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At least 433 records · Page 24

Directed Evolution of an Adenylation Domain Alters Substrate Specificity and Generates a New Catechol Siderophore in Escherichia coli

Nonribosomal peptide synthetases (NRPS) biosynthesize numerous natural products with therapeutic, agricultural, and industrial significance. Reliably altering substrate selection in these enzymes has been a longstanding goal, as this would enable the production of tailor-made peptides with desired activities. In this study, the NRPS EntF and the associated biosynthesis of the siderophore enterobactin (ENT) were used as a model system to interrogate substrate selection by an adenylation (A) domain. We employed a directed evolution pipeline that harnesses an in vivo genetic selection for siderophore production to alter A domain substrate selection. Surprisingly, this led to the formation of a new, physiologically active catechol siderophore in Escherichia coli. We characterized the enzyme variants in vitro and demonstrated transferability of our findings to the well-studied TycC and GrsB NRPSs. Furthermore, this work identifies critical binding pocket residues that allow for altered substrate selection in our model system and expands upon our understanding of iron acquisition in E. coli.

59 BASIC BIOLOGICAL SCIENCES↗

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO 2 via beta oxidation and the oxidative Wood–Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps.

59 BASIC BIOLOGICAL SCIENCES↗

Catalyst: Fast and flexible modeling of reaction networks

We introduce Catalyst.jl, a flexible and feature-filled Julia library for modeling and high-performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating stochastic chemical kinetics (jump process), chemical Langevin equation (stochastic differential equation), and reaction rate equation (ordinary differential equation) representations for CRNs. Through comprehensive benchmarks, we demonstrate that Catalyst simulation runtimes are often one to two orders of magnitude faster than other popular tools. More broadly, Catalyst acts as both a domain-specific language and an intermediate representation for symbolically encoding CRN models as Julia-native objects. This enables a pipeline of symbolically specifying, analyzing, and modifying CRNs; converting Catalyst models to symbolic representations of concrete mathematical models; and generating compiled code for numerical solvers. Leveraging ModelingToolkit.jl and Symbolics.jl, Catalyst models can be analyzed, simplified, and compiled into optimized representations for use in numerical solvers. Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid Design and Engineering of Smart and Secure Microbiological Systems (Final Report)

The design and application of successfully engineered biosystems requires an understanding of how engineered microbes will interact with other organisms – either as one-on-one competitors or in the context of microbial consortia. Engineering microorganisms from first principles for non-laboratory, environmental applications is inherently challenging because: (1) engineered systems tend to quickly revert back to their wild-type behaviors; and (2) these systems typically pay a price in reduced fitness, making them uncompetitive against invasive contaminating species (i.e., metabolic burden). For this project, we used a synthetic biology-based strategy to investigate the organization, control, stabilization, and destabilization of natural and engineered microbes. This approach enabled development of (1) single-strain systems capable of detecting and responding to target organisms in the environment; (2) a pipeline for refining and engineering biological constructs in new, non-model host organisms; and (3) improved systems for rapidly designing, engineering, and assaying new biological modules. This coupled approach to safeguard system design is predictable and portable across bacterial species and is focused on microbes that are part of the beneficial plant microbiome. A long-term goal beyond the proposed research is to enable the rational engineering of microbial communities based on first principles of biological design that mimic the smart performance of microorganisms observed in natural systems.

59 BASIC BIOLOGICAL SCIENCES↗

Prediction of Silicon Content in a Blast Furnace via Machine Learning: A Comprehensive Processing and Modeling Pipeline

Silicon content plays an important role in determining the operational efficiency of blast furnaces (BFs) and their downstream processes in integrated steelmaking; however, existing sampling methods and first-principles models are somewhat limited in their capability and flexibility. Current data-based prediction models primarily rely on a limited set of manually selected furnace parameters. Additionally, different BFs present a diverse set of operating parameters and state variables that are known to directly influence the hot metal’s silicon content, such as fuel injection, blast temperature, and raw material charge composition, among other process variables that have their own impacts. The expansiveness of the parameter set adds complexity to parameter selection and processing. This highlights the need for a comprehensive methodology to integrate and select from all relevant parameters for accurate silicon content prediction. Providing accurate silicon content predictions would enable operators to adjust furnace conditions dynamically, improving safety and reducing economic risk. To address these issues, a two-stage approach is proposed. First, a generalized data processing scheme is proposed to accommodate diverse furnace parameters. Second, a robust modeling pipeline is used to establish a machine learning (ML) model capable of predicting hot metal silicon content with reasonable accuracy. The method employed herein predicted the average Si content of the upcoming furnace cast with an accuracy of 91% among 200 target predictions for a specific furnace provisioned by the XGBoost model. This prediction is achieved using only the past shift’s operating conditions, which should be available in real time. This performance provides a strong baseline for the modeling approach with potential for further improvement through provision of real-time features.

Chemistry↗

The FRB-searching Pipeline of the Tianlai Cylinder Pathfinder Array

This paper presents the design, calibration, and survey strategy of the Fast Radio Burst (FRB) digital backend and its real-time data processing pipeline employed in the Tianlai Cylinder Pathfinder Array. The array, consisting of three parallel cylindrical reflectors and equipped with 96 dual-polarization feeds, is a radio interferometer array designed for conducting drift scans of the northern celestial semi-sphere. The FRB digital backend enables the formation of 96 digital beams, effectively covering an area of approximately 40 square degrees with the 3 dB beam. Our pipeline demonstrates the capability to conduct an automatic search of FRBs, detecting at quasi-real-time and classifying FRB candidates automatically. The current FRB searching pipeline has an overall recall rate of 88%. During the commissioning phase, we successfully detected signals emitted by four well-known pulsars: PSR B0329+54, B2021+51, B0823+26, and B2020+28. We report the first discovery of an FRB by our array, designated as FRB 20220414A. We also investigate the optimal arrangement for the digitally formed beams to achieve maximum detection rate by numerical simulation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Deep-Learning-Based Segmentation of Keyhole in In-Situ X-ray Imaging of Laser Powder Bed Fusion

In laser powder bed fusion processes, keyholes are the gaseous cavities formed where laser interacts with metal, and their morphologies play an important role in defect formation and the final product quality. The in-situ X-ray imaging technique can monitor the keyhole dynamics from the side and capture keyhole shapes in the X-ray image stream. Keyhole shapes in X-ray images are then often labeled by humans for analysis, which increasingly involves attempting to correlate keyhole shapes with defects using machine learning. However, such labeling is tedious, time-consuming, error-prone, and cannot be scaled to large data sets. To use keyhole shapes more readily as the input to machine learning methods, an automatic tool to identify keyhole regions is desirable. In this paper, a deep-learning-based computer vision tool that can automatically segment keyhole shapes out of X-ray images is presented. The pipeline contains a filtering method and an implementation of the BASNet deep learning model to semantically segment the keyhole morphologies out of X-ray images. The presented tool shows promising average accuracy of 91.24% for keyhole area, and 92.81% for boundary shape, for a range of test dataset conditions in Al6061 (and one AliSi10Mg) alloys, with 300 training images/labels and 100 testing images for each trial. Prospective users may apply the presently trained tool or a retrained version following the approach used here to automatically label keyhole shapes in large image sets.

36 MATERIALS SCIENCE↗

Topological Analysis of Temporal Hypergraphs

In this work we study the topological properties of temporal hypergraphs. Hypergraphs provide a higher dimensional generalization of a graph that is capable of capturing multi-way connections. As such, they have become an integral part of network science. A common use of hypergraphs is to model events as hyperedges in which the event can involve many elements as nodes. This provides a more complete picture of the event in comparison to the standard dyadic connection limitation of a graph. However, a common attribution to events is temporal information as an interval for when the event occurred. Consequently, a temporal hypergraph is born which accurately captures both the temporal information of events as well as their multi-way connections. Common tools for studying these temporal hypergraphs typically use summary statistics of snapshots from a sliding window procedure to capture changes in the underlying dynamics. However, these do not provide insight into how the changing structure of the hypergraph evolves and which components of the temporal hypergraph persist and are influential to the underlying system. To alleviate this need we leverage zigzag persistence from the field of Topological Data Analysis (TDA) to study the change in topological structure of time-evolving hypergraphs. We apply our pipeline to both a cyber security and social network dataset and show how the topological structure of their temporal hypergraphs change and can be used to understand the underlying dynamics.

hypergraphs, topological data analysis, zigzag per↗

L-PBF High-Throughput Data Pipeline Approach for Multi-modal Integration

Abstract Metal-based additive manufacturing requires active monitoring solutions for assessing part quality. Multiple sensors and data streams, however, generate large heterogeneous data sets that are impractical for manual assessment and characterization. In this work, an automated pipeline is developed that enables feature extraction from high-speed camera video and multi-modal data analysis. The framework removes the need for manual assessment through the utilization of deep learning techniques and training models in a weakly supervised paradigm. We demonstrate this pipeline’s capability over 700,000 high-speed camera frames. The pipeline successfully extracts melt pool and spatter geometries and links them to corresponding pyrometry, radiography, and processparameter information. 715 individual prints are examined to reveal melt pool areas that exceeds 0.07 mm 2 and pyrometry signal over a threshold (375 pyrometry units) were more likely to have defects. These automated processes enable massive throughput of characterization techniques.

36 MATERIALS SCIENCE↗

Reagent-free Hyperspectral Diagnosis of SARS-CoV-2 Infection in Saliva Samples

Rapid, reagent-free pathogen-agnostic diagnostics that can be performed at the point of need are vital for preparedness against future outbreaks. Yet, many current strategies are pathogen-specific and require several reagents. We present hyperspectral sensing, using light to non-invasively measure the composition of several molecules to form a spectral signature, to overcome these barriers. To generate these spectral signatures, we present the ProSpectral TM V1, a novel, miniaturized hyperspectral platform with high spectral resolution with two mini-spectrometers. Furthermore, we developed state-of-the-art ML pipelines for near real-time analysis of spectral signatures in saliva samples. We found that we could accurately identify SARS-CoV-2 infection status in double-blinded saliva samples and demonstrate 100% accuracy on a hold out test dataset. To our knowledge, this establishes the fastest hyperspectral diagnostic platform and in a small form factor, and executable with liquid samples, without ligands or reagents, all while maintaining PCR level specificity and sensitivity.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitivity of Next-Generation CMB Surveys to Neutrinos and Other Light Relics

Neutrinos and other light relics leave characteristic imprints in the cosmic microwave background anisotropies, making their observation a sensitive probe of the particle content and thermal history of the early universe. The energy density in these relativistic species is parameterized by their effective number $N_\mathrm{eff}$. Measuring this parameter at the percent level, which is a long-standing science goal of CMB-S4 and other experiments, would test a wide range of well-motivated physics within and beyond the Standard Model of particle physics. In this paper, we present Fisher-matrix forecasts of the projected sensitivity to $N_\mathrm{eff}$ of several CMB-S4 survey configurations considered during its extensive design phase. The conceptual design reaches $σ(N_\mathrm{eff}) < 0.03$ over its seven-year observing period, while the revised configuration achieves the same precision over a longer timescale. We complement these results with a cosmic-variance-limited survey over the same multipole range to quantify the room for improvement accessible with additional instrumental, observational, and theoretical efforts. Finally, we discuss the broad implications of precise $N_\mathrm{eff}$ measurements for the radiation sector, big bang nucleosynthesis, light thermal relics, and other early-universe physics. The forecasts presented in this work are performed with the publicly released DRAFT (Dark Radiation Anisotropy Flowdown Team) tool. It provides an end-to-end pipeline from simulated foreground maps and component separation to delensing and projected sensitivities for any cosmological parameter, and it can be directly applied to other cosmic microwave background survey designs.

Trendafilova, Cynthia [Case Western Reserve U., CE↗

Relating Molecular Properties to the Persistence of Marine Dissolved Organic Matter with Liquid Chromatography–Ultrahigh-Resolution Mass Spectrometry

Marine dissolved organic matter (DOM) contains a complex mixture of small molecules that eludes rapid biological degradation. Spatial and temporal variations in the abundance of DOM reflect the existence of fractions that are removed from the ocean over different time scales, ranging from seconds to millennia. However, it remains unknown whether the intrinsic chemical properties of these organic components relate to their persistence. Here, we elucidate and compare the molecular compositions of distinct DOM fractions with different lability along a water column in the North Atlantic Gyre. Our analysis utilized ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry at 21 T coupled to liquid chromatography and a novel data pipeline developed in CoreMS that generates molecular formula assignments and metrics of isomeric complexity. Clustering analysis binned 14 857 distinct molecular components into groups that correspond to the depth distribution of semilabile, semirefractory, and refractory fractions of DOM. The more labile fractions were concentrated near the ocean surface and contained more aliphatic, hydrophobic, and reduced molecules than the refractory fraction, which occurred uniformly throughout the water column. These findings suggest that processes that selectively remove hydrophobic compounds, such as aggregation and particle sorption, contribute to variable removal rates of marine DOM.

54 ENVIRONMENTAL SCIENCES↗

Integration of machine learning with neutron scattering for the Hamiltonian tuning of spin ice under pressure

Quantum materials research requires co-design of theory with experiments and involves demanding simulations and the analysis of vast quantities of data, usually including pattern recognition and clustering. Artificial intelligence is a natural route to optimise these processes and bring theory and experiments together. Here, we propose a scheme that integrates machine learning with high-performance simulations and scattering measurements, covering the pipeline of typical neutron experiments. Our approach uses nonlinear autoencoders trained on realistic simulations along with a fast surrogate for the calculation of scattering in the form of a generative model. We demonstrate this approach in a highly frustrated magnet, Dy 2 Ti 2 O 7 , using machine learning predictions to guide the neutron scattering experiment under hydrostatic pressure, extract material parameters and construct a phase diagram. Our scheme provides a comprehensive set of capabilities that allows direct integration of theory along with automated data processing and provides on a rapid timescale direct insight into a challenging condensed matter system.

36 MATERIALS SCIENCE↗

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

Describing Point Defect Topology in 2D Energy Materials Through Computer Vision

Point defects such as vacancies and impurity atoms strongly impact the performance of 2D materials. Traditional efforts often rely on manual detection, a process that is time-intensive, prone to human error, and challenging to scale. Here we leverage machine learning (ML) methods to identify and quantify vacancies within 2D transition metal carbides (Ti3C2, MXenes), aiming to expedite detection while improving accuracy. MXenes exhibit valuable defect-defined electrochemical properties, but we currently lack statistical understanding of defect topology needed to fully harness these materials. Here we employ a convolutional neural network for semantic segmentation of experimental MXene images, opening an opportunity to conduct a rigorous statistical study on defect hierarchy while investigating local relaxation in the lattice. We show how the integration of ML can yield fundamental insight into point defects, providing a powerful tool that will play an increasingly crucial role in the future of materials science. ML is often not just a matter of straightforward application, and pretrained models proved ineffective in this case. Instead, we trained our own neural network (NN) and applied data augmentation techniques and fine-tuning to the training dataset. Since labeled microscopy data is often scarce, we developed training data from a previously published wide-frame MXene image, using customized Gaussian fitting to locate atomic positions. Our trained model was then applied to a large dataset of experimental images, enabling a statistical study of defect configurations across three samples prepared with different HF etchant concentrations (5%, 9.1%, and 12.5%), as shown in Fig. 1. This also allowed us to investigate local strain around vacancies, though we find that we are limited by the precision of measurements using high-angle annular dark field (HAADF) images, as shown in Fig. 2. This study demonstrates how ML enables large-scale, quantitative analysis of atomic defects - an otherwise infeasible task with traditional methods. While our NN was specialized for Ti3C2 MXenes, the pipeline we developed provides a foundation for future ML models tailored to other materials. Ultimately, we envision embedding the NN onto the microscope to give real-time feedback to the user. To make this a reality, continued work is necessary to fully understand the NN's capabilities and limitations. This study gets one step closer to our goals of automated experimentation moving away from traditional methods of manual labeling. As ML capabilities advance, we hope to continue adapting and applying these techniques in microscopy.

2D materials↗

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI‐driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS‐based multiomics data. While centered on MS‐based omics, this holistic AI‐driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI‐driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems‐level understanding of biological processes and accelerating a myriad of biodiscoveries.

47 OTHER INSTRUMENTATION↗

Irradiation Testing of Sensors - ASI Program Review 2022

This is a powerpoint presentation for the annual Advanced Sensors and Instrumentation (ASI) program webinar. The following is a summary of the presentation. Advanced instrumentation enables testing of nuclear fuels and materials in support of the US advanced nuclear technology industry. A number of promising sensor technologies are in the pipeline. The early part of sensor development can be done outside of the reactor environment, but full technical readiness requires experience gained from in-core performance testing. Customers usually have only one shot to conduct their irradiation experiments. Because of the high costs test sponsors are frequently reluctant to incorporate unproven technologies in reactor experiments. Therefore, it is vital to demonstrate newly-developed sensors in operational conditions, prior to incorporating them into long-term high-value experiments. Successful completion of these activities will create new monitoring capabilities in high-power test reactors (such as ATR) as well as specialty reactors such as TREAT.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The SPAN512 mid-latitude pulsar survey at the Nançay Radio Telescope

The large number of ongoing surveys for pulsars and transients at various radio observatories is motivated by the science obtained from these sources. Timing and polarisation analysis of relativistic binaries can place strong constraints on theories of gravity. The observation of a growing number of millisecond pulsars (MSPs) spread over the celestial sphere may allow the detection of a stochastic gravitational wave background arising from supermassive black hole binaries. A more complete sample of young pulsars improves our knowledge of neutron star birth and evolution. Transients such as fast radio bursts can serve to probe the intergalactic medium. The SPAN512 pulsar survey covers intermediate Galactic latitudes using the L-band receiver of the Nançay Radio Telescope (NRT). The survey covers 224 sq. deg. of the sky for a total exposure time of 2200 h. Population syntheses predict the discovery of 3 to 19 new normal pulsars and a few MSPs. We present detailed modelling of the NRT beam with its L-band receiver and its sensitivity which we used to precisely assess the expected survey yield. We used the flexible Pulsar Arecibo L-band Feed Array data processing pipeline to search the 47 TB of SPAN512 data for pulsars and transients. The SPAN512 survey discovered two new MSPs and one new middle-aged pulsar. We focus on the analysis of the 2.4-ms spin period pulsar J2205+6012 for which we also report the detection of gamma-ray pulsations. Its narrow pulse width (35µs at an observing frequency of 2.55 GHz) allows for sub-microsecond timing precision over 8 yr, with exciting prospects for pulsar timing array programs.

79 ASTRONOMY AND ASTROPHYSICS↗