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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Comparing Individualized Survival Predictions From Random Survival Forests and Multistate Models in the Presence of Missing Data: A Case Study of Patients With Oropharyngeal Cancer

Background: In recent years, interest in prognostic calculators for predicting patient health outcomes has grown with the popularity of personalized medicine. These calculators, which can inform treatment decisions, employ many different methods, each of which has advantages and disadvantages. Methods: We present a comparison of a multistate model (MSM) and a random survival forest (RSF) through a case study of prognostic predictions for patients with oropharyngeal squamous cell carcinoma. The MSM is highly structured and takes into account some aspects of the clinical context and knowledge about oropharyngeal cancer, while the RSF can be thought of as a black-box non-parametric approach. Key in this comparison are the high rate of missing values within these data and the different approaches used by the MSM and RSF to handle missingness. Results: We compare the accuracy (discrimination and calibration) of survival probabilities predicted by both approaches and use simulation studies to better understand how predictive accuracy is influenced by the approach to (1) handling missing data and (2) modeling structural/disease progression information present in the data. We conclude that both approaches have similar predictive accuracy, with a slight advantage going to the MSM. Conclusions: Although the MSM shows slightly better predictive ability than the RSF, consideration of other differences are key when selecting the best approach for addressing a specific research question. These key differences include the methods’ ability to incorporate domain knowledge, and their ability to handle missing data as well as their interpretability, and ease of implementation. Ultimately, selecting the statistical method that has the most potential to aid in clinical decisions requires thoughtful consideration of the specific goals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2010

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher’s exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 59 and 39 half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

A Novel, Free-Space Optical Interconnect Employing Vertical-Cavity Surface Emitting Laser Diodes and InGaAs Metal-Semiconductor-Metal Photodetectors for Gbit/s RF/Microwave Systems

Emerging technologies and continuing progress in vertical-cavity surface emitting laser (VCSEL) diode and metal-semiconductor-metal (MSM) photodetector research are making way for novel, high-speed forms of optical data transfer in communication systems. VCSEL diodes operating at 1550 nm have only recently become commercially available, while MSM photodetectors are pushing the limits of contact lithography with interdigitated electrode widths reaching sub micron levels. We propose a novel, free-space optical interconnect operating at about 1Gbit/s utilizing VCSEL diodes and MSM photodetectors. We report on development, progress, and current work, which are as follows: first, analysis of the divergent behavior of VCSEL diodes for coupling to MSM photodetectors with a 50 by 50 m active area and second, the normalized frequency response of the VCSEL diode as a function of the modulating frequency. Third, the calculated response of MSM photodetectors with varying electrode width and spacing on the order of 1 to 3 m as well as the fabrication and characterization of these devices. The work presented here will lead to the formation and characterization of a fully integrated 1Gbit/s free-space optical interconnect at 1550 nm and demonstrates both chip level and board level functionality for RF/microwave digital systems.

Savich, Gregory R.↗
DOE OSTI2018

Multicolour photodetector based on a ZnSe/ZnTe/GaAs heterostructure

Structural, optical, and photoelectric properties of a ZeSe/ZnTe/GaAs heterostructure and a metal – semiconductor – metal detector (MSM-detector) based on this heterostructure are investigated. The composition and thickness of individual layers of the heterostructure are determined by the methods of energy dispersive analysis and Raman spectroscopy, and the optical properties are studied using the photoluminescence spectra. The ZeSe/ZnTe/GaAs heterostructure MSM-detector is highly sensitive. In particular, at a wavelength of 620 nm, the detector response signal corresponds to an ampere – watt sensitivity of 0.19 A W{sup −1} and an external quantum efficiency of 38 %. The MSM-detector photoresponse demonstrates three peaks located at wavelengths of 510, 620, and 870 nm. For the MSM-diode with a pin contact width of 2.8 μm, distances between them of 2.8 μm, and a total photosensitive area of 100 × 100 μm, the dark current density at room temperature constitutes 10{sup −8} A cm{sup −2}. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Electronic and optical device applications of hollow cathode plasma assisted atomic layer deposition based GaN thin films

Electronic and optoelectronic devices, namely, thin film transistors (TFTs) and metal–semiconductor–metal (MSM) photodetectors, based on GaN films grown by hollow cathode plasma-assisted atomic layer deposition (PA-ALD) are demonstrated. Resistivity of GaN thin films and metal-GaN contact resistance are investigated as a function of annealing temperature. Effect of the plasma gas and postmetallization annealing on the performances of the TFTs as well as the effect of the annealing on the performance of MSM photodetectors are studied. Dark current to voltage and responsivity behavior of MSM devices are investigated as well. TFTs with the N{sub 2}/H{sub 2} PA-ALD based GaN channels are observed to have improved stability and transfer characteristics with respect to NH{sub 3} PA-ALD based transistors. Dark current of the MSM photodetectors is suppressed strongly after high-temperature annealing in N{sub 2}:H{sub 2} ambient.

42 ENGINEERING↗
DOE OSTI2015

Actuation method and apparatus, micropump, and PCR enhancement method

An actuation apparatus includes at least one magnetic shape memory (MSM) element containing a material configured to expand and/or contract in response to exposure to a magnetic field. Among other things, the MSM element may be configured to pump fluid through a micropump by expanding and/or contracting in response to the magnetic field. The magnetic field may rotate about an axis of rotation and exhibit a distribution having a component substantially perpendicular to the axis of rotation. Further, the magnetic field distribution may include at least two components substantially orthogonal to one another lying in one or more planes perpendicular to the axis of rotation. The at least one MSM element may contain nickel, manganese, and gallium. A polymerase chain reaction (PCR) may be enhanced by contacting a PCR reagent and DNA material with the MSM element.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Influence of reabsorption and reemission on stimulated Raman scattering of polymethine dyes in multiple scattering media

It is shown that reabsorption of the luminescence radiation in the range of its overlapping with the absorption spectrum and the following reemission to a long-wavelength range may noticeably affect the process of stimulated Raman scattering (SRS) in polymethine dyes in multiple scattering media (MSM). This is related to the fact that SRS in such media occurs jointly with the random lasing (RL), which favors SRS and makes up with it a united nonlinear process. Reemission into the long-wavelength spectrum range amplified in MSM causes the RL spectrum to shift to longer wavelengths and initiates the long-wavelength band of RL, in which a main part of the lasing energy is concentrated. This weakens or completely stops the SRS if the band is beyond the range of possible spectral localisation of Stokes lines. This process depends on the efficiency of light scattering, dye concentration, temperature and pump intensity; hence, there exist optimal values of these parameters for obtaining SRS in MSM. (nonlinear optical phenomena)

36 MATERIALS SCIENCE↗
DOE OSTI2014

TU-F-BRF-06: 3D Pancreas MRI Segmentation Using Dictionary Learning and Manifold Clustering

Purpose: The recent advent of MRI guided radiotherapy machines has lent an exciting platform for soft tissue target localization during treatment. However, tools to efficiently utilize MRI images for such purpose have not been developed. Specifically, to efficiently quantify the organ motion, we develop an automated segmentation method using dictionary learning and manifold clustering (DLMC). Methods: Fast 3D HASTE and VIBE MR images of 2 healthy volunteers and 3 patients were acquired. A bounding box was defined to include pancreas and surrounding normal organs including the liver, duodenum and stomach. The first slice of the MRI was used for dictionary learning based on mean-shift clustering and K-SVD sparse representation. Subsequent images were iteratively reconstructed until the error is less than a preset threshold. The preliminarily segmentation was subject to the constraints of manifold clustering. The segmentation results were compared with the mean shift merging (MSM), level set (LS) and manual segmentation methods. Results: DLMC resulted in consistently higher accuracy and robustness than comparing methods. Using manual contours as the ground truth, the mean Dices indices for all subjects are 0.54, 0.56 and 0.67 for MSM, LS and DLMC, respectively based on the HASTE image. The mean Dices indices are 0.70, 0.77 and 0.79 for the three methods based on VIBE images. DLMC is clearly more robust on the patients with the diseased pancreas while LS and MSM tend to over-segment the pancreas. DLMC also achieved higher sensitivity (0.80) and specificity (0.99) combining both imaging techniques. LS achieved equivalent sensitivity on VIBE images but was more computationally inefficient. Conclusion: We showed that pancreas and surrounding normal organs can be reliably segmented based on fast MRI using DLMC. This method will facilitate both planning volume definition and imaging guidance during treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Microsimulation model calibration using incremental mixture approximate Bayesian computation

Microsimulation models (MSMs) are used to inform policy by predicting population-level outcomes under different scenarios. MSMs simulate individual-level event histories that mark the disease process (such as the development of cancer) and the effect of policy actions (such as screening) on these events. MSMs often have many unknown parameters; calibration is the process of searching the parameter space to select parameters that result in accurate MSM prediction of a wide range of targets. We develop Incremental Mixture Approximate Bayesian Computation (IMABC) for MSM calibration which results in a simulated sample from the posterior distribution of model parameters given calibration targets. IMABC begins with a rejection-based ABC step, drawing a sample of points from the prior distribution of model parameters and accepting points that result in simulated targets that are near observed targets. Next, the sample is iteratively updated by drawing additional points from a mixture of multivariate normal distributions and accepting points that result in accurate predictions. Posterior estimates are obtained by weighting the final set of accepted points to account for the adaptive sampling scheme. We demonstrate IMABC by calibrating CRC-SPIN 2.0, an updated version of a MSM for colorectal cancer (CRC) that has been used to inform national CRC screening guidelines.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Masked Symbol Modeling for Demodulation of Oversampled Baseband Communication Signals in Impulsive Noise-Dominated Channels

Recent breakthroughs in natural language processing show that attention mech- anism in Transformer networks, trained via masked-token prediction, enables models to capture the semantic context of the tokens and internalize the grammar of language. While the application of Transformers to communication systems is a burgeoning field, the notion of context within physical waveforms remains under-explored. This paper addresses that gap by re-examining inter-symbol con- tribution (ISC) caused by pulse-shaping overlap. Rather than treating ISC as a nuisance, we view it as a deterministic source of contextual information embedded in oversampled complex baseband signals. We propose Masked Symbol Model- ing (MSM), a framework for the physical (PHY) layer inspired by Bidirectional Encoder Representations from Transformers methodology. In MSM, a subset of symbol-aligned samples is randomly masked, and a Transformer predicts the missing symbol identifiers using the surrounding “in-between” samples. Through this objective, the model learns the latent syntax of complex baseband waveforms. We illustrate MSM’s potential by applying it to the task of demodulating sig- nals corrupted by impulsive noise, where the model infers corrupted segments by leveraging the learned context. Our results suggest a path toward receivers that interpret, rather than merely detect communication signals, opening new avenues for context-aware PHY layer design.

Bedir, Oguz↗
NASA NTRS1976

Design principles of a rotating medium speed mechanism

Design principles of a medium speed mechanism (MSM) are presented, including discussion on the relative merits of beryllium and aluminium as structural materials. Rotating at a speed of 60 rpm, the application envisaged for the MSM was as a despin bearing for the despun platform or despun antenna of a spin stabilized satellite. The MSM was built and tested to qualification level and is currently undergoing real time life testing.

Hostenkamp, R. G.↗
NASA NTRS1996

New Concentric Electrode Metal-Semiconductor-Metal Photodetectors

A new metal-semiconductor-metal (MSM) photodetector geometry is proposed. The new device has concentric metal electrodes which exhibit a high degree of symmetry and a design flexibility absent in the conventional MSM device. The concentric electrodes are biased to alternating potentials as in the conventional interdigitated device. Because of the high symmetry configuration, however, the new device also has a lower effective capacitance. This device and the conventional MSM structure are analyzed within a common theoretical framework which allows for the comparison of the important performance characteristics.

Towe, Elias↗
NASA NTRS1994

Theoretical Study of the Effect of an AlGaAs Double Heterostructure on Metal-Semiconductor-Metal Photodetector Performance

The impulse and square-wave input response of different GaAs metal-semiconductor-metal photodetector (MSM) designs are theoretically examined using a two dimensional drift- diffusion numerical calculation with a thermionic-field emission boundary condition model for the heterojunctions. The rise time and the fall time of the output signal current are calculated for a simple GaAs, epitaxially grown, MSM device as well as for various double-heterostructure barrier devices. The double heterostructure devices consist of an AlGaAs layer sandwiched between the top GaAs active, absorption layer and the bottom GaAs substrate. The effect of the depth of the AlGaAs layer on the speed and responsivity of the MSM devices is examined. It is found that there is an optimal depth, at fixed applied bias, of the AlGaAs layer within the structure that provides maximum responsivity at minimal compromise in speed.

Salem, Ali F.↗
NASA NTRSDate not supplied

Risk-Reduction Autonomy Implementation to Enable NASA Artemis Missions

To achieve NASA’s Artemis program mission objectives a high level of autonomy and ubiquitous autonomy throughout the systems that are being developed will be necessary. The autonomous systems of Artemis will require a distributed autonomy capability, with autonomous systems organized functionally in a hierarchical architecture, where systems at higher levels of the hierarchy have authority over systems at lower levels. The challenge of developing autonomy technologies and concepts of operations for Artemis has been undertaken by the NASA Gateway Working Group. This group has developed requirements, architectures, concepts of operations, and interface control documents, in the context of a hierarchical distributed architecture that includes the following: a Vehicle System Manager (VSM) that autonomously manages the entire Gateway; Module System Managers (MSMs) that autonomously manage each module; and System Managers (SMs) that autonomously manage systems within a module(i.e. ECLSS).A substantially high level of autonomy needs to be achieved by each element of the hierarchy (VSM, MSM, SM)to meet requirements for uncrewed operations; this includes conditions that will have minimal and/or delayed ground intervention (i.e. requirements for sustainability for months of operation without crew or ground support). To advance an implementation of this autonomy design (Gateway Autonomy Design –GAD), a collaboration was established between the Autonomous Systems Laboratory (ASL) at NASA Stennis Space Center and Lockheed Martin. The objectives of this partnership were the following: (1)to implement autonomy at the VSM, MSM, and SM levels;(2) to implement communications among a VSM, 2 MSMs, ORION (a visiting vehicle somewhat equivalent to a module) and 1 SM (a power system), and (3) test autonomous operations with representative use cases. A SM backed by a high-fidelity simulation was created to facilitate demonstrations of use cases that originated in a system of a module. Communication between the VSM and MSMs was implemented according to Concepts of Operations and Interface Control Documents (ICDs). Demonstrations were conducted to address nominal and off-nominal operations and multi-module interactions with VSM. Additionally, user interfaces were created to provide awareness about ongoing processes and results while enhancing the demonstration. Demonstrations included the following use cases: (1)Orion as visiting vehicle registers with VSM;(2) VSM reschedules a module’s timelines when another module’s MSM task fails; and (3) a module’s Power System Manager (PSM) standalone demonstration that included component failure diagnostics, tracing component failure to effected components, which in turn, reports failure information up to the VSM for acknowledgement and display. This paper will describe the detailed technology and autonomous systems developed, and the integrated multi-module demonstrations conducted. Also, challenges that must be met to fully implement the GAD defined by Gateway will be addressed.

Autonomous Systems↗
NASA NTRSDate not supplied

Risk-Reduction Autonomy Implementation to Enable NASA Artemis Missions

To achieve NASA’s Artemis program mission objectives a high level of autonomy that is ubiquitous throughout the systems that are being developed will be necessary. The autonomous systems of Artemis will require a distributed autonomy capability, with autonomous systems organized functionally in a hierarchical architecture, where systems at higher levels of the hierarchy have authority over systems at lower levels. The challenge of developing autonomy technologies and Concepts of Operations (ConOps) for Artemis has been undertaken by the NASA Gateway Working Group. This group has developed requirements, architectures, ConOps, and interface control documents (ICDs), in the context of a hierarchical distributed architecture that includes the following: a Vehicle System Manager (VSM) that autonomously manages the entire Gateway; Module System Managers (MSMs) that autonomously manage each module; and System Managers (SMs) that autonomously manage systems within a module (i.e. ECLSS). A substantially high level of autonomy needs to be achieved by each element of the hierarchy (VSM, MSM, SM) to meet requirements for uncrewed operations; this includes conditions that will have minimal and/or delayed ground intervention (i.e. requirements for sustainability for months of operation without crew or ground support). To advance an implementation of this autonomy design (Gateway Autonomy Design – GAD), a collaboration was established between the Autonomous Systems Laboratory (ASL) at NASA Stennis Space Center and Lockheed Martin. The objectives of this partnership were the following: (1) to implement autonomy at the VSM, MSM, and SM levels; (2) to implement communications among a VSM, 2 MSMs, ORION (a visiting vehicle somewhat equivalent to a module) and 1 SM (a power system), and (3) test autonomous operations with representative use cases. A SM backed by a high-fidelity simulation was created to facilitate demonstrations of use cases that originated in a system of a module. Communication between the VSM and MSMs was implemented according to Concepts of Operations and Interface Control Documents (ICDs). Demonstrations were conducted to address nominal and off-nominal operations and multi-module interactions with the VSM. Additionally, user interfaces were created to provide awareness about ongoing processes and results while enhancing the demonstration. Demonstrations included the following use cases: (1) Orion as visiting vehicle registers with VSM; (2) VSM reschedules a module’s timelines when another module’s MSM task fails; and (3) a module’s Power System Manager (PSM) demonstration that included component failure diagnostics, tracing component failure to effected components, which in turn, reports failure information up to the VSM for acknowledgement and display. This paper will describe the detailed technology and autonomous systems developed, and the integrated multi-module demonstrations conducted. Also, challenges that must be met to fully implement the GAD defined by Gateway will be addressed.

Fernando Figueroa↗
DOE OSTI2012

Development of reactivity feedback effect measurement techniques under sub-critical condition in fast reactors

The first-of-a-kind reactor has been licensed by a safety examination of the plant design based on the measured data in precedent mock-up experiments. The validity of the safety design can be confirmed without a mock-up experiment, if the reactor feed-back characteristics can be measured before operation, with the constructed reactor itself. The 'Synthesis Method', a systematic and sophisticated method of sub-criticality measurement, is proposed in this work to ensure the safety margin before operation. The 'Synthesis Method' is based on the modified source multiplication method (MSM) combined with the noise analysis method to measure the reference sub-criticality level for MSM. A numerical simulation for the control-rod reactivity worth and the isothermal feed-back reactivity was conducted for typical fast reactors of 100 MWe-size, 300 MWe-size, 750 MWe-size, and 1500 MWe-size to investigate the applicability of Synthesis Method. The number of neutron detectors and their positions necessary for the measurement were investigated for both methods of MSM and the noise analysis by a series of parametric survey calculations. As a result, it was suggested that a neutron detector located above the core center and three or more neutron detectors located above the radial blanket region enable the measurement of sub-criticality within 10% uncertainty from -$0.5 to -$2 and within 15% uncertainty for the deeper sub-criticality. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗