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At least 1,027 records · Page 57

The need for an integrated multi-OMICs approach in microbiome science in the food system

Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop “Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research” gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.

60 APPLIED LIFE SCIENCES↗

Herbicide‐resistant weed management with robots: A weed ecological–economic model

The heavy reliance on herbicides for weed control has led to an increase in resistant weeds in the United States. Robotic weed control is emerging as an alternative technology for removing weeds mechanically using artificial intelligence. We develop an integrated weed ecological and economic dynamic (I‐WEED) model to examine the biophysical and economic drivers of adopting robotic weed management and simulate the optimal timing and intensity of robotic adoption within and across growing seasons. We specify a cohort‐based weed growth model that relates yield damages to effective weed density and treats the susceptibility of weeds to herbicides as a renewable resource that can be regenerated by using mechanical weeding robots, due to a fitness cost that makes resistant weeds less prolific. Compared to myopic weed management which ignores resistance development, forward‐looking management leads to earlier adoption of robots and treating robots as complements instead of substitutes to herbicides. This weed management results in adopting fewer robots, deploying robots on a smaller portion of the land, higher profitability, and lower yield loss in the long run, relative to myopic management. Counterintuitively, myopic management leads to a lower resistance level through its higher robot adoption intensity. We also find that a lower level of initial weed seed resistance and/or a higher fitness cost result in a higher level of resistance because they create incentives for farmers to delay the adoption of robotic weed control. Our analysis shows the importance of jointly considering the interactions between weed ecology and economics in analyzing the incentives and effects of robotic weed management on weed resistance.

agricultural robotics↗

Multi‐Model Ensembles in Ecosystem Modeling: Challenges and Best Practices for Decision‐Making

Ecosystem models are increasingly central to the decision-making for environmental policy, conservation planning, and climate-related investments. Yet, the growing reliance on Multi-Model Ensembles (MMEs) of ecosystem models by practitioners and policymakers, sometimes under tight timelines and imperfect information, has frequently outpaced the scientific rigor required to ensure ensemble reliability. Here, MMEs refer to approaches that combine targeted predictions from multiple models with the expectation of improving robustness and quantifying predictive uncertainty. Poorly designed MMEs may create a false sense of confidence and lead to suboptimal policy and market decisions. This perspective argues that robust decision-making-relevant MMEs must be grounded on two pillars: (1) rigorous Model Intercomparison Projects (MIPs), which identify inter-model agreement and disagreement, characterize model uncertainties, and evaluate robustness with observationally based benchmarks—MIPs' diagnostic evaluation is so critical that it must be needed to drive MME's decision in model selection and weighting, especially when only a limited number of models available; and (2) co-design by both stakeholders and scientists to ensure that scenarios, metrics and uncertainty requirements provide decision-relevant information. Building upon the past success and lessons from the existing MIPs-MMEs efforts (e.g., climate/Earth system/crop), we derived the theoretical basis for MMEs, addressed their specific challenges in ecosystem modeling, and highlighted proper consideration of model numbers and diversity, risk of model inter-dependence, effective calibration of model parameters, possible overdue of some ecosystem model development, critical roles of open benchmark data across a wide range of conditions, and suggested use of Artificial Intelligence to support MIPs-MMEs. We highlighted the under-recognized opportunity for MIPs and MMEs to drive scientific progress and innovation through identifying better performing models, systematic benchmarking, feedback loops, and targeted model improvement. By following actionable best practice guidelines, MMEs can evolve from ad hoc aggregation of models into a trusted backbone of environmental policy and decision-making.

ecosystem modeling↗

The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization

Abstract Background Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine. Hypothesis/Objectives A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine. Animals No live animals were used. Methods The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence–readiness. Results VBO is an open, community-driven ontology representing over 19 500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and Clinical Importance The adoption of VBO as a standard for breed names in databases and veterinary electronic health records enhances veterinary data interoperability and computability, supporting precision medicine.

Veterinary Sciences↗

Learning error distribution kernel‐enhanced neural network methodology for multi‐intersection signal control optimization

Traffic congestion has substantially induced significant mobility and energy inefficiency. Many research challenges are identified in traffic signal control and management associated with artificial intelligence (AI)-based models. For example, developing AI-driven dynamic traffic system models that accurately capture high-resolution traffic attributes and formulate robust control algorithms for traffic signal optimization is difficult. Additionally, uncertainties in traffic system modeling and control processes can further complicate traffic signal system controllability. To partially address these challenges, this study presents a novel, hybrid neural network model enhanced with a probability density function kernel shaping technique to formulate traffic system dynamics better and improve comprehensive traffic network modeling and control. The numerical experimental tests were conducted, and the results demonstrate that the proposed control approach outperforms the baseline control strategies and reduces overall average delays by 11.64% on average. By leveraging the capabilities of this innovative model, this study aims to address major challenges related to traffic congestion and energy inefficiency toward more effective and adaptable AI-based traffic control systems.

Wang, Hong [Oak Ridge National Laboratory (ORNL), ↗

In-Situ Calibrated Digital Process Twin Models for Resource Efficient Manufacturing

The chief objective of manufacturing process improvement efforts is to significantly minimize process resources such as time, cost, waste, and consumed energy while improving product quality and process productivity. This paper presents a novel physics-informed optimization approach based on artificial intelligence (AI) to generate digital process twins (DPTs). The utility of the DPT approach is demonstrated in the case of finish machining of aerospace components made from gamma titanium aluminide alloy (γ-TiAl). This particular component has been plagued with persistent quality defects, including surface and sub-surface cracks, which adversely affect resource efficiency. Previous process improvement efforts have been restricted to anecdotal post-mortem investigation and empirical modeling, which fail to address the fundamental issue of how and when cracks occur during cutting. In this work, the integration of in-situ process characterization with modular physics-based models is presented, and machine learning algorithms are used to create a DPT capable of reducing environmental and energy impacts while significantly increasing yield and profitability. Based on the preliminary results presented here, we report an improvement in the overall embodied energy efficiency of over 84%, 93% in process queuing time, 2% in scrap cost, and 93% in queuing cost has been realized for γ-TiAl machining using our novel approach.

42 ENGINEERING↗

A Monte-Carlo Method for Evaluating the Economic Performance of Plastics Recycling Systems Using Historical Pricing

The management of plastic waste is a considerable emerging global concern. Conventional plastics recycling rates range from 5–10% in the US, which results in considerable material being sent to landfill. New sorting technologies using artificial intelligence have the potential to dramatically increase the ability of waste management companies to sort out valuable fractions of plastic waste and create high-purity streams for secondary markets. However, several fractions of the plastics recycling stream, i.e., low-density polyethylene, polypropylene, and polystyrene, do not have well-developed markets. These materials may be sent to pyrolysis facilities for thermal recycling, but the economics of the pyrolysis industry are currently uncertain. This work aims to identify the breakeven price of the plastic fractions that would be sent to pyrolysis in order to determine the economic viability of the sorting facility. The work will use Monte Carlo analysis to evaluate several scenarios and understand how compositional variation, price variability, and facility attributes affect the breakeven price. Here, the presorting conditions in Materials Recovery Facilities strongly affects the profitability of the sorting facility. High residual high density polyethylene (HDPE) and polyethylene terephthalate (PET) content in presorted bales are important revenue drivers for the facility, even in presorted 3-7 bales. Key variables that lead to profitability include a high sale price of polyethylene terephthalate, a high sale price of high-density polyethylene, and if polypropylene can be sold to recycling markets (as opposed to pyrolysis facilities).

Plastics↗

Meta-optic accelerators for object classifiers

Rapid advances in deep learning have led to paradigm shifts in a number of fields, from medical image analysis to autonomous systems. These advances, however, have resulted in digital neural networks with large computational requirements, resulting in high energy consumption and limitations in real-time decision-making when computation resources are limited. Here, we demonstrate a meta-optic–based neural network accelerator that can off-load computationally expensive convolution operations into high-speed and low-power optics. In this architecture, metasurfaces enable both spatial multiplexing and additional information channels, such as polarization, in object classification. End-to-end design is used to co-optimize the optical and digital systems, resulting in a robust classifier that achieves 93.1% accurate classification of handwriting digits and 93.8% accuracy in classifying both the digit and its polarization state. This approach could enable compact, high-speed, and low-power image and information processing systems for a wide range of applications in machine vision and artificial intelligence.

42 ENGINEERING↗

Disordered topological graphs enhancing nonlinear phenomena

Complex networks play a fundamental role in understanding phenomena from the collective behavior of spins, neural networks, and power grids to the spread of diseases. Topological phenomena in such networks have recently been exploited to preserve the response of systems in the presence of disorder. We propose and demonstrate topological structurally disordered systems with a modal structure that enhances nonlinear phenomena in the topological channels by inhibiting the ultrafast leakage of energy from edge modes to bulk modes. We present the construction of the graph and show that its dynamics enhances the topologically protected photon pair generation rate by an order of magnitude. Disordered nonlinear topological graphs will enable advanced quantum interconnects, efficient nonlinear sources, and light-based information processing for artificial intelligence.

42 ENGINEERING↗

AIVT: Inference of turbulent thermal convection from measured 3D velocity data by physics-informed Kolmogorov-Arnold networks

We propose the artificial intelligence velocimetry-thermometry (AIVT) method to reconstruct a continuous and differentiable representation of the temperature and velocity in turbulent convection from measured three-dimensional (3D) velocity data. AIVT is based on physics-informed Kolmogorov-Arnold networks and trained by optimizing a loss function that minimizes residuals of the velocity data, boundary conditions, and governing equations. We apply AIVT to a set of simultaneously measured 3D temperature and velocity data of Rayleigh-Bénard convection, obtained by combining particle image thermometry and Lagrangian particle tracking. This enables us to directly compare machine learning results to true volumetric, simultaneous temperature and velocity measurements. We demonstrate that AIVT can reconstruct and infer continuous, instantaneous velocity and temperature fields and their gradients from sparse experimental data at a high resolution, providing an additional approach for understanding thermal turbulence.

Science & Technology - Other Topics↗

Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning

Prediction of peptide secondary structure is challenging because of complex molecular interactions, sequence-specific behavior, and environmental factors. Traditional design strategies, based on hydrophobicity and structural propensity, can be biased and could indeed prevent discovery of interesting, diverse, and unconventional peptides with desired nanostructure assembly. Using β sheet formation in pentapeptides as a case study, we used an integrated high-throughput experimental workflow and an artificial intelligence–driven active learning framework to improve prediction accuracy of self-assembly. By focusing on sequences where machine learning (ML) predictions deviate from conventional design strategies, we synthesized and tested 268 pentapeptides, successfully finding 96 forming β sheet assemblies, including unconventional sequences (e.g., ILFSM, LMISI, MITIY, MISIW, and WKIYI) not predicted by traditional methods. Our ML models outperformed conventional β sheet propensity tables, revealing useful chemical design rules. A web interface is provided to facilitate community access to these models. This work highlights the value of ML-driven approaches in overcoming the limitations of current peptide design strategies.

Talluri, Y. Nissi [Indian Inst. of Technology (IIT↗

Attention to quantum complexity

The imminent era of error-corrected quantum computing demands robust methods to characterize quantum state complexity from limited, noisy measurements. We introduce the Quantum Attention Network (QuAN), a classical artificial intelligence (AI) framework leveraging attention mechanisms tailored for learning quantum complexity. Inspired by large language models, QuAN treats measurement snapshots as tokens while respecting permutation invariance. Combined with our parameter-efficient miniset self-attention block, this enables QuAN to access high-order moments of bit-string distributions and preferentially attend to less noisy snapshots. We test QuAN across three quantum simulation settings: driven hard-core Bose-Hubbard model, random quantum circuits, and toric code under coherent and incoherent noise. QuAN directly learns entanglement and state complexity growth from experimental computational basis measurements, including complexity growth in random circuits from noisy data. In regimes inaccessible to existing theory, QuAN unveils the complete phase diagram for noisy toric code data as a function of both noise types, highlighting AI’s transformative potential for assisting quantum hardware.

Kim, Hyejin [Cornell Univ., Ithaca, NY (United Sta↗

A high-throughput experimentation platform for data-driven discovery in electrochemistry

Automating electrochemical analyses combined with artificial intelligence is poised to accelerate discoveries in renewable energy sciences and technologies. This study presents an automated high-throughput electrochemical characterization (AHTech) platform as a cost-effective and versatile tool for rapidly assessing liquid analytes. The Python-controlled platform combines a liquid handling robot, potentiostat, and customizable microelectrode bundles for diverse, reproducible electrochemical measurements in microtiter plates, minimizing chemical consumption and manual effort. To showcase the capability of AHTech, we screened a library of 180 small molecules as electrolyte additives for aqueous zinc metal batteries, generating data for training machine learning models to predict Coulombic efficiencies. Key molecular features governing additive performance were elucidated using Shapley Additive exPlanations and Spearman’s correlation, pinpointing high-performance candidates like cis-4-hydroxy-d-proline, which achieved an average Coulombic efficiency of 99.52% over 200 cycles. The workflow established herein is highly adaptable, offering a powerful framework for accelerating the exploration and optimization of extensive chemical spaces across diverse energy storage and conversion fields.

Lin, Dian-Zhao [Johns Hopkins University, Baltimor↗

Multifunctional electrochemical memory stabilized by phase coexistence

Our growing computing needs, especially in applications that heavily rely on artificial intelligence (AI), motivate a search for new components that could substantially augment the performance of general-purpose digital computers. Beyond ON/OFF switching, new components with linear multistate analog resistive tuning, nonlinear volatile switching, spiking, oscillatory, stochastic and other complex functionalities could enable highly efficient neuromorphic computing schemes for AI information processing. Compared to the extreme multifunctionality of biological neurons, realizing all the above characteristics in a single, scalable analog component remains a grand challenge. Here we investigate electrochemical gating combined with localized thermal activation to program and switch a single, vertically integrated and dimensionally scaled electrothermal chemical random access memory (ETCRAM) with a channel and reservoir composed of phase-separated vanadium oxide. Closely related to electrochemical RAM (ECRAM), ETCRAM uses an integrated gate-heater electrode to overcome kinetic barriers that help retain states at ambient temperatures. In addition to synapse-like stable and programmable analog resistance states arising from redox-tunable phase coexistence, a single component exhibits neuron-like nonlinear conductance switching with a tunable threshold and self-driven dynamics owing to the thermally driven metal-insulator phase transition in vanadium dioxide. More broadly, we demonstrate that electrochemically stabilized phase coexistence could unlock analog electronics with novel functionality, stability, reconfigurability, and scalability.

Oh, Sangheon [Sandia National Lab. (SNL-CA), Liver↗

NF-κB perturbation reveals unique immunomodulatory functions in Prx1 + fibroblasts that promote development of atopic dermatitis

Skin is composed of diverse cell populations that cooperatively maintain homeostasis. Up-regulation of the nuclear factor κB (NF-κB) pathway may lead to the development of chronic inflammatory disorders of the skin, but its role during the early events remains unclear. Here, through analysis of single-cell RNA sequencing data via iterative random forest leave one out prediction, an explainable artificial intelligence method, we identified an immunoregulatory role for a unique paired related homeobox-1 (Prx1) + fibroblast subpopulation. Disruption of Ikkb–NF-κB under homeostatic conditions in these fibroblasts paradoxically induced skin inflammation due to the overexpression of C-C motif chemokine ligand 11 (CCL11; or eotaxin-1) characterized by eosinophil infiltration and a subsequent T H 2 immune response. Because the inflammatory phenotype resembled that seen in human atopic dermatitis (AD), we examined human AD skin samples and found that human AD fibroblasts also overexpressed CCL11 and that perturbation of Ikkb–NF-κB in primary human dermal fibroblasts up-regulated CCL11. Monoclonal antibody treatment against CCL11 was effective in reducing the eosinophilia and T H 2 inflammation in a mouse model. Together, the murine model and human AD specimens point to dysregulated Prx1 + fibroblasts as a previously unrecognized etiologic factor that may contribute to the pathogenesis of AD and suggest that targeting CCL11 may be a way to treat AD-like skin lesions.

60 APPLIED LIFE SCIENCES↗

Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort

The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 “critical” (in the intensive care unit under mechanical ventilation) and 25 “non-critical” (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The critical importance of software for HEP

Particle physics has an ambitious and broad global experimental programme for the coming decades. Large investments in building new facilities are already underway or under consideration. Scaling the present processing power and data storage needs by the foreseen increase in data rates in the next decade for HL-LHC is not sustainable within the current budgets. As a result, a more efficient usage of computing resources is required in order to realise the physics potential of future experiments. Software and computing are an integral part of experimental design, trigger and data acquisition, simulation, reconstruction, and analysis, as well as related theoretical predictions. A significant investment in computing and software is therefore critical. Advances in software and computing, including artificial intelligence (AI) and machine learning (ML), will be key for solving these challenges. Making better use of new processing hardware such as graphical processing units (GPUs) or ARM chips is a growing trend. This forms part of a computing solution that makes efficient use of facilities and contributes to the reduction of the environmental footprint of HEP computing. The HEP community already provided a roadmap for software and computing for the last EPPSU, and this paper updates that, with a focus on the most resource critical parts of our data processing chain.

97 MATHEMATICS AND COMPUTING↗

Scanning Probe Microscopy in the Information Age

Scanning probe microscopy (SPM) has brought scientific exploration, visualization, and control to nanoscale. A plethora of measurement approaches and techniques devised around SPM enabled probing structure and functionalities crucial for virtually all areas of science. While high-resolution electron microscopy techniques preceded scanning probes, SPM effectively opened the door to probing the structure–property relationship on length scales spanning 100s of micrometers down to a single atom. As the complexity of the material systems and the scientific questions increased, so too did the SPM techniques. Substantial efforts have been dedicated toward the development of better instrumentation platforms, probes, and novel spectroscopic measurements; however, many opportunities related to data processing and acquisition in SPM are just being realized now. This chapter will describe the recent progress in data-driven SPM by giving a broad overview of the field, the foundation of the scanning tunneling microscope (STM) and the atomic force microscope (AFM), as well as a description behind the operating principles and dynamic modes. A comprehensive overview of the multi-frequency techniques, Band excitation, and general acquisition mode SPM is given, setting the context for the application of big data, machine learning, and artificial intelligence in the field of dynamic SPM.

Collins, Liam↗