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At least 1,369 records · Page 76

DeepDiagnostics: A Software Package for Streamlined Posterior Evaluation

Automated prediction techniques like simulation-based inference (SBI) are important tasks for science experiments that produce large amounts of complex, raw data. However, their development remains in its early stages because the uncertainties of these techniques lack sufficient trustworthiness and interpretability. Packages for SBI provide a growing set of diagnostics; however, the software requirements are substantial, as they are tied to the inference technology itself, and the APIs lack adaptability. We introduce the DeepDiagnostics package for diagnosing posteriors from analytic likelihood-based methods and SBI methods, such as neural posterior estimation. DeepDiagnostics produces a comprehensive set of high-quality visualizations and metrics in a highly accessible, easy-to-use, and flexible package. We address all of these goals by providing a command-line inference tool and a Python API that is controlled through a configuration file. The package includes common diagnostics, such as parity plots, corner (covariance) plots, simulation-based calibration (SBC) diagnostics (including posterior coverage and rank histograms), Lemos et al. s PQMass and TARP, Masserano et al. s WALDO, Linhart et al. s LC2ST, as well as credible region diagnostics developed by our group.

Voetberg, Maggie [Fermilab]↗

Designing a User Interface for Real-Time Magnetometer Data Acquisition

The Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) is a next-generation quantum sensor designed to search for ultralight dark matter and explore new frontiers in quantum mechanics. Due to the experiment s sensitivity to magnetic interference, a magnetometer trolley system was developed to scan magnetic fields along a vacuum tube. Interacting with the system required command-line inputs, creating usability challenges. To improve accessibility and streamline data acquisition, I developed a graphical user interface (GUI) using Python and the customtkinter library. The GUI supports real-time data display, state/mode switching, command execution, and CSV file management. I collaborated with another intern to integrate data visualization features into the GUI, allowing users to generate 3D plots of post-acquisition magnetic field data. In the future, I aim to fix the real-time plotting feature as it results in an unresponsive GUI.

Mendez, Milagros [DuPage Coll.]↗

Accelerated Snowmelt Protocol to Simulate Climate Change Induced Impacts on Snowpack Dependent Ecosystems

Field studies that simulate the effects of climate change are important for a predictive understanding of ecosystem responses to a changing environment. Among many concerns, regional warming can result in advanced timing of spring snowmelt in snowpack dependent ecosystems, which could lead to longer snow-free periods and drier summer soils. Past studies investigating these impacts of climate change have manipulated snowmelt with a variety of techniques that include manual snowpack alteration with a shovel, infrared radiation, black sand and fabric covers. Within these studies however, sufficient documentation of methods is limited, which can make experimental reproduction difficult. Here, we outline a detailed plot-scale protocol that utilizes a permeable black geotextile fabric deployed on top of an isothermal spring snowpack to induce advanced snowmelt. The method offers a reliable and cost-effective approach to induce snowmelt by passively increasing solar radiation absorption at the snow surface. In addition, control configurations with no snowpack manipulation are paired adjacent to the induced snowmelt plot for experimental comparison. Past and ongoing deployments in Colorado subalpine ecosystems indicate that this approach can accelerate snowmelt by 14-23 days, effectively mimicking snowmelt timing at lower elevations. This protocol can be applied to a variety of studies to understand the hydrological, ecological, and geochemical impacts of regional warming in snowpack dependent ecosystems.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Deep Peat Heating (DPH) to Whole Ecosystem Warming (WEW) Metagenomes for Peat Samples Collected June 2016

This data set provides links to the results of metagenomic analyses of 44 peat samples collected on 13 June 2016 from SPRUCE experiment treatment and ambient plots. Experimental plots had received approximately 24 months of belowground warming (deep peat heating (DPH), Hanson et al. 2015) with the last 9 of those months including air warming for implementation of whole ecosystems warming (WEW – Hanson et al. 2016). The SPRUCE experiment site is located in an ombrotrophic bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). WEW Metagenomes: Data from these metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system and are available at the accession numbers provided below (Table 2) and in the accompanying inventory file. The easiest way to find results on IMG is at this link, https://img.jgi.doe.gov/cgi-bin/m/main.cgi, and then enter “June2016WEW” as a search term in the “Quick Genome Search:” box at the top of the page. This work was done in collaboration between ORNL, USFS and the DOE Joint Genome Institute (JGI) study that is targeting understanding the microbial metagenomes of “fungal, bacterial, and archaeal communities mediating C cycling and trace gas flux in peatland ecosystems subject to climate change” (Proposal ID: 1445).

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Total Gaseous Mercury Fluxes and Peat Mercury Concentrations, 2014-2015

This data set reports the results of total gaseous mercury (TGM) flux monitoring conducted in a sub-set of the SPRUCE experimental study enclosures (Plots 4, 6, 10, 13, 17 and 19) located in the S1 Bog. These plots were selected to represent duplicates of the +0, +4.5 and +9°C experimental temperature treatments. Monitoring of TGM fluxes was conducted in May-June 2014, August 2014 and June 2015 to capture the influence of the deep (2 m below the ground surface) peat warming experiment. These sampling events were conducted prior to the initiation of deep peat warming (May-June 2014), once target peat temperatures were achieved at depth (August 2014) and at the conclusion of the deep warming experiment prior to the initiation of whole ecosystem warming (June 2015). This data set also presents the total mercury (Hg) concentration for peat samples collected during the group sampling campaigns, involving a team of SPRUCE investigators and collaborators, in June 2014 (prior to deep peat warming experiment), September 2014 (target temperatures achieved at depth) and June 2015 (end of deep warming experiment and prior to whole ecosystem warming). Peat samples for total mercury analysis were collected from Enclosures 4, 6, 8, 10, 11, 13, 16, 17, 19, 20.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Xylem Native Embolism and Leaf Traits of Picea mariana and Larix laricina, 2019

This data set contains measurements of native embolism in branch xylem and associated branch and leaf traits from Picea mariana (Black Spruce) and Larix laricina (Tamarack) from September-October 2019 at the SPRUCE experiment (Hanson et al. 2017). Data are presented in one comma-separated (*.csv) file. Native embolism, a measurement of in-situ embolism in the xylem tissue that blocks water movement, measurements were conducted at the end of the growing season on cut branches using the hydraulic pipette method (see Peters et al. 2023 for full method). In short, branch segments were connected to hydraulic apprentice and flow rates of perfusion liquid were measured using graduated pipettes and stopwatch. After initial conductance measurements, branch segments were flushed using vacuum infiltration and hydraulic conductance was remeasured to calculate the percent loss in conductance due to embolism (PLC). Three branch segments (distal, middle, and proximal) were measured from each branch representing different diameters size classes. This dataset also contains leaf area associated with each measured branch segment, calculate leaf mass per area (LMA), sapwood specific conductivity (Ks), leaf area specific conductivity (Kl) and the sapwood area to leaf area ratio (Huber value). Measurements were made on mature trees from all ten treatment enclosures. One branch from each of five trees per species were used from each enclosure where available. Some plots do not contain five individual Larix laricina, in which case all available trees were sampled. All measurements were conducted in late September/early October 2019, at the end of growing season but before Larix laricina needle senescence. There are 10 experimental plots at SPRUCE: five temperature treatments (+0, +2.25, +4.5, +6.75, +9°C) at ambient CO2, and the same five temperature treatments at elevated CO2 (+500 ppm). These data were collected after the treatments had been running in full for three years, meaning much of the material measured was grown under treatment conditions.

Huber value↗

SupplementalFilesCPTAC_ProteogenomicOvarianPaper_2020_02_27

Interactive plots (in HTML/javascript) as supplemental files for the paper titled: Proteogenomic Characterization of Ovarian High-Grade Serous Cancer Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. The plots represent the differential expression of proteins (File 1) and phosphopeptides (File 2) comparing tumor to normal tissue.

59 BASIC BIOLOGICAL SCIENCES↗

Angle-resolved polarized Raman spectroscopy study of phosphorene nanoribbons

We present a systematic angle-resolved polarized Raman spectroscopy (ARPRS) study of black phosphorus (BP) nanostructures formed via electrochemical sodium- and lithium-ion intercalation. Sodium intercalation leads to bundles of densely packed, highly uniform phosphorene nanoribbons (PNRs) separated by parallel amorphous channels, whereas lithium intercalation results in shorter, irregular nanoribbon-like segments with lower aspect ratios. In both cases, six additional Raman peaks (P1–P6) appear alongside the three primary Raman-active modes of BP (A$^{1}_{g}$, B 2g , and A$^{2}_{g}$). These peaks are attributed to the amorphous regions, as confirmed by their isotropic angular dependence in ARPRS measurements. The three BP modes show pronounced angular variations that differ significantly between the two intercalated samples. In sodium-intercalated BP, A$^{1}_{g}$ and A$^{2}_{g}$ modes retain a dumbbell-like angular dependence under parallel polarization with enhanced anisotropy and reduced symmetry under crossed polarization. At the same time, the B 2g mode transitions from four-lobed (cloverleaf) polar plot to a butterfly-like one. In contrast, lithium-intercalated BP exhibits weaker anisotropy and less distinct angular polar plots for all three modes. These differences reflect the sensitivity of phonon behavior to underlying nanostructure morphology. The vibrational frequencies density of states (FDOS) calculations attribute the B 2g mode transformation to phonon band folding and mode mixing in PNRs. This study demonstrates the power of ARPRS in probing phonon-structure relationships and highlights the influence of edge geometry and quantum confinement on phonon dispersion in PNRs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Walker Branch Watershed: Daily Climate and Soil Temperature Data

This data set reports daily climate and soil temperature data for Walker Branch Watershed. As part of the long-term Walker Branch project, daily climate and soil temperature data were collected using instruments on a meteorological tower located in an upper slope of the watershed. This data set contains one data file of daily climate and soil temperature data from 1993 through 2010. Measurement collection began in 1993 as part of the Throughfall Displacement Experiment (TDE) in the control (ambient) plot. Measurements include daily integrated values for above canopy incident photosynthetically active radiation, above canopy incident total radiation, air temperature, relative humidity, rainfall, soil temperature at 10-15 cm, and wind speed. Measurements of incoming rainfall, irradiance, and photosynthetic photon flux density were obtained in a nearby clearing until 1998 when above canopy observations were added to the ambient plot tower. The Walker Branch Watershed is located on the U.S. Department of Energy's Oak Ridge Reservation in eastern Tennessee.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE S1 Bog Peat Depth Determined by Push Probe and GPR: 2009-2010

This data set reports the thickness of peat for the S1 Bog measured directly with manual push probes on September 21 and 22, 2009, and measured by ground penetrating radar (GPR) across transects from January 26 to February 2, 2010 and June 2 to June 9, 2010. Also included are interpolated values of peat depth from both probe and GPR data for the S1 Bog at 1 meter square horizontal resolution.The key objectives of these geophysical field surveys were to define the S1 peat depth, basin geometry, and to provide additional subsurface information for selecting the optimal locations for experimental plots (i.e., rows of chambers). GPR was specifically used to obtain better estimates of peat depths to refine the existing 3-D model of the S1 basin geometry and to provide high-density data on peat stratigraphy and examine variations in mineral soil near the proposed experimental plots.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE S1 Bog Vegetation Allometric and Biomass Data: 2010-2011

This data set reports the results of measurements on sampled aboveground tissues of trees (Picea mariana and Larix laricina), shrubs (Ledum, Chamaedaphne, and Vaccinium), and ground layer vegetation (all species) of the S1 Bog located in areas adjacent to planned experimental study plots. Ground layer vegetation was sampled from both hummocks and hollows, within a 0.25 m2 plot, to evaluate total standing biomass of bog vegetation at or near the peak of annual production. Vegetation was harvested, processed, and measured in July of 2010 and again in June of 2011.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Deep Peat Heating (DPH) Environmental Data, February 2014 through July 2015

This data set provides a record of the half-hourly automated environmental data collected for 14 SPRUCE plots (4, 5, 6, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, and 21) during the Deep Peat Heating (DPH) study. In June 2014, deep soil heating was initiated at 5 warming levels (+0, +2.25, +4.5, +6.75 and +9 °C) with 2 replicate plots per level. Measurements were underway before the initiation of heating treatments and continued through July 27 of 2015 at the transition to whole-ecosystem warming manipulations. The DPH study was undertaken to evaluate possible rapid responses of deep peat carbon (C) stocks, microbial communities, and biogeochemical cycling processes to unprecedented temperatures. Warming levels at depth were achieved over a 25 (+ 2.25 °C) to 60-day (+9 °C) period depending on the target treatment temperatures.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE S1 Bog Areal Coverage of Hummock and Hollow Microtopography Assessed Along Three Transects in the S1 Bog

Aerial coverage of hummocks and hollows was estimated in July 2012 in ten 4 m x 4 m plots each along three 60-m transects in the S1 Bog. Hollows were defined as the lowest elevation within plots and were typically at or near the height of the water table, hummocks included area above hollows, including the sides of the hummocks. The experimental work was conducted in a Picea mariana [black spruce] - Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).

54 ENVIRONMENTAL SCIENCES↗

Factors That Control the Formation of Dendrites and Other Morphologies on Lithium Metal Anodes

Lithium metal is a promising anode material for next-generation rechargeable batteries, but non-uniform electrodeposition of lithium is a significant barrier. These non-uniform deposits are often referred to as lithium “dendrites,” although their morphologies can vary. We have surveyed the literature on lithium electrodeposition through three classes of electrolytes: liquids, polymers and inorganic solids. We find that the non-uniform deposits can be grouped into six classes: whiskers, moss, dendrites, globules, trees, and cracks. These deposits were obtained in a variety of cell geometries using both unidirectional deposition and cell cycling. The main result of the study is a figure where the morphology of electrodeposited lithium is plotted as a function of two variables: shear modulus of the electrolyte and current density normalized by the limiting current density. We show that specific morphologies are confined to contiguous regions on this two-dimensional plot.

25 ENERGY STORAGE↗

A mathematical approach to survey electrochemical impedance spectroscopy for aging in lithium-ion batteries

Electrochemical impedance spectroscopy (EIS) is a valuable technique to detect the health status and aging phenomena in lithium-ion batteries (LiB). Equivalent circuit modeling (ECM) is conventionally used when interpreting EIS data and gaining physical insights into the aging mechanisms. However, performing ECM is resource intensive and expert-level of knowledge is usually required to select suitable models and fitting parameters. This article presents a quick and user-friendly data analysis algorithm as an alternative to ECM by mathematically fitting geometric features in Nyquist plots and obtaining the growth trends of the features. The evolving trends in the Nyquist plots, such as chord lengths of the arcs and interception points, are consistent with the growth of resistance components obtained using ECM with R 2 values from 0.67 to 0.99, and therefore can be used as indicators of battery aging. Our results show that the quick-fitting approach is suitable for analyzing a series of EIS data acquired during battery cycling and identifying the underlying aging mechanisms.

Chen, Bor-Rong↗

Large Trees Dominate Carbon Storage in Forests East of the Cascade Crest in the United States Pacific Northwest

Large-diameter trees store disproportionally massive amounts of carbon and are a major driver of carbon cycle dynamics in forests worldwide. In the temperate forests of the western United States, proposed changes to Forest Plans would significantly weaken protections for a large portion of trees greater than 53 cm (21 inches) in diameter (herein referred to as “large-diameter trees”) across 11.5 million acres (~4.7 million ha) of National Forest lands. This study is among the first to report how carbon storage in large trees and forest ecosystems would be affected by a proposed policy. We examined the proportion of large-diameter trees on National Forest lands east of the Cascade Mountains crest in Oregon and Washington, their contribution to overall aboveground carbon (AGC) storage, and the potential reduction in carbon stocks resulting from widespread harvest. We analyzed forest inventory data collected on 3,335 plots and found that large trees play a major role in the accumulated carbon stock of these forests. Tree AGC (kg) increases sharply with tree diameter at breast height (DBH; cm) among five dominant tree species. Large trees accounted for 2.0 to 3.7% of all stems (DBH ≥ 1” or 2.54 cm) among five tree species; but held 33 to 46% of the total AGC stored by each species. Pooled across the five dominant species, large trees accounted for 3% of the 636,520 trees occurring on the inventory plots but stored 42% of the total AGC. A recently proposed large-scale vegetation management project that involved widespread harvest of large trees, mostly grand fir, would have removed ~44% of the AGC stored in these large-diameter trees, and released a large amount of carbon dioxide to the atmosphere. Given the urgency of keeping additional carbon out of the atmosphere and continuing carbon accumulation from the atmosphere to protect the climate system, it would be prudent to continue protecting ecosystems with large trees for their carbon stores, and also for their co-benefits of habitat for biodiversity, resilience to drought and fire, and microclimate buffering under future climate extremes.

21-inch rule↗

Structural complexity and primary production resistance are coupled in a temperate forest

The capacity of forests to resist structural change and retain material legacies–the biotic and abiotic resources that persist through disturbance–is crucial to sustaining ecosystem function after disturbance. However, the role of forest structure as both a material legacy and feature supporting carbon (C) cycling stability following disturbance has not been widely investigated. We used a large-scale disturbance manipulation to ask whether legacies of lidar-derived canopy structures drive 3-year primary production responses to disturbance. As part of the Forest Resilience Threshold Experiment (FoRTE) in northern Michigan, USA we simulated phloem-disrupting disturbances producing a range of severities and affecting canopy trees of different sizes. We quantified the legacies of forest structure using two approaches: one measuring the change in structure and primary production from pre-to post-disturbance and the second estimating resistance as log transformed ratios of control and treatment values. We found that total aboveground wood net primary production (ANPP w ) was similar across disturbance severities as legacy trees rapidly increased rates of primary production. Experiment-wide, the disturbance had limited effects on change in mean structural complexity values; however, high variance underscored large differences in the magnitude and direction of complexity's response at the plot-scale. Plot-scale structural complexity, but not vegetation area index (VAI), resistance strongly predicted ANPP w resistance while temporal VAI and structural complexity changes did not. We conclude that the presence of material legacies in the form of forest structure may affect primary production stability following disturbance and that how legacies are quantified may affect the interpretation of disturbance response.

lidar—remote sensing↗

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

54 ENVIRONMENTAL SCIENCES↗