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At least 703 records · Page 39

Phosphoproteomics Modifications in Women with Rheumatoid Arthritis─Application of Web-Based Software to Enhance Data Visualization

Individuals with rheumatoid arthritis (RA) are at increased risk of functional disability, cardiovascular disease, and obesity, all of which are influenced by dysregulated skeletal muscle. Here, this pilot study aims to identify phosphoproteomics changes in RA skeletal muscle and visualize modifications through development of a web-based app designed to promote user-friendly data interpretation and visualization. NanoLC–MS/MS analysis was performed on vastus lateralis biopsies from three women with RA and matched healthy controls. Differential analysis was performed using the Limma R package. Kinase substrate enrichment analysis (KSEA) predicted changes in kinase activity. RA muscle displayed 35 upregulated and 60 downregulated phosphosites, including the cytoskeletal proteins TTN (Ser33201, Ser33013, Ser20925), NEB (Ser2219, Thr254, Ser33013, Ser20925), FLNA (Ser1459), and LASP1 (Ser146). Compared to healthy controls, KSEA predicted decreased activity of several kinases in RA muscle, including PRKACA and CDKs. All such changes were visualized by use of our web-based app. Overall, phosphoproteome analysis reveals signaling alterations in RA skeletal muscle linked to cytoskeletal proteins, representing candidate disease biomarkers; these modifications can be explored through use of our web-based software.

phosphoproteomics↗

Top-down proteomics

Proteoforms arising from posttranslational modifications, genetic polymorphisms, and RNA splice variants, play a pivotal role as the key drivers in biology. Thus, a comprehensive understanding of proteoforms is essential for unraveling the intricacies of biological systems and bridging the gap between genotype and phenotype. By analyzing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and presents a next-generation approach for deciphering protein function, uncovering disease mechanisms, and advancing precision medicine. This Primer embarks on a journey into the world of TDP by encapsulating its historical context, underlying principles, recent advances, and an outlook on the future of TDP. The experimental section navigates instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques, and data collection. Results decipher raw data, visualize intact protein spectra, unravel data analysis, and explain proteoform identification, characterization, and quantitation, as well as statistical analysis. Various applications of TDP spanning the human proteoform project, biomedical, biopharmaceutical, and clinical applications are described. These are complemented by discussions on measurement reproducibility, limitations, and a forward-looking perspective outlining uncharted waters where the field can advance, and potential exciting future applications of TDP.

Roberts, David S.↗

ACME Priority Metrics (A-PRIME)

A-PRIME, is a collection of scripts designed to provide Accelerated Climate Model for Energy (ACME) model developers and analysts with a variety of analysis of the model needed to determine if the model is producing the desired results, depending on the goals of the simulation. The software is csh scripts based at the top level to enable scientist to provide the input parameters. Within the scripts, the csh scripts calls code to perform the postprocessing of the raw data analysis and create plots for visual assessment.

Evans, KatherineJ.↗

SciDAC's Earth System Grid Center for Enabling Technologies Semiannual Progress Report October 1, 2010 through March 31, 2011

This report summarizes work carried out by the Earth System Grid Center for Enabling Technologies (ESG-CET) from October 1, 2010 through March 31, 2011. It discusses ESG-CET highlights for the reporting period, overall progress, period goals, and collaborations, and lists papers and presentations. To learn more about our project and to find previous reports, please visit the ESG-CET Web sites: http://esg-pcmdi.llnl.gov/ and/or https://wiki.ucar.edu/display/esgcet/Home. This report will be forwarded to managers in the Department of Energy (DOE) Scientific Discovery through Advanced Computing (SciDAC) program and the Office of Biological and Environmental Research (OBER), as well as national and international collaborators and stakeholders (e.g., those involved in the Coupled Model Intercomparison Project, phase 5 (CMIP5) for the Intergovernmental Panel on Climate Change (IPCC) 5th Assessment Report (AR5); the Community Earth System Model (CESM); the Climate Science Computational End Station (CCES); SciDAC II: A Scalable and Extensible Earth System Model for Climate Change Science; the North American Regional Climate Change Assessment Program (NARCCAP); the Atmospheric Radiation Measurement (ARM) program; the National Aeronautics and Space Administration (NASA), the National Oceanic and Atmospheric Administration (NOAA)), and also to researchers working on a variety of other climate model and observation evaluation activities. The ESG-CET executive committee consists of Dean N. Williams, Lawrence Livermore National Laboratory (LLNL); Ian Foster, Argonne National Laboratory (ANL); and Don Middleton, National Center for Atmospheric Research (NCAR). The ESG-CET team is a group of researchers and scientists with diverse domain knowledge, whose home institutions include eight laboratories and two universities: ANL, Los Alamos National Laboratory (LANL), Lawrence Berkeley National Laboratory (LBNL), LLNL, NASA/Jet Propulsion Laboratory (JPL), NCAR, Oak Ridge National Laboratory (ORNL), Pacific Marine Environmental Laboratory (PMEL)/NOAA, Rensselaer Polytechnic Institute (RPI), and University of Southern California, Information Sciences Institute (USC/ISI). All ESG-CET work is accomplished under DOE open-source guidelines and in close collaboration with the project's stakeholders, domain researchers, and scientists. Through the ESG project, the ESG-CET team has developed and delivered a production environment for climate data from multiple climate model sources (e.g., CMIP (IPCC), CESM, ocean model data (e.g., Parallel Ocean Program), observation data (e.g., Atmospheric Infrared Sounder, Microwave Limb Sounder), and analysis and visualization tools) that serves a worldwide climate research community. Data holdings are distributed across multiple sites including LANL, LBNL, LLNL, NCAR, and ORNL as well as unfunded partners sites such as the Australian National University (ANU) National Computational Infrastructure (NCI), the British Atmospheric Data Center (BADC), the Geophysical Fluid Dynamics Laboratory/NOAA, the Max Planck Institute for Meteorology (MPI-M), the German Climate Computing Centre (DKRZ), and NASA/JPL. As we transition from development activities to production and operations, the ESG-CET team is tasked with making data available to all users who want to understand it, process it, extract value from it, visualize it, and/or communicate it to others. This ongoing effort is extremely large and complex, but it will be incredibly valuable for building 'science gateways' to critical climate resources (such as CESM, CMIP5, ARM, NARCCAP, Atmospheric Infrared Sounder (AIRS), etc.) for processing the next IPCC assessment report. Continued ESG progress will result in a production-scale system that will empower scientists to attempt new and exciting data exchanges, which could ultimately lead to breakthrough climate science discoveries.

54 ENVIRONMENTAL SCIENCES↗

Reduced Order Model Implementation in the Risk-Informed Safety Margin Characterization Toolkit

The RISMC project aims to develop new advanced simulation-based tools to perform Probabilistic Risk Analysis (PRA) for the existing fleet of U.S. nuclear power plants (NPPs). These tools numerically model not only the thermo-hydraulic behavior of the reactor primary and secondary systems but also external events temporal evolution and components/system ageing. Thus, this is not only a multi-physics problem but also a multi-scale problem (both spatial, µm-mm-m, and temporal, ms-s-minutes-years). As part of the RISMC PRA approach, a large amount of computationally expensive simulation runs are required. An important aspect is that even though computational power is regularly growing, the overall computational cost of a RISMC analysis may be not viable for certain cases. A solution that is being evaluated is the use of reduce order modeling techniques. During the FY2015, we investigated and applied reduced order modeling techniques to decrease the RICM analysis computational cost by decreasing the number of simulations runs to perform and employ surrogate models instead of the actual simulation codes. This report focuses on the use of reduced order modeling techniques that can be applied to any RISMC analysis to generate, analyze and visualize data. In particular, we focus on surrogate models that approximate the simulation results but in a much faster time (µs instead of hours/days). We apply reduced order and surrogate modeling techniques to several RISMC types of analyses using RAVEN and RELAP-7 and show the advantages that can be gained.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Analyzing Multifaceted Scientific Data with Topological Analytics (Final Technical Report)

This final technical report describes the activities undertaken through Department of Energy, Office of Science, Advanced Scientific Computing Research Early Career award DE-SC-0019039, “Analyzing Multifaceted Scientific Data with Topological Analytics." This report summarizes contributions made toward the research of visualization, machine learning, and topological data analysis of complex simulation data.

97 MATHEMATICS AND COMPUTING↗

CyanoCyc cyanobacterial web portal

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists’ work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

59 BASIC BIOLOGICAL SCIENCES↗

A re-analysis of the causes of Boeing 727 'black hole landing' crashes

A review is presented of Kraft and Elworth's (1969) investigation and analysis of night visual approaches; their data is reanalyzed, and the reliability of the visual angle hypothesis is discussed. To increase pilot awareness of the hazardous illusions inherent in black hole landings, it was suggested that pilots should monitor their altimeters more often during night approaches. It was also recommended that greater attention should be given to airport design, so that the effects of black hole conditions could be minimized.

Schwirzke, Martin F. J.↗

Multiresolution and Explicit Methods for Vector Field Analysis and Visualization

This is a request for a second renewal (3d year of funding) of a research project on the topic of multiresolution and explicit methods for vector field analysis and visualization. In this report, we describe the progress made on this research project during the second year and give a statement of the planned research for the third year. There are two aspects to this research project. The first is concerned with the development of techniques for computing tangent curves for use in visualizing flow fields. The second aspect of the research project is concerned with the development of multiresolution methods for curvilinear grids and their use as tools for visualization, analysis and archiving of flow data. We report on our work on the development of numerical methods for tangent curve computation first.

Nielson, Gregory M.↗

Expert System Software Assistant for Payload Operations

The broad objective of this expert system software based application was to demonstrate the enhancements and cost savings that can be achieved through expert system software utilization in a spacecraft ground control center. Spacelab provided a valuable proving ground for this advanced software technology; a technology that will be exploited and expanded for future ISS operations. Our specific focus was on demonstrating payload cadre command and control efficiency improvements through the use of "smart" software which monitors flight telemetry, provides enhanced schematic-based data visualization, and performs advanced engineering data analysis.

Rogers, Mark N.↗

Dust Accumulation and Solar Panel Array Performance on the Mars Exploration Rover (MER) Project

One of the most fundamental design considerations for any space vehicle is its power supply system. Many options exist, including batteries, fuel cells, nuclear reactors, radioisotopic thermal generators (RTGs), and solar panel arrays. Solar arrays have many advantages over other types of power generation. They are lightweight and relatively inexpensive, allowing more mass and funding to be allocated for other important devices, such as scientific instruments. For Mars applications, solar power is an excellent option, especially for long missions. One might think that dust storms would be a problem; however, while dust blocks some solar energy, it also scatters it, making it diffuse rather than beamed. Solar cells are still able to capture this diffuse energy and convert it into substantial electrical power. For these reasons, solar power was chosen to be used on the 1997 Mars Pathfinder mission. The success of this mission set a precedent, as NASA engineers have selected solar power as the energy system of choice for all future Mars missions, including the Mars Exploration Rover (MER) Project. Solar sells have their drawbacks, however. They are difficult to manufacture and are relatively fragile. In addition, solar cells are highly sensitive to different parts of the solar spectrum, and finding the correct balance is crucial to the success of space missions. Another drawback is that the power generated is not a constant with respect to time, but rather changes with the relative angle to the sun. On Mars, dust accumulation also becomes a factor. Over time, dust settles out of the atmosphere and onto solar panels. This dust blocks and shifts the frequency of the incoming light, degrading solar cell performance. My goal is to analyze solar panel telemetry data from the two MERs (Spirit and Opportunity) in an effort to accurately model the effect of dust accumulation on solar panels. This is no easy process due to the large number of factors involved. Changing solar flux (the amount of solar energy reaching the planet), solar spectrum, solar angle, rover tilt, and optical depth (the opacity of the atmosphere due to dust) were the most significant. Microsoft Excel and Visual Basic are used for data analysis. The results of this work will be used to improve the dust accumulation and atmosphere effects model that was first created after the Mars Pathfinder mission. This model will be utilized and applied when considering the design of solar panel array systems on future Mars projects. Based on this data, and depending upon the tenure and application of the mission, designers may also elect to employ special tools to abate dust accumulation, or decide that the expected level of accumulation is acceptable.

Turgay, Eren H.↗

Photometric and Spectral Study of the Saturnian Satellites

Photometric and spectra analysis of data from the Cassini Visual and Infrared Mapping Spectrometer (VIMS) has yielded intriguing findings regarding the surface properties of several of the icy Saturnian satellites. Spectral cubes were obtained of these satellites with a wavelength distribution in the IR far more extensive than from any previous observations. Disk-integrated solar phase curves were constructed in several key IR wavelengths that are indicative of key properties of the surface of the body, such as macroscopic roughness, fluffiness (or the porosity of the surface), global albedo and scattering properties of surface particles. Polynomial fits to these phase curves indicate a linear albedo trend of the curvature of the phase functions. Rotational phase functions from Enceladus were found to exhibit a double-peaked sinusoidal curve, which shows larger amplitudes for bands corresponding to water ice and a linear amplitude-albedo trend. These functions indicate regions on the surface of the satellite of more recent geologic activity. In addition, recent images of Enceladus show tectonic features and an absence of impact craters on Southern latitudes which could be indicative of a younger surface. Investigations into the properties of these features using VIMS are underway.

Newman, Sarah F.↗

NASA Tech Briefs, October 2007

Topics covered include; Wirelessly Interrogated Position or Displacement Sensors; Ka-Band Radar Terminal Descent Sensor; Metal/Metal Oxide Differential Electrode pH Sensors; Improved Sensing Coils for SQUIDs; Inductive Linear-Position Sensor/Limit-Sensor Units; Hilbert-Curve Fractal Antenna With Radiation- Pattern Diversity; Single-Camera Panoramic-Imaging Systems; Interface Electronic Circuitry for an Electronic Tongue; Inexpensive Clock for Displaying Planetary or Sidereal Time; Efficient Switching Arrangement for (N + 1)/N Redundancy; Lightweight Reflectarray Antenna for 7.115 and 32 GHz; Opto-Electronic Oscillator Using Suppressed Phase Modulation; Alternative Controller for a Fiber-Optic Switch; Strong, Lightweight, Porous Materials; Nanowicks; Lightweight Thermal Protection System for Atmospheric Entry; Rapid and Quiet Drill; Hydrogen Peroxide Concentrator; MMIC Amplifiers for 90 to 130 GHz; Robot Would Climb Steep Terrain; Measuring Dynamic Transfer Functions of Cavitating Pumps; Advanced Resistive Exercise Device; Rapid Engineering of Three-Dimensional, Multicellular Tissues With Polymeric Scaffolds; Resonant Tunneling Spin Pump; Enhancing Spin Filters by Use of Bulk Inversion Asymmetry; Optical Magnetometer Incorporating Photonic Crystals; WGM-Resonator/Tapered-Waveguide White-Light Sensor Optics; Raman-Suppressing Coupling for Optical Parametric Oscillator; CO2-Reduction Primary Cell for Use on Venus; Cold Atom Source Containing Multiple Magneto- Optical Traps; POD Model Reconstruction for Gray-Box Fault Detection; System for Estimating Horizontal Velocity During Descent; Software Framework for Peer Data-Management Services; Autogen Version 2.0; Tracking-Data-Conversion Tool; NASA Enterprise Visual Analysis; Advanced Reference Counting Pointers for Better Performance; C Namelist Facility; and Efficient Mosaicking of Spitzer Space Telescope Images.

Source record↗

Vesta Mineralogy: VIR maps Vesta's surface

The Dawn mission will have completed Survey orbit around 4 Vesta by the end of August 2011. We present a preliminary analysis of data acquired by the Visual and InfraRed Spectrometer (VIR) to map Vesta mineralogy. Thermal properties and mineralogical data are combined to provide constraints on Vesta's formation and thermal evolution. delivery of exogenic materials, space weathering processes, and origin of the howardite. eucrite, and diogenite (HED) meteorites.

Coradina, A.↗

Data Cube Application Algorithms For The United Nations Sustainable Development Goals (UN-SDGS)

In 2015, all United Nations (UN) Member States adopted the 2030 Agenda for Sustainable Development. The Agenda provides a shared blueprint for peace and prosperity for people and for the planet, considering our current situation and helping to create a plan. The core of this agenda is a set of seventeen Sustainable Development Goals (SDGs), which represent an urgent call for action by all countries -both developed and developing - in a global partnership. The Committee on Earth Observation Satellites (CEOS) Systems Engineering Office (SEO) team has recently developed and released a set of innovative notebooks addressing UN SDGs 6.6.1 (spatial extents of water-related ecosystems), 11.3.1 (ratio of land consumption rate to population growth rate), and 15.3.1 (proportion of land that is degraded over total land area). These notebooks empower users by providing features that will assist with streamlining analysis ready data retrieval, processing, and visualization. The main contributions in this paper are: (1) briefly describing the framework of the UN SDG notebooks, (2) enumerating the notebooks’ salient features, and (3) discussing current limitations and proposing approaches to overcome these limitations.

Open Data Cube↗

High Performance Descriptive Semantic Analysis of Semantic Graph Databases

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to understand their inherent semantic structure, whether codified in explicit ontologies or not. Our group is researching novel methods for what we call descriptive semantic analysis of RDF triplestores, to serve purposes of analysis, interpretation, visualization, and optimization. But data size and computational complexity makes it increasingly necessary to bring high performance computational resources to bear on this task. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multi-threaded architecture of the Cray XMT platform, conventional servers, and large data stores. In this paper we describe that architecture and our methods, and present the results of our analyses of basic properties, connected components, namespace interaction, and typed paths such for the Billion Triple Challenge 2010 dataset.

99 GENERAL AND MISCELLANEOUS↗

'Big Data' Collaboration: Exploring, Recording and Sharing Enterprise Knowledge

As data sources and data size proliferate, knowledge discovery from "Big Data" is starting to pose several challenges. In this paper, we address a specific challenge in the practice of enterprise knowledge management while extracting actionable nuggets from diverse data sources of seemingly-related information. In particular, we address the challenge of archiving knowledge gained through collaboration, dissemination and visualization as part of the data analysis, inference and decision-making lifecycle. We motivate the implementation of an enterprise data-discovery and knowledge recorder tool, called SEEKER based on real world case-study. We demonstrate SEEKER capturing schema and data-element relationships, tracking the data elements of value based on the queries and the analytical artifacts that are being created by analysts as they use the data. We show how the tool serves as digital record of institutional domain knowledge and a documentation for the evolution of data elements, queries and schemas over time. As a knowledge management service, a tool like SEEKER saves enterprise resources and time by avoiding analytic silos, expediting the process of multi-source data integration and intelligently documenting discoveries from fellow analysts.

Big Data↗

Big Data as a Service from an Urban Information System

Big Data has already proven itself as a valuable tool that lets geographers and urban researchers utilize large data re- sources to generate new insights. However, wider adoption of Big Data techniques in these areas is impeded by a number of difficulties in both knowledge discovery and data and sci- ence production. Typically users face such problems as dis- parate and scattered data, data management, spatial search- ing, insufficient computational capacity for data-driven anal- ysis and modelling, and the lack of tools to quickly visual- ize and summarize large data and analysis results. Here we propose an architecture for an Urban Information Sys- tem (UrbIS) that mitigates these problems by utilizing the Big Data as a Service (BDaaS) concept. With technolog- ical roots in High-performance Computing (HPC), BDaaS is based on the idea of outsourcing computations to dif- ferent computing paradigms, scalable to super-computers. UrbIS aims to incorporate federated metadata search, in- tegrated modeling and analysis, and geovisualization into a single seamless workflow. The system is under active devel- opment and is built around various emerging technologies that include hybrid and NoSQL databases, massively par- allel systems, GPGPU computing, and WebGL-based geo- graphic visualization. UrbIS is designed to facilitate using Big Data across multiple cities to better understand how ur- ban areas impact the environment and how climate change and other environmental change impact urban areas.

Sorokine, Alexandre↗