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At least 325 records · Page 18

Surface Water Quality Data from Beaver-Impacted Streams; Trail Creek and East River, Colorado 2025

This data package contains surface water chemistry measurements collected in 2025 to evaluate how beaver damming and low-tech process-based stream restoration influence water quality and metal mobility in mountainous headwater systems of the Upper Colorado River Basin. Sampling was conducted at Trail Creek (Taylor Park watershed, Colorado), a tributary undergoing restoration through installation of low-tech process-based structures (i.e., beaver dam analogs), and at off-channel beaver ponds within the East River floodplain (East River watershed, Colorado). Samples were collected along longitudinal transects spanning upstream control reaches, beaver-influenced ponded reaches, and downstream segments. Additional samples were collected from near-surface pore waters within a beaver dam seepage face. The dataset includes concentrations of major and trace elements measured by inductively coupled plasma–mass spectrometry (ICP-MS) and inductively coupled plasma–optical emission spectrometry (ICP-OES), major anions measured by ion chromatography (IC), and dissolved organic carbon (DOC; reported as non-purgeable organic carbon, NPOC). Samples were size-fractionated at 0.45 micrometers (µm), 0.22 µm, and 0.02 µm to distinguish particulate (>0.45 µm), colloidal (0.22–0.02 µm), and dissolved (<0.02 µm) fractions. The data package consists of comma-separated value (.csv) files containing tabulated chemical concentration data, sample metadata (site identifiers, geographic coordinates, sampling dates, fraction type), and quality control flags. All files are provided in open, non-proprietary formats that can be accessed using standard data analysis software such as Microsoft Excel, R, Python, MATLAB, or other programs capable of reading .csv files. Units, detection limits, and analytical methods are documented in accompanying metadata files. The dataset is designed to support analyses of (1) how beaver impoundment and restoration structures alter elemental partitioning and transport, (2) the role of iron and organic carbon in mediating trace metal mobility, and (3) reach-scale changes in water quality across restoration gradients. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

Anions↗

Measuring thermal curing induced shrinkage of material extrusion based additive manufacturing silicone elastomer lattices by X-ray computed tomography

Thermal curing induces shrinkage in material extrusion based additive manufacturing silicone elastomer samples, resulting in discrepancies between as printed and final geometries. Knowing the extent to which the samples change in shape and size allows us to make appropriate modifications to the printing design to better control the geometry of the samples. We present an X-ray computed tomography (CT) based approach to determine filament-level shrinkage due to thermal curing of silicone elastomer samples printed with direct ink writing (DIW). The approach relies on custom-designed build plates that are resistant to the elevated curing temperatures and that have sufficiently distinct X-ray absorption characteristics from the silicone elastomer to ensure adequate segmentation of the latter in X-ray imaging data. We implement the approach to evaluate shrinkage in DIW ‘log pile’ samples with three distinct strand arrangements and demonstrate of how filament-level information can be extracted from the X-ray CT data.

Additive manufacturing↗

Emergence of nosocomial associated opportunistic pathogens in the gut microbiome after antibiotic treatment

Introduction: According to the Centers for Disease Control’s 2015 Hospital Acquired Infection Hospital Prevalence Survey, 1 in 31 hospital patients was infected with at least one nosocomial pathogen while being treated for unrelated issues. Many studies associate antibiotic administration with nosocomial infection occurrence. However, to our knowledge, there is little to no direct evidence of antibiotic administration selecting for nosocomial opportunistic pathogens. Aim: This study aims to confirm gut microbiota shifts in an animal model of antibiotic treatment to determine whether antibiotic use favors pathogenic bacteria. Methodology: We utilized next-generation sequencing and in-house metagenomic assembly and taxonomic assignment pipelines on the fecal microbiota of a urinary tract infection mouse model with and without antibiotic treatment. Results: Antibiotic therapy decreased the number of detectable species of bacteria by at least 20-fold. Furthermore, the gut microbiota of antibiotic treated mice had a significant increase of opportunistic pathogens that have been implicated in nosocomial infections, like Acinetobacter calcoaceticus/baumannii complex, Chlamydia abortus, Bacteroides fragilis, and Bacteroides thetaiotaomicron. Moreover, antibiotic treatment selected for antibiotic resistant gene enriched subpopulations for many of these opportunistic pathogens. Conclusions: Oral antibiotic therapy may select for common opportunistic pathogens responsible for nosocomial infections. In this study opportunistic pathogens present after antibiotic therapy harbored more antibiotic resistant genes than populations of opportunistic pathogens before treatment. Our results demonstrate the effects of antibiotic therapy on induced dysbiosis and expansion of opportunistic pathogen populations and antibiotic resistant subpopulations of those pathogens. Follow-up studies with larger samples sizes and potentially controlled clinical investigations should be performed to confirm our findings.

59 BASIC BIOLOGICAL SCIENCES↗

Autosampler software

control software for an automated liquid chromatography sample injection and separation system. It is related to a PNNL invention report 31630-E, Method for direct delivering trace samples from smallsize wells to liquid chromatography and mass spectrometry. The main purpose of the control software is to enable automated sample injection from a nanowell device.

Liyu, Andrey↗

Inferring precocial Chinook Salmon production through single‐parentage assignments

Abstract Objective Parentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We applied single‐parentage assignments to a naturally spawning population of Chinook Salmon Oncorhynchus tshawytscha to quantify production of anadromous returns by unsampled precocial males. Methods We used an approach that focused on two important aspects of parentage analyses: (1) addressing the presence of family structure within the set of sampled parents and (2) controlling for false‐positive and false‐negative assignments. Result Results indicated that 30% of reproductively successful males were precocial males, which produced 20% of the returning anadromous offspring. Conclusion This study provides a framework for applying single‐parent assignments in a salmonid study system while explicitly addressing sources of assignment errors.

Steele, Craig A.↗

Facile fabrication of 2D material multilayers and vdW heterostructures with multimodal microscopy and AFM characterization

Reliable transfer processes that enable manipulation of two-dimensional (2D) materials, e.g., transition metal dichalcogenides (TMDCs) and MXenes, from one substrate to another has been a necessity for successful device fabrication. Here, with both mechanical exfoliation and chemical vapor deposition (CVD) widely used, a versatile, clean, deterministic, and yet simple transfer technique is highly needed. To address such need, we developed a transfer method that takes advantage of wettability contrast between interfaces without the use of sacrificial layers or chemical processes. More importantly, a setup was developed to carry out this transfer method with high sample selectivity and fine control of the position and orientation of transferred TMDC crystals, a feature required for fabrication of the devices based on vertical 2D heterostructures. Using both exfoliated and CVD grown materials and subsequent atomic force microscopy (AFM), photoluminescence (PL), confocal Raman and tip enhanced Raman spectroscopy (TERS) characterization, we ascertained the quality of interfaces resulting from the transfer process while preserving excellent 2D material integrity. PL and TERS maps revealed nanometer-scale heterogeneities in the interfaces of fabricated heterostructures, which should enable further perfection of the transfer technique. TERS/TEPL information were employed to identify areas suitable for nanodevice fabrication, making the reported transfer and characterization methods ideal for making high quality assembly of 2D heterostructure more accessible, which should facilitate exploration of vertical 2D heterostructures for applications in electronics, batteries, solar cells, and twistronics.

2D material transfer↗

High-Throughput Microfluidics Platform for Intracellular Delivery and Sampling of Biomolecules from Live Cells

Nondestructive cell membrane permeabilization systems enable the intracellular delivery of exogenous biomolecules for cell engineering tasks as well as the temporal sampling of cytosolic contents from live cells for the analysis of dynamic processes. Here, in this paper, we report a microwell array format live-cell analysis device (LCAD) that can perform localized-electroporation induced membrane permeabilization, for cellular delivery or sampling, and directly interfaces with surface-based biosensors for analyzing the extracted contents. We demonstrate the capabilities of the LCAD via an automated high-throughput workflow for multimodal analysis of live-cell dynamics, consisting of quantitative measurements of enzyme activity using self-assembled monolayers for MALDI mass spectrometry (SAMDI) and deep-learning enhanced imaging and analysis. By combining a fabrication protocol that enables robust assembly and operation of multilayer devices with embedded gold electrodes and an automated imaging workflow, we successfully deliver functional molecules (plasmid and siRNA) into live cells at multiple time-points and track their effect on gene expression and cell morphology temporally. Furthermore, we report sampling performance enhancements, achieving saturation levels of protein tyrosine phosphatase activity measured from as few as 60 cells, and demonstrate control over the amount of sampled contents by optimization of electroporation parameters using a lumped model. Lastly, we investigate the implications of cell morphology on electroporation-induced sampling of fluorescent molecules using a deep-learning enhanced image analysis workflow.

59 BASIC BIOLOGICAL SCIENCES↗

Scalable fabrication of an array-type fixed-target device for automated room temperature X-ray protein crystallography

X-ray crystallography is one of the leading tools to analyze the 3-D structure, and therefore, function of proteins and other biological macromolecules. Traditional methods of mounting individual crystals for X-ray diffraction analysis can be tedious and result in damage to fragile protein crystals. Furthermore, the advent of multi-crystal and serial crystallography methods explicitly require the mounting of larger numbers of crystals. To address this need, we have developed a device that facilitates the straightforward mounting of protein crystals for diffraction analysis, and that can be easily manufactured at scale. Inspired by grid-style devices that have been reported in the literature, we have developed an X-ray compatible microfluidic device that can be used to trap protein crystals in an array configuration, while also providing excellent optical transparency, a low X-ray background, and compatibility with the robotic sample handling and environmental controls used at synchrotron macromolecular crystallography beamlines. At the Stanford Synchrotron Radiation Lightsource (SSRL), these capabilities allow for fully remote-access data collection at controlled humidity conditions. Furthermore, we have demonstrated continuous manufacturing of these devices via roll-to-roll fabrication to enable cost-effective and efficient large-scale production.

chemical engineering↗

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗

Ab Initio Bulk Free Energy Surface of Proper Ferroelectrics

We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core of our approach is the metadynamics algorithm that extracts the polarization dependence of the FES from all-atom molecular dynamics simulations without an a priori ansatz. The rest of the FES is derived from the metadynamics trajectories that span the relevant phase space. We demonstrate our approach in the case of lead titanate. The errors across the phase transition, due to DFT numerics, all-atom molecular dynamics, and free energy evaluation by enhanced sampling, can be systematically controlled and are of the order of 1 meV/atom. The accuracy of the resulting ab initio FES is only limited by the adopted functional approximation of DFT.

Xie, Pinchen [Lawrence Berkeley National Laborator↗

Growth, mortality, wood density, biomass data from BIONTE inventories in Manaus, Brazil

BIONTE (BIOmass and NuTrient Experiment) is a selective logging experiment established at the Experimental Station of Tropical Forestry (EEST, aka “ZF2”) field research station in the mid 1980s in the central Amazon (Higuchi et al. 1997, Amaral et al. 2019). Led by the National Institute for Amazon Research (INPA) in Brazil, the project aimed at assessing the effects of logging intensity on forest dynamics and enabling the creation of a model of forest management for the Central Amazon. The experiment included three levels of increasing selective logging intensity and controls, with 1 hectare sample plots (12 total) located at the center of 4 hectare treatment plots. The site’s Köppen classification is tropical rainforest (Af), characterized by high temperatures and humidity, with mean annual temperatures around 27 ℃ and mean annual precipitation around 2200 mm of rain. The vegetation has a high floristic diversity, the soils of the region are poor in nutrients, and the topography is characterized by plateaus (where BIONTE is located), and also valley bottoms and slopes. The inventory (growth and mortality) and biomass data included here covers the 1990 to 2019 period, with wood density being averaged from existing datasets. This dataset includes a data file in .csv file format and a .txt file, BIONTE_mortality-rates_headers.txt, that provides descriptions for the data file headers.

54 ENVIRONMENTAL SCIENCES↗

Development of Material Studies at the LANL UCN Facility Focusing on Actinide Hydriding and Fission Damage

The aging of as-built actinide surfaces in static and dynamic environments is a complex problem of high importance to LANL’s core mission. Many standard material science tools used to study this problem are ideal for highly controlled, lab-made samples. The goal of this work is to use ultracold neutrons to bridge the gap between lab made and as-built surface aging studies. This capability is unique to LANL and will support our core mission.

36 MATERIALS SCIENCE↗

Investigating Soil Organic Matter Complexation using Spectral Induced Polarization

Spectral induced polarization (SIP) laboratory experiments were conducted to determine the sensitivity of this method to the formation of soil organic matter (SOM) complexes, with a long-term goal of field-scale monitoring. There are few SIP experiments that have explored this topic, yet understanding the dynamic behavior and interactions of SOM at the field scale could provide insight into soil fertility and health which influences crop yields, microorganisms that degrade organic pollutants, and carbon stabilization. We present the results of three experiments where the iron oxide, ferrihydrite (Fhy), was used to coat different media, and then the OM compound pentaglycine (PG) was pulse injected to form SOM complexes. SIP data was collected during these injections to capture any surface complexation changes. These experiments were performed in 1) a fluidic cell containing a micromodel, 2) a column containing Fhy coated ceramic beads and 3) a column containing Fhy coated Accusand®. Our results show a higher frequency response (defined here as > 1 Hz) in all three experiments, with the largest amplitude response after the first PG injection (Figure S.1). The repeatability of this response is encouraging and supporting data collected on the Accusand® experiment provides preliminary insight into the mechanisms controlling the SIP signatures. Sampling of fluid conductivity $σ_w$ and pH may indicate deprotonation of SOM occurring or rapid adsorption and release of protons from the Fhy sites. However additional experiments are needed to identify and confirm the primary and secondary reactions impacting the SIP response. We are looking towards other opportunities to continue this work, particularly to repeat experiments while collecting supporting datasets.

58 GEOSCIENCES↗

The Preparation and Characterization of Co–Ni Nanoparticles and the Testing of a Heterogenized Co–Ni/Alumina Catalyst for CO Hydrogenation

Samples of well-controlled nanoparticles consisting of alloys of cobalt and nickel of different atomic ratios were synthesized using wet chemical methods with oleylamine as the solvent and the reducing agent. These materials were characterized by a variety of techniques, including high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), X-ray energy dispersive spectroscopy (EDS), and X-ray diffraction (XRD). Small amounts of heterogenized catalysts were prepared using alumina as the support. However, the potential for use of Co–Ni catalysts in CO hydrogenation was explored using a larger amount of Co–Ni/alumina catalyst prepared from standard aqueous impregnation methods and tested in a continuously stirred tank reactor (CSTR) for Fischer–Tropsch synthesis (FTS). Results are compared to a reference catalyst containing only cobalt. The heterogenized catalysts were characterized using synchrotron methods, including temperature programmed reduction with extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge spectroscopy (TPR-EXAFS/XANES). The characterization results support intimate contact between Co and Ni, strongly suggesting alloy formation. In FTS testing, drawbacks of Ni addition included decreased CO conversion on a per gram catalyst basis, although Ni did not significantly impact the turnover number of cobalt, and produced slightly higher light gas selectivity. Benefits of Ni addition included an inverted induction period relative to undoped Co/Al2O3, where CO conversion increased with time on-stream in the initial period, and the stabilization of cobalt nanoparticles at a lower weight % of Co.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluation of High-Temperature Martensitic Steels for Heavy-Duty Diesel Piston Applications

Five different commercially available high-temperature martensitic steels were evaluated for use in a heavy-duty diesel engine piston application and compared to existing piston alloys 4140 and microalloyed steel 38MnSiVS5 (MAS). Finite element analyses (FEA) were performed to predict the temperature and stress distributions for severe engine operating conditions of interest, and thus aid in the selection of the candidate steels. Complementary material testing was conducted to evaluate the properties relevant to the material performance in a piston. The elevated temperature strength, strength evolution during thermal aging, and thermal property data were used as inputs into the FEA piston models. Additionally, the long-term oxidation performance was assessed relative to the predicted maximum operating temperature for each material using coupon samples in a controlled-atmosphere cyclic-oxidation test rig. A current commercial steel piston alloy, quenched and tempered martensitic steel 4140, was tested in a single-cylinder research engine for a baseline oxidation and mechanical performance assessment using an abbreviated (50h) durability test plan. The predicted suitability of a candidate piston material in an engine is primarily based on its elevated temperature strength, oxidation resistance, and the complex influence of thermal conductivity, the latter of which is substantially lower for the candidate materials considered in this research relative to the traditional alloys. Although the lower thermal conductivity causes the candidate alloys to operate in higher temperature ranges under identical engine operating conditions and piston geometries, increasing the likelihood of partially or completely negating their strength and oxidation resistance advantages relative to 4140 and MAS steels, this evaluation indicates that several of the candidate piston alloys are predicted to enable improved oxidation resistance under more severe engine operating conditions relative to the current piston materials. However, further evaluation is required to determine if the elevated temperature fatigue strength and durability of these alloys are suitable for more severe engine conditions.

36 MATERIALS SCIENCE↗

Prostate cancer-associated secreted proteins

Methods are provided for treating a subject with prostate cancer and/or diagnosing a subject at risk for prostate cancer, which can include measuring increased expression of at least two prostate cancer-related molecules in a sample obtained from a subject, including the prostate cancer-related molecules AGR2, AGR3, CRISP3, CCL3, CEACAM5, CEACAM6, IL24, MMP9, CXCL14, CD90, POSTN, and SFRP4. The methods can include administering at therapy to a subject with prostate cancer. Methods are provided for treating a subject with intermediate- or high-risk prostate cancer, which can include measuring increased expression of MMP9 in a sample obtained from a subject compared to a control representing expression of MMP9 expected in a sample from a subject who has low-risk prostate cancer.

59 BASIC BIOLOGICAL SCIENCES↗

Alteration of the Cesium-137 soil profile by wild boar rooting after the Fukushima Daiichi Nuclear Power Plant accident

Large amounts of Cesium-137 ( 137 Cs, physical half-life ca. 30 years) were released into the environment from the 2011 Fukushima Daiichi Nuclear Power Plant (FDNPP) accident in Japan. Initially contaminants from the accident were deposited on the surface soil layers in terrestrial ecosystems, but over time vertical migration of 137 Cs has occurred, with most 137 Cs now distributed a few centimeters below the soil surface. Wild boar (Sus scrofa) rooting likely alters the distribution of contaminants in soil profiles. Such impacts may be particularly pronounced in areas contaminated from the FDNPP accident, given the increase in abundance of wild boar in these areas. Our objective was to determine whether rooting by wild boar alters the distribution of 137 Cs contamination within soil profiles through collection of soil cores from control sites and two different types of rooting samples, “new depressions” and “old depressions” within the difficult-to-return zone surrounding the FDNPP. The 137 Cs ratio [activity concentration of 137 Cs at each depth / the maximum activity concentration of 137 Cs in each core sample] rapidly decreased after reaching a peak at the control sites. However, the 137 Cs ratio at all rooted sites decreased more slowly, and 137 Cs was distributed deeper into the soil layers than control sites, across both new and old rooting sites. Moreover, the 137 Cs soil profiles varied greatly among core samples and sampling sites. Furthermore, these results demonstrate that soil disturbance from wild boar rooting can directly influence the distribution of contaminants within soil profiles. However, the extent to which deeper layers are affected by contamination depends on the unique characteristics (i.e., depth of rooting) of each wild boar rooting disturbance. Further studies are needed to examine the effects of long-term rooting on the alteration of 137 Cs in soil profiles.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Controllable strain-driven topological phase transition and dominant surface-state transport in HfTe5

Abstract The fine-tuning of topologically protected states in quantum materials holds great promise for novel electronic devices. However, there are limited methods that allow for the controlled and efficient modulation of the crystal lattice while simultaneously monitoring the changes in the electronic structure within a single sample. Here, we apply significant and controllable strain to high-quality HfTe 5 samples and perform electrical transport measurements to reveal the topological phase transition from a weak topological insulator phase to a strong topological insulator phase. After applying high strain to HfTe 5 and converting it into a strong topological insulator, we found that the resistivity of the sample increased by 190,500% and that the electronic transport was dominated by the topological surface states at cryogenic temperatures. Our results demonstrate the suitability of HfTe 5 as a material for engineering topological properties, with the potential to generalize this approach to study topological phase transitions in van der Waals materials and heterostructures.

36 MATERIALS SCIENCE↗