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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes

Fruiting body development (FBD) of mushroom-forming fungi has attracted tremendous interest. However, the genetic and molecular basis of FBD is poorly known. Here, using Lentinula edodes (shiitake) as a model, we deciphered the genetic architecture underlying fruiting body-related traits (FBRTs) by combined genomic, genetic and phenotypic data. Using RNA-Seq of fruiting bodies from 110 dikaryons in a bi-parental mapping population, we constructed an ultra-high-density genetic map of L. edodes (Lemap2.0) with a total length of 810.14 cM, which covered 81.7% of the shiitake genome. A total of 94 scaffolds of the shiitake genome were aligned to Lemap2.0 and re-anchored into nine pseudochromosomes. Then via quantitative trait locus (QTL) analysis, we disclosed an outline of the genetic architecture of FBD in shiitake. Twenty-nine QTLs and three main genomic regions associated with FBD of shiitake were identified. Using meta-QTL analysis, seven pleiotropic QTLs for multiple traits were detected, which contributed to the correlations of FBRTs. In the mapped QTLs, the expression of 246 genes were found to significantly correlate with the phenotypic traits. Thirty-three of them were involved in FBD and could represent candidate genes controlling the shape and size of fruiting bodies. Collectively, our findings have advanced our understanding of the genetic regulation of FBD in shiitake and mushroom-forming fungi at large.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Mapping environmental sensitivity: A systematic online approach to support environmental assessment and planning

Environmental sensitivity analysis provides a framework for systematically and objectively determining the potential for significant environmental impacts. The higher the natural or acquired sensitivity of the receiving environment, the less capable it is to cope with human-induced change. Given that sensitivity is context- and spatially-specific, Geographic Information Systems have been applied to develop an operational Webtool to analyse it. The Webtool enables a rapid and replicable spatial examination of environmental sensitivities and potential for land-use conflicts that supports Strategic Environmental Assessment and, ultimately, informed planning and decision-making. The novelty is on the provision of an online geoprocessing Widget that enables creation of context-specific maps. Pilot testing the Webtool in land-use and renewable energy planning through stakeholder engagement has validated its applicability. Stakeholders confirmed that it enables replicating and, in some cases, improving in-house SEA mapping processes while saving time and effort. However, its full reliance on publicly available spatial datasets renders completeness and resolution issues. The Webtool provides a critical starting-point for sectoral planning discussions and for developing plan/programme alternatives that avoid or minimise potentially incompatible or unsustainable zonings, while promoting consistency and transparency in impact assessment. - Highlights: •Sensitivity mapping can enhance baseline information for environmental assessments. •A novel online geoprocessing tool supports systematic sensitivity assessment. •It enables combining context-specific environmental criteria and value judgments. •Pilot testing it through stakeholder engagement has validated its applicability. •The tool promotes assessment consistency and transparency but data issues remain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Introducing a risk aggregation rationale for mapping risks to aquifers from point- and diffuse-sources–proof-of-concept using contamination data from industrial lagoons

Highlights: • Aquifer risk mapping is introduced for contaminants acting as point/diffuse-sources. • Innovations are framed by risk cells based on Source-Pathway-Receptor-Source (SPRC). • Point-source (Risk Cell 1) and diffuse-source (Risk Cell 2) use sets of algorithms. • Algorithms include MODPATH, DRASTIC, GWPI and are integrated on a modular basis. • Risk Cells 1/2 are aggregated giving fit-for-purpose results as proof-of-concept. - Abstract: Proof-of-concept for a methodology is presented on mapping risks to aquifers impacted from point- and diffuse-sources, where mapping or indexing refers to relative but not absolute values. The methodology is generic but tested by investigating impacts of a risk exposure from industrial wastewater lagoons. The methodology is innovative for using the qualitative Source-Pathways-Receptors-Consequences (SPRC) framework to aggregate risks from both point-sources and diffuse-sources through breaking down a study area into SPRC risk cells. In this paper, two risk cells are required as: (i) Cell 1 is directly impacted from a point-source; and (ii) Cell 2 is impacted by diffuse-sources to slowly contaminate the aquifer by infiltration over a large area. Indexing both types of risk cells generically comprise three tiered processes: (i) binary indexing establishes if a grid cell is at a potential risk or not; (ii) graded indexing measures the strength of the risk pathways from source to receptors; and (iii) local indexing measures intrinsic potentials at the grid cell to propagate the risk. These three processes apply to both point- and diffuse-sources but with different mathematical formulations. The proof-of-concept for the methodology of risk aggregation using the SPRC framework is supported by results of a study area, in which a set of performance metrics are used by comparing with the measurements. The results are found to be fit-for-purpose for serving as proactive management tools and to provide a deeper insight into potential impacts of adverse effects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Synchrotron-based X-ray fluorescence microscopy mapping the ionome of a toxic freshwater cyanobacterium

Harmful algal blooms (HABs) pose a major environmental concern across the globe. In abundance, cyanobacteria, or so-called green-blue algae can produce extremely dangerous cyanotoxins that harm humans and animals. This study focused on the mapping and distribution of intracellular macro-and micronutrients of the widespread freshwater cyanobacteria Microcystis aeruginosa (M. aeruginosa). Towards a better understanding of trace metal uptake and homeostasis throughout the cell cycle, we quantitatively mapped the spatial distribution of the elements P, K, Fe, Ca, Zn, Mn, and Cu across the ultrastructure of frozen-hydrated single cells using state-of-theart X-ray nanofluorescence imaging at the Advanced Photon Source (APS) at Argonne National Laboratory. Further, bulk cellular nutrient and trace metal content correlated well with the total intracellular elemental content in individual cells obtained by quantitative synchrotron X-ray fluorescence measurements. Multi-dimensional mappings showed P and K atoms colocalized as discrete semicircular hotspots that were analyzed with respect to their stoichiometry. Elevated Cu and Ca concentrations were detected along division plane of cells. P and K were found to have similar spatial elemental distribution with about 65% and 69% of the total cellular P and K, respectively, located at the hotspots. The P and K colocalization were refined further using nanotomography, showing a K envelope surrounding the P core. Inorganic P and organic P compounds were specified using solution-state 31 P nuclear magnetic resonance (NMR) spectroscopy from M. aeruginosa. Of the total extracted P determined by 31 P NMR spectroscopy, 47% were found to be nucleotides while only 11% were polyphosphates. Multimodal X-ray imaging provides a better understanding of intracellular biochemical processes in cyanobacteria, helping us monitor and combat an emerging environmental threat.

31P NMR spectroscopy↗
DOE OSTI2017

A risk map methodology to assess the spatial and temporal distribution of leakage into groundwater from Geologic Carbon Storage

The risks to potable aquifers due to brine leakage through plugged and abandoned (P&A) wells is highly uncertain and a potentially significant contributor to the risk profile in Geologic Carbon Storage (GCS). This uncertainty stems from the unknown location of wells and the large variance of P&A wellbore permeability, making the spatial assessment of P&A brine leakage risk challenging. A new methodology is presented to generate “risk maps”, or spatial distributions of brine leakage risk to groundwater resources as defined with no-impact or Maximum Contaminant Level (MCL) thresholds. The methodology utilizes probability theory, thereby avoiding the use of computationally expensive Monte Carlo simulations while maintaining flexibility in modeling techniques. These maps provide quantitative probabilities of risk as a function of time to inform site selection and monitoring during and post-injection, conducive to the US EPA's permitting of class-VI wells and the so-called “area of review”, AoR. As a demonstration of the methodology, a numerical model of a hypothetical fully-coupled system spanning from the injection reservoir to the USDW is used to assess the evolution of brine leakage through P&A wells. Risk maps of CO 2 leakage can also be generated with this methodology for a comprehensive assessment of GCS leakage risk.

58 GEOSCIENCES↗
DOE OSTI2022

Nanoindentation mapping defects filtration for heterogeneous materials using generative adversarial networks

Advanced composite materials with multiple phases and heterogeneous microstructure necessitate spatial mapping characterization of elastic modulus to develop constitutive relations and overall mechanical response. Such modulus mapping can be obtained using the nanoindentation technique, where the indenter tip raster over the selected microstructure region. Typically, a surface preparation procedure is done in the specimens to ensure proper contact between the indenter tip and sample surface. However, a near-perfect surface finish is unachievable in heterogeneous materials, primarily with ceramic reinforcements, due to the differential material removal rate during polishing. Thus, the nanoindenter records localized erroneous measurements due to differences in surface roughness and corresponding force response. This study establishes a novel deep learning-based strategy to rectify incorrect experimental spatial measurements acquire during nanoindentation modulus mapping. Here, the integrated bicubic interpolation and generative adversarial networks (GANs) model was trained using 14 ceramic and 18 metallic data sets, each comprising 65,536 measurements. The developed algorithm was validated against experimental measurements on four unknown specimens. The standard deviation in measured elastic modulus reduces by ~50% in ceramics and ~72% in metallic samples. This computational framework proposes a novel approach to reducing uncertainty in materials’ properties using state-of-the-art computer vision techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.

3D cell mapping↗
DOE OSTI2014

Methodology to design a municipal solid waste generation and composition map: A case study

Highlights: • To draw a waste generation and composition map of a town a lot of factors must be taken into account. • The methodology proposed offers two different depending on the available data combined with geographical information systems. • The methodology has been applied to a Spanish city with success. • The methodology will be a useful tool to organize the municipal solid waste management. - Abstract: The municipal solid waste (MSW) management is an important task that local governments as well as private companies must take into account to protect human health, the environment and to preserve natural resources. To design an adequate MSW management plan the first step consist in defining the waste generation and composition patterns of the town. As these patterns depend on several socio-economic factors it is advisable to organize them previously. Moreover, the waste generation and composition patterns may vary around the town and over the time. Generally, the data are not homogeneous around the city as the number of inhabitants is not constant nor it is the economic activity. Therefore, if all the information is showed in thematic maps, the final waste management decisions can be made more efficiently. The main aim of this paper is to present a structured methodology that allows local authorities or private companies who deal with MSW to design its own MSW management plan depending on the available data. According to these data, this paper proposes two ways of action: a direct way when detailed data are available and an indirect way when there is a lack of data and it is necessary to take into account bibliographic data. In any case, the amount of information needed is considerable. This paper combines the planning methodology with the Geographic Information Systems to present the final results in thematic maps that make easier to interpret them. The proposed methodology is a previous useful tool to organize the MSW collection routes including the selective collection. To verify the methodology it has been successfully applied to a Spanish town.

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

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Locating Undocumented Wells Using Historical Oil and Gas Exploration Maps: A Case Study in Osage County, Oklahoma

Undocumented oil and gas wells lack reliable information about their locations and characteristics, making them difficult to identify. These wells can result in unanticipated delays and costs in the development of nearby surface and subsurface resources, and, if improperly plugged, can cause contamination. This study leverages historical petroleum exploration maps to locate such wells, focusing on Osage County, Oklahoma. Two sets of early 20th century oil and gas exploration maps by the United States Geological Survey were georeferenced and analyzed using a computer vision model to detect well symbols. The locations of detected wells were compared to the location of known wells in the database from the Bureau of Indian Affairs Osage Agency to identify potential undocumented wells. The analysis yielded over 500 potential undocumented wells, with dry holes constituting the largest fraction. Field verification confirmed the presence of some undocumented wells. Comparison with prior work revealed limited overlap, underscoring the complementary value of historical oil and gas maps for locating undocumented wells. This approach demonstrates the utility of integrating historical cartographic resources with modern geospatial and machine learning techniques to improve the identification and management of undocumented wells.

Energy - Petroleum↗
DOE OSTI2018

Nanoscale mapping of hydrogen evolution on metallic and semiconducting MoS 2 nanosheets

Hydrogen evolution reaction (HER) on molybdenum disulfide (MoS 2 ) nanosheets is enhanced for the metallic (1T) phase relative to the thermodynamically stable semiconducting (2H) phase. To measure this difference, we employ scanning electrochemical microscopy (SECM) for high-resolution mapping (<20 nm spatial resolution) of surface reactivity for mixed-phase and pure 2H-only MoS 2 nanosheets. For mixed-phase MoS 2 nanosheets, we find major differences in reactivity of the two phases for electron transfer involving ferrocenemethanol, allowing us to locate 1T and 2H regions and directly map the corresponding HER activity. In our measurements, we find that HER is immeasurably slow on the 2H basal plane and much faster on edges, whereas 1T portions are highly reactive across the entire portion. We also use scanning transmission electron microscopy-electron energy loss spectroscopy and scanning Kelvin probe microscopy to corroborate the phase domains and local workfunctions (surface potentials) within the MoS 2 nanosheets; the mixed-phase MoS 2 has a shallower workfunction compared to 2H MoS 2 , which could enable a greater driving force for H 2 generation. As a result, this powerful combination of techniques for spatially mapping surface reactivity and correlated phase domains should be applicable to a broad range of materials for HER and other catalysis reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2013

SIMS instrumentation and methodology for mapping of co-localized molecules

We describe an innovative mode for localizing surface molecules. In this methodology, individual C{sub 60} impacts at 50 keV are localized using an electron emission microscope, EEM, synchronized with a time-of-flight mass spectrometer for the detection of the concurrently emitted secondary ions. The instrumentation and methodologies for generating ion maps are presented. The performance of the localization scheme depends on the characteristics of the electron emission, those of the EEM and of the software solutions for image analysis. Using 50 keV C{sub 60} projectiles, analyte specific maps and maps of co-emitted species have been obtained. The individual impact sites were localized within 1-2 μm. A distinctive feature of recording individual impacts is the ability to identify co-emitted ions which originate from molecules co-located within ∼10 nm.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

An unconstrained Lagrangian formulation and conservation laws for the Schrödinger map system

We consider energy-critical Schrödinger maps from R{sup 2} into S{sup 2} and H{sup 2}. Viewing such maps with respect to orthonormal frames on the pullback bundle provides a gauge field formulation of the evolution. We show that this gauge field system is the set of Euler-Lagrange equations corresponding to an action that includes a Chern-Simons term. We also introduce the stress-energy tensor and derive conservation laws. In conclusion we offer comparisons between Schrödinger maps and the closely related Chern-Simons-Schrödinger system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

High-speed force mapping on living cells with a small cantilever atomic force microscope

The imaging speed of the wide-spread force mapping mode for quantitative mechanical measurements on soft samples in liquid with the atomic force microscope (AFM) is limited by the bandwidth of the z-scanner and viscous drag forces on the cantilever. Here, we applied high-speed, large scan-range atomic force microscopy and small cantilevers to increase the speed of force mapping by ≈10−100 times. This allowed resolving dynamic processes on living mouse embryonic fibroblasts. Cytoskeleton reorganization during cell locomotion, growth of individual cytoskeleton fibers, cell blebbing, and the formation of endocytic pits in the cell membrane were observed. Increasing the force curve rate from 2 to 300 Hz increased the measured apparent Young's modulus of the cells by about 10 times, which facilitated force mapping measurements at high speed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Disease mapping based on stochastic SIR-SI model for Dengue and Chikungunya in Malaysia

This paper describes and demonstrates a method for relative risk estimation which is based on the stochastic SIR-SI vector-borne infectious disease transmission model specifically for Dengue and Chikungunya diseases in Malaysia. Firstly, the common compartmental model for vector-borne infectious disease transmission called the SIR-SI model (susceptible-infective-recovered for human populations; susceptible-infective for vector populations) is presented. This is followed by the explanations on the stochastic SIR-SI model which involve the Bayesian description. This stochastic model then is used in the relative risk formulation in order to obtain the posterior relative risk estimation. Then, this relative estimation model is demonstrated using Dengue and Chikungunya data of Malaysia. The viruses of these diseases are transmitted by the same type of female vector mosquito named Aedes Aegypti and Aedes Albopictus. Finally, the findings of the analysis of relative risk estimation for both Dengue and Chikungunya diseases are presented, compared and displayed in graphs and maps. The distribution from risk maps show the high and low risk area of Dengue and Chikungunya diseases occurrence. This map can be used as a tool for the prevention and control strategies for both diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Damage mapping in structural health monitoring using a multi-grid architecture

This paper presents a multi-grid architecture for tomography-based damage mapping of composite aerospace structures. The system employs an array of piezo-electric transducers bonded on the structure. Each transducer may be used as an actuator as well as a sensor. The structure is excited sequentially using the actuators and the guided waves arriving at the sensors in response to the excitations are recorded for further analysis. The sensor signals are compared to their baseline counterparts and a damage index is computed for each actuator-sensor pair. These damage indices are then used as inputs to the tomographic reconstruction system. Preliminary damage maps are reconstructed on multiple coordinate grids defined on the structure. These grids are shifted versions of each other where the shift is a fraction of the spatial sampling interval associated with each grid. These preliminary damage maps are then combined to provide a reconstruction that is more robust to measurement noise in the sensor signals and the ill-conditioned problem formulation for single-grid algorithms. Experimental results on a composite structure with complexity that is representative of aerospace structures included in the paper demonstrate that for sufficiently high sensor densities, the algorithm of this paper is capable of providing damage detection and characterization with accuracy comparable to traditional C-scan and A-scan-based ultrasound non-destructive inspection systems quickly and without human supervision.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Analysis of unstable periodic orbits and chaotic orbits in the one-dimensional linear piecewise-smooth discontinuous map

In this paper, we analytically examine the unstable periodic orbits and chaotic orbits of the 1-D linear piecewise-smooth discontinuous map. We explore the existence of unstable orbits and the effect of variation in parameters on the coexistence of unstable orbits. Further, we show that this structuring is different from the well known period adding cascade structure associated with the stable periodic orbits of the same map. Further, we analytically prove the existence of chaotic orbit for this map.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Maps of the little bangs through energy density and temperature fluctuations

Heavy-ion collisions at ultra-relativistic energies are often referred to as little bangs. We propose for the first time to map the heavy-ion collisions at ultra-relativistic energies, similar to the maps of the cosmic microwave background radiation, using fluctuations of energy density and temperature in small phase space bins. We study the evolution of fluctuations at each stage of the collision using an event-by-event hydrodynamic framework. We demonstrate the feasibility of making fluctuation maps from experimental data and its usefulness in extracting considerable information regarding the early stages of the collision and its evolution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗