Development of a timing and data link for EIC Common Hardware Platform
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43 PARTICLE ACCELERATORS↗
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Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.
97 MATHEMATICS AND COMPUTING↗
Risk assessment of safety-critical data communication in digital safety feature control system - 205
As one of the safety-critical systems in Advanced Power Reactor-1400 (APR-1400) nuclear power plant (NPP), the Engineered Safety Feature-Component Control System (ESF-CCS) employs safety data link and network communication for transmitting safety component actuation to effectively facilitate various safety-critical field controllers. However, data communication failure risk in the ESF-CCS has yet to be fully quantified, the probability that a safety-critical system in digitalized NPP becomes unsafe due to a network failure must be evaluated to quantify the risk of digital I and C system. In this study, a fault tree model was developed to assess the data link and data network failure-induced unavailability of a safety-critical system function used to generate an automated control signal for actuating design basis accident mitigation equipment. Especially, the risk of data communication failure in a digital safety feature control system was analyzed in consideration of interconnection between safety-critical controllers and the fault-tolerant algorithm implemented in the network configuration. Based on the developed fault tree model, case studies were performed to quantitatively assess the unavailability of ESF-CCS signal generation due to safety data link and network failure and their risk effect on safety signal generation unavailability. This study is expected to provide risk information on the safety-critical data communication in a digitalized NPP instrumentation and control system. (authors)
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Simit: A Language for Physical Simulation
With existing programming tools, writing high-performance simulation code is labor intensive and requires sacrificing readability and portability. Here, the alternative is to prototype simulations in a high-level language like Matlab, thereby sacrificing performance. The Matlab programming model naturally describes the behavior of an entire physical system using the language of linear algebra. However, simulations also manipulate individual geometric elements, which are best represented using linked data structures like meshes. Translating between the linked data structures and linear algebra comes at significant cost, both to the programmer and to the machine. High-performance implementations avoid the cost by rephrasing the computation in terms of linked or index data structures, leaving the code complicated and monolithic, often increasing its size by an order of magnitude. In this article, we present Simit, a new language for physical simulations that lets the programmer view the system both as a linked data structure in the form of a hypergraph and as a set of global vectors, matrices, and tensors depending on what is convenient at any given time. Simit provides a novel assembly construct that makes it conceptually easy and computationally efficient to move between the two abstractions. Using the information provided by the assembly construct, the compiler generates efficient in-place computation on the graph. We demonstrate that Simit is easy to use: a Simit program is typically shorter than a Matlab program; that it is high performance: a Simit program running sequentially on a CPU performs comparably to hand-optimized simulations; and that it is portable: Simit programs can be compiled for GPUs with no change to the program, delivering 4 to 20× speedups over our optimized CPU code.
97 MATHEMATICS AND COMPUTING↗
Global sensitivity analysis, probabilistic calibration, and predictive assessment for the data assimilation linked ecosystem carbon model
In this paper we propose a probabilistic framework for an uncertainty quantification (UQ) study of a carbon cycle model and focus on the comparison between steady-state and transient simulation setups. A global sensitivity analysis (GSA) study indicates the parameters and parameter couplings that are important at different times of the year for quantities of interest (QoIs) obtained with the data assimilation linked ecosystem carbon (DALEC) model. We then employ a Bayesian approach and a statistical model error term to calibrate the parameters of DALEC using net ecosystem exchange (NEE) observations at the Harvard Forest site. The calibration results are employed in the second part of the paper to assess the predictive skill of the model via posterior predictive checks.
54 ENVIRONMENTAL SCIENCES↗
A multigigabit link layer protocol for single picosecond latency determinism using AMD ultrascale+ GTH and GTY transreceivers
recision timing distribution systems require determin istic and repeatable high speed serial data link latency. The EIC Timing Data Link will employ a specialized link layer protocol for deterministic multigigabit communication us ing AMD Ultrascale+ GTH and GTY transceivers. Link la tency must also be measurable to accurately compensate in real time for latency variations of the physical medium. The point-to-point link is full duplex and fully synchronous with a latency control algorithm to align the internal clocks of each system with picosecond resolution. Deterministic clock domain crossing between systems is ensured using static timing analysis of the elastic buffer control signals.
43 PARTICLE ACCELERATORS↗
Towards Cache-Enabled, Order-Aware, Ontology-Based Stream Reasoning Framework
While streaming data have become increasingly more popular in business and research communities, semantic models and processing software for streaming data have not kept pace. Traditional semantic solutions have not addressed transient data streams. Semantic web languages (e.g., RDF, OWL) have typically addressed static data settings and linked data approaches have predominantly addressed static or growing data repositories. Streaming data settings have some fundamental differences; in particular, data are consumed on the fly and data may expire. Stream reasoning, a combination of stream processing and semantic reasoning, has emerged with the vision of providing "smart" processing of streaming data. C-SPARQL is a prominent stream reasoning system that handles semantic (RDF) data streams. Many stream reasoning systems including C-SPARQL use a sliding window and use data arrival time to evict data. For data streams that include expiration times, a simple arrival time scheme is inadequate if the window size does not match the expiration period. In this paper, we propose a cache-enabled, order-aware, ontology-based stream reasoning framework. This framework consumes RDF streams with expiration timestamps assigned by the streaming source. Our framework utilizes both arrival and expiration timestamps in its cache eviction policies. In addition, we introduce the notion of "semantic importance" which aims to address the relevance of data to the expected reasoning, thus enabling the eviction algorithms to be more context- and reasoning-aware when choosing what data to maintain for question answering. We evaluate this framework by implementing three different prototypes and utilizing five metrics. The trade-offs of deploying the proposed framework are also discussed.
Data Discovery↗
Sensor payloads for small unmanned aerial vehicles
Small unmanned aerial systems (sUAS) are ideal for delivering sensors into areas that are inaccessible or too dangerous for human entry or manned aircraft over-flights. The systems can fly low and slow for enhanced sensitivity, and they can get into tight spaces where ordinary aircraft would never attempt to fly. We have configured and flown sensor payloads for radiation, chemical, and optical detection on small fixed wing and rotary wing aircraft. For radiation detection we have flown packages consisting of sodium iodide (NaI), lanthanum bromide (LaBr3), and cadmium-zinc-telluride (CZT) gamma spectrometers, and we have also flown a CZT gamma imaging detector. The chemical sensing package consists of surface catalytic detectors for real-time chemical sensing, and a multi-tube chemical sampler that can be post-flight analyzed with a gas chromatograph mass spectrometer (GCMS). The optical package comprises a small spectrometer with wavelength sensitivity from 200 nm to 900 nm, and it has successfully collected burst light spectra from small explosive detonations. All the sensor packages provide telemetry, GPS coordinates, LIDAR distance ranging, and absolute time of day to microsecond accuracy. Payload weights range from less than 1 kg up to 5.5 kg, and they have flown on Sandstorm and T-28 fixed wing drones, on a custom-built heavy-lift hex-copter, a 3DR Solo quad-copter, and a T-Rex 700 helicopter. Communications are over 2.4 GHz, 915 MHz radios, and 4G LTE cellular data links. Real time data feeds from the sensor payloads to web browser clients anywhere in the world are possible via a virtual server on the Amazon AWS cloud.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Systems, devices and methods for communicating data with unmanned aerial vehicles using underlay broadcast channel
An unmanned aerial vehicle (UAV) and base station are disclosed that communicate within a first cell via schedule requests to set up transmission of up-link data. The UAV additionally communicates up-link data via a grant-free underlay broadcast channel to one or more neighboring base stations of the terrestrial cellular network. Transmitters, receivers, related methods are also disclosed for modulation and demodulation of the transmission packets.
Moradi, Hussein↗
Compiler verification meets cross-language linking via data abstraction
Many real programs are written in multiple different programming languages, and supporting this pattern creates challenges for formal compiler verification. We describe our Coq verification of a compiler for a high-level language, such that the compiler correctness theorem allows us to derive partial-correctness Hoare-logic theorems for programs built by linking the assembly code output by our compiler and assembly code produced by other means. Our compiler supports such tricky features as storable cross-language function pointers, without giving up the usual benefits of being able to verify different compiler phases (including, in our case, two classic optimizations) independently. Here, the key technical innovation is a mixed operational and axiomatic semantics for the source language, with a built-in notion of abstract data types, such that compiled code interfaces with other languages only through axiomatically specified methods that mutate encapsulated private data, represented in whatever formats are most natural for those languages.
97 MATHEMATICS AND COMPUTING↗
Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response
Ubiquitination is a common protein post-translational modification that regulates many key cellular functions. Here we investigated the dynamics of ubiquitinated proteins after an inflammatory stimulation of RAW264.7 macrophage-like cells with bacterial lipopolysaccharide. We demonstrate that levels of global ubiquitination, and K48 and K63 polyubiquitination change after lipopolysaccharide stimulation. A quantitative proteomic analysis identified 1199 ubiquitinated proteins, 78 of which had significantly changed ubiquitination levels after lipopolysaccharide stimulation. We next identified a subset of proteins that were targeted for degradation after lipopolysaccharide stimulation, by integrating the ubiquitinome data with global proteomics and transcriptomics results. Using cellular assays and western blot analyses we biochemically validated DBC1, a histone deacetylase inhibitor not previously linked to inflammation, as a degradation substrate, which is targeted via an orchestrated mechanism utilizing caspases and the proteasome. The degradation of DBC1 releases histone deacetylase activity, linking lipopolysaccharide activation to chromatin remodeling in caspase- and proteasome-mediated signaling.
Environmental Molecular Sciences Laboratory↗
Localization of the regulatory particle subunit Sem1 in the 26S proteasome
Highlights: •26S proteasome subunit Sem1 was mapped using cryo-EM and cross-linking data. •C-terminal helix of Sem1 located near winged helix motif of Rpn7. •N-terminal part of Sem1 tethers Rpn7, Rpn3 and lid helical bundle. •Sem1 binds differently to PCI-domains of proteasome subunit Rpn7 and TREX-2 subunit Thp1. -- Abstract: The ubiquitin–proteasome system is responsible for regulated protein degradation in the cell with the 26S proteasome acting as its executive arm. The molecular architecture of this 2.5 MDa complex has been established recently, with the notable exception of the small acidic subunit Sem1. Here, we localize the C-terminal helix of Sem1 binding to the PCI domain of the subunit Rpn7 using cryo-electron microscopy single particle reconstruction of proteasomes purified from yeast cells with sem1 deletion. The approximate position of the N-terminal region of Sem1 bridging the cleft between Rpn7 and Rpn3 was inferred based on site-specific cross-linking data of the 26S proteasome. Our structural studies indicate that Sem1 can assume different conformations in different contexts, which supports the idea that Sem1 functions as a molecular glue stabilizing the Rpn3/Rpn7 heterodimer.
60 APPLIED LIFE SCIENCES↗
Future radiotherapy practice will be based on evidence from retrospective interrogation of linked clinical data sources rather than prospective randomized controlled clinical trials
No abstract prepared.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Response to “Comment on ‘Future radiotherapy practice will be based on evidence from retrospective interrogation of linked clinical data sources rather than prospective randomized controlled clinical trials’” [Med. Phys. 41(3) 030601 (3pp.) (2014)]
No abstract prepared.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Response to “Comment on ‘Future radiotherapy practice will be based on evidence from retrospective interrogation of linked clinical data sources rather than prospective randomized controlled clinical trials’” [Med. Phys. 41(3), 030601 (3pp.) (2014)]
No abstract prepared.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Drone Video Platform—Collision Avoidance, Situational Awareness, and Communications
Small unmanned aerial systems are ideal for delivering sensors into areas that are inaccessible or too dangerous for human entry or manned aircraft over-flights. The systems can fly low and slow for enhanced sensitivity and in tight spaces where ordinary aircraft could never fit. We have configured and flown sensor payloads for radiation, chemical, and optical detection on small fixed-wing and rotary-wing aircraft. All the sensor packages provide telemetry, GPS coordinates, LIDAR distance ranging, and absolute time of day to microsecond accuracy. Payload weights range from less than 1 kg up to 5.5 kg. Currently, communications are over 2.4 GHz and 915 MHz radios, as well as over 4G LTE cellular data links. Real-time data feeds from the sensor payloads to web browser clients anywhere in the world are possible via a virtual EC2 server on the Amazon AWS cloud. In FY 2019, the Nevada National Security Site teamed with Virginia Tech, H3D Corp., and Unmanned Systems, Inc. to accomplish the four flight missions described in this report. A large part of this year’s mission goals were to demonstrate the ability to fly beyond visual line of sight (BVLOS).
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗