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At least 181 records · Page 10

A standardized quantitative analysis strategy for stable isotope probing metagenomics

ABSTRACT Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg , an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, “who is eating what?” and “who is active?” within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism’s taxonomic identity and genome composition while providing quantitative estimates of the microorganism’s isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

54 ENVIRONMENTAL SCIENCES↗

Submillimetric Spectroscopic Observations of Volatiles in Comet C-2004 Q2 (Machholz)

Submillimeter spectroscopic observations of comets provide an important tool for understanding their chemical composition and enable a taxonomic classification. Aims. We aim to determine the production rates of several parent- and product volatiles and the C-12/C-13 isotopic carbon ratio in the long-period comet C/2004 Q2 (Machholz), which is likely to originate from the Oort Cloud. Methods. The line emission from several molecules in the coma was measured with high signal-to-noise ratio in January 2005 at heliocentric distance of 1.2 AU by means of high-resolution spectroscopic observations using the Submillimeter Telescope (SMT) at the Arizona Radio Observatory (ARO). Results. We have obtained production rates of several volatiles (CH3OH, HCN, H(sup 13)CN, HNC, H2CO, CO, and CS) by comparing the observed and simulated line-integrated intensities. We calculated the synthetic profiles using a radiative transfer code that includes collisions between neutrals and electrons, and the effects of radiative pumping of the fundamental vibrational levels by solar infrared radiation. Furthermore, multiline observations of the CH3OH J = 7-6 series allow us to estimate the rotational temperature using the rotation diagram technique. We find that the CH3OH population distribution of the levels sampled by these lines can be described by a rotational temperature of 40 +/- 3 K. Derived mixing ratios relative to hydrogen cyanide are CO/CH3OH/H2CO/CS/HNC/HC-13N/HCN= 30.9/24.6/4.8/0.57/0.031/0.013/1 assuming a pointing offset of 8" due to the uncertain ephemeris at the time of the observations and the telescope pointing error. Conclusions. The measured relative molecular abundances in C/2004 Q2 (Machholz) are between low- to typical values of those obtained in Oort Cloud comets, suggesting that it has visited the inner solar system previously and undergone thermal processing. The HNC/HCN abundance ratio of approx 3.1% is comparable to that found in other comets, accounting for the dependence on the heliocentric distance, and could possibly be explained by ion-molecule chemical processes in the low-temperature atmosphere. From a tentative HC-13N detection, the measured value of 97 +/- 30 for the HC-12N/HC-13N isotopologue pair is consistent with a telluric value. The outgassing variability observed in the HCN production rates over a period of two hours is consistent with the rotation of the nucleus derived using different observational techniques.

chemical composition↗

Damping Wing-Like Features in the Spectra of High Redshift Quasars: a Challenge for Fully-Coupled Simulations

Recently, several observational detections of damping-wing-like features at the edges of “dark gaps” in the spectra of distant quasars (the “Malloy-Lidz effect”) have been reported, rendering strong support for the existence of “neutral islands” in the universe at redshifts as low as z<5.5. We apply the procedure from one of these works, Zhu et al 2024, to the outputs of fully coupled cosmological simulations from two recent large projects, “Cosmic Reionization On Computers” (CROC) and “Thesan”. Synthetic spectra in both simulations have statistics of dark gaps similar to observations, but do not exhibit the damping wing features. Moreover, a toy model with neutral islands added “by hand” only reproduces the observational results when the fraction of neutral islands among all dark gaps approaches 90%. I.e., simulations and observations appear to produce two distinct “populations” of dark gaps. In addition, in the simulations, the neutral islands at z=5.9 should be short-lived and should not extend to z<5.5. A plausible explanation for this discrepancy is that both simulations underestimate the fluctuations in the photoionization rate and, hence, are missing a population of long-lived neutral islands, located in the large downward fluctuations of the photoionization rate.

79 ASTRONOMY AND ASTROPHYSICS↗

New Directions for Chemical Engineering

Over the past century, the work of chemical engineers has helped transform societies and the lives of individuals, from the synthetic fertilizers that helped feed the world to the development of novel materials used in fuels, electronics, medical devices, and other products. Chemical engineers' ability to apply systems-level thinking from molecular to manufacturing scales uniquely positions them to address today’s most pressing problems, including climate change and the overuse of resources by a growing population. New Directions for Chemical Engineering details a vision to guide chemical engineering research, innovation, and education over the next few decades. This report calls for new investments in U.S. chemical engineering and the interdisciplinary, cross-sector collaborations necessary to advance the societal goals of transitioning to a low-carbon energy system, ensuring our production and use of food and water is sustainable, developing medical advances and engineering solutions to health equity, and manufacturing with less waste and pollution. The report also calls for changes in chemical engineering education to ensure the next generation of chemical engineers is more diverse and equipped with the skills necessary to address the challenges ahead.

National Academies of Sciences, Engineering, and M↗

GenAI-Based Digital Twins Aided Data Augmentation Increases Accuracy in Real-Time Cokurtosis-Based Anomaly Detection of Wearable Data

Early detection of potential infectious disease outbreaks is crucial for developing effective interventions. In this study, we introduce advanced anomaly detection methods tailored for health datasets collected from wearables, offering insights at both individual and population levels. Leveraging real-world physiological data from wearables, including heart rate and activity, we developed a framework for the early detection of infection in individuals. Despite the availability of data from recent pandemics, substantial gaps remain in data collection, hindering method development. To bridge this gap, we utilized Wasserstein Generative Adversarial Networks (WGANs) to generate realistic synthetic wearable data, augmenting our dataset for training. Subsequently, we use these augmented datasets to implement a cokurtosis-based technique for anomaly detection in multivariate time-series data. Our approach includes a comprehensive assessment of uncertainties in synthetic data compared to the actual data upon which it was modeled, as well as the uncertainty associated with fine-tuning anomaly detection thresholds in physiological measurements. Through our work, we present an enhanced method for early anomaly detection in multivariate datasets, with promising applications in healthcare and beyond. This framework could revolutionize early detection strategies and significantly impact public health response efforts in future pandemics.

Data-Driven Digital Twins↗

Aboveground and Belowground Responses to Cyanobacterial Biofertilizer Supplement in a Semi-Arid, Perennial Bioenergy Cropping System

The need for sustainable agricultural practices to meet the food, feed, and fuel demands of a growing global population while reducing detrimental environmental impacts has driven research in multi-faceted approaches to agricultural sustainability. Perennial cropping systems and microbial biofertilizer supplements are two emerging strategies to increase agricultural sustainability that are studied in tandem for the first time in this study. During the establishment phase of a perennial switchgrass stand in SW Montana, USA, we supplemented synthetic fertilization with a nitrogen-fixing cyanobacterial biofertilizer (CBF) and were able to maintain aboveground crop productivity in comparison to a synthetic only (urea) fertilizer treatment. Soil chemical analysis conducted at the end of the growing season revealed that late-season nitrogen availability in CBF-supplemented field plots increased relative to urea-only plots. High-throughput sequencing of bacterial/archaeal and fungal communities suggested fine-scale responses of the microbial community and sensitivity to fertilization among arbuscular mycorrhizal fungi, Planctomycetes, Proteobacteria, and Actinobacteria. Given their critical role in plant productivity and soil nutrient cycling, soil microbiome monitoring is vital to understand the impacts of implementation of alternative agricultural practices on soil health.

biofertilizer↗

Improving Predictive Capability in REHEDS Simulations with Fast, Accurate, and Consistent Non-Equilibrium Material Properties

Predictive design of REHEDS experiments with radiation-hydrodynamic simulations requires knowledge of material properties (e.g. equations of state (EOS), transport coefficients, and radiation physics). Interpreting experimental results requires accurate models of diagnostic observables (e.g. detailed emission, absorption, and scattering spectra). In conditions of Local Thermodynamic Equilibrium (LTE), these material properties and observables can be pre-computed with relatively high accuracy and subsequently tabulated on simple temperature-density grids for fast look-up by simulations. When radiation and electron temperatures fall out of equilibrium, however, non-LTE effects can profoundly change material properties and diagnostic signatures. Accurately and efficiently incorporating these non-LTE effects has been a longstanding challenge for simulations. At present, most simulations include non-LTE effects by invoking highly simplified inline models. These inline non-LTE models are both much slower than table look-up and significantly less accurate than the detailed models used to populate LTE tables and diagnose experimental data through post-processing or inversion. Because inline non-LTE models are slow, designers avoid them whenever possible, which leads to known inaccuracies from using tabular LTE. Because inline models are simple, they are inconsistent with tabular data from detailed models, leading to ill-known inaccuracies, and they cannot generate detailed synthetic diagnostics suitable for direct comparisons with experimental data. This project addresses the challenge of generating and utilizing efficient, accurate, and consistent non-equilibrium material data along three complementary but relatively independent research lines. First, we have developed a relatively fast and accurate non-LTE average-atom model based on density functional theory (DFT) that provides a complete set of EOS, transport, and radiative data, and have rigorously tested it against more sophisticated first-principles multi-atom DFT models, including time-dependent DFT. Next, we have developed a tabular scheme and interpolation methods that compactly capture non-LTE effects for use in simulations and have implemented these tables in the GORGON magneto-hydrodynamic (MHD) code. Finally, we have developed post-processing tools that use detailed tabulated non-LTE data to directly predict experimental observables from simulation output.

36 MATERIALS SCIENCE↗

Modeling the microplastic distribution along the Delaware River Estuary: Accumulation patterns and hydrodynamic influences

Microplastic pollution is an escalating environmental concern, particularly in densely populated estuary regions, where it poses significant threats to aquatic life and human health. The dispersion patterns of microplastic particles along estuaries are influenced and complicated by multiple environmental factors such as river flow, tidal mixing, salt intrusion, and estuarine circulation. This study examines the accumulation and dispersion patterns by modeling three typical classes of microplastics in the Delaware River Estuary: synthetic fibers, sinking plastic films, and rising plastic pellets. Our findings reveal specific areas with high microplastic accumulation for each type. Notably, the upper estuary regions exhibit significant retention of rising microplastics, associated with a region with reduced along-thalweg velocities downstream of Trenton, NJ and upstream of Philadelphia, PA. Conversely, synthetic fibers and sinking plastic films accumulate in the flow convergence zone near the bottom salinity front, typically downstream of Philadelphia. All of the microplastic accumulation hot spot locations are controlled by the balance of river discharge and salinity intrusions. During the dry season, microplastic accumulation hot spots shift upstream in the estuary, whereas in the wet season, the strong river discharge pushes them downstream. Furthermore, on the other hand, tidal mixing, settling, and resuspension processes strongly impact the spreading of microplastics along the river.

Delaware River Estuary↗

Research, Development and Demonstration of Advanced Vehicle Technologies in Clean Motor Fuels (CRADA Final Report)

NREL/DOE has been funding research, development, and demonstration (RD&D) projects to facilitate the deployment of alternative fuels into the marketplace in order to achieve three objectives: 1) enhance the reduction of mobile source emissions in California and the U.S.; 2) increase U.S. competitiveness and economic prosperity; and 3) preserve the environment through the reduction of emissions and toxins from the motor vehicle population. The Lewis-Presley Air Quality Management Act requires the South Coast Air Quality Management District to establish a program to encourage participation in projects to increase the utilization of clean-burning fuels. The parties seek to collaborate on a joint RD&D project to perform a field test on a small vehicle fleet operating on Fischer-Tropsch synthetic diesel fuel. Recently the 106th U.S. Congress designated "gas-to-liquid" (GTL) transportation fuels that are produced from domestic products as alternative fuels under the Energy Policy Act of 1992 (EPACT). Niche markets could develop quickly for these fuel products, perhaps especially for the use of Fischer-Tropsch synthetic fuels in centrally fueled vehicle fleets in California. NREL and its project partners from the U.S. Department of Energy and West Virginia University have recently conducted what we believe to be the first-ever controlled tests of Fischer-Tropsch synthetic fuels in heavy vehicles. These tests have shown that Fischer-Tropsch fuels can be substituted in unmodified trucks and buses without any detectable loss in drivability and performance. Compared to a California diesel fuel baseline, neat Shell Fischer-Tropsch fuel emitted about 12% lower NOx and 24% lower particulate matter over a five-mile driving route while maintaining the same fuel economy on an energy equivalent basis. Whereas these exhaust emissions reductions from these previous studies have been impressive, far greater exhaust emissions reductions can be achieved if the vehicles are retrofitted with emissions control technologies that are enabled by Fischer-Tropsch fuels. For this program, a test fleet would be selected and retrofitted with continuously regenerating traps (CRT’s) or diesel particulate filters (DPF's). The University of West Virginia, under a separate subcontract to SCAQMD will have the responsibility to test and measure the emissions from the test fleet of vehicles.

33 ADVANCED PROPULSION SYSTEMS↗

Reducing Sample Size While Improving Equity in Vaccine Clinical Trials: A Machine Learning-Based Recruitment Methodology with Application to Improving Trials of Hepatitis C Virus Vaccines in People Who Inject Drugs

Despite the availability of direct-acting antivirals that cure individuals infected with the hepatitis C virus (HCV), developing a vaccine is critically needed in achieving HCV elimination. HCV vaccine trials have been performed in populations with high incidence of new HCV infection such as people who inject drugs (PWID). Developing strategies of optimal recruitment of PWID for HCV vaccine trials could reduce sample size, follow-up costs and disparities in enrollment. We investigate trial recruitment informed by machine learning and evaluate a strategy for HCV vaccine trials termed PREDICTEE—Predictive Recruitment and Enrichment method balancing Demographics and Incidence for Clinical Trial Equity and Efficiency. PREDICTEE utilizes a survival analysis model applied to trial candidates, considering their demographic and injection characteristics to predict the candidate’s probability of HCV infection during the trial. The decision to recruit considers both the candidate’s predicted incidence and demographic characteristics such as age, sex, and race. We evaluated PREDICTEE using in silico methods, in which we first generated a synthetic candidate pool and their respective HCV infection events using HepCEP, a validated agent-based simulation model of HCV transmission among PWID in metropolitan Chicago. We then compared PREDICTEE to conventional recruitment of high-risk PWID who share drugs or injection equipment in terms of sample size and recruitment equity, with the latter measured by participation-to-prevalence ratio (PPR) across age, sex, and race. Comparing conventional recruitment to PREDICTEE found a reduction in sample size from 802 (95%: 642–1010) to 278 (95%: 264–294) with PREDICTEE, while also reducing screening requirements by 30%. Simultaneously, PPR increased from 0.475 (95%: 0.356–0.568) to 0.754 (95%: 0.685–0.834). Even when targeting a dissimilar maximally balanced population in which achieving recruitment equity would be more difficult, PREDICTEE is able to reduce sample size from 802 (95%: 642–1010) to 304 (95%: 288–322) while improving PPR to 0.807 (95%: 0.792–0.821). PREDICTEE presents a promising strategy for HCV clinical trial recruitment, achieving sample size reduction while improving recruitment equity.

60 APPLIED LIFE SCIENCES↗

Projecting U.S. coastal storm surge risks and impacts with deep learning

Storm surge is one of the deadliest hazards posed by tropical cyclones (TCs), yet assessing its current and future risk is difficult due to the phenomenon’s rarity and physical complexity. Recent advances in artificial intelligence applications to natural hazard modeling suggest a new avenue for addressing this problem. We develop a deep learning storm surge model to efficiently estimate coastal surge risk in the United States from 900 000 synthetic TC events, accounting for projected changes in TC behavior and sea levels. The derived historical 100 year surge (the event with a 1% yearly exceedance probability) agrees well with historical observations and other modeling techniques. When coupled with an inundation model, we find that heightened TC intensities and sea levels by the end of the century result in a 50% increase in population at risk. Key findings include markedly heightened risk in Florida, and critical thresholds identified in Georgia and South Carolina.

RAFT↗

Single-cell measurement of plasmid copy number and promoter activity

Abstract Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources, all of which provide critical insights for cellular engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Inductively Coupled Nonthermal Plasma Synthesis of Size-Controlled γ-Al 2 O 3 Nanocrystals

Gamma alumina (γ-Al 2 O 3 ) is widely used as a catalyst and catalytic support due to its high specific surface area and porosity. However, synthesis of γ-Al 2 O 3 nanocrystals is often a complicated process requiring high temperatures or additional post-synthetic steps. Here, we report a single-step synthesis of size-controlled and monodisperse, facetted γ-Al 2 O 3 nanocrystals in an inductively coupled nonthermal plasma reactor using trimethylaluminum and oxygen as precursors. Under optimized conditions, we observed phase-pure, cuboctahedral γ-Al 2 O 3 nanocrystals with defined surface facets. Nuclear magnetic resonance studies revealed that nanocrystal surfaces are populated with AlO 6 , AlO 5 and AlO 4 units with clusters of hydroxyl groups. Nanocrystal size tuning was achieved by varying the total reactor pressure yielding particles as small as 3.5 nm, below the predicted thermodynamic stability limit for γ-Al 2 O 3 .

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Determination of the mean energy of fast electron losses and anisotropies through thick-target emission on WEST

Abstract A new method to obtain the mean energy of fast electron losses in fusion plasmas using a versatile multi-energy hard x-ray (HXR) detector is presented. The method is based on measuring the thick-target emission of tungsten in the divertor region produced by fast electron losses interacting with the target and modeling the tungsten spectra by a Monte Carlo code which simulates the interaction between a beam of electrons and a solid target. The mean energy of the fast electron losses is determined through the comparison between the experimental and synthetic emission. The results show that fast electron losses during lower hybrid current drive discharges at WEST have a mean energy of 90–140 keV and represent only 2% of the total heat flux at the target. Additionally, anisotropic HXR emission has been detected for the first time at the WEST core and edge plasma, with opposite directions. It is due to the forward-peak emission of two distinctive populations of fast electrons: co-current fast electrons in the core and counter-current fast electron losses at the inner strike point. In view of future experiments like ITER where electron cyclotron current drive will generate a fast electron population, this technique could serve as a real-time monitor of fast electron losses and eventually feed an actuator on the current drive generation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

pH dependent reactivity of boehmite surfaces from first principles molecular dynamics

pH dependent interfacial chemistry depends upon the distribution and respective pKa values of different surface active sites. This is highly relevant to the chemistry of nanoparticle morphologies that expose faces with varying surface termination. Recent synthetic advances for nanoparticles of various minerals, including AlO(OH) (boehmite), present an excellent opportunity to compare and contrast predicted surface pKa on low Miller index planes so as to reinterpret reported interfacial properties (i.e., point of zero charge – PZC) and reactivity. This work employs ab initio molecular dynamics and empirical models to predict site-specific pKa values of accurate (benchmarked) surface models of boehmite. Using the different surface site populations, the PZC is determined and the influence this has upon reported interfacial chemistry is described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Laboratory Method for Assessing Audibility and Localization of Rotorcraft Fly-In Noise

The low frequency content of rotorcraft noise allows it to be heard over great distances. This factor contributes to the disruption of natural quiet in national parks and wilderness areas, and can lead to annoyance in populated areas. Further, it can result in the sound being heard at greater distances compared to higher altitude fixed wing aircraft operations. Human response studies conducted in the field are challenging since test conditions are difficult to control. This paper presents a means of quantitatively determining the audibility and localization of rotorcraft fly-in noise, under a specified ambient noise condition, within a controlled laboratory environment. It is demonstrated using synthetic fly-in noise of a light utility helicopter. The method is shown to resolve differences in audibility distances due to different ground impedances, propagation modeling methods, and directivity angles. Further, it demonstrates the efficacy of an accelerated test method.

Rizzi, Stephen A.↗

Abundances in late-type giants.

The narrow-band photometry of Spinrad and Taylor (1969) is analyzed by the synthetic spectra technique. Surface gravities, Doppler broadening velocities, effective temperatures, and metal abundances are determined for 131 K giants. Evolutionary tracks and gravities determined from the photometry are used to give space positions, space velocities, and absolute magnitudes of the 131 stars. We conclude that a class of stars exists with metals and/or nitrogen significantly enhanced with respect to the sun; further that these stars have average space motions similar to those of moderately old Population I stars. The Doppler broadening velocity is found to be a strong function of temperature for K giants, and in some cases, possibly a function of surface gravity.

Gottlieb, D. M.↗

Developing a Genetic Variant Calling Pipeline for Quantifying the Complex Mutagenic Load Accumulated in BioNutrients-1 Production Pack Samples

Microorganisms hold great promise for on demand production of labile nutrients and pharmaceuticals as well recycling and in situ resource utilization. The utilization of microorganisms for such tasks on space missions is hindered by the limited data on how microbes respond to spaceflight. For example, the genetic stability of microorganisms, and the genomic engineered traits added to deliver desired functions, over long-term storage in the spacecraft environment is poorly understood. The BioNutrients-1 (BN-1) mission conducted a 5-year study of desiccated storage in Low Earth Orbit (LEO) to evaluate the suitability of eight synthetic biology chassis organisms for long-duration space missions. We are employing high-depth, whole genome sequencing (WGS) to determine the mutagenic load that accumulated during long-term storage. Mutation analysis pipelines are well established for homogenous culture grown from a single colony, but the mutational landscape of the BN-1 samples present a unique analysis challenge, as every cell in the BN-1 samples had a unique genetic journey of DNA damage and repair. Consequently, sequence variants are expected at low allele frequency within samples. To address this genetic complexity, we apply two distinct computational approaches to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO. For reference genome free mutation detection, we utilized DiscoSNP++, which is a de Bruijn graph approach. For reference genome-based mutation detection we utilize GATK for Microbes, which is a Bayesian probabilistic approach. We will benchmark these approaches against the mutations originally identified using CRISP, a method optimized for pooled samples. Ultimately, quantifying the mutation load imposed by storage or growth on the ISS will help identify chassis organisms with both high levels of genome stability and viability, which are desirable traits for implementation of bioproduction in long-duration missions.

SNP↗