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At least 379 records · Page 21

A free association semantic task for fNIRS-based perinatal depression assessment

Perinatal depression (PD) is a highly prevalent psychological disorder that has a detrimental effect on infant and maternal physical and mental health, but effective and objective assessment of PD is still insufficient. In recent years, the functional near-infrared spectroscopy (fNIRS) has been acknowledged as an effective non-invasive tool for clinical assessment of depression. This study proposed a free association semantic task (FAST) paradigm for fNIRS-based assessment of PD. To better address the emotion characteristics of PD, the participants are required to generate a dynamic concept chain based on positive, negative or neutral seed words, while 48-channel fNIRS recordings over frontal and bilateral temporal regions. Results from twenty-two late-pregnant women revealed that, the oxyhemoglobin (oxy-Hb) changes during the FAST with the positive and negative seed words over the frontal region were correlated with PD severity, which was different from the correlation patterns in the FAST with neutral seed word and the classical verbal fluency test (VFT). Furthermore, distinct correlation patterns were also observed in the FAST with the positive and negative seed words, manifested in fNIRS channels corresponding to the right dorsolateral prefrontal cortex (DLPFC) and right inferior frontal gyrus (IFG), respectively. Moreover, regression analyses showed that the FAST with positive and negative seed words can well explain the severity of PD. Our findings suggest the proposed FAST paradigm as a promising approach for PD assessment.

Chen, Danni↗

Quantification of energy and cost reduction from decreasing dissolved oxygen levels in full‐scale water resource recovery facilities

Abstract Aeration systems often lack the efficiency to maintain a desired residual dissolved oxygen (DO) concentration in the tank in part because little consideration is given to the dynamic daily and seasonal loading conditions. Although advanced aeration controllers exist, the majority of plants have DO set points typically based on common practice and literature values rather than site‐specific conditions, which can result in DO set points higher than those necessary to meet treatment objectives. DO set point reduction strategies have primarily been proposed through either static or dynamic simulations. In this study, the substantial improvements associated with DO set point reduction are demonstrated at full scale. A yearlong characterization of full‐scale aeration dynamics captured the effect of diurnal and seasonal fluctuations on oxygen transfer and energy demand and so facilitated the estimation of the potential savings of DO reduction strategies. Full‐scale validation provided direct evidence of DO reduction strategies inducing an overall enhancement of oxygen transfer efficiency along the different bioreactors, while confirming that energy savings as high as 20% were feasible. This study quantifies the influence of oxygen transfer efficiency on operating choices and site‐specific conditions (control strategy, loading conditions, and influent flow variability). Practitioner points We quantified the energy reduction and cost savings associated with a DO reduction in an aeration tank. For each 0.2 mg/L of DO decreased, the average power demand reduction per unit water treated exceeded 17%. Field measurements of dynamic alpha values eliminate the uncertainty in estimating aeration energy and cost savings from DO variations.

Pasini, Federico↗

A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights

Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host–symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N 2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host–symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host–symbiont interplay.

Entomology↗

Characteristics of an Introduced Walleye Population with Implications for Suppression

Abstract The management of introduced fishes, including Walleye Sander vitreus, whether for control or enhancement, requires understanding of population dynamics at the invasion front. Walleye recently established in the Pend Oreille basin, Idaho, threaten the existing salmonid-based fish community and associated recreational fishery. Therefore, the objectives of this study were to describe population growth and associated life history characteristics. Walleye were sampled in October of 2011, 2014, and 2017 using a standardized gill netting survey protocol to describe trends in relative abundance and evaluate population dynamics. Relative abundance increased exponentially from 1.4 to 4.3 fish/net over the 6-year monitoring period. This population was characterized by fast somatic growth, robust body condition, and early age at maturity at or near the biological maxima for Walleye. Among the survey years, mean length at age 2 varied for female (359–441 mm) and male (358–426 mm) Walleye and relative weight varied from 91 to 98. The sampled Walleye matured at 1 to 4 years of age, and recruitment became more consistent as abundance increased. These density-dependent metrics suggest that the Walleye population is still at low density relative to carrying capacity. The information that was gained from this study was used to better understand potential risks and guide management decisions related to experimental population suppression that is now underway. Suppression under these conditions must overcome the recruitment capabilities of the population. We conclude that natural mortality is likely regulated by density-dependent processes. Therefore, at current (low) density, fishing mortality may be entirely additive and compensation is unlikely to further complicate management.

Ryan, Robert G.↗

Nevada Higher Education Benefits from US Department of Energy (DOE) Environmental Management (EM) Nevada Program's Transfer of Geologic Samples - 20442

The Nevada National Security Site (NNSS), formerly the Nevada Test Site, was the location of 100 historic atmospheric and 828 historic underground nuclear tests from 1951 to 1992. Related to this historic nuclear testing, geologic and hydrologic studies of the site were conducted utilizing the skills and the expertise of the U.S. Geological Survey (USGS) and national laboratories (Los Alamos National Laboratory, Lawrence Livermore National Laboratory), who were principal in leading the development of weapons and were responsible for specific underground testing programs. The subsurface samples and technical/scientific data associated with NNSS geologic studies (past and present) are preserved and stored at the USGS Mercury Core Library and Data Center located at the NNSS. Currently, the facility stores over 2,000,000 linear feet of cores and cuttings from more than 2,600 drill holes that can be accessed for study. Most of the samples and historic geologic work was focused directly on subsurface geologic settings that relate directly to historic underground nuclear testing. Since 1992, the United States has observed a unilateral moratorium on full-scale nuclear testing, and the U.S. Department of Energy (DOE) Environmental Management (EM) Nevada Program is now responsible for hydrogeologic characterization of the potential impacts to the natural groundwater systems that may have resulted from historic underground nuclear tests. As part of this effort, the EM Nevada Program Underground Test Area (UGTA) Activity has drilled and completed over 58 deep (2,000 - 7,000 ft.) characterization wells, totaling in excess of 170,000 linear feet of cuttings and core samples. Cutting samples were collected as triplicate samples for each respective depth interval, to account for potential later nondestructive/destructive analysis and to preserve samples for regulatory purposes. Recently, it was recognized by the EM Nevada Program that opportunities may exist to reduce the cost and floor space required for the storage of geologic samples at the Mercury Core Library without impacting the integrity and representative nature of the samples necessary for project execution. An initiative was sponsored by EM Nevada Program to evaluate several options: 1) disposal of a portion of cuttings and cores in a land fill setting; 2) reduction in sample volume through skeletonizing core and cuttings from wells to a representative but much smaller number of samples; and 3) solicit potential interest in the academic community where other geoscientists could freely access the samples for studies. The Nevada state university system through the Nevada Bureau of Mines and Geology responded positively to the opportunity to receive these NNSS samples from the EM Nevada Program. In June 2019, approximately 17,000 geologic samples, representing greater than 170,000 linear feet of drilling and weighing over 20,000 pounds, were shipped from the NNSS to the Great Basin Science Sample and Records Library located in Reno, Nevada. The benefits resulting from this transfer were realized by the EM Nevada Program in terms of cost and space savings for geologic sample storage at the NNSS. The transfer did not impact the EM Nevada Program mission as access to representative geologic samples for regulatory and scientific purposes was preserved. Moreover, the Nevada Bureau of Mines and Geology acquired a significant resource of subsurface geologic samples and supporting technical data to support academic and scientific studies in a complex volcanic setting in southwest Nevada. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Association of clonal hematopoiesis mutations with clinical outcomes: A systematic review and meta-analysis

Clonal hematopoiesis (CH) mutations are common among individuals without known hematologic disease. CH mutations have been associated with numerous adverse clinical outcomes across many different studies. We systematically reviewed the available literature for clinical outcomes associated with CH mutations in patients without hematologic disease. We searched PubMed, EMBASE, and Scopus for eligible studies. Three investigators independently extracted the data, and each study was verified by a second author. Risk of bias was assessed using the Newcastle-Ottawa Scale. We identified 32 studies with 56 cohorts that examine the association between CH mutations and clinical outcomes. We conducted meta-analyses comparing outcomes among individuals with and without detectable CH mutations. We conducted meta-analyses for cardiovascular diseases (nine studies; HR = 1.61, 95% CI = 1.26–2.07, p = .0002), hematologic malignancies (seven studies; HR = 5.59, 95% CI = 3.31–9.45, p < .0001), therapy-related myeloid neoplasms (four studies; HR = 7.55, 95% CI = 4.3–13.57, p < .001), and death (nine studies; HR = 1.34, 95% CI = 1.2–1.5, p < .0001). The cardiovascular disease analysis was further stratified by variant allele fraction (VAF) and gene, which showed a statistically significant association only with a VAF of ≥ 10% (HR = 1.42, 95% CI = 1.24–1.62, p < .0001), as well as statistically significant associations for each gene examined with the largest magnitude of effect found for CH mutations in JAK2 (HR = 3.5, 95% CI = 1.84–6.68, p < .0001). Analysis of the association of CH mutations with hematologic malignancy demonstrated a numeric stepwise increase in risk with increasing VAF thresholds. This analysis strongly supports the association of CH mutations with a clinically meaningful increased risk of adverse clinical outcomes among individuals without hematologic disease, particularly with increasing VAF thresholds.

60 APPLIED LIFE SCIENCES↗

Cost of Fish Exclusion and Passage Technologies for Hydropower

Hydropower represents a reliable source of renewable energy and accounts for approximately 7% of the total electrical generation in the United States. Future expansion of hydropower is likely to be in the form of either smaller new stream development projects or powering existing non-powered dams. For these new projects to be successful, careful analysis of risks, costs, and uncertainty to offset reduced power production as well as ensuring the protection and safe passage of migratory fish to gain public support, will be required. Exclusion and passage are two common approaches to protect fish from entrainment and impingement at hydropower facilities. The thresholds for entrainment risk and requirements for exclusion and passage often differ depending on the species involved, the characteristics of the facility, and the goals of stakeholders. While the costs associated with environmental mitigations represent a large proportion of the total costs required for the licensing of hydropower facilities, little quantitative information is present within the literature regarding the specific costs of fish exclusion and passage. Working with FOA awardee Natel Energy, scientists at Oak Ridge National Laboratory were tasked with assessing the capital construction costs for downstream fish exclusion and passage infrastructure. This report used keyword searches of an existing environmental mitigation cost data set and manual extraction of additional cost data associated with protection, mitigation, and enhancement (PM&E) measures related to positive barrier screening and passage from regulatory licensing documents available in the Federal Energy Regulatory Commission (FERC) eLibrary. This approach yielded a total of 50 PM&E mitigation measures with estimated capital construction costs pertaining to positive barrier screens, 142 pertaining to passage studies, and 26 pertaining to passage-related studies. PM&E measures associated with positive barrier screens represented <10% of the 171 total FERC project dockets available in the data set. These data were highly skewed toward conventional relicensing projects, as <7% were associated with new stream development (NSD) projects. Results from these data indicate highly variable costs associated with fish screening, with flow-normalized costs one to two orders of magnitude higher for screening with the highest exclusion capability (≤0.09 in. spacing) compared with coarser screening (1 to 2 in.). Furthermore, estimated capital costs of passage infrastructure were positively related to the scale of the project based on installed capacity for some, but not all, types of passage. These data provide an initial baseline for estimating exclusion and passage costs for hydropower development and may help developers consider options for more fish-friendly generation technologies, though gaps remain relating to a lack of data, particularly for NSD projects. More data may still be available within the FERC eLibrary, but significant effort will be required to manually identify and extract the data for future analyses.

13 HYDRO ENERGY↗

Engine-in-the-Loop Study of a Hierarchical Predictive Online Controller for Connected and Automated Heavy-Duty Vehicles

This paper presents a cohesive set of engine-in-the-loop (EIL) studies examining the use of hierarchical model-predictive control for fuel consumption minimization in a class-8 heavy-duty truck intended to be equipped with Level-1 connectivity/automation. This work is motivated by the potential of connected/automated vehicle technologies to reduce fuel consumption in both urban/suburban and highway scenarios. The authors begin by presenting a hierarchical model-predictive control scheme that optimizes multiple chassis and powertrain functionalities for fuel consumption. These functionalities include: vehicle routing, arrival/departure at signalized intersections, speed trajectory optimization, platooning, predictive optimal gear shifting, and engine demand torque shaping. The primary optimization goal is to minimize fuel consumption, but the hierarchical controller explicitly accounts for other key objectives/constraints, including operator comfort and safe inter-vehicle spacing. This work is experimentally experimentally validated via a sequence of EIL studies intended for evaluating the computational costs and fuel savings associated with these algorithms. These EIL studies involve the closed-loop validation of the proposed control strategies, both individually and combined. These studies show that this hierarchy of algorithms is capable of running online, with the round-trip communication delay inherent in EIL simulation being one of the key factors affecting the EIL results. Moreover, the EIL studies are encouraging, both in terms of the successful hierarchical integration of the underlying algorithms and also in the resulting fuel savings seen in the EIL tests. In particular, the EIL results suggest that an aggressive overall goal of reducing vehicle fuel consumption by 15-20% or more is potentially achievable, especially in urban/suburban scenarios.

33 ADVANCED PROPULSION SYSTEMS↗

Parametric Study of Used Nuclear Oxide Fuel Constituent Dissolution in Molten LiCl-KCl-UCl 3

Prior work identified dissolution of used nuclear oxide fuel constituents from a uranium oxide matrix into molten LiCl-KCl-UCl 3 at 500°C, prompting a subsequent series of three progressive studies (including an initial scoping study, an electrolytic dissolution study, and a chemical-seeded dissolution study) to further investigate associated parameters and mechanisms. Thermodynamic calculations were performed to identify possible reaction mechanisms and their propensities in used oxide fuel constituent dissolution. Used nuclear oxide fuels with varying preconditions from fast and thermal test reactors were separately immersed in the subject salt system to assess fuel constituent migration from the bulk fuel matrix to the salt phase in an initial scoping study. Dissolution of expected fuel constituents, including alkali, alkaline earth, lanthanide, and transuranium oxides, into the chloride salt phase varied widely, ranging from 12% to 99% in the initial study. Uranium isotope blending between the salt phase and bulk fuel matrix was also observed, which was attributed to reducing conditions in the fuel matrix. Electrolytic and chemical-seeded dissolution studies were subsequently performed to effect reducing conditions in the fuel. Other parameters, including temperature (at 500°C, 650°C, 725°C, and 800°C) and uranium trichloride concentrations (at 6, 9, and 19 wt% uranium), were investigated in the latter two studies, resulting in fuel constituent dissolution above 90%. Extents of dissolution were based on initial and final fuel constituent concentrations in the oxide fuels following operations in the salt and subsequent removal of the salt via distillation. Finally, in this series of progressive studies, oxide fuel preconditioning and in situ reducing conditions, along with elevated temperature and uranium trichloride concentrations, were the primary parameters promoting used nuclear oxide fuel constituent dissolution in accordance with identified reaction mechanisms.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Tea consumption and risk of bladder cancer in the Bladder Cancer Epidemiology and Nutritional Determinants (BLEND) Study: Pooled analysis of 12 international cohort studies

Tea has been shown to be associated with reduced risk of several diseases including cardiovascular diseases, stroke, metabolic syndrome, and obesity. However, the results on the relationship between tea consumption and bladder cancer are conflicting. This research aimed to assess the association between tea consumption and risk of bladder cancer using a pooled analysis of prospective cohort data. Individual data from 532,949 participants in 12 cohort studies, were pooled for analyses. Cox regression models stratified by study centre was used to estimate hazard ratios (HR) and corresponding 95% CIs. Fractional polynomial regression models were used to examine the dose–response relationship. A higher level of tea consumption was associated with lower risk of bladder cancer incidence (compared with no tea consumption: HR = 0.87, 95% C.I. = 0.77–0.98 for low consumption; HR = 0.86, 95% C.I. = 0.77–0.96 for moderate consumption; HR = 0.84, 95% C.I. = 0.75–0.95 for high consumption). When stratified by sex and smoking status, this reduced risk was statistically significant among men and current and former smokers. In addition, dose–response analyses showed a lower bladder cancer risk with increment of 100 ml of tea consumption per day (HR-increment = 0.97; 95% CI = 0.96–0.98). A similar inverse association was found among males, current and former smokers while never smokers and females showed non-significant results, suggesting potential sex-dependent effect. Higher consumption of tea is associated with reduced risk of bladder cancer with potential interaction with sex and smoking status. Further studies are needed to clarify the mechanisms for a protective effect of tea (e.g. inhibition of the survival and proliferation of cancer cells and anti-inflammatory mechanisms) and its interaction with smoking and sex.

60 APPLIED LIFE SCIENCES↗

Laboratory time series moisture manipulative experiment from sediment across San Antonio, Texas: time series aerobic respiration and geochemistry

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration. The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS Allison Veach collaboration (AV1). The data package associated with the AV1 study is available at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2529428. AV1 sampling occurred across 7 perennial and 7 intermittent streams in San Antonio, Texas. Each stream/site was visited both in summer during base flow (July-September 2023) and winter during peak flow (January-February 2024). This study uses subsamples from a subset of AV1 samples. The original field samples were labeled as AV1_###. Subsequent subsamples for this study were labeled as EV_###. The labels from the field samples and the EV subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EV_001 is a subsample from AV1_001). See the critical details section below for more details on sample naming. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) effect size; (2) iron (II); (3) gravimetric moisture; (4) respiration rates; (5) raw dissolved oxygen values and plots; (6) specific conductance; (7) pH; (8) temperature; (9) a summary containing mean, median, and standard deviation values of each data type for each treatment (wet and dry); and (10) methods codes. All files are .csv or.pdf.

54 ENVIRONMENTAL SCIENCES↗

Timeseries Photos of a Variably Inundated Stream: Umtanum Creek, Washington, United States

This dataset is associated with a broader study using game camera timeseries photos collected to evaluate stream variable inundation via changes in width (i.e. wet fraction). Four game cameras were deployed along Umtanum Creek (Washington, United States) to track changes in stream inundation over time. Drone imagery was collected at the same location on October 18, 2024 which was used to construct a digital elevation model (DEM) of the streambed topography. The associated paper and data can be found at https://doi.org/10.1016/j.envsoft.2025.106715 (Bao et al., 2025a)) and https://doi.org/10.15485/2589885 (Bao et al., 2025b), respectively. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to this readme, this data package also includes a file-level metadata (FLMD) files that describes each file and a data dictionaries (DD) that describe all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) readme; (4) field metadata; (5) field protocol; and (5) folders containing game camera photos. Game camera photos are organized into folders for each camera (CDL, CUL, CDR, CUR; see readme for information on camera naming) by the month photos were collected. All files are .csv, .jpg, or .pdf.

AI image segmentation↗

Electron energy distributions in the extended gas nebulae associated with high-z AGN: Maxwell–Boltzmann versus κ distributions

ABSTRACT Emission line observations together with photoionization models provide important information about the ionization mechanisms, densities, temperatures, and metallicities in active galactic nuclei (AGN)-ionized gas. Photoionization models usually assume Maxwell–Boltzmann (M–B) electron energy distributions (EED), but it has been suggested that using κ distributions may be more appropriate and could potentially solve the discrepancies in temperatures and abundances found in HII regions and planetary nebulae. We consider the impact of the presence of κ distributions in photoionized nebulae associated with AGN and study how this might affect spectral modelling and abundance analyses for such regions. Using the photoionization code MAPPINGS 1e, we compute models adopting M–B and κ distributions of electron energies and compare the behaviour of emission line ratios for different values of κ, gas metallicity, density, ionization parameter, and SED slope. We find that the choice of EED can have a large impact on some UV and optical emission lines emitted by photoionized nebulae associated with AGN, and that the impact of adopting a κ distribution is strongly dependent on gas metallicity and ionization parameter. We compile a sample of line ratios for 143 type 2 AGN and compare our models against the observed line ratios. We find that for 98 objects, κ distributions provide a better fit to the observed line ratios than M–B distributions. In addition, we find that adopting κ-distributed electron energies results in significant changes in the inferred gas metallicity and ionization parameter in a significant fraction of objects.

Morais, S. G. (ORCID:0000000200927813)↗

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species

This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. Herein, a total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.

59 BASIC BIOLOGICAL SCIENCES↗

DISCo-microbe: design of an identifiable synthetic community of microbes

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).

16S rRNA↗

A Study of Model-Based Protective Fast-Charging and Associated Degradation in Commercial Smartphone Cells: Insights on Cathode Degradation as a Result of Lithium Depositions on the Anode

The ever expanding mobile consumer electronic market has accelerated the need for safe and efficient fast-charging approaches that improve the overall speed of battery charging without hastened deterioration of the battery performance. Herein, the impact of a resource inexpensive, physics-based, electrochemically optimized fast-charging algorithm (charging time < 2 h) for mobile devices is investigated. A critical difference in the amount and morphology of lithium deposits on the anode for cells fast-charged without an optimized algorithm is observed and found to be the main cause of capacity decay. Furthermore, an in-depth study of the LiCoO 2 cathode regions opposite to pronounced lithium deposits on the anode reveals a “mirroring” phenomenon, i.e., a frozen monoclinic phase, and inactivity to relithiation. In operando hard X-ray absorption spectroscopy reveals that degraded spots on harvested cathodes seem to be activated again and participate in the intercalation process when lithiated at low rates from lithium foil counter electrodes. On the other hand, tests at higher C-rates, closer to the actual fast-charging rate, reveal only negligible oxidation state changes and therefore poor performance.

25 ENERGY STORAGE↗

In planta single-molecule imaging and holographic force spectroscopy to study real-time, multimodal turnover dynamics of polysaccharides and associated carbohydrate metabolites

Cellular production of polysaccharides from simple sugar molecules serves critical roles in a variety of metabolic processes essential to the survival of every living organism. In the context of photosynthetically fixed carbon, cell wall polysaccharides synthesis is particularly of interest for increased biomass accumulation for human food, animal feed, and bioenergy related applications. Despite a long history of research in plant cell biology, our understanding of in planta cell wall biosynthesis and its regulation is far from complete due to lack of a comprehensive microscopy toolkit that encompass the multiple spatial and temporal scales in which cell wall polysaccharides fibrils are synthesized and assembled into intricate cell wall networks. In this project, a multidisciplinary team of scientists from Rutgers University, Vanderbilt University, and Oak Ridge National Laboratory carried out innovative multimodal, multiscale microscopy studies of cell wall synthesis using single-molecule force-spectroscopy, super-resolution fluorescence microscopy, and in vivo live cell imaging. Our novel multimodal and holistic imaging approach revealed plant cell wall polysaccharides synthesis processes in unprecedented detail across multiple spatiotemporal scales, from a single-molecule to a single-cell. Besides, the team has made technical and scientific innovations across multiple research fields—microscopy, bioengineering, single-molecule biophysics, and plant biology, etc.—to accomplish the goals. The results from this project will greatly advance the mechanistic and holistic understanding of in planta cell wall synthesis, which will accelerate the development of better transgenic crops for bioenergy applications. Moreover, the new toolbox, combining powerful advanced microscopy assays with cell/protein engineering, will have broader impacts on molecular and cellular biology fields by paving the way for studying cellular processes occurring across multiple physical scales with multimodal microscopy methodologies.

59 BASIC BIOLOGICAL SCIENCES↗

Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping

Abstract High-throughput transcriptomics (HTTr) uses gene expression profiling to characterize the biological activity of chemicals in in vitro cell-based test systems. As an extension of a previous study testing 44 chemicals, HTTr was used to screen an additional 1,751 unique chemicals from the EPA’s ToxCast collection in MCF7 cells using 8 concentrations and an exposure duration of 6 h. We hypothesized that concentration-response modeling of signature scores could be used to identify putative molecular targets and cluster chemicals with similar bioactivity. Clustering and enrichment analyses were conducted based on signature catalog annotations and ToxPrint chemotypes to facilitate molecular target prediction and grouping of chemicals with similar bioactivity profiles. Enrichment analysis based on signature catalog annotation identified known mechanisms of action (MeOAs) associated with well-studied chemicals and generated putative MeOAs for other active chemicals. Chemicals with predicted MeOAs included those targeting estrogen receptor (ER), glucocorticoid receptor (GR), retinoic acid receptor (RAR), the NRF2/KEAP/ARE pathway, AP-1 activation, and others. Using reference chemicals for ER modulation, the study demonstrated that HTTr in MCF7 cells was able to stratify chemicals in terms of agonist potency, distinguish ER agonists from antagonists, and cluster chemicals with similar activities as predicted by the ToxCast ER Pathway model. Uniform manifold approximation and projection (UMAP) embedding of signature-level results identified novel ER modulators with no ToxCast ER Pathway model predictions. Finally, UMAP combined with ToxPrint chemotype enrichment was used to explore the biological activity of structurally related chemicals. The study demonstrates that HTTr can be used to inform chemical risk assessment by determining in vitro points of departure, predicting chemicals’ MeOA and grouping chemicals with similar bioactivity profiles.

Toxicology↗