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At least 1,009 records · Page 56

Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations

The interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical information loss. This is particularly important in the analysis of large phenotypic datasets (phenomics). Here we introduce Multi-Attribute Subset Selection (MASS), an algorithm which separates a matrix of phenotypes (e.g., yield across microbial species and environmental conditions) into predictor and response sets of conditions. Using mixed integer linear programming, MASS expresses the response conditions as a linear combination of the predictor conditions, while simultaneously searching for the optimally descriptive set of predictors. We apply the algorithm to three microbial datasets and identify environmental conditions that predict phenotypes under other conditions, providing biologically interpretable axes for strain discrimination. MASS could be used to reduce the number of experiments needed to identify species or to map their metabolic capabilities. The generality of the algorithm allows addressing subset selection problems in areas beyond biology.

59 BASIC BIOLOGICAL SCIENCES↗

SOAREX-8 Suborbital Experiments 2015 - A New Paradigm for Small Spacecraft Communication

In 2015 NASA plans to launch a payload to 280 Km altitude on a sounding rocket from the Wallops Flight Facility. This payload will contain several novel technologies that work together to demonstrate methodologies for space sample return missions and for nanosatellite communications in general. The payload will deploy and test an Exo-Brake, which slows the payload aerodynamically, providing eventual de-orbit and recovery of future ISS samples through a Small Payload Quick Return project. In addition, this flight addresses future Mars mission entry technology, space-to-space communications using the Iridium Short Messaging Service (SMS), GPS tracking, and wireless sensors using the ZigBee protocol. SOAREX-8 is being assembled and tested at Ames Research Center (ARC) and the NASA Engineering and Safety Center (NESC) is funding sensor and communications work. Open source Arduino technology and software are used for system control. The ZigBee modules used are XBee units that connect analog sensors for temperature, air pressure and acceleration measurement wirelessly to the payload telemetry system. Our team is developing methods for power distribution and module mounting, along with software for sensor integration, data assembly and downlink. We have demonstrated relaying telemetry to the ground using the Iridium satellite constellation on a previous flight, but the upcoming flight will be the first time we integrate useful flight test data from a ZigBee wireless sensor network. Wireless sensor data will measure the aerodynamic efficacy of the Exo-Brake permitting further on orbit flight tests of improved designs. The Exo-Brake is 5 sq m in area and will be stored in a container and deployed during ascent once the payload is jettisoned from the launch vehicle. We intend to further refine the hardware and continue testing on balloon launches, future sounding rocket flights and on nanosatellite missions. The use of standards-based and open source hardware/software has allowed for this project to be completed with a very modest budget and a challenging schedule. There is a wealth of hardware and software available for both the Arduino platform and the XBee, all low-cost or open-source. Along with the Exo-Brake hardware and deployment discussion, this paper will describe in detail the system architecture emphasizing the successful use of open source hardware and software to minimize effort and cost. Testing procedures, radio frequency interference (RFI) mitigation, success criteria and expected results will also be discussed. The use of Iridium short messaging capability for space-to-space links, standards-based wireless sensor networks, and other innovative communications technology are also presented.

aerobrake↗

Transitioning the NASA SLR Network to Event Timing Mode for Reduced Systematics, Improved Stability and Data Precision

NASA's legacy Satellite Laser Ranging (SLR) network produces about one-third of the global SLR data to support spacegeodesy. This network of globally distributed stations has been using Time Interval Units (TIU) for range measurements for thelast 25 + years. To improve the reliability of the SLR network and satisfy the need for stable millimeter precision data, a phasedreplacement of the TIUs in the network with picosecond-precise Event Timer Modules was initiated in 2015. This schemeallowed the time of flight and laser transmit epoch measurement to one picosecond resolution. For a network with globalscientific impact, transitioning to a new data generation metrological scheme requires significant data scrutiny and long-termscience data validation. Any long-term testing/measurement has the potential to interrupt the station's daily operational dataflow to the International Laser Ranging Service (ILRS) as the station under test will have to put its test data into quarantine.We have demonstrated a very effective way to test and implement the new device without removing the old hardware andwithout the need for the orbit analysis. This operationally noninvasive scheme performed concurrent test measurements enablinguninterrupted operational data flow to the users, while allowing simultaneous test data capture for short- and long-termsystematics and stability analysis. Extensive analysis of the test data was performed by the NASA SLR engineering team andthe ILRS Analysis Standing Committee, to uncover biases and any dependencies on the satellite ranges (for nonlinear scaleissues). Multi-ETM comparison was also performed at two of the SLR stations through the interchange of hardware to establishthe inter-device range biases and stability. Such benchmarked hardware was subsequently sent to the remaining stationsto allow traceability and normalize the network performance. The range bias intercomparison performed using the multiyearSLR data analysis agreed well with the engineering changes, thus validating the approach to flush out station-specific rangingsystematics affecting precise orbit determination. Such an improvement and rebalancing of the current network will allowan orderly transition of the current NASA SLR network operating at a maximum rate of 10 Hz to the NASA next generationSpace Geodesy Satellite Laser Ranging (SGSLR) network operating at 2 kHz (McGarry et al. in J Geod, 2018. https ://doi.org/10.1007/s0019 0-018-1191-6; Merkowitz et al. in J Geod, 2018. https ://doi.org/10.1007/s0019 0-018-1204-5).

Varghese, Thomas↗

System and method for structural characterization of materials by supervised machine learning-based analysis of their spectra

A method of supervised machine learning-based spectrum analysis information, using a neural network trained with spectrum information, to identify a specified feature of a given material, a system for supervised machine learning-based spectrum analysis, and a method of training a neural network to analyze spectrum data. The method of supervised machine learning-base spectrum analysis comprises inputting into the neural network spectrum data obtained from a sample of the given material; and the neural network processing the spectrum data, in accordance with the training of the neural network, and outputting one or more values for the specified feature of the sample of the material. In an embodiment, the training set of data includes x-ray absorption spectroscopy data for the given material. In an embodiment, the training set of data includes electron energy loss spectra (EELS) data.

Frenkel, Anatoly↗

Semi-supervised permutation invariant particle-level anomaly detection

The development of analysis methods to distinguish potential beyond the Standard Model phenomena in a model-agnostic way can significantly enhance the discovery reach in collider experiments. However, the typical machine learning (ML) algorithms employed for this task require fixed length and ordered inputs that break the natural permutation invariance in collision events. To address this, a semi-supervised anomaly detection tool is presented that takes a variable number of particle-level inputs and leverages a signal model to encode this information into a permutation invariant, event-level representation via supervised training with a Particle Flow Network (PFN). Data events are then encoded into this representation and given as input to an autoencoder for unsupervised ANomaly deTEction on particLe flOw latent sPacE (ANTELOPE), classifying anomalous events based on a low-level and permutation invariant input modeling. Performance of the ANTELOPE architecture is evaluated on simulated samples of hadronic processes in a high energy collider experiment, showing good capability to distinguish disparate models of new physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A machine learning pipeline for membrane segmentation of cryo-electron tomograms

We describe how to use several machine learning techniques organized in a learning pipeline to segment and identify cell membrane structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging technique that tries to piece together disconnected components belonging to the same membrane structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here works well for extracting membrane surfaces in two real tomogram datasets.

97 MATHEMATICS AND COMPUTING↗

Benchmark probabilistic solar forecasts: Characteristics and recommendations

We illustrate and compare commonly used benchmark, or reference, methods for probabilistic solar forecasting that researchers use to measure the performance of their proposed techniques. A thorough review of the literature indicates wide variation in the benchmarks implemented in probabilistic solar forecast studies. To promote consistent and sensible methodological comparisons, we implement and compare ten variants from six common benchmark classes at two temporal scales: intra-hourly forecasts and hourly resolution forecasts. Using open-source Surface Radiation Budget Network (SURFRAD) data from 2018, these benchmark methods are compared using proper probabilistic metrics and common diagnostic tools. Practical implementation issues, such as the impact of missing data and applicability for operational forecasting, are also discussed. Furthermore, we make recommendations for practitioners on the appropriate selection of benchmark methods to properly showcase state-of-the-art improvements in forecast reliability and sharpness. All code and open-source data are available on Github for reproducibility and for other researchers to apply the same benchmark methods to their own data.

14 SOLAR ENERGY↗

Accurate and reliable thermochemistry by data analysis of complex thermochemical networks using Active Thermochemical Tables: the case of glycine thermochemistry

Active Thermochemical Tables (ATcT) were successfully used to resolve the existing inconsistencies related to the thermochemistry of glycine, based on statistically analyzing and solving a thermochemical network that includes >3350 chemical species interconnected by nearly 35 000 thermochemically-relevant determinations from experiment and high-level theory. Here, the current ATcT results for the 298.15 K enthalpies of formation are −394.70 ± 0.55 kJ mol −1 for gas phase glycine, −528.37 ± 0.20 kJ mol −1 for solid α-glycine, −528.05 ± 0.22 kJ mol −1 for β-glycine, −528.64 ± 0.23 kJ mol −1 for γ-glycine, −514.22 ± 0.20 kJ mol −1 for aqueous undissociated glycine, and −470.09 ± 0.20 kJ mol −1 for fully dissociated aqueous glycine at infinite dilution. In addition, a new set of thermophysical properties of gas phase glycine was obtained from a fully corrected nonrigid rotor anharmonic oscillator (NRRAO) partition function, which includes all conformers. Corresponding sets of thermophysical properties of α-, β-, and γ-glycine are also presented.

Active Thermochemical Tables↗

Grad–Shafranov equilibria via data-free physics informed neural networks

A large number of magnetohydrodynamic (MHD) equilibrium calculations are often required for uncertainty quantification, optimization, and real-time diagnostic information, making MHD equilibrium codes vital to the field of plasma physics. In this paper, we explore a method for solving the Grad–Shafranov equation by using physics-informed neural networks (PINNs). For PINNs, we optimize neural networks by directly minimizing the residual of the partial differential equation as a loss function. We show that PINNs can accurately and effectively solve the Grad–Shafranov equation with several different boundary conditions, making it more flexible than traditional solvers. This method is flexible as it does not require any mesh and basis choice, thereby streamlining the computational process. We also explore the parameter space by varying the size of the model, the learning rate, and boundary conditions to map various tradeoffs such as between reconstruction error and computational speed. Additionally, we introduce a parameterized PINN framework, expanding the input space to include variables such as pressure, aspect ratio, elongation, and triangularity in order to handle a broader range of plasma scenarios within a single network. Parameterized PINNs could be used in future work to solve inverse problems such as shape optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Automated imaging of the annihilation of a transverse domain wall in patterned magnetic thin films

Imaging the magnetic domain wall behavior in patterned thin films under external stimuli can enable understanding the underlying energy landscape and the role of local microstructure and defects. We present an automated workflow for in situ Lorentz transmission electron microscopy to image magnetic domain walls at the nanometer length scale and at a time resolution in the sub-millisecond regime—the latter of which is limited by the speed of the available camera. Our workflow is modular and can be broadly applied to various types of in situ experiments, taking us a step closer to the future of autonomous imaging of nanomagnetic films with electron microscopy. Using our workflow, we show the transformation of a transverse domain wall with sub-millisecond time resolution under the application of an in situ transverse magnetic field, a study of whose dynamics are essential in the design of future domain wall mediated spintronic device applications.

Algebraic topology↗

HDX–MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker

Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen,Nat. Rev. Mol. Cell Biol.18, 285–298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond,J. Biol. Chem.294, 7151–7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Ribacket al.,Cell168, 1028–1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen–deuterium exchange/mass spectrometry to investigate the mechanism of Pab1’s condensation. Pab1’s four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate’s interaction network. Our data yield a picture of Pab1’s stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.

Science & Technology - Other Topics↗

Development of HELIOS/BIPR/PARCS/MCNP6 Computation Route for WWER RPV Neutron Fluence Analysis and Validation Against Ex-Vessel Detector Measurement Data

Here, a computational route was developed for precise calculation of fast neutron fluence on a WWER-type reactor pressure vessel (RPV). The method is based on the transfer of neutronics data from HELIOS-2 lattice calculations and nodal diffusion neutronics data (power, density, and temperature) from BIPR7.1 and PARCS 3.36/PATHS core calculations into a three-dimensional (pinwise axially distributed) fixed neutron source for modeling of transport of fast neutrons from the reactor core to the outer surface of the RPV using MCNP6.2. Validation of the proposed computational method was carried out based on comparative analysis of MCNP6.2-predicted and neutron dosimetry–measured reaction rates [ 54 Fe(n,p) 54 Мn, 93 Nb(n,n') 93 mNb, and 58 Ni(n,р) 58 Со] on the outer surface of the Armenian Nuclear Power Plant (ANPP) Unit 2 RPV. Validation revealed that the MCNP6.2-predicted fast neutron fluence results are very sensitive to the ENDF-B neutron data. Particularly, MCNP6.2 with ENDF/B-VIII.0 significantly underpredicts (20% to 30%) fast neutron fluence while using ENDF/B-VII.1 data overpredicts it. Adding revised beta-released evaluations of 54 Fe, 56 Fe, 57 Fe, and 16 O from the International Nuclear Data Evaluation Network (INDEN) to ENDF/B-VIII.0 allows one to obtain reasonable agreement with measurement results for all types of measured reaction rates.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗