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35 records · Page 2

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Wildfire smoke exposure and early childhood respiratory health: a study of prescription claims data

Abstract Wildfire smoke is associated with short-term respiratory outcomes including asthma exacerbation in children. As investigations into developmental wildfire smoke exposure on children’s longer-term respiratory health are sparse, we investigated associations between developmental wildfire smoke exposure and first use of respiratory medications. Prescription claims from IBM MarketScan Commercial Claims and Encounters database were linked with wildfire smoke plume data from NASA satellites based on Metropolitan Statistical Area (MSA). A retrospective cohort of live infants (2010–2016) born into MSAs in six western states (U.S.A.), having prescription insurance, and whose birthdate was estimable from claims data was constructed ( N = 184,703); of these, gestational age was estimated for 113,154 infants. The residential MSA, gestational age, and birthdate were used to estimate average weekly smoke exposure days ( smoke-day ) for each developmental period: three trimesters, and two sequential 12-week periods post-birth. Medications treating respiratory tract inflammation were classified using active ingredient and mode of administration into three categories:: 'upper respiratory', 'lower respiratory', 'systemic anti-inflammatory'. To evaluate associations between wildfire smoke exposure and medication usage, Cox models associating smoke-days with first observed prescription of each medication category were adjusted for infant sex, birth-season, and birthyear with a random intercept for MSA. Smoke exposure during postnatal periods was associated with earlier first use of upper respiratory medications (1–12 weeks: hazard ratio (HR) = 1.094 per 1-day increase in average weekly smoke-day, 95%CI: (1.005,1.191); 13–24 weeks: HR = 1.108, 95%CI: (1.016,1.209)). Protective associations were observed during gestational windows for both lower respiratory and systemic anti-inflammatory medications; it is possible that these associations may be a consequence of live-birth bias. These findings suggest wildfire smoke exposure during early postnatal developmental periods impact subsequent early life respiratory health.

Dhingra, Radhika↗

HPC4Mfg with ACS

Distillation in the chemical industry accounts for roughly 10% of energy use in the U.S. While porous mass separating agents (MSAs) appear capable of achieving the same separations for a fraction of the energy, the fundamental lack of a well-understood relationship between the behavior of fluid mixtures confined in MSA pores and the selectivity of MSA-based processes presents a major barrier to their widespread industrial application. This work is the first study to systematically and self-consistently explore a range of parameters describing various molecule-material interactions in MSA-based separations. Through high performance computing (HPC), this study has yielded a fundamental understanding of the influence of confined fluid behavior on selectivity. The results also serve as a knowledge base for subsequent investigations needed to transform the framework for rational design of MSA-based separation processes. This will significantly reduce the energy required for separations central to chemical manufacturing.

36 MATERIALS SCIENCE↗

Microwave soil moisture measurements and analysis

An effort to develop a model that simulates the distribution of water content and of temperature in bare soil is documented. The field experimental set up designed to acquire the data to test this model is described. The microwave signature acquisition system (MSAS) field measurements acquired in Colby, Kansas during the summer of 1978 are pesented.

Newton, R. W.↗

Off-the-shelf real-time monitoring of satellite constellations in a visual 3-D environment

The multimission spacecraft analysis system (MSAS) data monitor is a generic software product for future real-time data monitoring and analysis. The system represents the status of a satellite constellation through the shape, color, motion and position of graphical objects floating in a three dimensional virtual reality environment. It may be used for the monitoring of large volumes of data, for viewing results in configurable displays, and for providing high level and detailed views of a constellation of monitored satellites. It is considered that the data monitor is an improvement on conventional graphic and text-based displays as it increases the amount of data that the operator can absorb in a given period, and can be installed and configured without the requirement for software development by the end user. The functionality of the system is described, including: the navigation abilities; the representation of alarms in the cybergrid; limit violation; real-time trend analysis, and alarm status indication.

Schwuttke, Ursula M.↗

BOREAS HYD-8 DEM Data Over the NSA-MSA and SSA-MSA in the UTM Projection

The BOREAS HYD-8 team focused on describing the scaling behavior of water and carbon flux processes at local and regional scales. These DEMs were produced from digitized contours at a cell resolution of 100 meters. Vector contours of the area were used as input to a software package that interpolates between contours to create a DEM representing the terrain surface. The vector contours had a contour interval of 25 feet. The data cover the BOREAS MSAs of the SSA and NSA and are given in a UTM map projection. Most of the elevation data from which the DEM was produced were collected in the 1970s or 1980s. The data are stored in binary, image format files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Wang, Xue-Wen↗

BOREAS HYP-8 DEM Data Over The NSA-MSA and SSA-MSA in The AEAC Projection

These data were derived from the original Digital Elevation Models (DEMs) produced by the Boreal Ecosystem-Atmosphere Study (BOREAS) Hydrology (HYD)-8 team. The original DEMs were in the Universal Transverse Mercator (UTM) projection, while this product is projected in the Albers Equal-Area Conic (AEAC) projection. The pixel size of the data is 100 meters, which is appropriate for the 1:50,000-scale contours from which the DEMs were made. The original data were compiled from information available in the 1970s and 1980s. This data set covers the two Modeling Sub-Areas (MSAs) that are contained within the Southern Study Area (SSA) and the Northern Study Area (NSA). The data are stored in binary, image format files. The DEM data over the NSA-MSA and SSA-MSA in the AEAC projection are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

Knapp, David E.↗

Seasonal-scale Observational Data Analysis and Atmospheric Phenomenology for the Cold Land Processes Experiment

The Cold Land Processes Experiment (CLPX) experiment emphasized the development of a strong synergism between process-oriented understanding, land surface models and microwave remote sensing. Our work sought to investigate which topographically- generated atmospheric phenomena are most relevant to the CLPX MSA's for the purpose of evaluating their climatic importance to net local moisture fluxes and snow transport through the use of high-resolution data assimilation/atmospheric numerical modeling techniques. Our task was to create three long-term, scientific quality atmospheric datasets for quantitative analysis (for all CLPX researchers) and provide a summary of the meteorologically-relevant phenomena of the three MSAs (see Figure) over northern Colorado. Our efforts required the ingest of a variety of CLPX datasets and the execution an atmospheric and land surface data assimilation system based on the Navier-Stokes equations (the Local Analysis and Prediction System, LAPS, and an atmospheric numerical weather prediction model, as required) at topographically- relevant grid spacing (approx. 500 m). The resulting dataset will be analyzed by the CLPX community as a part of their larger research goals to determine the relative influence of various atmospheric phenomena on processes relevant to CLPX scientific goals.

Poulos, Gregory S.↗

Increased User Satisfaction Through an Improved Message System

With all of the enhancements in software methodology and testing, there is no guarantee that software can be delivered such that no user errors occur, How to handle these errors when they occur has become a major research topic within human-computer interaction (HCI). Users of the Multimission Spacecraft Analysis Subsystem(MSAS) at the Jet Propulsion Laboratory (JPL), a system of X and motif graphical user interfaces for analyzing spacecraft data, complained about the lack of information about the error cause and have suggested that recovery actions be included in the system error messages...The system was evaluated through usability surveys and was shown to be successful.

Human-computer interaction error handling direct m↗

A Multi-Mission Approach to Spacecraft Analysis

This paper describes the design of the JPL institutional Multi-Mission Spacecraft Analysis System (MSAS) and its initial adaptation to the Cassini mission.

spacecraft analysis multi-mission approach↗

On the ionospheric impact of recent storm events on satellite-based augmentation systems in middle and low-latitude sectors

The Ionospheric correction algorithms have been characterized extensively for the mid-latitude region of the ionosphere where benign conditions usually exist. The United States Federal Aviation Administration's (FAA) Wide Area Augmentation System (WAAS) for civil aircraft navigation is focused primarily on the Conterminous United States (CONUS). Other Satellite-based Augmentation Systems (SBAS) include the European Geostationary Navigation Overlay Service (EGNOS) and the Japanese Global Navigation Satellite System (MSAS). Researchers are facing a more serious challenge in addressing the ionospheric impact on navigation using SBAS in other parts of the world such as the South American region on India. At equatorial latitudes, geophysical conditions lead to the so-called Appleton-Hartree (equatorial) anomaly phenomenon, which results in significantly larger ionospheric range delays and range delay spatial gradients than is observed in the CONUS or European sectors. In this paper, we use GPS measurements of geomagnetic storm days to perform a quantitative assessment of WAAS-type ionospheric correction algorithms in other parts of the world such as the low-latitude Brazil and mid-latitude Europe. For the study, we access a world-wide network of 400+ dual frequency GPS receivers.

validation↗

The Ionospheric Impact of the October 2003 Storm Event on WAAS

The United States Federal Aviation Administration's (FAA) Wide Area Augmentation System (WAAS) for civil aircraft navigation is focused primarily on the Conterminous United States (CONUS). Other Satellite- Based Augmentation Systems (SBAS) include the European Geostationary Navigation Overlay Service (EGNOS) and the Japanese Global Navigation Satellite System (MSAS). Navigation using WAAS requires accurate calibration of ionospheric delays. to provide delay corrections for single frequency GPS users, the wide area differential GPS systems depend upon accurate determination of ionospheric total electron content (TEC) along radio links. Dual frequency transmissions from GPS satellites have been used for many years to measure and map ionospheric TEX on regional and global scales.

modeling↗

Electrostatic Microshutter Arrays

Based on the Microshutter Array (MSA) subsystems developed at NASA Goddard Space Flight Center (GSFC) for the James Webb Space Telescope (JWST), Next Generation Microshutter Array (NGMSA) has been developed to be used as multi-object selectors for future telescopes in space applications. Microshutter arrays function as transmission devices. Selected shutters fully open at 90 degrees permitting income light going through, while the rest of shutters keep closed. The programmable microshutter open and close make the device perform as a multi object selector that can be used on space telescopes. Utilizing a multi object selector, the telescope efficiency can be increased to 100 times or more. Like JWST MSAs, NGMSA features torsion hinges, light shields, front and back electrodes for shutter actuation, latch, and closing. The difference is that JWST MSA utilized the magnetic actuation while NGMSA the electrostatic actuation.

Micro-electro-mechanical-system (MEMS)↗

Mars Sample Receiving Facility Research and Development to Enable Preservation, Safe Containment, and Scientific Research of Martian Samples on Earth

NASA and ESA are working together to plan a joint campaign to potentially bring back the first Martian samples to Earth in the early 2030s. On the surface of Mars, the Mars 2020Perseverance Rover is selecting and packaging samples that could be returned to Earth for careful examination by an international team of scientists. In preparation for this historic sample return, advance planning is underway to design and build a Mars Sample Receiving Facility (SRF) in the mid-2020s. In 2022, a Mars Sample Receiving Facility Assessment Study(MSAS) will be conducted to further define construction modality and capability options for a facility in the conterminous United States. Since Mars Sample Return (MSR) is currently categorized as a planetary protection restricted Earth return, this new facility would feature biosafety level 4 (BSL-4)-like high containment to protect Earth’s biosphere from any potential hazard. In addition, the facility also requires integration of cleanroom technologies to mitigate against terrestrial contamination and preserve sample integrity for science investigations. The integration of both clean handling and high containment requires significant technology research and development (R&D) by the mid-2020s to support the definition and planning of a SRF before commencing the site specific design phase. The SRF project will need to solidify the inorganic, organic, and biological contamination control (CC) requirements for the facility. This could entail a translation of Mars 2020 mission CC requirements for geologic material to engineering requirements for surfaces and airborne molecular contamination inside isolators and cleanrooms. In tandem, the project will need to determine precision cleaning and sterilization approaches for cleanrooms, isolators, equipment, and tools. Initial material selections for the facility construction materials, cleanrooms, isolators, and BSL-4 suits/garments are an important activity. The recent construction of the OSIRIS-REx and Hayabusa2 curation cleanroom laboratories greatly benefited from early materials testing, before the design phase, to reduced organic outgassing and particulate shedding inside the laboratory. While the early biohazard investigations in the SRF may deem the samples safe to release to laboratories throughout the world, sterilization methods need to be defined to safely release Martian samples. One key aspect of enabling simultaneous sample containment and cleanliness is the concept of a Double-Walled Isolator (DWI) that ESA has been pursuing. Further R&D is needed about DWIs, sample handling, and instrumentation interfaces before beginning the SRF site specific design phase. A working isolator/DWI engineering model should be developed and fabricated. Isolator sizes, connections, pass-through antechambers, and configurations and basic interfaces with instruments and tools as well as the use of robotic, mechanical, and/or human manipulation need to be considered. Inert high purity gas supply (one-pass or recirculation) and other isolator utilities must be determined. Special accommodations for large instruments (e.g., XCT,SEM, etc.) need to be developed. Techniques for opening the sample tubes packaged by M2020and extracting the headspace gas while keeping samples pristine will be challenging, requiring additional R&D, and engagement of the M2020 project. In addition, careful micromanipulation for subdivision and packaging of samples will also need to be included. These combined R&D activities are important before commencing the SRF design phase to ensure safe biohazard containment, sample preservation, and science integrity for the samples that would be studied in the SRF and in laboratories around the world.

mars sample return↗

Engineered Edge Effect Stress Redistribution in Suspended Thin Film Stacks for Flatness Control

This paper presents the systematic study of edge effect stresses and interaction between thin film stacks to achieve flat suspended thin film structures. Finite element modeling (FEM) was used for rapid analysis of support structures on microshutter array (MSA) shutter blades. The design application aims to flatten the blades to provide ultra-high contrast to optical detectors using MSAs as field masks. This is the first comprehensive study of microscopic surface feature edge effect and film-to-film stress interaction in micro electromechanical systems (MEMS). This study demonstrates flattening of thin film stacks by stress redistribution by induced shear force at the edge of strategically designed reinforcement structures.

Thin Film MEMS↗