5-HT) in the regulation of the hypothalamic-pituitary-adrenocortical system are surveyed. Lesion experiments which seek to determine functional maps of serotonergic input to areas involved in regulation are reported. Investigations of the effects of 5-HT levels on the plasma ACTH response to stress and the diurnal variation in basal plasma corticosterone are summarized, and the question of whether serotonergic transmission is involved in the regulation of all aspects of pituitary-adrenal function is considered with attention to the stimulatory and inhibitory action of 5-HT.

Vernikos-Danellis, J.↗
NASA NTRSDate not supplied

Towards Energy Scale Calibration and Drift Correction of TES Detectors for Athena X-IFU

The Athena X-Ray Integral Field Unit (X-IFU) comprises a 2376-pixel array of transition edge sensors (TES) read out with time-division multiplexing (TDM). X-IFU will provide spatially resolved, high-resolution spectroscopy (2.5 eV full-width-half-maximum up to 7 keV) over the energy range 0.2 to 12 keV, with an absolute energy scale accuracy of 0.4 eV. The energy scale function maps the optimally filtered pulse height, in arbitrary engineering units, to real calibrated energy. Uncertainties in the calibration can result from imperfect fitting of the energy scale between the known calibration points. Furthermore, temporal changes in the TES operating environment, such as heat-sink temperature, magnetic field and bias voltage, can cause significant variations in the detector gain function over time. If not properly corrected, this can result in degradation of the energy resolution, and systematic errors in the absolute energy scale. The non-linear nature of TES detectors, coupled with the possibility of multiple simultaneously occurring sources of drift, can make effective corrections over the full bandpass of the instrument extremely challenging. Athena X-IFU will employ an on-board calibration source that provides known reference x-ray lines. This provides real-time monitoring of the gain stability of the detector system and information that can be used to correct for gain drifts. For X-IFU the baseline approach is to measure a series of calibration curves under different environmental conditions, which bound the expected drifts the instrument is predicted to see over the course of the mission. Using the information from the in-flight calibration source, these energy scale functions can be interpolated to generate a new corrected energy scale as a function of time. In this paper we discuss progress towards demonstrating that the X-IFU energy scale requirements can be met. We present measurements on ~ 200 pixels in a prototype X-IFU array read out with 8-column x 32-row TDM. We use a rotating target source containing 12 fluorescent targets to generate x-ray lines covering the energy range 4 keV (Sc-Kα) to 12 keV (Br-Kα). We present measurements of the non-linear energy scale function and show how variations in heat-sink temperature, TES bias voltage and magnetic field affect the shape of TES energy scale differently and introduce different residual gain errors over the bandpass. We explore different drift correction algorithms that use either a single or multiple referential lines to track and correct the gain from these various sources of drift. In addition to the pulse-height, the DC ‘baseline’ level of the TES can contain information about its bias conditions. Thus, we test a multi-parameter gain correction algorithm that attempts to incorporate both the pulse height and the additional baseline information into the algorithm.

Stephen J Smith↗
DOE OSTI2020

Inversion of Time-Lapse Seismic Reservoir Monitoring Data Using CycleGAN: A Deep Learning-Based Approach for Estimating Dynamic Reservoir Property Changes

Carbon capture and storage is being pursued globally as a geoengineering measure for reducing the emission of anthropogenic CO 2 the atmosphere. Comprehensive monitoring, verification, and accounting programs must be established for demonstrating the safe storage of injected CO 2 . One of the most commonly deployed monitoring techniques is time-lapse seismic reservoir monitoring (also known as 4-D seismic), which involves comparing 3-D seismic survey data taken at the same study site but over different times. Analyses of 4-D seismic data volumes can help improve the quality of storage reservoir characterization, track the movement of injected CO 2 plume, and identify potential CO 2 spillover/leakage from the storage reservoirblue. However, the derivation of high-resolution CO 2 saturation maps from 4-D seismic data is a highly nonlinear and ill-posed inverse problem, often requiring significant computational effort. In this research, we apply a physics-based deep learning method to facilitate the solution of both the forward and inverse problems in seismic inversion while honoring physical constraints. A cycle generative adversarial neural network (CycleGAN) model is trained to learn the bidirectional functional mappings between the reservoir dynamic property changes and seismic attribute changes, such that both forward and inverse solutions can be obtained efficiently from the trained model. We show that our CycleGAN-based approach not only improves the reliability of 4-D seismic inversion but also expedites the quantitative interpretation. Our deep learning-based workflow is generic and can be readily used for reservoir characterization and reservoir model updates involving the use of 4-D seismic data.

58 GEOSCIENCES↗
NASA NTRS1992

Mechanically verified hardware implementing an 8-bit parallel IO Byzantine agreement processor

Consider a network of four processors that use the Oral Messages (Byzantine Generals) Algorithm of Pease, Shostak, and Lamport to achieve agreement in the presence of faults. Bevier and Young have published a functional description of a single processor that, when interconnected appropriately with three identical others, implements this network under the assumption that the four processors step in synchrony. By formalizing the original Pease, et al work, Bevier and Young mechanically proved that such a network achieves fault tolerance. We develop, formalize, and discuss a hardware design that has been mechanically proven to implement their processor. In particular, we formally define mapping functions from the abstract state space of the Bevier-Young processor to a concrete state space of a hardware module and state a theorem that expresses the claim that the hardware correctly implements the processor. We briefly discuss the Brock-Hunt Formal Hardware Description Language which permits designs both to be proved correct with the Boyer-Moore theorem prover and to be expressed in a commercially supported hardware description language for additional electrical analysis and layout. We briefly describe our implementation.

Moore, J. Strother↗
NASA NTRS2000

Incremental Parallelization of Non-Data-Parallel Programs Using the Charon Message-Passing Library

Message passing is among the most popular techniques for parallelizing scientific programs on distributed-memory architectures. The reasons for its success are wide availability (MPI), efficiency, and full tuning control provided to the programmer. A major drawback, however, is that incremental parallelization, as offered by compiler directives, is not generally possible, because all data structures have to be changed throughout the program simultaneously. Charon remedies this situation through mappings between distributed and non-distributed data. It allows breaking up the parallelization into small steps, guaranteeing correctness at every stage. Several tools are available to help convert legacy codes into high-performance message-passing programs. They usually target data-parallel applications, whose loops carrying most of the work can be distributed among all processors without much dependency analysis. Others do a full dependency analysis and then convert the code virtually automatically. Even more toolkits are available that aid construction from scratch of message passing programs. None, however, allows piecemeal translation of codes with complex data dependencies (i.e. non-data-parallel programs) into message passing codes. The Charon library (available in both C and Fortran) provides incremental parallelization capabilities by linking legacy code arrays with distributed arrays. During the conversion process, non-distributed and distributed arrays exist side by side, and simple mapping functions allow the programmer to switch between the two in any location in the program. Charon also provides wrapper functions that leave the structure of the legacy code intact, but that allow execution on truly distributed data. Finally, the library provides a rich set of communication functions that support virtually all patterns of remote data demands in realistic structured grid scientific programs, including transposition, nearest-neighbor communication, pipelining, gather/scatter, and redistribution. At the end of the conversion process most intermediate Charon function calls will have been removed, the non-distributed arrays will have been deleted, and virtually the only remaining Charon functions calls are the high-level, highly optimized communications. Distribution of the data is under complete control of the programmer, although a wide range of useful distributions is easily available through predefined functions. A crucial aspect of the library is that it does not allocate space for distributed arrays, but accepts programmer-specified memory. This has two major consequences. First, codes parallelized using Charon do not suffer from encapsulation; user data is always directly accessible. This provides high efficiency, and also retains the possibility of using message passing directly for highly irregular communications. Second, non-distributed arrays can be interpreted as (trivial) distributions in the Charon sense, which allows them to be mapped to truly distributed arrays, and vice versa. This is the mechanism that enables incremental parallelization. In this paper we provide a brief introduction of the library and then focus on the actual steps in the parallelization process, using some representative examples from, among others, the NAS Parallel Benchmarks. We show how a complicated two-dimensional pipeline-the prototypical non-data-parallel algorithm- can be constructed with ease. To demonstrate the flexibility of the library, we give examples of the stepwise, efficient parallel implementation of nonlocal boundary conditions common in aircraft simulations, as well as the construction of the sequence of grids required for multigrid.

VanderWijngaart, Rob F.↗
NASA NTRS2004

Accessing FMS Functionality: The Impact of Design on Learning

In modern commercial and military aircraft, the Flight Management System (FMS) lies at the heart of the functionality of the airplane. The nature of the FMS has also caused great difficulties learning and accessing this functionality. This study examines actual Air Force pilots who were qualified on the newly introduced advanced FMS and shows that the design of the system itself is a primary source of difficulty learning the system. Twenty representative tasks were selected which the pilots could be expected to accomplish on an ' actual flight. These tasks were analyzed using the RAFIV stage model (Sherry, Polson, et al. 2002). This analysis demonstrates that a great burden is placed on remembering complex reformulation of the task to function mapping. 65% of the tasks required retaining one access steps in memory to accomplish the task, 20% required two memorized access steps, and 15% required zero memorized access steps. The probability that a participant would make an access error on the tasks was: two memorized access steps - 74%, one memorized access step - 13%, and zero memorized access steps - 6%. Other factors were analyzed as well, including experience with the system and frequency of use. This completed the picture of a system with many memorized steps causing difficulty with the new system, especially when trying to fine where to access the correct function.

Fennell, Karl↗
DOE OSTI2021

The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa

Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Prediction and uncertainty quantification of shale well performance using multifidelity Monte Carlo

Uncertainty quantification is an integral component of reservoir management, especially considering the inherent uncertainty in subsurface systems. While a standard practice to estimate the uncertainty, Monte Carlo (MC) simulation is computationally intense when the sampling population comprises high-fidelity simulations. Alternatively, the Multi-fidelity Monte Carlo (MFMC) simulation overcomes this computational intensity by integrating low- and high-fidelity simulations. Our goal is to minimize the number of expensive high-fidelity simulations while maintaining accuracy and using numerous fast and cheap low-fidelity simulations to efficiently sample to input parameter space of interest. We selected gas production from unconventional wells to demonstrate the potential speedups and accuracy of the MFMC approach. The model fidelity usually determines the trade-off between accuracy and efficiency. While the high-fidelity model is more accurate, the low-fidelity model is more efficient. Our high-fidelity simulation includes reservoir simulations of a hydraulically fractured well. On the other hand, our low-fidelity model comprises the parallel-plate flow model. We used differential programming to efficiently solve the 1D flow model, where automatic differentiation is used to efficiently compute the gradients. We matched the production profile of high-fidelity simulations with our low-fidelity simulations. Then, we used a support vector regression to map the high- and low-fidelity input parameters. The mapping function is essential to tune the low-dimensional parameter space of the low-fidelity model to the high-dimensional parameter space of the high-fidelity model. We found that we can use a combination of 9 high fidelity and 10,000 low fidelity simulations to efficiently and accurately simulate pressure management. This method is at least two orders of magnitude faster than only using high-fidelity simulations. Finally, from a broader perspective, MFMC could efficiently estimate the uncertainty of various systems and models, integrating low- and high-fidelity models.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2024

A deep learning-based workflow for fast prediction of 3D state variables in geological carbon storage: A dimension reduction approach

Deep learning (DL) models are extensively used as surrogate models for high-fidelity simulations of multiphase fluid flow in porous media at large scales, enabling fast forecasts of the spatial–temporal evolution of three-dimensional (3D) state variables in geological carbon storage (GCS). However, training these models in high-dimensional space remains computationally demanding and prone to overfitting because of limited training data. This paper presents a novel workflow to address these challenges by integrating dimension reduction (DR) methods. Here, the proposed workflow employed pre-trained DR models to extract the latent variables of geological models and state variables and utilized the multi-layer perceptron (MLP) for constructing mapping functions between the input and output variables in latent spaces. Subsequently, the pre-trained reconstruction models converted the MLP-predicted latent state variables to their original high-dimensional form. Furthermore, we proposed a novel strategy for the DR and reconstruction of 3D saturation fields to account for the unique data characteristics of sparsity, nonuniformity, and discontinuity. The proposed strategy applied PCA and inverse PCA for 2D average saturation fields and developed a DL-based 3D reconstruction model, leveraging three 2D average saturation fields as input to produce a 3D saturation field as output. The pre-training of DR and reconstruction models and training of MLP models were conducted on 84 Gulf of Mexico (GoM) simulations and evaluated on 12 testing simulations. Each simulation contained 720 monthly time steps, with the first 360 months as the injection period and the rest as the post-injection period. The proposed workflow, incorporating DR and DL models, accurately predicts the normalized 3D pressure fields, achieving mean square error (MSE) of 2.92 × 10 -7 compared to the ground truth obtained from a full-physics simulator. Furthermore, the proposed strategy outperformed PCA and convolutional autoencoder (CAE) models on 3D saturation fields, resulting in minor workflow prediction errors with an MSE of 2.93 × 10 -5 . The results suggest the proposed workflow provides sufficient predictive fidelity across temporal and spatial scales, and enables a speedup of 160 times compared to the full-physics simulator, facilitating improved decision-making and risk assessment for large-scale GCS management in real-time scenarios.

3D reconstruction model↗
DOE OSTI2020

Dissolution of a cylindrical disk in Hele-Shaw flow: a conformal-mapping approach

Here we apply conformal mapping to find the evolving shapes of a dissolving cylinder in a potential flow. Similar equations can be used to describe melting in a flowing liquid phase. Results are compared with microfluidic experiments and numerical simulations. Shapes predicted by conformal mapping agree almost perfectly with experimental observations, after a modest (20 %) rescaling of the time. Finite-volume simulations show that the differences with experiment are connected to the underlying assumptions of the analytical model: potential flow and diffusion-limited dissolution. Approximate solutions of the equations describing the evolution of the shape of the undissolved solid can be derived from a Laurent expansion of the mapping function from the unit circle. Asymptotic expressions for the evolution of the area of the disk and the shift in its centre of mass have been derived at low and high Péclet number. Analytic approximations to the leading-order Laurent coefficients provide additional insight into the mechanisms underlying pore-scale dissolution.

58 GEOSCIENCES↗
DOE OSTI2021

Trap-Assisted Dopant Compensation Prevents Shunting in Poly-Si Passivating Interdigitated Back Contact Silicon Solar Cells

Using a trap-assisted compensation model, we explain why polycrystalline Si (poly-Si) passivating contacts are able to achieve low leakage current between the doped fingers of interdigitated back contact (IBC) monocrystalline Si solar cells despite mixing of boron and phosphorus dopants in the isolation region. The fill factor of IBC solar cells is strongly affected by the electrical isolation region between n- and p-type fingers, as this region is critical in minimizing shunting losses. During fabrication of monocrystalline Si solar cells with poly-Si passivating contacts, the intrinsic poly-Si isolation region inevitably gets contaminated with both p- and n-type dopants. Using dopant profiles measured with time-of-flight secondary ion mass spectrometry and scanning probe measurements of the isolation region, we demonstrate that despite the dopant spreading during cell processing, a well-compensated region between the doped fingers exists that prevents shunting. The trap-assisted dopant compensation mechanism significantly widens the compensated region to tens of microns, where the residual dopant densities are below the trap density. This enables a high-resistivity region, resulting in low shunt current. Using one-dimensional (1-D) finite element diode simulations, we identify the design parameters and experimental conditions under which a sufficiently resistive region can form. Furthermore, our measurements of 2-D local resistivity and work function maps across the isolation region using scanning spreading resistance microscopy and Kelvin probe force microscopy demonstrate the existence of a highly resistive, wide compensated region and confirm our proposed compensation mechanism. For our structures, this region is ~25 µm in width within a ~150 µm wide finger isolation region with nearly 3 orders of magnitude higher resistivity than the regions dominated by a single type of dopant.

14 SOLAR ENERGY↗
DOE OSTI2024

Bridging Hydrological Ensemble Simulation and Learning Using Deep Neural Operators

Ensemble-based simulation and learning (ESnL) has long been used in hydrology for parameter inference, but computational demands of process-based ESnL can be quite high. To address this issue, we propose a deep neural operator learning approach. Neural operators are generic machine learning algorithms that can learn functional mappings between infinite-dimensional spaces, providing a highly flexible tool for scientific machine learning. Our approach is built upon DeepONet, a specific deep neural operator, and is designed to address several common problems in hydrology, namely, model parameter estimation, prediction at ungaged locations, and uncertainty quantification. Here we demonstrate the effectiveness of our DeepONet-based workflow using an existing large model ensemble created for an eastern U.S. watershed that is instrumented with 10 streamflow gages. Results suggest DeepONet achieves high efficiency in learning an ML surrogate model from the model ensemble, with the modified Kling-Gupta Efficiency exceeding 0.9 on holdout test sets. Parameter inference, carried out using the trained DeepONet surrogate model and genetic algorithm, also yields robust results. Additionally, we formulate and train a separate DeepONet model for physics-informed, seq-to-seq streamflow forecasting, which further reduces biases in the pre-trained DeepONet surrogate model. While this study focuses primarily on a single watershed, our approach is general and may be extended to enable learning from model ensembles across multiple basins or models. Thus, this research represents a significant contribution to the application of hybrid machine learning in hydrology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Novel genetic risk factors influence progression of islet autoimmunity to type 1 diabetes

Type 1 diabetes arises from the autoimmune destruction of insulin-producing beta-cells of the pancreas, resulting in dependence on exogenously administered insulin to maintain glucose homeostasis. In this study, our aim was to identify genetic risk factors that contribute to progression from islet autoimmunity to clinical type 1 diabetes. We analyzed 6.8 million variants derived from whole genome sequencing of 160 islet autoantibody positive subjects, including 87 who had progressed to type 1 diabetes. The Cox proportional-hazard model for survival analysis was used to identify genetic variants associated with progression. We identified one novel region, 20p12.1 (TASP1; genome-wide P < 5 × 10 –8 ) and three regions, 1q21.3 (MRPS21–PRPF3), 2p25.2 (NRIR), 3q22.1 (COL6A6), with suggestive evidence of association (P < 8.5 × 10 –8 ) with progression from islet autoimmunity to type 1 diabetes. Once islet autoimmunity is initiated, functional mapping identified two critical pathways, response to viral infections and interferon signaling, as contributing to disease progression. These results provide evidence that genetic pathways involved in progression from islet autoimmunity differ from those pathways identified once disease has been established. These results support the need for further investigation of genetic risk factors that modulate initiation and progression of subclinical disease to inform efforts in development of novel strategies for prediction and intervention of type 1 diabetes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗