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At least 217 records · Page 12

Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository

NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as various means to download and access the data including programmatically through the GeneLab Open API (GLOpenAPI). The open access of datasets in NASA’s OSDR provides a unique opportunity for the scientific community, as well as citizen scientists and students, to continue using OSDR resources to further unlock profound insights into the consequences of space travel on the human body. Through implementation of security measures to protect sensitive human data, the OSDR seeks to strengthen the science exchange between the Biological and Physical Sciences Program and the Human Research Program, per recommendation 4-1 of the 2023-2032 Decadal Survey, and encourage further sharing and dissemination of astronaut data to provide the scientific community with the resources needed to lay the groundwork for developing targeted mitigation strategies to help withstand the rigors of long-duration spaceflight.

Amanda Marie Saravia-butler↗

Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository

NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as instructions for how to download and access the data. The I4 datasets described here re present the first ever comprehensive collection of commercial astronaut data.

Amanda M Saravia-Butler↗

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗

The SAGA Survey. II. Building a Statistical Sample of Satellite Systems around Milky Way–like Galaxies

In this work, we present the Stage II results from the ongoing Satellites Around Galactic Analogs (SAGA) Survey. Upon completion, the SAGA Survey will spectroscopically identify satellite galaxies brighter than M r,o = -12.3 around 100 Milky Way (MW) analogs at z ~ 0.01. In Stage II, we have more than quadrupled the sample size of Stage I, delivering results from 127 satellites around 36 MW analogs with an improved target selection strategy and deep photometric imaging catalogs from the Dark Energy Survey and the Legacy Surveys. We have obtained 25,372 galaxy redshifts, peaking around z = 0.2. These data significantly increase spectroscopic coverage for very low redshift objects in 17 < r o < 20.75 around SAGA hosts, creating a unique data set that places the Local Group in a wider context. The number of confirmed satellites per system ranges from zero to nine and correlates with host galaxy and brightest satellite luminosities. We find that the number and luminosities of MW satellites are consistent with being drawn from the same underlying distribution as SAGA systems. The majority of confirmed SAGA satellites are star-forming, and the quenched fraction increases as satellite stellar mass and projected radius from the host galaxy decrease. Overall, the satellite quenched fraction among SAGA systems is lower than that in the Local Group. We compare the luminosity functions and radial distributions of SAGA satellites with theoretical predictions based on cold dark matter simulations and an empirical galaxy–halo connection model and find that the results are broadly in agreement.

79 ASTRONOMY AND ASTROPHYSICS↗

Proceedings of the Workshop for Applied Nuclear Data Activities WANDA 2022

On February 28 – March 4, 2022, the Nuclear Data Interagency Working Group (NDIAWG) hosted the 5-day virtual Workshop for Applied Nuclear Data (WANDA2022) to facilitate interagency collaboration on nuclear data for applications. This year’s focus was nuclear data for space applications, but also included photon reactions and transport, reactions on unstable nuclei, and data adjustment topics. The annual WANDA workshops are planned by the Nuclear Data Working Group (NDWG) with the goal of assembling users and producers of nuclear data to provide input to identify and prioritize nuclear data needs and to suggest solutions to address those needs. The workshop consisted of talks by agency program managers, six topic focused road mapping sessions and a review of NDIAWG-funded projects. More than 350 attendees represented national laboratories, universities, and federal agencies, as well as international organizations and industry. The proceedings presented herein summarize the workshop’s content, highlight important outcomes, and document attendees’ recommendations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

RAID 7 disk array

Each RAID level reflects a different design architecture. Associated with each is a backdrop of imposed limitations, as well as possibilities which may be exploited within the architectural constraints of that level. There are three unique features that differentiate RAID 7 from all other levels. RAID 7 is asynchronous with respect to usage of I/O data paths. Each I/O drive (includes all data and one parity drives) as well as each host interface (there may be multiple host interfaces) has independent control and data paths. This means that each can be accessed completely, independently, of the other. This is facilitated by a separate device cache for each device/interface as well. RAID 7 is asynchronous with respect to device hierarchy and data bus utilization. Each drive and each interface is connected to a high speed data bus controlled by the embedded operating system to make independent transfers to and from central cache. RAID 7 is asynchronous with respect to the operation of an embedded real time process oriented operating system. This means that exclusive and independent of the host, or multiple host paths, the embedded OS manages all I/O transfers asynchronously across the data and parity drives. A key factor to consider is that of the RAID 7's ability to anticipate and match host I/O usage patterns. This yields the following benefits over RAID's built around micro-code based architectures. RAID 7 appears to the host as a normally connected Big Fast Disk (BFD). RAID 7 appears, from the perspective of the individual disk devices, to minimize the total number of accesses and optimize read/write transfer requests. RAID 7 smoothly integrates the random demands of independent users with the principles of spatial and temporal locality. This optimizes small, large, and time sequenced I/O requests which results in users having an I/O performance which approaches performance to that of main memory.

Stout, Lloyd↗

General-Purpose Data-Formatting Input/Output System

Multiplexable input/output (I/O) system developed as interface between host computer and real-time, fixed-base simulator cockpit. Unit designed to be general-purpose interface and operated through virtually any 8- or 16-bit, transistor/transistor-logic-level, parallel-I/O port with or without handshaking. Accepts byte-coded data in form of data blocks from host computer and routes data to various system I/O modules like discrete outputs, lamp drivers, and seven-segment-display drivers. Formats and routes data from input modules back to host computer. Other modules designed to drive alphanumeric displays and communications interfaces and to serve as analog-to-digital and digital-to-analog converter modules.

Busquets, Anthony M.↗

COVID-19 biomarkers based on respiratory microbiome content

COVID-19 patient care management would greatly benefit from new tools that enable accurate assessment of disease severity and stage, potentially enabling a personalized medicine approach. Detection of the SARS-CoV-2 virus itself, or even quantitation of viral loads, is not sufficient for accurate assessment of disease state beyond diagnosis of infection [eg, doi:10.1093/cid/ciaa344]. Levels of usual suspect protein biomarkers associated with host response to infection [eg, C-reactive protein (CRP); cytokines like IL-6, TNF-alpha, and IL-10; complement proteins like C3a and C5a], and of individual blood cell types (eg, leukocytes, lymphocytes, and subsets thereof), show limited correlation with disease severity and stage, with high patient-to-patient and study-to-study variability [eg, doi:10.1093/cid/ciaa248]. High-dimensional panels of biomarkers should have greater predictive power and resilience to unavoidable sources of variability; however, their assembly from proteins and cell types is extremely difficult, due to technical limitations in analyte measurement, especially with regard to starting material requirements and detection sensitivity. Host response profiling through Next Generation Sequencing (NGS) of gene expression patterns (ie, RNA-Seq) is a promising approach, but at the time of this project there were only two publicly available datasets of relevance [doi:10.1093/cid/ciaa203, doi:10.1080/22221751.2020.1747363], and close inspection of them revealed that each had at least one major flaw that severely undermined its value in supporting robust analysis of host response to SARS-CoV- 2 infection. However, the first of these studies [doi:10.1093/cid/ciaa203] fortuitously collected NGS data not only from host cells, but also from bacteria present in bronchoalveolar lavage fluid (BALF) recovered from COVID-19 patients; and because the respiratory microbiome (in terms of bacterial species content) is far less complex than the human transcriptome, the NGS data collected were sufficient to provide coverage depth supporting robust analysis. Surprisingly, the authors of the study did not carry out a detailed analysis of these data and their potential for revealing important new information about COVID-19. Therefore, we carried out a meta-analysis of the dataset as a first step in evaluating the potential for profiling of respiratory microbiome dynamics as a means of accurately assessing COVID-19 disease state.

59 BASIC BIOLOGICAL SCIENCES↗

Interactive data line study and experiment

The paper considers the utility of having remote terminals on a Landsat image processing system and the development of efficient data transfer strategies such as data compression. The approach is to link an image processing terminal (located in a mobile van) to a multiuser host computer via the Communications Technology Satellite and a leased phone line. The host computer will share time between the remote state users and local users. The terminal includes a minicomputer, a color video display, and a communications interface, and the user has access to all of the resources of the host facility via the data link. While at present the terminal acts in the display-only mode, the computing capability of the terminal can be varied from display-only up to a stand-alone image processing system. An analysis of trade-offs between data link and remote terminal capacities is described with attention to the evaluation of the system by state users and the selection of a system architecture suitable to unique needs.

Rasmussen, D. N.↗

Linking transients to their host galaxies – II. A comparison of host galaxy properties and rate dependencies across supernova types

ABSTRACT We use the latest data set of supernova (SN) host galaxies to investigate how the host properties – stellar mass, star formation rate (SFR), metallicity, absolute magnitude, and colour–differ across SN types, with redshift-driven selection effects controlled. SN Ib and Ic host galaxies, on average, are more massive, metal-rich, and redder than SN II hosts. For subtypes, SN Ibn and Ic-BL have bluer hosts than their normal SN Ib and Ic siblings; SN IIb has consistent host properties with SN Ib, while hosts of SN IIn are more metal-rich than those of SN II. Hydrogen-deficient superluminous SNe feature bluer and lower luminosity hosts than most subtypes of core-collapse supernova (CC SN). Assuming simple proportionality of CC SN rates and host SFRs does not recover the observed mean host properties; either a population of long-lived progenitors or a metallicity-dependent SN production efficiency better reproduces the observed host properties. Assuming the latter case, the rates of SN II are insensitive to host metallicity, but the rates of SN Ib and Ic are substantially enhanced in metal-rich hosts by a factor of $\sim 10$ per dex increase in metallicity. Hosts of SN Ia are diverse in their observed properties; subtypes including SN Ia-91T, Ia-02cx, and Ia-CSM prefer star-forming hosts, while subtypes like SN Ia-91bg and Ca-rich prefer quiescent hosts. The rates of SN Ia-91T, Ia-02cx, and Ia-CSM are closely dependent on, or even proportional to, their host SFRs, indicating relatively short-lived progenitors. Conversely, the rates of SN Ia-91bg and Ca-rich transients are proportional to the total stellar mass, favouring long-lived progenitors.

Qin, Yu-Jing (ORCID:0000000336586026)↗

NASA’s Atmospheric Science Data Center’s Approach to a Cloud-Based Model of Ingest, Archival, and Distribution of TEMPO Data: Methods, Challenges, and Best Practices

The National Aeronautics and Space Administration's (NASA) Atmospheric Science Data Center (ASDC) at NASA Langley Research Center in Hampton, VA provides atmospheric science data products and services to the science community, including enhanced search and subsetting capabilities for numerous datasets. The ASDC is the official Distributed Active Archive Center (DAAC) of record for the upcoming Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument. TEMPO will be situated on a geostationary satellite positioned at a longitude near the center of the conterminous United States and focused on North America, making hourly swaths of its field of regard from east to west. ASDC’s data products are currently hosted locally and services (e.g., spatial and temporal subsetting) are managed on premises. The ASDC is planning to provide TEMPO data and services in the cloud through the Earthdata Search platform. This presentation will discuss the ASDC’s approach to a cloud-based model of ingest, archival, and distribution of TEMPO data. Methods, challenges, best practices, lessons learned, and future plans will be discussed.

Iman Nasif↗

Performance Prediction of Big Data Transfer Through Experimental Analysis and Machine Learning

Big data transfer in next-generation scientific applications is now commonly carried out over connections with guaranteed bandwidth provisioned in High-performance Networks (HPNs) through advance bandwidth reservation. To use HPN resources efficiently, provisioning agents need to carefully schedule data transfer requests and allocate appropriate bandwidths. Such reserved bandwidths, if not fully utilized by the requesting user, could be simply wasted or cause extra overhead and complexity in management due to exclusive access. This calls for the capability of performance prediction to reserve bandwidth resources that match actual needs. Towards this goal, we employ machine learning algorithms to predict big data transfer performance based on extensive performance measurements, which are collected over a span of several years from a large number of data transfer tests using different protocols and toolkits between various end sites on several real-life physical or emulated HPN testbeds. We first identify a comprehensive list of attributes involved in a typical big data transfer process, including end host system configurations, network connection properties, and control parameters of data transfer methods. We then conduct an in-depth exploratory analysis of their impacts on application-level throughput, which provides insights into big data transfer performance and motivates the use of machine learning. We also investigate the applicability of machine learning algorithms and derive their general performance bounds for performance prediction of big data transfer in HPNs. Experimental results show that, with appropriate data preprocessing, the proposed machine learning-based approach achieves 95% or higher prediction accuracy in up to 90% of the cases with very noisy real-life performance measurements.

Yun, Daqing↗

Performance Prediction of Big Data Transfer Through Experimental Analysis and Machine Learning

Big data transfer in next-generation scientific ap- plications is now commonly carried out over connections with guaranteed bandwidth provisioned in High-performance Net- works (HPNs) through advance bandwidth reservation. To use HPN resources efficiently, provisioning agents need to carefully schedule data transfer requests and allocate appropriate band- widths. Such reserved bandwidths, if not fully utilized by the requesting user, could be simply wasted or cause extra overhead and complexity in management due to exclusive access. This calls for the capability of performance prediction to reserve bandwidth resources that match actual needs. Towards this goal, we employ machine learning algorithms to predict big data transfer perfor- mance based on extensive performance measurements, which are collected over a span of several years from a large number of data transfer tests using different protocols and toolkits between various end sites on several real-life physical or emulated HPN testbeds. We first identify a comprehensive list of attributes involved in a typical big data transfer process, including end host system configurations, network connection properties, and control parameters of data transfer methods. We then conduct an in-depth exploratory analysis of their impacts on application- level throughput, which provides insights into big data transfer performance and motivates the use of machine learning. We also investigate the applicability of machine learning algorithms and derive their general performance bounds for performance prediction of big data transfer in HPNs. Experimental results show that, with appropriate data preprocessing, the proposed machine learning-based approach achieves 95% or higher pre- diction accuracy in up to 90% of the cases with very noisy real-life performance measurements.

Yun, Daqing↗

Energy Emergency and Preparedness Data: Frequently Asked Questions (FAQs) and Quick Guidance on Crisis Communications

State Energy Offices and Public Utility Commissions rely on timely, accurate, and actionable information to perform their energy emergency response duties and execute their roles as state energy security planners. In support of this need, the National Association of State Energy Officials (NASEO) and the National Association of Regulatory Utility Commissions (NARUC) hosted an Energy Security and Data Analysis Workshop in Washington, DC to identify energy security response and planning data sources; and to share successful methods of data use and integration in state, federal, and private sector tools. Following the workshop, NASEO and NARUC hosted two topical data-centric webinars based on state priorities to identify best practices in Geographic Information Systems (GIS) and Crisis Communications programs leveraged in energy assurance planning and response. The Crisis Communications webinar covered best practice tactics for how states can respond during energy emergencies and other crises. Based on the workshop and webinars, this document summarizes commonly used data sources and includes frequently asked questions which may be used by state energy officials (i.e., consisting of staff from Public Utility Commissions and Governor-designated State Energy Offices) to help guide them in developing or improving their Crisis Communications capabilities. A strong public information program is a key crisis management tool. Timely and accurate information helps prevent confusion and uncertainty and encourages public support and cooperation. As energy subject matter experts, state energy officials are vital in the distilling, clarifying, and conveying energy sector information and implications to decision-makers and the public. Other participants in an effective public information program include the Governor’s Office, other state agencies, local governments, energy providers, local businesses, state legislature, and the federal government. It is essential to provide stakeholders and the public with information about the nature, severity, and duration of an emergency because inadequate understanding and awareness can lead to undesirable actions that could further exacerbate the situation. Before a state government can provide information to the public, it must gather information, describe the emergency accurately, and develop recommendations to manage the situation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Volcanic Gas Emissions Mapping Using a Mass Spectrometer System

The visualization of hazardous gaseous emissions at volcanoes using in-situ mass spectrometry (MS) is a key step towards a better comprehension of the geophysical phenomena surrounding eruptive activity. In-Situ gas data consisting of helium, carbon dioxide, sulfur dioxide, and other gas species, were acquired with an MS system. MS and global position system (GPS) data were plotted on ground imagery, topography, and remote sensing data collected by a host of instruments during the second Costa Rica Airborne Research and Technology Applications (CARTA) mission This combination of gas and imaging data allowed 3-dimensional (3-D) visualization of the volcanic plume end the mapping of gas concentration at several volcanic structures and urban areas This combined set of data has demonstrated a better tool to assess hazardous conditions by visualizing and modeling of possible scenarios of volcanic activity. The MS system is used for in-situ measurement of three-dimensional gas concentrations at different volcanic locations with three different transportation platforms, aircraft, auto, and hand carried. The demonstration for urban contamination mapping is also presented as another possible use for the MS system.

Griffin, Timothy P.↗

IDB Data Loader

The International Database of Reference Gamma-Ray Spectra of Various Nuclear Matter is designed to hold curated gamma spectral data and will be hosted by the International Atomic Energy Agency on its public facing web site. Currently, the database to be hosted is given to the International Atomic Energy Agency by Sandia. This document describes the application used by Sandia to load spectral data into a database.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

An Overview in the Development of a Multi-Sensor Data Science System for Monitoring a Solvent Extraction Process

To enhance nuclear nonproliferation stewardship, Idaho National Laboratory is building the Beartooth nuclear fuel cycle processing test bed. The Beartooth test bed will allow researchers the opportunity to study nuclear fuel processing operations including the use of centrifugal contactors in solvent extraction processes. The test bed is designed to support data collection and machine learning to monitor process operations. As part of this project, researchers will study data collected from a host of sensors that have not been typically used to monitor solvent extraction processes such as vibration, acoustic, colormetric, and thermal measurement data. The goal of this research is to employ machine learning and data analytics to study the confluence of signals collected from both traditionally and non-traditionally used sensors to provide operator process awareness and discover process anomalies. An overview of planned sensors and experiments that will focus on signal discovery will be presented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

An Overview in the Development of a Multi-Sensor Data Science System for Monitoring a Solvent Extraction Process

To enhance nuclear nonproliferation stewardship, Idaho National Laboratory is building the Beartooth nuclear fuel cycle processing test bed. The Beartooth test bed will allow researchers the opportunity to study nuclear fuel processing operations including the use of centrifugal contactors in solvent extraction processes. The test bed is designed to support data collection and machine learning to monitor process operations. As part of this project, researchers will study data collected from a host of sensors that have not been typically used to monitor solvent extraction processes such as vibration, acoustic, colormetric, and thermal measurement data. The goal of this research is to employ machine learning and data analytics to study the confluence of signals collected from both traditionally and non-traditionally used sensors to provide operator process awareness and discover process anomalies. An overview of planned sensors and experiments that will focus on signal discovery will be presented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗