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At least 703 records · Page 39

Real-time breath analysis towards a healthy human breath profile

Abstract The direct analysis of molecules contained within human breath has had significant implications for clinical and diagnostic applications in recent decades. However, attempts to compare one study to another or to reproduce previous work are hampered by: variability between sampling methodologies, human phenotypic variability, complex interactions between compounds within breath, and confounding signals from comorbidities. Towards this end, we have endeavored to create an averaged healthy human ‘profile’ against which follow-on studies might be compared. Through the use of direct secondary electrospray ionization combined with a high-resolution mass spectrometry and in-house bioinformatics pipeline, we seek to curate an average healthy human profile for breath and use this model to distinguish differences inter- and intra-day for human volunteers. Breath samples were significantly different in PERMANOVA analysis and ANOSIM analysis based on Time of Day, Participant ID, Date of Sample, Sex of Participant, and Age of Participant ( p < 0.001). Optimal binning analysis identify strong associations between specific features and variables. These include 227 breath features identified as unique identifiers for 28 of the 31 participants. Four signals were identified to be strongly associated with female participants and one with male participants. A total of 37 signals were identified to be strongly associated with the time-of-day samples were taken. Threshold indicator taxa analysis indicated a shift in significant breath features across the age gradient of participants with peak disruption of breath metabolites occurring at around age 32. Forty-eight features were identified after filtering from which a healthy human breath profile for all participants was created.

60 APPLIED LIFE SCIENCES↗

LBNF/DUNE Liquid Argon Roadmap

The Deep Underground Neutrino Experiment (DUNE) is an international flagship venture to unlock the mysteries of neutrinos. Hosted at the Sanford Underground Research Facility (SURF) and supported by the Long-Baseline Neutrino Facility (LBNF), DUNE relies on nearly 75,000 tonnes of ultrapure liquid argon (LAr) housed in state-of-the-art cryostats. Transporting such vast quantities of LAr to its destination a mile underground in Lead, SD, is a logistical and engineering challenge. The process begins with securing large quantities of liquid argon from suppliers located far from the site, with major sources situated near Houston, TX and Chicago, IL. The receiving facility, located atop a mountain with steep, often snow-covered access roads, provides limited maneuverability for trucks and can only handle two deliveries simultaneously. The facility serves as an entry point for argon to the greater LBNF cryogenic system. It is furnished with truck unloading stations, limited buffer storage of some 280 tonnes capacity, and vaporizers. The last are crucial for converting liquid argon into gas for transfer down the Ross Shaft, eliminating the need for cryogens in the vertical pipeline. These constraints, along with other operational factors, cap the delivery rate at 70 tonnes per day. Once underground, the argon is purified and recondensed before filling the cryostats. This roadmap outlines the integrated supply chain and cryogenic systems that enable the delivery of LAr to support DUNE’s groundbreaking physics research.

Maciazka, Matt [Fermilab]↗

Twisted bilayered graphenes at magic angles and Casimir interactions: correlation-driven effects

Twisted bilayered graphenes (TBGs) at magic angles are systems housing long ranged periodicity of moiré patterns together with short ranged periodicity associated with the individual graphenes. Such materials are a fertile ground for novel states largely driven by electronic correlations. Here we find that the ubiquitous Casimir force can serve as a platform for macroscopic manifestations of the quantum effects stemming from the magic angle bilayered graphenes properties and their phases determined by electronic correlations. In conclusion, by utilizing comprehensive calculations for the electronic and optical response, we find that Casimir torque can probe anisotropy from the Drude conductivities in nematic states, while repulsion in the Casimir force can help identify topologically nontrivial phases in magic angle TBGs.

36 MATERIALS SCIENCE↗

A comparative analysis of US state-level policies and programs to advance energy justice

Abstract The US energy system is undergoing massive changes that have environmental, technological, and societal implications. Decisions and actions taken now will dramatically alter the trajectory of our future energy system. Though new technologies can lessen the dangers of anthropogenic climate change, an effective and sustainable transition requires addressing social justice issues as a priority. To this end, many states have implemented policies and programs that address energy justice. A formal survey of state-level energy justice policies and programs is needed to better understand the methods used to assist communities targeted and the impacts of these efforts. Such an analysis should include an analysis of the metrics used to judge the effectiveness of the enacted policies and programs. In this paper, we analyze the energy justice policies and programs of seven different US states. From this analysis, we identify three important aspects of state energy policies. First, most policies and programs do not articulate their goals, nor cite metrics to judge their successes. This lack of transparency and accountability is a major roadblock to truly just solutions. Second, states focus on a very narrow range of solutions for energy justice issues. The most prevalent being utility bill assistance, which does not address the systemic and enduring challenges faced by many low-income or historically marginalized communities. Lastly, comprehensive energy policy does not acknowledge and address housing, employment, education, and healthcare inequities that exacerbate energy system inequities. The work presented in this paper sheds light on the progress of state-level energy justice policies and programs across the United States, and we argue more work needs to be done to understand best practices in energy justice policymaking.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Fast convolutional neural networks on FPGAs with hls4ml

We introduce an automated tool for deploying ultra low-latency, low-power deep neural networks with convolutional layers on field-programmable gate arrays (FPGAs). By extending the hls4ml library, we demonstrate an inference latency of 5 µs using convolutional architectures, targeting microsecond latency applications like those at the CERN Large Hadron Collider. Considering benchmark models trained on the Street View House Numbers Dataset, we demonstrate various methods for model compression in order to fit the computational constraints of a typical FPGA device used in trigger and data acquisition systems of particle detectors. In particular, we discuss pruning and quantization-aware training, and demonstrate how resource utilization can be significantly reduced with little to no loss in model accuracy. We show that the FPGA critical resource consumption can be reduced by 97% with zero loss in model accuracy, and by 99% when tolerating a 6% accuracy degradation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Synergizing human expertise and AI efficiency with language model for microscopy operation and automated experiment design

With the advent of large language models (LLMs), in both the open source and proprietary domains, attention is turning to how to exploit such artificial intelligence (AI) systems in assisting complex scientific tasks, such as material synthesis, characterization, analysis and discovery. Here, we explore the utility of LLMs, particularly ChatGPT4, in combination with application program interfaces (APIs) in tasks of experimental design, programming workflows, and data analysis in scanning probe microscopy, using both in-house developed APIs and APIs given by a commercial vendor for instrument control. We find that the LLM can be especially useful in converting ideations of experimental workflows to executable code on microscope APIs. Beyond code generation, we find that the GPT4 is capable of analyzing microscopy images in a generic sense. At the same time, we find that GPT4 suffers from an inability to extend beyond basic analyses for more in-depth technical experimental design. We argue that an LLM specifically fine-tuned for individual scientific domains can potentially be a better language interface for converting scientific ideations from human experts to executable workflows. Such a synergy between human expertise and LLM efficiency in experimentation can open new doors for accelerating scientific research, enabling effective experimental protocols sharing in the scientific community.

97 MATHEMATICS AND COMPUTING↗

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

Abstract Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

Environmental Sciences & Ecology↗

EMDB—the Electron Microscopy Data Bank

Abstract The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

59 BASIC BIOLOGICAL SCIENCES↗

Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government

Challenges facing food production and agricultural systems are increasingly interconnected with economic, security, health, and equity issues, among others. Threats such as extreme weather, economic volatility, and shrinking water resources and arable land, influence our ability to maintain a safe and resilient food supply. One promising solution to these threats is controlled environment agriculture (CEA). In many cases, CEA can drastically reduce the amount of water and land used in crop production while increasing productivity. Operations may be established in nearly any environment and harvests can take place year-round, supporting food system resiliency and sustainability. CEA sits at the nexus of a number of disciplines and industries, making it well suited for transdisciplinary and multi-institutional research coordination. Herein, authors from multiple US government agencies present CEA as a case study in improving cross-agency research collaboration. The federal government houses a range of scientific expertise and research capabilities, positioning scientists to lead national and global efforts in transdisciplinary, interagency approaches to complex challenges. Navigating cross-agency collaboration can be a challenge, especially coordinating across different scientific disciplines, geographic locations, and funding mechanisms. To enhance multiagency efforts, collaborators could prioritize (i) organizing personnel and resources, (ii) enhancing existing multiagency collaborations, and (iii) focusing on further opportunities for coordination. Adopting these approaches could enable federal researchers to reinforce and advance academic and industry efforts to address current CEA challenges while solidifying the United States as a leader in this arena.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Evaluation of Skyshine from an Accelerator Facility: Dependence on Distance and Angle

Neutron skyshine from Linac Coherent Light Source II 4 GeV electron beam operation at SLAC National Accelerator Laboratory can contribute to prompt radiation exposure to the public at distances far beyond the accelerator tunnel housing. One of the shielding design requirements at SLAC is that the annual dose to a member of the public is no more than 0.05 mSv y -1 . Our work uses Monte Carlo code FLUKA to simulate the generation of neutrons from 4 GeVelectron beam losses on a thick copper target inside a generalized geometry of the Linac Coherent Light Source II Beam Transport Hall accelerator tunnel section. The effective dose from neutron skyshine was characterized as a function of both distance from the tunnel wall (up to 1 km away) and angle relative to the beam direction (between 0° and 180°). Furthermore, this new methodology for evaluating neutron skyshine dose is applicable to high-energy GeV-range electron accelerator facilities both at SLAC and elsewhere.

43 PARTICLE ACCELERATORS↗

Temporal Characterization of Tritium Smear Activities

Tritium collection efficiency varies as a function of smear media. The use of porous smear materials leads to an increase in the measured tritium activity as a function of time when the measurement is performed with liquid scintillation counters. Operational inclusion of the efficiency differences and the time dependence of the tritium smear activity is necessary to preclude inadvertently releasing materials or areas. Thomas Jefferson National Laboratory Radiological Control Department identified a contaminated stainless steel containment vessel that previously housed a target containing more than 37 TBq of tritium. The item was systematically sectioned and surveyed to compare three smear types: water-wetted cotton swabs, water-wetted paper smears, and ethanol-wetted Styrofoam wipes (NUC-Wipes™). The total activity of each section was determined using repeated decontamination. The time dependence of the measured activity was also studied. The measured activity of both paper smears and cotton swabs showed significant time dependence. The cotton swabs also showed significantly reduced collection efficiency. Given the widespread use of both of these media in routine contamination surveys, site operational limits were derived using fitted curves for time dependence and average efficiency results. In conclusion, the use of these more restrictive limits allows for rapid measurement of tritium smears while ensuring regulatory compliance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Brilliant angle-independent structural colours preserved in weevil scales from the Swiss Pleistocene

Extant weevils exhibit a remarkable colour palette that ranges from muted monochromatic tones to rainbow-like iridescence, with the most vibrant colours produced by three-dimensional photonic nanostructures housed within cuticular scales. Although the optical properties of these nanostructures are well understood, their evolutionary history is not fully resolved, in part due to a poor knowledge of their fossil record. Here, we report three-dimensional photonic nanostructures preserved in brightly coloured scales of two weevils, belonging to the genus Phyllobius or Polydrusus , from the Pleistocene (16–10 ka) of Switzerland. The scales display vibrant blue, green and yellow hues that resemble those of extant Phyllobius/Polydrusus . Scanning electron microscopy and small-angle X-ray scattering analyses reveal that the subfossil scales possess a single-diamond photonic crystal nanostructure. In extant Phyllobius/Polydrusus , the near-angle-independent blue and green hues function primarily in crypsis. The preservation of far-field, angle-independent structural colours in the Swiss subfossil weevils and their likely function in substrate matching confirm the importance of investigating fossil and subfossil photonic nanostructures to understand the evolutionary origins and diversification of colours and associated behaviours (e.g. crypsis) in insects.

54 ENVIRONMENTAL SCIENCES↗

Wealth inequality in the prehispanic northern US Southwest: from Malthus to Tyche

Persistent differences in wealth and power among prehispanic Pueblo societies are visible from the late AD 800s through the late 1200s, after which large portions of the northern US Southwest were depopulated. In this paper we measure these differences in wealth using Gini coefficients based on house size, and show that high Ginis (large wealth differences) are positively related to persistence in settlements and inversely related to an annual measure of the size of the unoccupied dry-farming niche. We argue that wealth inequality in this record is due first to processes inherent in village life which have internally different distributions of the most productive maize fields, exacerbated by the dynamics of systems of balanced reciprocity; and second to decreasing ability to escape village life owing to shrinking availability of unoccupied places within the maize dry-farming niche as villages get enmeshed in regional systems of tribute or taxation. We embed this analytical reconstruction in the model of an ‘Abrupt imposition of Malthusian equilibrium in a natural-fertility, agrarian society’ proposed by Puleston et al. (Puleston C, Tuljapurkar S, Winterhalder B. 2014 PLoS ONE 9, e87541 (doi:10.1371/journal.pone.0087541)), but show that the transition to Malthusian dynamics in this area is not abrupt but extends over centuries. This article is part of the theme issue ‘Evolutionary ecology of inequality’.

99 GENERAL AND MISCELLANEOUS↗

Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil

As the world population increases, improvements in crop growth and yield will be needed to meet rising food demands, especially in countries that have not developed agricultural practices optimized for their own soils and crops. In many African countries, farmers improve agricultural productivity by applying synthetic fertilizers and pesticides to crops, but their continued use over the years has had serious environmental consequences including air and water pollution as well as loss of soil fertility. To reduce the overuse of synthetic amendments, we are developing inocula for crops that are based on indigenous soil microbes, especially those that enhance plant growth and improve agricultural productivity in a sustainable manner. We first isolated environmental DNA from soil samples collected from an agricultural region to study the composition of the soil microbiomes and then used Vigna unguiculata (cowpea), an important legume crop in Botswana and other legumes as “trap” plants using the collected soil to induce nitrogen-fixing nodule formation. We have identified drought-tolerant bacteria from Botswana soils that stimulate plant growth; many are species of Bacillus and Paenibacillus . In contrast, the cowpea nodule microbiomes from plants grown in these soils house mainly rhizobia particularly Bradyrhizobium , but also Methylobacterium spp. Hence, the nodule microbiome is much more limited in non-rhizobial diversity compared to the soil microbiome, but also contains a number of potential pathogenic bacteria.

Kosty, Melissa↗

Electric accumulation of millicharged particles

A terrestrial population of millicharged particles that interact significantly with normal matter can arise if they make up a dark matter subcomponent or if they are light enough to be produced in cosmic-ray air showers. Such particles thermalize to terrestrial temperatures through repeated scatters with normal matter in Earth’s environment. We show that a simple electrified shell (for example, a Van de Graaff generator) functions as an efficient accumulator of such room-temperature millicharged particles, parametrically enhancing their local density by as much as 12 orders of magnitude. This can be used to boost the sensitivity of any detector housed in the shell’s interior, such as ion traps and tests of Coulomb’s law. In a companion paper, we apply this specifically to Cavendish tests of Coulomb’s law, and we show that a well-established setup can probe a large region of unexplored parameter space, with sensitivity to the irreducible density of millicharged particles generated from cosmic rays that outperforms future accelerator searches for sub-GeV masses.

Berlin, Asher [Fermilab] (ORCID:0000000211561482)↗

Permanent magnets for the return loop of the Cornell-Brookhaven energy recovery linac test accelerator

214 neodymium permanent magnets have been manufactured for the return loop of the CBETA multi-turn ERL at Cornell University. There are 5 types of quadrupole and combined-function gradient magnets using a variant of the circular Halbach design. These are made out of NdFeB material and glued into an aluminium housing with water channels for temperature stabilisation. The NdFeB wedges and magnet construction were done by outside companies, while the final “tuning” using inserts containing 64 iron rods per magnet was done at BNL over a period of about 6 months. Average relative field errors of 2.2×10 -4 were achieved on the beam region. The magnet strengths vary by type but are of order 10 T/m for quadrupole component and up to 0.3 T for the dipole. This paper reports on the field quality and timeline achieved in this production process

43 PARTICLE ACCELERATORS↗

Performance of Oak Ridge National Laboratory spallation neutron source proton power upgrade cavities and cryomodule production

The Proton Power Upgrade initiative at Oak Ridge National Lab’s Spallation Neutron Source aims to greatly boost the capability of proton beam power. This upgrade involves the integration of seven additional cryomodules, each housing four six-cell high-beta ( β = 0.81 ) superconducting radio frequency cavities. These cavities, manufactured and processed by Research Instruments in Germany, underwent meticulous treatment, including electropolishing as the bulk and final vital step. Upon delivery to Jefferson Lab, a total of 28 cavities for seven cryomodules, along with an additional four cavities for a spare cryomodule, underwent thorough vertical qualification tests, meeting the required specifications. Following cavity tanking and subsequent rf testing, the assembly of eight cryomodules was successfully executed, with all 32 cavities demonstrating compliance with acceptance criteria. The transportation of the cryomodule to SNS for high-power testing in the tunnel yielded exceptional results. Notably, the performance surpassed specifications, in terms of quality factor and accelerating gradient. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗