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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Analysis of biofilm assembly by large area automated AFM

Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Information theory and machine learning illuminate large‐scale metabolomic responses of Brachypodium distachyon to environmental change

SUMMARY Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC‐MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC‐MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ–condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)‐based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML‐based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co‐accumulation analysis further identified condition‐specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio‐Analytic Resource for Plant Biology website ( https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi‐bin/efpWeb.cgi ), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sea Ice Rheology Experiment (SIREx): 1. Scaling and Statistical Properties of Sea-Ice Deformation Fields

As the sea-ice modeling community is shifting to advanced numerical frameworks, developing new sea-ice rheologies, and increasing model spatial resolution, ubiquitous deformation features in the Arctic sea ice are now being resolved by sea-ice models. Initiated at the Forum for Arctic Modeling and Observational Synthesis, the Sea Ice Rheology Experiment (SIREx) aims at evaluating state-of-the-art sea-ice models using existing and new metrics to understand how the simulated deformation fields are affected by different representations of sea-ice physics (rheology) and by model configuration. Part 1 of the SIREx analysis is concerned with evaluation of the statistical distribution and scaling properties of sea-ice deformation fields from 35 different simulations against those from the RADARSAT Geophysical Processor System (RGPS). For the first time, the viscous-plastic (and the elastic-viscous-plastic variant), elastic-anisotropic-plastic, and Maxwell-elasto-brittle rheologies are compared in a single study. We find that both plastic and brittle sea-ice rheologies have the potential to reproduce the observed RGPS deformation statistics, including multi-fractality. Model configuration (e.g., numerical convergence, atmospheric representation, spatial resolution) and physical parameterizations (e.g., ice strength parameters and ice thickness distribution) both have effects as important as the choice of sea-ice rheology on the deformation statistics. It is therefore not straightforward to attribute model performance to a specific rheological framework using current deformation metrics. In light of these results, we further evaluate the statistical properties of simulated Linear Kinematic Features in a SIREx Part 2 companion paper.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

PermitTEC v0.1: Standardized Metadata Corpus of NEPA Litigation Documents

The National Environmental Policy Act of 1969, as amended (NEPA), mandates that federal agencies assess and document potential environmental impacts before deciding on proposed actions. While significant progress has been made in cataloging and standardizing NEPA documents themselves, the legal challenges that frequently arise from these decisions remain poorly cataloged and largely inaccessible for systematic analysis. Litigation challenging NEPA compliance can substantially delay project timelines, reshape agency decision-making, and establish precedents that influence future environmental reviews — yet no standardized, machine-readable corpus exists that links litigation records to the NEPA projects they contest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Wide Area 3D Measurement System for Analysis of 3013 Inner Container Closure Weld Region

One of the main focus areas of the 3013 Surveillance Program is a thorough evaluation of the inner container closure weld region (ICCWR) opened for destructive examination (DE). As part of the protocol to investigate the corrosion in the ICCWR, a laser confocal microscope (LCM) is used to perform close visual examination of the surface and to measure corrosion features on the surface. However, in FY20, the introduction of the Wide Area 3D Measurement System (WAMS) was tested as a method for faster inspection of the ICCWR. Optimization of the WAMS parameters for data collection was carried out using a generic tear-drop type sample containing large and fine Stress Corrosion Cracking (SCC) fractures and high resolution images were compared to the image obtained with the LCM. Although the image with the LCM shows higher resolution than the WAMS images, the small features can be still identified in the WAMS images. The advantage of collecting data for the full circumference using the WAMS is that it can take about a week to complete, which represents 1/16 of the time needed with the LCM. Nonetheless, both systems offer capabilities that combined can be utilized to expedite the examination of the ICCWR. The WAMS can be utilized to obtain images for faster screening or identification of corrosion features on the surface while the LCM can be utilized to obtain higher resolution images of those areas identified by the WAMS.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Data and scripts associated with the manuscript "Using Mutual Information for Global Sensitivity Analysis on Watershed Modeling"

This package contains the data and scripts used in "Using Mutual Information for Global Sensitivity Analysis on Watershed Modeling" (Jiang et al., 2022). The ARW_SWAT.zip file contains the SWAT simulation and the sensitivity analysis result in the American River Watershed. The Portage_SWAT.zip file contains the SWAT simulation and the sensitivity analysis result in the Portage River Watershed. The src folder contains the source code of sensitivity analysis and plotting functions. The notebooks folder contains the Jupyter notebooks for performing sensitivity analysis and other post analyses.Global Sensitivity Analysis (GSA) often is applied to assess the sensitivity of model outputs to their inputs using ensemble simulations. However, increasing model complexity and the associated computational cost have limited the use of most GSA approaches for process-based watershed models. We propose to use Mutual Information (MI) as a computationally efficient GSA method for watershed modeling. Such MI computed from several hundred realizations usually can capture nonlinear relationships between inputs and outputs of interest. We perform MI-based watershed sensitivity analyses in studies of the Portage River Watershed in Ohio and the American River Watershed in Washington. In these studies, MI is used to evaluate the sensitivity of river discharges simulated by the Soil and Water Assessment Tool to no less than 20 parameters for each watershed. Our MI-based sensitivity analyses achieved convergence with about 300~500 realizations, a small fraction of the ensemble size (i.e., several thousand) required by the Sobol method. Nevertheless, MI yields similar sensitivity ranking compared to the Sobol method, especially for sensitive parameters. Our study thus sheds new light on the use of MI as an affordable GSA method for computationally intensive models such as the hyper-resolution, watershed hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Improving Convection Trigger Functions in Deep Convective Parameterization Schemes Using Machine Learning

Abstract Deficiencies in convection trigger functions, used in deep convection parameterizations in General Circulation Models (GCMs), have critical impacts on climate simulations. A novel convection trigger function is developed using the machine learning (ML) classification model XGBoost. The large‐scale environmental information associated with convective events is obtained from the long‐term constrained variational analysis forcing data from the Atmospheric Radiation Measurement (ARM) program at its Southern Great Plains (SGP) and Manaus (MAO) sites representing, respectively, continental mid‐latitude and tropical convection. The ML trigger is separately trained and evaluated per site, and jointly trained and evaluated at both sites as a unified trigger. The performance of the ML trigger is compared with four convective trigger functions commonly used in GCMs: dilute convective available potential energy (CAPE), undilute CAPE, dilute dynamic CAPE (dCAPE), and undilute dCAPE. The ML trigger substantially outperforms the four CAPE‐based triggers in terms of the F 1 score metric, widely used to estimate the performance of ML methods. The site‐specific ML trigger functions can achieve, respectively, 91% and 93% F 1 scores at SGP and MAO. The unified trigger also has a 91% F 1 score, with virtually no degradation from the site‐specific training, suggesting the potential of a global ML trigger function. The ML trigger alleviates a GCM deficiency regarding the overprediction of convection occurrence, offering a promising improvement to the simulation of the diurnal cycle of precipitation. Furthermore, to overcome the black box issue of the ML methods, insights derived from the ML model are discussed, which may be leveraged to improve traditional CAPE‐based triggers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Geochemistry of East River, Colorado floodplain sediments from Meander Z and Meander Y collected in 2017.

This dataset includes sediment geochemical characterization data from floodplain sediments collected as a part of the Watershed Function Scientific Focus Area (SFA) located in the Upper Colorado River Basin. The data were collected in order to investigate the role of biogeochemical cycling and other river corridor processes on riverine export of solutes. Sediment cores were collected from Meander Z (MZA, MZB) and Meander Y (MYP) just upstream of the confluence with Brush Creek in September 2017 to depths of approximately 40-95 cm in 15-20 cm intervals. Analyses include moisture content, particle size analysis, total inorganic and total organic carbon, and extractions by 1 M KCl (for adsorbed NH4), anoxic HCl (for Fe(II) content), ammonium oxalate (for amorphous Fe-oxide content), and dithionite (for crystalline Fe-oxide content). Sample locations are included in both a kmz file, which can be opened in Google Earth, and a csv file, and methods are included as a text document. All characterization data is summarized in a Microsoft Excel file, and is also included as individual .csv files for each extraction (ammonium oxalate, anoxic HCl, dithionite, and KCl) and for bulk sediment data (moisture content, particle size analysis, TIC, and TOC).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Application of Point Precipitation Frequency Estimates to Watersheds

This report documents work sponsored by the U.S. Nuclear Regulatory Commission (NRC) at the Oak Ridge National Laboratory (ORNL) as part of the RES project, “Application of Point Precipitation Frequency Estimates to Watersheds.” This project was implemented as part of the Probabilistic Flood Hazard Assessment (PFHA) Research Program. The objective of the PFHA Research Program is to develop tools and guidance on the use of PFHA methods to risk-inform NRC’s licensing of new facilities as well as licensing and oversight of currently operating facilities as they relate to flooding hazards. Many nuclear power plants (NPPs) are located on or near rivers so riverine flooding hazards need to be considered in their design and operation. Probabilistic riverine flood models are important tools for realistic assessment of flooding risks. However, these models require areal estimates of the depth, duration, and frequency of rainfall distributed over the watershed, which are not often available. Point precipitation frequency estimates are more widely available. For example, the National Oceanic and Atmospheric Administration (NOAA) has published NOAA Atlas 14, which provides point precipitation frequency estimates for 5-minute through 60-day durations at average recurrence intervals of 1-year through 1,000-year. The research documented in this report addresses areal reduction factors (ARFs), which can be used to convert the widely available point precipitation frequency estimates, to estimates of areal precipitation frequency over a watershed. The most widely used ARF source is Technical Paper 29 (TP-29) published by the then U.S. Weather Bureau in 1958. However, both the methods and the underlying precipitation data used to produce TP-29 are seriously out of date. For example, due to the small gauge network available at the time of TP-29’s compilation, ARF estimates developed are only for watersheds smaller than about 400 square miles. Due to the relatively short record lengths of precipitation data available, frequency considerations could not be accurately determined. Other factors such as regional climate and seasonality were not addressed. Several newer methods have been published since TP-29 was developed and both the type and quantity of precipitation data have increased significantly, along with computational resources and analytical tools such as geographic information systems. This report reviewed and assessed the available precipitation products and methods for conducting ARF analysis. The work applied up-to-date precipitation data products and analysis methods with a novel watershed-based approach to investigate how ARF estimates vary across different methods, data sources, geographical locations, return periods, and seasons. The overall findings reported here regarding basic ARF trends are in line with other recent studies showing that ARFs decrease with increasing area, increase with increasing duration, and decrease with increasing return period. This study found significant differences among the available ARF methods. This work also found a strong geographical variability across different US hydrologic regions, suggesting that the ARF are specific to regional climate patterns and geographical characteristics and should not be applied arbitrarily to other locations. The results also reveal the importance of data record length, especially for high return level ARFs. The work reported in NUREG/CR-7271 will assist NRC staff in assessing different classes of ARF methods in conjunction with available rainfall data sets. It will also support the development of guidance for application of point precipitation data in PFHAs. It should be noted that the ARF values presented in this report for any location or region were developed for the purposes of comparing methods and investigating the factors that influence ARFs. They should not be considered official and should not be used in leu of a site-specific analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Ecological Quality Evolution and Its Driving Factors in Yunnan Karst Rocky Desertification Areas

Rocky desertification is a key element affecting regional ecological quality. Rocky desertification in Southwest China directly affects the ecological security of the Yangtze River and Pearl River basins and also restricts regional economic and social development. In order to clarify the evolution laws and key influencing factors of ecological quality in Yunnan karst rocky desertification areas, a quantitative analysis based on the remote sensing-based ecological index (RSEI) model was conducted to explore the overall evolution characteristics and change laws of ecological quality in Yunnan karst rocky desertification areas in the past 30 years. The correlation between RSEI, rock outcrop rate (Fr), and driving factors was determined by redundancy analysis. The results showed the following: (1) RSEI in Yunnan karst rocky desertification areas generally showed a decreasing trend, with a fluctuation in the mid-term, followed by a tendency to recover. It fell into three stages: decline, trough, and recovery, with fitting coefficients of -0.121, -0.057, and 0.157, respectively. In contrast, Fr showed an opposite tendency, illustrating the inverse relationship between RSEI and Fr, and the rate of sequential succession was much faster than that of the reverse succession under human measures of intervention. (2) The mean value of RSEI of Yunnan karst rocky desertification areas was generally lower than that of the total Yunnan Province land areas and Yunnan non-karst rocky desertification areas, but the mean value of Fr was generally more than that of both the above-mentioned areas. In addition, the RSEI and Fr of Yunnan karst rocky desertification areas both showed lower stability values than those of both the above-mentioned areas. This generally suggested a low ecological quality and a high degree of desertification under a low stability in Yunnan karst rocky desertification areas. (3) The correlation of RSEI and Fr with driving factors followed the order of topographic factors, soil factors > water factors > anthropogenic factors. Anthropogenic factors were the driving force changing the state of rocky desertification, geological factors such as topography and soil to a larger extent determined the original macroscopic ecological relationship of rocky desertification, and water factors lay between the above two. The findings of this research will provide theoretical support and a basis for the improvement of ecological quality and comprehensive control of karst rocky desertification in Yunnan Province.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

Position-specific 13 C/ 12 C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids. Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The 13 C/ 12 C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ 13 C values relative to a working standard. This methodology constrains position-specific δ 13 C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ 13 C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7–5‰ for each carbon position. Position-specific δ 13 C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO 2 , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline. Here this study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Measurement of isosteric heat of gas adsorption and Brunauer–Emmett–Teller (BET) surface area using a quartz crystal microbalance

The study of gas adsorption on a solid surface evaluates the affinity between sorbate gas and sorbent substrate and factors that contribute to this. This report presents a test platform for adsorption experiments of various gases on various solid surfaces. Controlled environmental conditions enable investigations in materials surface science and increase the consistency among adsorption data. The system utilizes a quartz crystal microbalance to perform gravimetric analysis of deposition and adsorption, enabling investigation of the interaction of gaseous molecules with solid surfaces. In this study, a quartz crystal microbalance as gas adsorption detector was integrated with an environmental chamber to create a versatile tool for gas adsorption experiments on thin films. Experimental operation of this apparatus was demonstrated via acquisition of the adsorption isotherms of cyclohexane vapor on a gold surface at 55 and 70 °C. The result indicated International Union of Pure and Applied Chemistry Type II adsorption. Consequentially, application of the Brunauer–Emmett–Teller model to the isotherm data subject to predefined criteria for linear region selection yielded a surface area of the sorbent of 0.53 cm2 at 55 °C. From the monolayer region of the isotherms, the isosteric heat of adsorption of the cyclohexane vapor on gold was calculated to be 37 kJ mol-1.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Evaluating the sustainability of the 2017 US biofuel industry with an integrated techno-economic analysis and life cycle assessment

The United States produced more than 66.2 billion Liters of biofuel, primarily in the form of corn ethanol (61 billion Liters) and soybean biodiesel (6 billion Liters), for the transportation industry in 2017. No work currently exists that evaluates both the economic and environmental outcomes of this industry with adequate geospatial resolution and national scope. In this study, a model framework is constructed to perform Techno-Economic Analysis and Life Cycle Assessment using high-resolution input datasets to provide a granular estimation of corn ethanol and soybean biodiesel sustainability performance in most counties in the United States in 2017 (the most recent year for which data is available). Results show a total life cycle, greenhouse gas emission volume of 99.5 million Mg CO 2-eq produced in 2017 by these two biofuels (94.8 million Mg from corn ethanol, and 4.7 million Mg from soybean biodiesel), excluding indirect land use change emissions. Further, this volume corresponds to a combined carbon intensity of 65.3 gCO 2-eq /MJ, which is a greenhouse gas improvement compared to petroleum-based gasoline (the carbon intensity of conventional gasoline is 93.0 gCO 2-eq /MJ). However, these biofuels are produced at an additional economic cost ($1.8 billion over the displaced gas/diesel). Additionally, these biofuels generate unfavorable impacts in other environmental categories when compared to petroleum-based fuels, particularly in areas of water, land, and nitrogen intensity. This work enables stakeholders to assess the specific value of biofuels as a means of emission reduction and determine if the attained improvements are worth the associated opportunity costs.

09 BIOMASS FUELS↗
DOE OSTI2024

Assessing Gas-Phase Ion Reactivity of 50 Elements with NO and the Direct Application for 239 Pu in Complex Matrices Using ICP-MS/MS

Understanding the reactivity of metal cations with various reaction gases in ICP-MS/MS is important to determine the best gas to use for a given analyte/interference pair. In this study, nitric oxide (NO) was investigated as the reaction gas following previous experimental designs. The reactions with 50 elements were investigated to examine periodic trends in reactivity, validate theoretical modeling of reaction enthalpies as a method to screen reactant gases, and provide a baseline for potential in-line gas separation methods. ICP-MS/MS studies involving actinides are typically limited to Th, U and Pu, with analyses of Np and Am rarely reported in the literature. To date, only two previous methods have investigated the use of NO in ICP-MS/MS analyses. To showcase the utility of NO, a method was developed to measure 239 Pu in the presence of environmental matrix constituent and other actinides, like what could be expected from post-detonation debris, with no chemical separation prior to analysis. 239 Pu + was reacted to form 239 Pu 16 O + , eliminating interferences derived from the sample matrix by measuring 239 Pu + intensity at m/z = 255 ( 239 Pu 16 O + ). To validate NO for 238 U 1 H + interference removal in environmental matrices, standard reference materials were diluted to 1 mg per gram of solution and spiked to 0.05 pg/g of 239 Pu and 1 µg/g 238 U (Pu/U = 5 x 10 -8 ). Measured 239 Pu concentrations were within 6% of the spiked value. In conclusion, these results demonstrate that reliable 239 Pu measurements can be made at levels relevant to nuclear forensics without the need for extensive chemical matrix separation prior to analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Analysis of Infrastructures for Processing Plastic Waste using Pyrolysis-Based Chemical Upcycling Pathways

Modern mechanical recycling infrastructure for plastic is capable of processing only a small subset of waste plastics, reinforcing the need for parallel disposal methods such as landfilling and incineration. Emerging pyrolysis-based chemical technologies can "upcycle" plastic waste into high-value polymer and chemical products and process a broader range of waste plastics. In this work, we study the economic and environmental benefits of deploying an upcycling infrastructure in the continental United States for producing low-density polyethylene (LDPE) and polypropylene (PP) from post-consumer mixed plastic waste. Our analysis aims to determine the market size that the infrastructure can create, the degree of circularity that it can achieve, the prices for waste and derived products it can propagate, and the environmental benefits of diverting plastic waste from landfill and incineration facilities it can produce. We apply a computational framework that integrates techno-economic analysis, life cycle assessment, and value chain optimization. Our results demonstrate that the infrastructure generates an economy of nearly 20 billion USD and positive prices for plastic waste, opening opportunities for compensation to residents who provide plastic waste. Our analysis also indicates that the infrastructure can achieve a plastic-to-plastic degree of circularity of 34% and remains viable under various external factors (including technology efficiencies, capital investment budgets, and polymer market values). Finally, we present significant environmental benefits of upcycling over alternative landfill and incineration waste disposal methods, and comment on ongoing work expanding our modeling methodology to other chemical upcycling pathway case studies, including hydroformylation of specific plastics to chemicals.

Interdisciplinary↗