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Model-Based Systems

Engineers, who design systems using text specification documents, focus their work upon the completed system to meet Performance, time and budget goals. Consistency and integrity is difficult to maintain within text documents for a single complex system and more difficult to maintain as several systems are combined into higher-level systems, are maintained over decades, and evolve technically and in performance through updates. This system design approach frequently results in major changes during the system integration and test phase, and in time and budget overruns. Engineers who build system specification documents within a model-based systems environment go a step further and aggregate all of the data. They interrelate all of the data to insure consistency and integrity. After the model is constructed, the various system specification documents are prepared, all from the same database. The consistency and integrity of the model is assured, therefore the consistency and integrity of the various specification documents is insured. This article attempts to define model-based systems relative to such an environment. The intent is to expose the complexity of the enabling problem by outlining what is needed, why it is needed and how needs are being addressed by international standards writing teams.

Frisch, Harold P.↗

Can synthetic lethality approach be used with DNA repair genes for primary and secondary MDS?

Cancer-specific defects in DNA repair pathways create the opportunity to employ synthetic lethality approach. Recently, GEMA (gene expression and mutation analysis) approach detected insufficient expression of BRCA or NHEJ (non-homologous end joining) to predict PARP inhibitors response. We evaluated a possible role of DNA repair pathways using gene expression of single-strand break (XPA, XPC, XPG/ERCC5, CSA/ERCC8, and CSB/ERCC6) and double-strand break (ATM, BRCA1, BRCA2, RAD51, XRCC5, XRCC6, LIG4) in 92 patients with myelodysplastic syndrome (73 de novo, 9 therapy-related (t-MDS). Therapy-related MDS (t-MDS) demonstrated a significant downregulation of axis BRCA1-BRCA2-RAD51 comparing to normal controls (p = 0.048, p = 0.001, p = 0.001). XRCC6 showed significantly low expression in de novo MDS comparing to controls (p = 0.039) and for patients who presented chromosomal abnormalities (p = 0.047). Downregulation of LIG4 was consistently associated with poor prognostic markers in de novo MDS (hemoglobin < 8 g/dL (p = 0.040), neutrophils < 800/mm{sup 3} (p < 0.001), patients with excess of blasts (p = 0.001), very high (p = 0.002)/high IPSS-R (p = 0.043) and AML transformation (p < 0.001). We also performed an evaluation of GEPIA Database in 30 cancer types and detected a typical pattern of downregulation as here presented in primary or secondary MDS. All these results suggest synthetic lethality approach can be tested with DNA repair genes (beyond that of BRCA1/2 status) for de novo and therapy-related myelodysplastic syndrome and may encourage clinical trials evaluating the use of PARP1 inhibitors in MDS. Graphic Abstract: .

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Characterization of the Deltaproteobacteria in contaminated and uncontaminated stream sediments and identification of potential mercury methylators

Microbial communities were examined in surface stream sediments at 5 contaminated sites and 1 control site near Oak Ridge, TN, USA, to identify bacteria that could be contributing to mercury (Hg) methylation. The phylogenetic composition of the sediment bacterial community was examined over 3 quarterly sampling periods (36 samples) using 16S rRNA gene pyrosequencing. Only 3064 sequences (0.85% of the total community) were identified as Deltaproteobacteria, the only group known to methylate Hg, using the Ribosomal Database Project classifier at the 99% confidence threshold. Constrained ordination techniques indicated statistically significant positive linear correlations between Desulfobulbus spp., Desulfonema spp. and Desulfobacca spp. and methyl-Hg concentrations at the Hg-contaminated sites. In contrast, the distribution of organisms related to Byssovorax spp. was significantly correlated to inorganic carbon, nitrate and uranium concentrations but not to Hg or methyl-Hg. Overall, the abundance and richness of Deltaproteobacteria sequences were higher in uncontaminated sediments, while the majority of the members present at the contaminated sites were either known potential metal-reducers/methylators or metal tolerant species. Given the abundance relative to other known Hg methylators and the association with methyl-Hg, Desulfobulbus spp. is considered a prime candidate for involvement in Hg methylation in these streams.

59 BASIC BIOLOGICAL SCIENCES↗

DART 7.0 User Guide

The Desktop Analysis Reporting Tool (DART) is a software package that allows users to easily view and analyze daily files that span long periods. DART gives users the capability to quickly determine the state of health of a radiation portal monitor (RPM), troubleshoot and diagnose problems, and view data in various time frames to perform trend analysis. In short, it converts the data strings written in the daily files into meaningful tables and plots. The standalone version of DART (“soloDART”) utilizes a database engine that is included with the application; no additional installations are necessary. There is also a networked version of DART (“polyDART”) that is designed to maximize the benefit of a centralized data repository while distributing the workload to individual desktop machines. This networked approach requires a more complex database manager Structured Query Language (SQL) Server; however, SQL Server is not currently provided with DART. Regardless of which version is used, DART will import daily files from RPMs, store the relevant data in its database, and it can produce reports for status, trend analysis, and reporting purposes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Anomaly Detection for Discrete Sequences: A Survey

This survey attempts to provide a comprehensive and structured overview of the existing research for the problem of detecting anomalies in discrete/symbolic sequences. The objective is to provide a global understanding of the sequence anomaly detection problem and how existing techniques relate to each other. The key contribution of this survey is the classification of the existing research into three distinct categories, based on the problem formulation that they are trying to solve. These problem formulations are: 1) identifying anomalous sequences with respect to a database of normal sequences; 2) identifying an anomalous subsequence within a long sequence; and 3) identifying a pattern in a sequence whose frequency of occurrence is anomalous. We show how each of these problem formulations is characteristically distinct from each other and discuss their relevance in various application domains. We review techniques from many disparate and disconnected application domains that address each of these formulations. Within each problem formulation, we group techniques into categories based on the nature of the underlying algorithm. For each category, we provide a basic anomaly detection technique, and show how the existing techniques are variants of the basic technique. This approach shows how different techniques within a category are related or different from each other. Our categorization reveals new variants and combinations that have not been investigated before for anomaly detection. We also provide a discussion of relative strengths and weaknesses of different techniques. We show how techniques developed for one problem formulation can be adapted to solve a different formulation, thereby providing several novel adaptations to solve the different problem formulations. We also highlight the applicability of the techniques that handle discrete sequences to other related areas such as online anomaly detection and time series anomaly detection.

99 GENERAL AND MISCELLANEOUS↗

ISSARS Aerosol Database : an Incorporation of Atmospheric Particles into a Universal Tool to Simulate Remote Sensing Instruments

The Instrument Simulator Suite for Atmospheric Remote Sensing (ISSARS) entered its third and final year of development with an overall goal of providing a unified tool to simulate active and passive space borne atmospheric remote sensing instruments. These simulations focus on the atmosphere ranging from UV to microwaves. ISSARS handles all assumptions and uses various models on scattering and microphysics to fill the gaps left unspecified by the atmospheric models to create each instrument's measurements. This will help benefit mission design and reduce mission cost, create efficient implementation of multi-instrument/platform Observing System Simulation Experiments (OSSE), and improve existing models as well as new advanced models in development. In this effort, various aerosol particles are incorporated into the system, and a simulation of input wavelength and spectral refractive indices related to each spherical test particle(s) generate its scattering properties and phase functions. These atmospheric particles being integrated into the system comprise the ones observed by the Multi-angle Imaging SpectroRadiometer(MISR) and by the Multiangle SpectroPolarimetric Imager(MSPI). In addition, a complex scattering database generated by Prof. Ping Yang (Texas A&M) is also incorporated into this aerosol database. Future development with a radiative transfer code will generate a series of results that can be validated with results obtained by the MISR and MSPI instruments; nevertheless, test cases are simulated to determine the validity of various plugin libraries used to determine or gather the scattering properties of particles studied by MISR and MSPI, or within the Single-scattering properties of tri-axial ellipsoidal mineral dust particles database created by Prof. Ping Yang.

Instrument Simulator Suite for Atmospheric Remote ↗

Sperm quality and environment: A retrospective, cohort study in a Northern province of Italy

Background: Several studies proposed a relationship between environmental factors and semen quality, as well as the negative effect of air pollution on spermatogenesis and gonadal function. No specific studies evaluated the environmental influence on semen quality in a specific geographical area. Aim: to evaluate the environmental influence on male sperm parameters in a Northern Italian population referred for semen analysis in the National Health System. The objective of the study is the assessment of the relationship of both air pollution and environmental parameters with quality-related sperm variables, during the coldest months of the year when air is usually most polluted, due to low ventilation and poor rainfall. Study design: A retrospective, observational, cohort study was carried out in the province of Modena, located in the Emilia-Romagna region of Northern Italy. Methods: Semen analyses (n=406), environmental temperature, air humidity and air particulate matter (PM) measurements from the 1st of November 2014 to the 19th of February 2015 were acquired to the first database. Since spermatogenesis lasts over two months, a second, wider database was arranged, evaluating environmental exposure in the 3 months before semen collection (from August 1st 2014). All data included in the database were registered by geo-coding the residential address of the patients and the site of registration of environmental factors. The geo-codification of parameters was performed using Fusion Tables of Google available at (https://www.google.com/fusiontables/data? dsrcid=implicit), considering the exact time of measurement. Results: Average air temperature was inversely related to sperm concentration and to total sperm number (p<0.001). Semen volume was inversely related only to the minimum (p<0.001) and not to maximum recorded temperature (p=0.110). Air humidity was not related to sperm quantity and quality. PM{sub 2.5} was directly related to total sperm number (p<0.001). PM{sub 10} was directly related to both semen volume (0<0.001), and typical forms (p<0.001), inversely related to atypical forms (p<0.001), but related neither to sperm concentration (p=0.430) nor to sperm motility. The extended analyses considering environmental parameters in the 3 months before semen collection, confirmed the relationship between air temperature and sperm quantity, whereas no influence was found between PM and sperm quality. Conclusion: An influence of environmental temperature on semen quantity is suggested, without a clear effect of air pollution, as assessed through PM{sub 10} levels, on sperm parameter variations.

54 ENVIRONMENTAL SCIENCES↗

Hybrid Wing Body Aircraft System Noise Assessment with Propulsion Airframe Aeroacoustic Experiments

A system noise assessment of a hybrid wing body configuration was performed using NASA s best available aircraft models, engine model, and system noise assessment method. A propulsion airframe aeroacoustic effects experimental database for key noise sources and interaction effects was used to provide data directly in the noise assessment where prediction methods are inadequate. NASA engine and aircraft system models were created to define the hybrid wing body aircraft concept as a twin engine aircraft with a 7500 nautical mile mission. The engines were modeled as existing technology high bypass ratio turbofans. The baseline hybrid wing body aircraft was assessed at 22 dB cumulative below the FAA Stage 4 certification level. To determine the potential for noise reduction with relatively near term technologies, seven other configurations were assessed beginning with moving the engines two fan nozzle diameters upstream of the trailing edge and then adding technologies for reduction of the highest noise sources. Aft radiated noise was expected to be the most challenging to reduce and, therefore, the experimental database focused on jet nozzle and pylon configurations that could reduce jet noise through a combination of source reduction and shielding effectiveness. The best configuration for reduction of jet noise used state-of-the-art technology chevrons with a pylon above the engine in the crown position. This configuration resulted in jet source noise reduction, favorable azimuthal directivity, and noise source relocation upstream where it is more effectively shielded by the limited airframe surface, and additional fan noise attenuation from acoustic liner on the crown pylon internal surfaces. Vertical and elevon surfaces were also assessed to add shielding area. The elevon deflection above the trailing edge showed some small additional noise reduction whereas vertical surfaces resulted in a slight noise increase. With the effects of the configurations from the database included, the best available noise reduction was 40 dB cumulative. Projected effects from additional technologies were assessed for an advanced noise reduction configuration including landing gear fairings and advanced pylon and chevron nozzles. Incorporating the three additional technology improvements, an aircraft noise is projected of 42.4 dB cumulative below the Stage 4 level.

Thomas, Russell H.↗

Trajectory analysis via a geometric feature space approach

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.

97 MATHEMATICS AND COMPUTING↗

Speleogenesis, geometry, and topology of caves: A quantitative study of 3D karst conduits

Karst systems are hierarchically spatially organized three-dimensional (3D) networks of conduits behaving as drains for groundwater flow. Recently, geostatistical approaches proposed to generate karst networks from data and parameters stemming from analogous observed karst features. Other studies have qualitatively highlighted relationships between speleogenetic processes and cave patterns. However, few studies have been performed to quantitatively define these relationships. This paper reports a quantitative study of cave geometries and topologies that takes the underlying speleogenetic processes into account. In order to study the spatial organization of caves, a 3D numerical database was built from 26 caves, corresponding to 621 km of cumulative cave passages representative of the variety of karst network patterns. The database includes 3D speleological surveys for which the speleogenetic context is known, allowing the polygenic karst networks to be divided into 48 monogenic cave samples and classified into four cave patterns: vadose branchwork (VB), water-table cave (WTC), looping cave (LC), and angular maze (AM). Eight morphometric cave descriptors were calculated, four geometrical parameters (width-height ratio, tortuosity, curvature, and vertical index) and four topological ones (degree of node connectivity, α and γ graph indices, and ramification index) respectively. The results were validated by statistical analyses (Kruskal-Wallis test and PCA). The VB patterns are clearly distinct from AM ones and from a third group including WTC and LC. A quantitative database of cave morphology characteristics is provided, depending on their speleogenetic processes. These characteristics can be used to constrain and/or validate 3D geostatistical simulations. This study shows how important it is to relate the geometry and connectivity of cave networks to recharge and flow processes. Conversely, the approach developed here provides proxies to estimate the evolution of the vadose zone to epiphreatic and phreatic zones in limestones from the quantitative analysis of existing cave patterns.

58 GEOSCIENCES↗

Adverse Events Involving Radiation Oncology Medical Devices: Comprehensive Analysis of US Food and Drug Administration Data, 1991 to 2015

Purpose: Radiation oncology relies on rapidly evolving technology and highly complex processes. The US Food and Drug Administration collects reports of adverse events related to medical devices. We sought to characterize all events involving radiation oncology devices (RODs) from the US Food and Drug Administration's postmarket surveillance Manufacturer and User Facility Device Experience (MAUDE) database, comparing these with non–radiation oncology devices. Methods and Materials: MAUDE data on RODs from 1991 to 2015 were sorted into 4 product categories (external beam, brachytherapy, planning systems, and simulation systems) and 5 device problem categories (software, mechanical, electrical, user error, and dose delivery impact). Outcomes included whether the device was evaluated by the manufacturer, adverse event type, remedial action, problem code, device age, and time since 510(k) approval. Descriptive statistics were performed with linear regression of time-series data. Results for RODs were compared with those for other devices by the Pearson χ{sup 2} test for categorical data and 2-sample Kolmogorov-Smirnov test for distributions. Results: There were 4234 ROD and 4,985,698 other device adverse event reports. Adverse event reports increased over time, and events involving RODs peaked in 2011. Most ROD reports involved external beam therapy (50.8%), followed by brachytherapy (24.9%) and treatment planning systems (21.6%). The top problem types were software (30.4%), mechanical (20.9%), and user error (20.4%). RODs differed significantly from other devices in each outcome (P<.001). RODs were more likely to be evaluated by the manufacturer after an event (46.9% vs 33.0%) but less likely to be recalled (10.5% vs 37.9%) (P<.001). Device age and time since 510(k) approval were shorter among RODs (P<.001). Conclusions: Compared with other devices, RODs may experience adverse events sooner after manufacture and market approval. Close postmarket surveillance, improved software design, and manufacturer–user training may help mitigate these events.

07 ISOTOPE AND RADIATION SOURCES↗

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo design have generated accurate predictions of 3D folded chain structures, generalization to synthetic polymers remains intractable due to the requirement of large structural databases and the intrinsically disordered nature of polymer building blocks. In this work, polypeptoids, a class of peptidomimetic synthetic polymers, are utilized to build a general workflow for the study of relationships between monomer sequence and dynamic 3D chain structure in solution. Furthermore, this work demonstrates how control over the monomer sequence can alter the conformational landscape of synthetic polymers to deviate dramatically from classical chain statistics. Specifically, the distribution of end-to-end distances, as measured by double electron-electron resonance spectroscopy in dilute solvent, is systematically skewed towards shorter distances with an increasing number of hydrophobes and further refined by hydrophobe arrangement in amphiphilic polypeptoid chains.

36 MATERIALS SCIENCE↗

Rapid Threat Organism Recognition Pipeline

The RAPTOR computational pipeline identifies microbial nucleic acid sequences present in sequence data from clinical samples. It takes as input raw short-read genomic sequence data (in particular, the type generated by the Illumina sequencing platforms) and outputs taxonomic evaluation of detected microbes in various human-readable formats. This software was designed to assist in the diagnosis or characterization of infectious disease, by detecting pathogen sequences in nucleic acid sequence data from clinical samples. It has also been applied in the detection of algal pathogens, when algal biofuel ponds became unproductive. RAPTOR first trims and filters genomic sequence reads based on quality and related considerations, then performs a quick alignment to the human (or other host) genome to filter out host sequences, then performs a deeper search against microbial genomes. Alignment to a protein sequence database is optional. Alignment results are summarized and placed in a taxonomic framework using the Lowest Common Ancestor algorithm.

Solberg, OwenD.↗

PANTHER: Trajectory Analysis

We want to organize a body of trajectories in order to identify, search for, classify and predict behavior among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as total distance traveled and distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generally be mapped easily to behaviors of interest to humans that are searching large databases. Most of these geometric features are invariant under rigid transformation. We demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories, predict destination and apply unsupervised machine learning algorithms.

42 ENGINEERING↗

Abstract - Cooperative Research and Development Agreement between Environmental Defense Fund and National Energy Technology Laboratory

Here, we summarize an effort to develop a global oil and gas infrastructure (GOGI) taxonomy and geodatabase, using a combination of big data computing, custom search and data integration algorithms, and expert driven spatio-temporal analytics to identify, access, and evaluate open oil and gas data resources and uncertainty trends worldwide. This approach leveraged custom National Energy Technology Laboratory (NETL) tools and capabilities in collaboration with Environmental Defense Fund (EDF) and Carbon Limits subject matter expertise, to identify over 380 datasets and integrate more than 4.8 million features into the GOGI database. In addition to acquisition of open oil and gas infrastructure data, information was collected and analyzed to assess the spatial, temporal, and source quality of these resources, and estimate their completeness relative to the top 40 hydrocarbon producing and consuming countries.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Progress Report on SFR Metallic Fuel Data Qualification

This report summarizes the progress of SFR metallic fuel qualification related activities, which are focused on providing quality assurance relevant information applicable to experiments irradiated during the Integral Fast Reactor (IFR) program. A background of metallic fuel performance data and the associated databases, including the EBR-II Fuels Irradiation & Physics Database (FIPD) and Out-of-Pile Transient Database (OPTD), is included. The legacy data in the databases, including as-built, post-irradiation examination (PIE), operating parameters, and out-of-pile experiment data are introduced. The SFR metallic fuel Quality Assurance Program Plan (QAPP) and its implementation to qualify these legacy data is described in detail. Important PIE data QA documents and the specifications of four types of PIE measurements (contact profilometry, laser profilometry, neutron radiography and gamma scan) are provided. Examples of the implementation of the QAPP to qualify each of those types of PIE data are provided.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Survey of Aging and Monitoring Concerns for Cables and Splices Due to Cable Repair and Replacement

The purpose of this report is to survey aging and monitoring concerns for electrical cable splices in nuclear power plants (NPPs) in long term operation. As portions of existing electrical cable runs in nuclear are replaced over time due to localized events, the total number of splices in NPPs is expected to increase. Relative to cables, the body of knowledge regarding aging of splices and splices in combination with aging cables in nuclear service environments in long-term operations is low. A few reports have considered the aging of cable system components other than cables (Jacobus 1990; Nelson 1998; Villaran and Lofaro 2002), but the nuclear industry has two decades of operating experience since these were published to further enlighten this issue. Herein we discuss electrical cables and splices commonly found in U.S. nuclear power plants, their qualification in safety-related application, and methods for monitoring their health condition. Common environmental stresses that can give rise to cable and splice failure are discussed. The Nuclear Regulatory Commission (NRC) Licensee Event Reports (LER) database was used to identify documented issues of cable and splice failure. The trend in the resultant data over time is considered to see if failures are increasing as plants age. Observations and conclusions of this work include: 1. Cables and splices are highly reliable components. Occurrence rates for events of interest were low and nearly constant over the last 20 years. 2. Common-cause failure for evaluated cable events of interest was observed to primarily be associated with loose connections, which may manifest associated with workmanship issues, thermal cycling, and/or vibration. 3. Replacement of cables is more common than repair, leading to an increase in proportion of new generation cables in the plant over time. 4. Splices on degraded cables have been observed to be problematic. Due to aging NPP infrastructure, including electrical cables, it is expected that such issues will continue to increase. 5. Condition monitoring approaches, while shown to be fruitful for cables, have been shown to be insensitive to degradation of splice sleeves, which are critical to the continued performance of splices. Additional condition monitoring (CM) work is needed to evaluate methods which are sensitive to the degradation of splice components. 6. Extended Material Degradation Assessment (EMDA) knowledge gaps for electrical cables (Bernstein et al. 2014) have not been investigated for splices but may represent similar concerns such as for the accelerated aging process historically used in environmental qualification.

42 ENGINEERING↗

Knowledge Graph for End-to-End Traceability of an Integrated Human-Earth System Model

Integrated human-Earth system models inform energy-water-land system dynamics and policies, yet their results are difficult to trace through input-data, model structure, scenario configurations, and solved outputs. Because this information is siloed across disconnected artifacts, process-based IAMs have historically lacked a unified, queryable representation. Such lack of traceability prevents researchers from systematically isolating the multi-sector drivers of complex outcomes (such as tracing water-scarcity results back to distant energy-system dynamics) or conducting holistic uncertainty attribution across hundreds of interacting parameters. To address this concern, our work documents the software engineering process of a knowledge graph that unifies these four layers for the Global Change Analysis Model (GCAM-USA_Reference scenario, GCAM v9.1). The graph was built as a relational property graph in DuckDB from the run’s own artifacts: the input-preparation dependency map (gcamdata chunk map), the model’s XML input files, the run configuration, and the results database (BaseX), successfully mapping the model’s declared structure. The resulting graph comprises 204,321 nodes and 1,687,814 edges across 16 node types and 15 edge types, with approximately 16.3 million time-series values stored separately to maintain structural efficiency. To ensure representation fidelity, every edge carries an epistemic-status annotation recording the warrant for the relationship (structural, provenance, dependency, or model-derived), and a machine-readable provenance ledger classifying the origin of every schema element. Evaluation against a fixed five-benchmark suite with locked baselines reports zero structural orphans, zero dangling edge endpoints, and 100% of output-producing technologies traceable to raw input files. Two interactive interfaces present the graph, including a serverless browser application built on DuckDB-Wasm. By establishing the first end-to-end provenance framework for an IAM, this work enables researchers and scientists to systematically audit complex policy scenarios, debug model structures, and trace policy-relevant outputs to their data origins in real time.

Artifical Intelligence↗