Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “High resolution data analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Chlorophyll- a dynamics in the lower Amazon River: insights from in situ and hyperspectral remote sensing using OCI-PACE

Chlorophyll-a concentration (Chla) is a key indicator of phytoplankton biomass and aquatic trophic status. However, satellite-derived Chla in sediment-rich waters, such as those found in the Lower Amazon River, remains challenging. The present study characterizes in situ Chla levels and their relationships with geographic, physical, and biogeochemical parameters in the Lower Amazon. Data collected between 2014 and 2017 across four hydrological seasons included measurements of Chla, remote sensing reflectance, and water quality parameters such as total suspended sediment, conductivity, water surface temperature, dissolved oxygen, pH, dissolved organic carbon and coloured dissolved organic matter. An empirical model was developed to estimate Chla using simulated hyperspectral bands from NASA’s PACE mission, achieving high performance (R 2 = 0.76; RMSE = 0.11 μg·L −1 ). Red bands proved particularly effective for Chla retrieval, while the addition of ultraviolet bands further enhanced model accuracy. The application of the developed model to satellite imagery yielded results consistent with in situ observations for the same hydrologic season. Seasonal variation and geographic location were major factors influencing Chla dynamics. This study provides a novel contribution to Chla estimation in optically complex, highly turbid waters and highlights the potential of the PACE mission to enhance global aquatic ecosystem monitoring. In conclusion, by offering freely available hyperspectral data with high radiometric resolution, PACE represents a significant advancement in the realm of remote sensing of aquatic environments.

Amazon River↗
DOE OSTI2021

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C . geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C . geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C . geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C . geophilum , we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Application of a Chemical Index to Aerosol Mass Spectrometry: Delta Plots and Functional Group Distributions

A better understanding of the chemical properties of organic aerosol (OA) particles will improve our ability to characterize their sources and predict their lifetime. The high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) is widely used to measure OA in real time using thermal vaporization followed by electron ionization (EI). EI creates fragment ions that can be assigned to functional groups using delta analysis, a method of classifying mass spectra according to the presence of different chemically related ion series. In this study, we demonstrate the application of delta analysis to characterize molecular structures using a new visualization method. We also use delta analysis to quantify the functional group distribution with an average absolute error of ∼5–6% for individual standard molecules, comparable to the error observed for OA mixtures from biomass and coal combustion fit with Fourier transform infrared spectroscopy. Finally, we apply delta functional group analysis to AMS positive matrix factorization (PMF) factors across seven different field campaigns and find a similar composition across the more oxidized factors with about 55% acid and 26% alcohol groups. The analysis method described here can be applied to any HR-ToF-AMS data set to provide quantitative relative functional group distributions for OA mixtures.

aerosol↗
DOE OSTI2024

A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries

An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase α/β titanium alloy. The data were recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3 nm step size. The results show the expected Burgers orientation relationships between the α laths and β matrix, as well as the expected misorientations between α laths. A minor issue was found that one area was affected by 180° ambiguities in indexing occur due to this area being aligned too close to a zone axis of the α with twofold projection symmetry (not present in 3D) in the zero-order Laue Zone, and this should be avoided in data acquisition in the future. Nevertheless, this study demonstrates a good workflow for the analysis of nanocrystalline two- or multi-phase materials, which will be of widespread use in analysing two-phase titanium and other systems and how they evolve as a function of thermomechanical treatments.

36 MATERIALS SCIENCE↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to West Nile Virus Infection, Processed Experimental Dataset Catalog

West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flavivirus) by the National Institute of Allergy and Infectious Diseases (NIAID), and are known to cause severe infections in humans where lethal host-associated mechanisms are not clearly defined. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding a specific West Nile virus [NCBITAXON:11082] (WNV-NY99 382) experimental infection study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Development of an Attenuated Total Reflectance–Ultraviolet–Visible Probe for the Online Monitoring of Dark Solutions

Optical spectroscopy is a valuable tool for on-line monitoring of a variety of processes. Ultraviolet-visible (UV-vis) spectroscopy in particular, can monitor the concentration of analytes as well as identify speciation and oxidation state. However, it can be difficult to impossible to employ UV-vis based sensors on chemical systems that are very dark (i.e., high optical density) as exceedingly short pathlengths are required (for transmission approaches) or effective means of backscattering are needed (for reflectance approaches). Examples of processes that would benefit significantly from the use of optical sensors and encounter these challenges include used nuclear fuel recycling and molten salts with high concentrations of dissolved uranium. Utilizing an attenuated total reflectance (ATR) UV-vis approach can overcome these challenges and allow for the measurement of solutions orders of magnitude more concentrated than transmission UV-vis. However, determining ideal sensor specifications for varied processes can be time consuming and expensive. Here, in this study, we evaluate the ability for a novel ATR-UV-vis probe to measure very concentrated solutions of Co(II) and Ni(II) nitrate as well as organic dyes (methylene blue, acid red 1, and crystal violet). This sensor design provides a modular method for exploring possible “pathlengths” by altering the exposed ATR fiber length. Also studied were approaches to loading and measuring the sensor cell. These results are compared to a traditional 1 cm cuvette measured by transmission UV-vis. It was found that the ATR-UV-vis probe was capable of measuring solutions 600 times more concentrated than the 1 cm cuvette. Advanced data analysis in the form of multivariate curve resolution (MCR) was used to analyze the speciation of methylene blue over a large concentration range. The application of this novel ATR-UV-vis probe to the interrogation of dark solutions is a promising avenue for use in on-line monitoring of nuclear processes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

DESI DR1 Ly α 1D power spectrum: Validation of estimators

The Data Release 1 (DR1) of the Dark Energy Spectroscopic Instrument (DESI) is the largest sample to date for small-scale Lyα forest cosmology, accessed through its one-dimensional power spectrum (P 1D ). The Lyα forest P 1D is extracted from quasar spectra that are highly inhomogeneous (both in wavelength and between quasars) in noise properties due to intrinsic properties of the quasar, atmospheric and astrophysical contamination, and also sensitive to low-level details of the spectral extraction pipeline. We employ two estimators in DR1 analysis to measure P 1D : the optimal estimator and the fast Fourier transform (FFT) estimator. To ensure robustness of our DR1 measurements, we validate these two power spectrum and covariance matrix estimation methodologies against the challenging aspects of the data. First, using a set of 20 synthetic 1D realizations of DR1, we derive the masking bias corrections needed for the FFT estimator and the continuum fitting bias needed for both estimators. We demonstrate that both estimators, including their covariances, are unbiased with these corrections using the Kolmogorov-Smirnov test. Second, we substantially extend our previous suite of CCD image simulations to include 675,000 quasars, allowing us to accurately quantify the pipeline's performance. This set of simulations reveals biases at the highest k values, corresponding to a resolution error of a few percent. We base the resolution systematics error budget of DR1 P 1D on these values, but do not derive corrections from them since the simulation fidelity is insufficient for precise corrections.

Lyman alpha forest↗
DOE OSTI2022

Fuzzy dark matter and the Dark Energy Survey Year 1 data

ABSTRACT Gravitational weak lensing by dark matter haloes leads to a measurable imprint in the shear correlation function of galaxies. Fuzzy dark matter (FDM), composed of ultralight axion-like particles of mass m ∼ 10−22 eV, suppresses the matter power spectrum and shear correlation with respect to standard cold dark matter. We model the effect of FDM on cosmic shear using the optimized halo model HMCode, accounting for additional suppression of the mass function and halo concentration in FDM as observed in N-body simulations. We combine Dark Energy Survey Year 1 (DES-Y1) data with the Planck cosmic microwave background anisotropies to search for shear correlation suppression caused by FDM. We find no evidence of suppression compared to the preferred cold dark matter model, and thus set a new lower limit to the FDM particle mass. Using a log-flat prior and marginalizing over uncertainties related to the non-linear model of FDM, we find a new, independent 95 per cent C.L. lower limit log10m > −23 combining Planck and DES-Y1 shear, an improvement of almost two orders of magnitude on the mass bound relative to CMB-only constraints. Our analysis is largely independent of baryonic modelling, and of previous limits to FDM covering this mass range. Our analysis highlights the most important aspects of the FDM non-linear model for future investigation. The limit to FDM from weak lensing could be improved by up to three orders of magnitude with $\mathcal {O}(0.1)$ arcmin cosmic shear angular resolution, if FDM and baryonic feedback can be simultaneously modelled to high precision in the halo model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Ebola Virus Infection, Processed Experimental Dataset Catalog

Ebola virus (EBOV) is high risk biological agent, classified as a Category A priority pathogen (Flaviviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), known to cause hemorrhagic fever with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Ebola virus [NCBITAXON:186536] (Zaire/Makona or Zaire/Mayinga) experimental infection study. Human host samples types include peripheral blood mononuclear cells isolated from blood plasma ["PBMC", BTO:0001025], human hepatoma carcinoma cells ["HUH", BTO:0001950], human umbilical vein endothelial cells ["HUVEC", BTO:0001949], immortalized human hepatocyte cells ["IHH", BTO:0006147], and human histiocytic lymphoma cells ["U937", BTO:0001412].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Optimal 1D Ly α forest power spectrum estimation – II. KODIAQ, SQUAD, and XQ-100

ABSTRACT We measure the 1D Ly α power spectrum P1D from Keck Observatory Database of Ionized Absorption toward Quasars (KODIAQ), The Spectral Quasar Absorption Database (SQUAD), and XQ-100 quasars using the optimal quadratic estimator. We combine KODIAQ and SQUAD at the spectrum level, but perform a separate XQ-100 estimation to control its large resolution corrections in check. Our final analysis measures P1D at scales k < 0.1 s km−1 between redshifts $z$ = 2.0–4.6 using 538 quasars. This sample provides the largest number of high-resolution, high-S/N observations; and combined with the power of optimal estimator it provides exceptional precision at small scales. These small-scale modes (k ≳ 0.02 s km−1), unavailable in Sloan Digital Sky Survey and Dark Energy Spectroscopic Instrument analyses, are sensitive to the thermal state and reionization history of the intergalactic medium, as well as the nature of dark matter. As an example, a simple Fisher forecast analysis estimates that our results can improve small-scale cut-off sensitivity by more than a factor of 2.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Forest aboveground biomass estimation through integration of sentinel-2 and PALSAR-2 time series: assessing models trained on GEDI and field inventory benchmarks

Accurate and spatially explicit forest Aboveground Biomass (AGB) mapping through remote sensing is critical for quantifying terrestrial carbon stocks and informing effective forest management strategies. However, AGB estimation in dense forests with complex terrain remains challenging due to satellite sensor signal saturation problem (saturation issue occurs in high biomass forests), structural complexity, and limited ground truth for calibration. This study presents a novel framework that integrates multi-temporal Sentinel-2 optical imagery, ALOS PALSAR-2 Synthetic Aperture Radar (SAR) data, and topographic variables with explainable Machine Learning to map AGB across mountainous forests within subtropical and temperate oceanic climate zones of Mexico. We evaluate the effects of temporal granularity and sensor synergy by comparing multiple temporal inputs and sensor configurations (Sentinel-2, PALSAR-2, and their fusion), and assess model performance using two reference datasets: NASA GEDI LiDAR-derived biomass and Mexico’s National Forest and Soil Inventory (INFyS). Our results showed that models trained on INFyS consistently outperformed those trained on GEDI, highlighting limitations in GEDI’s reliability in biomass estimates within this study region. Furthermore, the integration of Sentinel-2 and PALSAR-2 provided improved predictions compared to single-sensor models, particularly when combined with temporally explicit yearly statistics. The best-performing model, which was trained on INFyS data, and considered both Sentinel-2 and PALSAR-2 yearly statistics, as well as topographic variables, achieved an R2 of 0.64, RMSE of 51.10 Mg/ha, and relative RMSE (rRMSE) of 58.69%. Explainable ML analysis identified Sentinel-2 spectral indices and topographic features as key predictors, while PALSAR-2 metrics provided complementary information, partially mitigating saturation effects in high-biomass areas. Specifically, integrating both sensors substantially improved AGB estimation in high biomass forest (≥200 Mg/ha), yielding 98% gains over optical-only model, with resulting estimates exceeding GEDI L4B by 29% and ESA-CCI-BIOMASS by 174%. Terrain-stratified analysis indicated close agreement with GEDI in low-slope areas, with increasing divergence as slope steepness increased, while estimates remained consistently higher than ESA-CCI-BIOMASS across all slope classes. The proposed approach advances multi-sensor fusion and temporal feature engineering for AGB mapping using open-access satellite datasets, providing a scalable and reproducible framework for annual biomass monitoring in topographically complex mountainous forests. The resulting 25 m resolution biomass product has the potential to provide spatially detailed information for forest monitoring and may support applications in carbon accounting and forest management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Filterscope Techniques for Parasitic Signal Screening

Here, the filterscope diagnostic uses bandpass filters and photomultiplier tubes (PMTs) to detect specific spectral emission lines. A filterscope was used to measure the W I 400.88 nm line emission as a function of ion energy on the Radio Frequency Plasma Interaction Experiment (RF PIE) for the purpose of assessing W erosion on plasma-facing components (PFCs). Different filter techniques are being explored and compared in order to effectively screen out nearby impurity lines, like the Ar II 401.39 nm line. The effectiveness of these techniques is determined by comparing the measurements to a high-resolution 1.0 m Czerny–Turner spectrometer with 0.012 nm spectral resolution. The ability to filter out nearby impurity emissions is useful when imaging PFCs in fusion devices including divertor and antenna guard limiters. Initial results with a helium plasma show little difference between the two techniques at higher bias voltages. In a helium plasma at lower dc bias voltages, a two-filter technique with filters at two separate wavelengths was shown to be more effective at screening out background signals. Data collected with an argon plasma however show the technique with overlapping filters on the line of interest is a closer match to spectrometer data at lower dc bias voltages.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

A phenology- and trend-based approach for accurate mapping of sea-level driven coastal forest retreat

The rapid replacement of upland forest by encroaching marshland is a striking manifestation of global sea-level rise (SLR). Timely and high-resolution information on the location and extent of transition forest (the ecotone between upland forest and marsh where tree mortality due to seawater intrusion begins) is fundamental to understanding the processes and patterns of SLR-driven landscape reorganization. Despite its significance, accurate characterization of salt-impacted transition forest remains challenging due to the complexity of coastal environments, scarcity of ground-truth data, and the lack of effective mapping algorithms. Here we use the full archive of Landsat images between 1984 and 2021 to investigate the spectral, temporal, and phenological characteristics of transition forest, and develop a robust framework for monitoring coastal vegetation shifts in the mid-Atlantic U.S., a global SLR hotspot. Here, we found that transition forest exhibits strong negative NDVI trends and a deviation of land surface phenology from marsh and upland forest that distinguishes itself from surrounding vegetation. By integrating temporal trends and land surface phenology, our results demonstrate superior discrimination between marsh and coastal forests to existing map products (e.g. NOAA Coastal Change Analysis Program, National Land Cover Database) that allows a reliable identification of the coastal treeline. We applied the approach to map regional land cover in 1985, 2000 and 2020 (overall classification accuracy >92%) and found that the area of coastal forest decreased by 22.0% from 1985 to 2020, the majority of which transitioned to marshland (92.3%, 5.3 × 10 3 ha). Based upon fine-scale patterns of coastal transgression, we created a practical workflow for spatially explicit quantification of forest retreat rates. Concurrent with rising sea level, coastal forests migrated upslope from 0.63 (± 0.27) m above sea level in 1985 to 0.78 (± 0.32) m above sea level in 2020, and horizontal forest retreat rates accelerated from 3.1 (range of 0–36) m yr -1 during 1985–2000 to 4.7 (0–55) m yr -1 during 2001–2020. As SLR continues to accelerate, our study may serve as a scalable solution for consistent tracking of coastal landscape evolution that is urgently needed for sustainable forest and wetland management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape

The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China)

1. Morphometrics are fundamental for the analysis of size and shape in fossils, particularly because soft parts or DNA are rarely preserved and hard parts such as shells are commonly the only source of information. Geometric morphometrics, that is, landmark analysis, is well established for the description of shape but it exhibits a couple of shortcomings resulting from subjective choices during landmarking (number and position of landmarks) and from difficulties in resolving shape at the level of micro-sculpture. 2. With the aid of high-resolution 3D scanning technology and analyses of fractal dimensions, we test whether such shortcomings of linear and landmark morphometrics can be overcome. As a model group, we selected a clade of modern viviparid gastropods from Lake Lugu, with shells that show a high degree of sculptural variation. Linear and landmark analyses were applied to the same shells in order to establish the fractal dimensions. 3. The genetic diversity of the gastropod clade was assessed. The genetic results suggest that the gastropod clade represents a single species. The results of all morphometric methods applied are in line with the genetic results, which is that no specific morphotype could be delimited. Apart from this overall agreement, landmark and fractal dimension analyses do not correspond to each other but represent data sets with different information. Generally, the fractal dimension values quantify the roughness of the shell surface, the resolution of the 3D scans determining the level. In our approach, we captured the micro-sculpture but not the first-order sculptural elements, which explains that fractal dimension and landmark data are not in phase. 4. We can show that analyzing fractal dimensions of gastropod shells opens a window to more detailed information that can be considered in evolutionary and ecological contexts. We propose that using low-resolution 3D scans may successfully substitute landmark analyses because it overcomes the subjective landmarking. Analyses of 3D scans with higher resolution than used in this study will provide surface roughness information at the mineralogical level. We suggest that fractal dimension analyses of a combination of differently resolved 3D models will significantly improve the quality of shell morphometrics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III

Abstract Plants make complex and potent therapeutic molecules 1,2 , but sourcing these molecules from natural producers or through chemical synthesis is difficult, which limits their use in the clinic. A prominent example is the anti-cancer therapeutic paclitaxel (sold under the brand name Taxol), which is derived from yew trees (Taxusspecies) 3 . Identifying the full paclitaxel biosynthetic pathway would enable heterologous production of the drug, but this has yet to be achieved despite half a century of research 4 . WithinTaxus’ large, enzyme-rich genome 5 , we suspected that the paclitaxel pathway would be difficult to resolve using conventional RNA-sequencing and co-expression analyses. Here, to improve the resolution of transcriptional analysis for pathway identification, we developed a strategy we term multiplexed perturbation × single nuclei (mpXsn) to transcriptionally profile cell states spanning tissues, cell types, developmental stages and elicitation conditions. Our data show that paclitaxel biosynthetic genes segregate into distinct expression modules that suggest consecutive subpathways. These modules resolved seven new genes, allowing a de novo 17-gene biosynthesis and isolation of baccatin III, the industrial precursor to Taxol, inNicotiana benthamianaleaves, at levels comparable with the natural abundance inTaxusneedles. Notably, we found that a nuclear transport factor 2 (NTF2)-like protein, FoTO1, is crucial for promoting the formation of the desired product during the first oxidation, resolving a long-standing bottleneck in paclitaxel pathway reconstitution. Together with a new β-phenylalanine-CoA ligase, the eight genes discovered here enable the de novo biosynthesis of 3’-N-debenzoyl-2’-deoxypaclitaxel. More broadly, we establish a generalizable approach to efficiently scale the power of co-expression analysis to match the complexity of large, uncharacterized genomes, facilitating the discovery of high-value gene sets.

Science & Technology - Other Topics↗
DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Analysis of Completion Design Impact on Cluster Efficiency and Pressure-Based Well Communication in HFTS-2 Delaware Basin

The Hydraulic Fracturing Test Site 2 (HFTS-2) is a joint industry project in the Delaware basin to advance hydraulic fracturing understanding and improve productivity in shale reservoirs. The project integrates multi-disciplinary approaches to evaluate different completion designs, well spacing, inter-well communication, and stimulated rock volume, among other factors. This paper focused on two major areas related to hydraulic fracture performance. First, an analysis of different completion designs on cluster efficiency based on near well Distributed Acoustic Sensing (DAS). Second, an evaluation of well and completion designs on inter-well fracture driven interactions (FDIs) based on downhole pressure monitoring. Fluid/sand distribution and cluster efficiency analyses were based on near wellbore DAS data collected from two adjacent horizontal wells completed in two different landing zones in the Wolfcamp formation. These wells had different completion designs aiming to evaluate the effect of normal vs. extended stage lengths, perforation hole tapering and limited entry. Standard deviation from ideal fluid/sand distribution and waterfall plots were used to evaluate cluster efficiency for each design and stage. Inter-well FDIs analysis was conducted among the horizontal wells and a vertical monitor well. One horizontal well served as the monitor well while the other horizontal well was being treated. The vertical well was instrumented with downhole pressure and temperature gauges to aid monitoring fracture height growth. The pressure response during and after fracturing was characterized based on maximum pressure increase value and slope. Pressure response vs. FDIs trigger factors such distance, cluster efficiency and stage fluid volume were also analyzed. Based on the different completion and perforation designs tested, DAS analysis suggests that limited entry design worked best. Extreme limited entry showed the potential of high perforation erosion and reduced cluster efficiency. Here, the limited entry and tapered perforation design demonstrated potential to improve the cluster efficiency for extended stage lengths. Pressure monitoring across formation units proved to be critical to understand fracture interactions and fracture vertical growth. Pressure communication across different formation units during hydraulic fracturing operation indicate fractures grew upwards during Wolfcamp wells fracturing. However, this pressure communication dissipated over time. High intensity FDIs were recorded when the frac stages Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/1-21URTC/D011S018R001/2477607/urtec-2021-5289-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5289 were closer to the pressure gauge location in the monitor wells. Some of these stages that produced high intensity FDIs also had high fluid volume per cluster and low cluster efficiency. The multi-disciplinary and high-quality data collected from HFTS-2 helped to further understand why completion approaches such as limited entry and tapered perforation design are successful in improving cluster efficiency. The DAS data combined with downhole high-resolution pressure measurements also helped to quantify the effect of lower cluster efficiency data on the incidence and intensity of FDIs.

58 GEOSCIENCES↗