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At least 739 records · Page 41

Efficient Agent-Based Models for Non-Genomic Evolution

Modeling dynamical systems composed of aggregations of primitive proteins is critical to the field of astrobiological science involving early evolutionary structures and the origins of life. Unfortunately traditional non-multi-agent methods either require oversimplified models or are slow to converge to adequate solutions. This paper shows how to address these deficiencies by modeling the protein aggregations through a utility based multi-agent system. In this method each agent controls the properties of a set of proteins assigned to that agent. Some of these properties determine the dynamics of the system, such as the ability for some proteins to join or split other proteins, while additional properties determine the aggregation s fitness as a viable primitive cell. We show that over a wide range of starting conditions, there are mechanisins that allow protein aggregations to achieve high values of overall fitness. In addition through the use of agent-specific utilities that remain aligned with the overall global utility, we are able to reach these conclusions with 50 times fewer learning steps.

Gupta, Nachi↗

Are Medications Involved in Vision and Intracrancial Pressure Changes Seen in Spaceflight?

The Food and Drug Association Adverse Event Reports (FDA AER) from 2009-2011 were used to create a database from millions of known and suspected medication-related adverse events among the general public. Vision changes, sometimes associated with intracranial pressure changes (VIIP), have been noted in some long duration crewmembers. Changes in vision and blood pressure (which can subsequently affect intracranial pressure) are fairly common side effects of medications. The purpose of this study was to explore the possibility of medication involvement in crew VIIP symptoms. Reports of suspected medication-related adverse events may be filed with the Food and Drug Administration (FDA) by medical professionals or consumers. Quarterly compilations of these reports are available for public download. Adverse Event Reporting System (AERS) reports from 1/1/2009- 6/30/2012 were downloaded and compiled into a searchable database for this study. Reports involving individuals under the age of 18 and older than 65 were excluded from this analysis. Case reports involving chronic diseases such as cancer, diabetes, multiple sclerosis and other serious conditions were also excluded. A scan of the medical literature for medication-related VIIP-like adverse events was used to create a list of suspect medications. These medications, as well as certain medications used frequently by ISS crew, were used to query the database. Queries for use of suspected medications were run, and the nature of the symptoms reported in those cases were tabulated. Symptoms searched in the FDA AERS were chosen to include the typical symptoms noted in crewmembers with VIIP. Vision symptoms searched were: visual acuity reduced, visual impairment, and vitreous floaters. Pressure changes included: abnormal sensation in eye, intracranial pressure increased, intraocular pressure increased, optic neuritis, optic neuropathy, and papilloedema. Limited demographic information is included with the FDA AERS; relevant data were also sorted by age and sex from each report. RESULTS Steroid-containing oral contraceptives had the highest number of reports associated with vision (n=166) and pressure symptoms (n=54). Corticosteroid-containing medications were also high; prednisone, for example, had 137 reports of vision issues and 79 of pressure issues. Pain relievers were also a medication class with vision and pressure-related adverse events reported. Common over-the-counter medications such as acetaminophen, aspirin and ibuprofen each had multiple reports for both vision and pressure symptoms. Antimicrobial medications ciprofloxacin and diflucan were also associated with a number of vision and pressure-related AERS. Unexpectedly, pseudoephedrine and promethazine were mentioned in fewer than 20 reports each over the 3.5 years of data examined. The FDA AERS represents a wealth of data, but there are several limitations to its use. The data are entered by the public or medical professionals, but are not checked for accuracy or completeness and may even be entered multiple times. The causal relationship between a particular adverse event and a particular medication is not tested. The cases represent a broad spectrum of demographics, occupations, and health histories, and thus do not model the astronaut population well. There is no information on the frequency of use of a medication for comparison purposes; it is not possible to assign a rate for any particular adverse event. Nonetheless, there are compelling trends. Use of corticosteroid-containing medications, pain relievers (even over-the-counter), and oral contraceptives were associated with higher numbers of vision- or intracranial pressure-related adverse events. In general, there were more vision problems than pressure problems reported. Certain medications that were once suspected of playing a role in the crew VIIP syndrome, namely pseudoephedrine and promethazine, were found to have extremely low numbers of VIIP-like AERS in the FDA data. However, crew use of corticosteroid-containing medications and pain relievers may warrant additional investigation

Faust, K. M.↗

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting

Many existing object counting methods rely on density map estimation (DME) of the discrete grid representation by decoding extracted image semantic features from designed convolutional neural networks (CNNs). Relying on discrete density maps not only leads to information loss dependent on the original image resolution, but also has a scalability issue when analyzing high-resolution images with cubically increasing memory complexity. Furthermore, none of the existing methods can offer reliable uncertainty quantification (UQ) for the derived count estimates. To overcome these limitations, we design UNcertainty-aware, hypernetwork-based Implicit neural representations for Counting (UNIC) to assign probabilities and the corresponding counting confidence over continuous spatial coordinates. We derive a sampling-based Bayesian counting loss function and develop the corresponding model training algorithm. UNIC outperforms existing methods on the Remote Sensing Object Counting (RSOC) dataset with reliable UQ and improved interpretability of the derived count estimates. Our code is available at https://github.com/SiyuanXu-tamu/UNIC.

97 MATHEMATICS AND COMPUTING↗

Diffusion lengths in irradiated N/P InP-on-Si solar cells

Indium phosphide (InP) solar cells were made on silicon (Si) wafers (InP/Si) by to take advantage of both the radiation-hardness properties of the InP solar cell and the light weight and low cost of Si wafers. The InP/Si cell application is for long duration and/or high radiation orbit space missions. Spire has made N/P InP/Si cells of sizes up to 2 cm by 4 cm with beginning-of-life (BOL) AM0 efficiencies over 13% (one-sun, 28C). These InP/Si cells have higher absolute efficiency and power density after a high radiation dose than gallium arsenide (GaAs) or silicon (Si) solar cells after a fluence of about 2e15 1 MeV electrons/sq. cm. In this work, we investigate the minority carrier (electron) base diffusion lengths in the N/P InP/Si cells. A quantum efficiency model was constructed for a 12% BOL AM0 N/P InP/Si cell which agreed well with the absolutely measured quantum efficiency and the sun-simulator measured AM0 photocurrent (30.1 mA/sq. cm). This model was then used to generate a table of AM0 photocurrents for a range of base diffusion lengths. AM0 photocurrents were then measured for irradiations up to 7.7e16 1 MeV electrons/sq. cm (the 12% BOL cell was 8% after the final irradiation). By comparing the measured photocurrents with the predicted photocurrents, base diffusion lengths were assigned at each fluence level. A damage coefficient K of 4e-8 and a starting (unirradiated) base electron diffusion length of 0.8 microns fits the data well. The quantum efficiency was measured again at the end of the experiment to verify that the photocurrent predicted by the model (25.5 mA/sq. cm) agreed with the simulator-measured photocurrent after irradiation (25.7 mA/sq. cm).

Wojtczuk, Steven↗

Gaussian mixture model clustering algorithms for the analysis of high-precision mass measurements

The development of the phase-imaging ion-cyclotron resonance (PI-ICR) technique for use in Penning trap mass spectrometry (PTMS) increased the speed and precision with which PTMS experiments can be carried out. In PI-ICR, data sets of the locations of individual ion hits on a detector are created showing how ions cluster together into spots according to their cyclotron frequency. Ideal data sets would consist of a single, 2D-spherical spot with no other noise, but in practice data sets typically contain multiple spots, non-spherical spots, or significant noise, all of which can make determining the locations of spot centers non-trivial. A method for assigning groups of ions to their respective spots and determining the spot centers is therefore essential for further improving precision and confidence in PI-ICR experiments. Here, we present the class of Gaussian mixture model (GMM) clustering algorithms as an optimal solution. We show that on simulated PI-ICR data, several types of GMM clustering algorithms perform better than other clustering algorithms over a variety of typical scenarios encountered in PI-ICR. The mass spectra of 163Gd, 163 mGd, 162 Tb, and 162 mTb measured using PI-ICR at the Canadian Penning trap mass spectrometer were checked using GMMs, producing results that were in close agreement with the previously published values.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Application of large eddy interaction model to channel flow

A procedure utilizing an expansion of proper orthogonal functions (or modes) to predict a fully developed flow in channel is derived. To examine numerical and conceptual difficulties, preliminary computations are performed with assigned mean velocity, and turbulence is expressed with only the first mode. The nonlinear interactions of the components of the first mode are treated specifically, with the influence of higher modes neglected; this treatment required adjustment of the skewness and effective Reynolds number to assure energy equilibrium of the first mode. Computational results show that the first mode possesses the structural character similar to that of the entire flow.

Hong, S. K.↗

Application of a large-eddy interaction model to channel flow

A procedure utilizing an expansion of proper orthogonal functions (or modes) to predict a fully developed flow in channel is derived. To examine numerical and conceptual difficulties, preliminary computations are performed with assigned mean velocity, and turbulence is expressed with only the first mode. The nonlinear interactions of the components of the first mode are treated specifically, with the influence of higher modes neglected; this treatment required adjustment of the skewness and effective Reynolds number to assure energy equilibrium of the first mode. Computational results show that the first mode possesses the structural character similar to that of the entire flow.

Hong, S. K.↗

Component modes damping assignment methodology for articulated, multiflexible body structures

To simulate the dynamical motion of articulated, multiflexible body structures, one can use multibody simulation packages such as DISCOS. To this end, one must supply appropriate reduced-order models for all of the flexible components involved. The component modes projection and assembly model reduction (COMPARE) methodology is one way to construct these reduced-order component models, which when reassembled capture important system input-to-output mapping of the full-order model at multiple system configurations of interest. In conjunction, we must also supply component damping matrices which when reassembled generate a system damping matrix that has certain desirable properties. The problem of determining the damping factors of components' modes to achieve a given system damping matrix is addressed here. To this end, we must establish from first principles a matrix-algebraic relation between the system's modal damping matrix and the components' modal damping matrices. An unconstrained/constrained optimization problem can then be formulated to determine the component modes' damping factors that best satisfy that matrix-algebraic relation. The effectiveness of the developed methodology, called ModeDamp, has been successfully demonstrated on a high-order, finite element model of the Galileo spacecraft.

Lee, Allan Y.↗

Synchrotron X-ray diffraction analysis of constituent phases in transition joint between nickel alloy 738LC and a MnFeCoNiCu alloy

Synchrotron x-ray diffraction (XRD) analysis was performed on transition joints between a single-phase MnFeCoNiCu alloy and Ni-base Alloy 738LC to efficiently identify the constituent phases across the interface, with different levels of material intermixing generated by laser-welding with variable power. Here, the intermixing extent was quantified by postmortem energy dispersive x-ray spectroscopy mapping. Diffraction-based analyses on complex composition spaces with limited prior data present significant challenges because elemental substitution in both disordered and ordered phases is more extensive than in conventional alloy spaces, which may effectuate relatively large shifts in the observed lattice parameters that convolute the analysis. Therefore, thermodynamic simulations and crystallographic literature data were employed to construct a system-specific diffraction library of twelve prospective phases for the composition space investigated. Subsequently, for predicted disordered cubic phases, statistical hard-sphere models were established to estimate the lattice parameters and predict diffraction peak positions for inclusion in the library. The library was then employed to analyze diffraction profiles measured from the variably intermixed transition joints, with focus on accounting for both high and low-intensity peaks. 99.0 % of diffraction peaks with relative intensity greater than 0.001 were assigned to phases from the system-specific library, exemplifying rigorous peak accounting and indicating that no unexpected phases were present. Up to six of the twelve library phases were experimentally found in the transition joints. The lattice parameters predicted by the statistical hard-sphere model based upon thermodynamic simulations agree reasonably well with the measured values for the disordered FCC matrix phase.

36 MATERIALS SCIENCE↗

Robust Assignment Of Eigensystems For Flexible Structures

Improved method for placement of eigenvalues and eigenvectors of closed-loop control system by use of either state or output feedback. Applied to reduced-order finite-element mathematical model of NASA's MAST truss beam structure. Model represents deployer/retractor assembly, inertial properties of Space Shuttle, and rigid platforms for allocation of sensors and actuators. Algorithm formulated in real arithmetic for efficient implementation. Choice of open-loop eigenvector matrix and its closest unitary matrix believed suitable for generating well-conditioned eigensystem with small control gains. Implication of this approach is that element of iterative search for "optimal" unitary matrix appears unnecessary in practice for many test problems.

Juang, Jer-Nan↗

A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors

Abstract TGA (TGACG-binding) transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigated the role of StTGA2.1, a potato (Solanum tuberosum) TGA lacking the full bZIP, which we named a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirmed that StTGA2.1 overexpression compensates for SA-deficiency, indicating a distinct mechanism of action compared with model plant species. To understand the underlying mechanisms, we showed that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigated the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirmed that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases (StPRX), which are known to play role in immune response. Finally, via structural modeling and molecular dynamics simulations, we hypothesized that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to distinct functions and that such events should be studied carefully in other protein families.

59 BASIC BIOLOGICAL SCIENCES↗

Shell structure of 43 S and collapse of the N = 28 shell closure

The single-particle structure of the N = 27 isotones provides insights into the shell evolution of neutron-rich nuclei from the doubly-magic 48 Ca toward the drip line. 43 S was studied employing the one-neutron knockout reaction from a radioactive 44 S beam. Using a combination of prompt and delayed γ-ray spectroscopy the level structure of 43 S was clarified. Momentum distributions were analyzed and allowed for spin and parity assignments. The deduced spectroscopic factors show that the 44 S ground-state configuration has a strong intruder component. Here, the results were confronted with shell model calculations using two effective interactions. General agreement was found between the calculations, but strong population of states originating from the removal of neutrons from the 2p 3/2 orbital in the experiment indicates that the breakdown of the N = 28 magic number is more rapid than the theoretical calculations suggest.

39 ≤ A ≤ 58↗

Dose-dependent structural and electron-density features in the lytic polysaccharide monooxygenase NcAA9D

Structural studies of copper-containing lytic polysaccharide monooxygenases (LPMOs) by X-ray crystallography are often complicated by radiation damage. In this study, we analyze a series of 36 X-ray crystal structures of NcAA9D, a Neurospora crassa AA9-family LPMO, determined from data collected at cryogenic temperature from a single crystal to investigate the progressive effects of radiation damage at the active site of this enzyme. We report new insights into the dose-dependence of active-site geometry in LPMOs and utilize the unique pre-bound dioxygen site of NcAA9D to analyze the impact of X-ray dose on the electron density of this species. It is well established that photoreduction of the LPMO active-site copper(II) leads to expulsion of its water ligands. We further characterize this displacement and the corresponding electron-density smearing, a phenomenon that can lead to the erroneous modeling of copper-bound dioxygen species. These findings suggest that radiation-dose series collected from a single crystal provide invaluable data to support unambiguous assignment of radiation-sensitive intermediates at the active site of LPMOs and other radiation-sensitive redox enzymes.

Miller, Samuel [ORNL] (ORCID:0009000459491817)↗

RWRtoolkit Narrative

This narrative presents a demonstration of RWRtools methods to the important bioenergy feedstock Panicum virgatum (Switchgrass) by leveraging networks from the model plant Arabidopsis thaliana. We used a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with Switchgrass shoot biomass. We then assigned these SNPs to Switchgrass genes, and using Phytozome (Goodstein et al., 2012), assigned these 38 Switchgrass GWAS genes to 32 Arabidopsis orthologs. These 32 genes are the starting set of genes (i.e. the seed gene set) for this demo narrative.

59 BASIC BIOLOGICAL SCIENCES↗

Oxygen isotope cosmothermometer.

Variations in oxygen isotopic abundances of meteoritic minerals, chondrules, whole meteorites, and planets are discussed in terms of a model involving isotopic exchange between primordial dust and a cooling solar nebular gas. From the temperature-dependence of the isotopic fractionation factors, temperatures have been assigned to the processes of initial condensation, chondrule formation, and planetary accretion. Separated phases from carbonaceous chondrites fall into three isotopic groups representing widely differing conditions of formation: (1) low-iron olivine and pyroxene, and calcium-aluminum silicates condensed at temperatures above 1000 K; (2) high-iron olivine and pyroxene melted to form chondrules after prior cooling and exchange to temperatures of 530-620 K; and (3) hydrous silicates condensed at temperatures below 400 K.

Onuma, N.↗

An alternative resource sharing scheme for land mobile satellite services

A preliminary comparison between the two competing channelization concepts for the Land Mobile Satellite Services (LMSS), namely frequency division (FD) and code division (CD), is presented. Both random access and demand-assigned approaches are considered under these concepts. The CD concept is compared with the traditional FD concept based on the system consideration and a projected traffic model. It is shown that CD is not particularly attractive for the first generation Mobile Satellite Services because of the spectral occupancy of the network bandwidth. However, the CD concept is a viable alternative for future systems such as the personal access satellite system (PASS) in the Ka-band spectrum where spectral efficiency is not of prime concern. The effects of power robbing and voice activity factor are incorporated. It was shown that the traditional rule of thumb of dividing the number of raw channels by the voice activity factor to obtain the effective number of channels is only valid asymptotically as the aggregated traffic approaches infinity.

Yan, Tsun-Yee↗

Robustness of reduced-order multivariable state-space self-tuning controller

In this paper, we present a quantitative analysis of the robustness of a reduced-order pole-assignment state-space self-tuning controller for a multivariable adaptive control system whose order of the real process is higher than that of the model used in the controller design. The result of stability analysis shows that, under a specific bounded modelling error, the adaptively controlled closed-loop real system via the reduced-order state-space self-tuner is BIBO stable in the presence of unmodelled dynamics.

Yuan, Zhuzhi↗

A Probabilistic Tool that Aids Logistics Engineers in the Establishment of High Confidence Repair Need-Dates at the NASA Shuttle Logistics Depot

The NASA Shuttle Logistics Depot (NSLD) is tasked with the responsibility for repair and manufacture of Line Replaceable Unit (LRU) hardware and components to support the Space Shuttle Orbiter. Due to shrinking budgets, cost effective repair of LRU's becomes a primary objective. To achieve this objective, is imperative that resources be assigned to those LRU's which have the greatest expectation of being needed as a spare. Forecasting the times at which spares are needed requires consideration of many significant factors including: failure rate, flight rate, spares availability, and desired level of support, among others. This paper summarizes the results of the research and development work that has been accomplished in producing an automated tool that assists in the assignment of effective repair start-times for LRU's at the NSLD. This system, called the Repair Start-time Assessment System (RSAS), uses probabilistic modeling technology to calculate a need date for a repair that considers the current repair pipeline status, as well as, serviceable spares and projections of future demands. The output from the system is a date for beginning the repair that has significantly greater confidence (in the sense that a desired probability of support is ensured) than times produced using other techniques. Since an important output of RSAS is the longest repair turn-around time that will ensure a desired probability of support, RSAS has the potential for being applied to operations at any repair depot where spares are on-hand and repair start-times are of interest. In addition, RSAS incorporates tenants of Just-in-Time (JIT) techniques in that the latest repair start-time (i.e., the latest time at which repair resources must be committed) may be calculated for every failed unit This could reduce the spares inventory for certain items, without significantly increasing the risk of unsatisfied demand.

Bullington, J. V.↗