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At least 757 records · Page 42

Establishing Data Analysis Pipeline for Bulk ATAC-Seq Datasets

We developed an analysis pipeline for transposase-accessible chromatin sequencing (ATAC-Seq) data derived from bulk samples, which brings together publicly available R packages in addition to command-line tools designed for analysis of bulk ATAC-Seq data and can be run on any computer running a Linux-like operating system such as Ubuntu or Apple OSX.

97 MATHEMATICS AND COMPUTING↗

Cyber Halo Innovation Research Program (CHIRP) Handbook: CHIRP Program Document 2026

The Cyber Halo Innovation Research Program (CHIRP) handbook outlines a comprehensive framework designed to advance space cybersecurity education, workforce development, recruitment efforts for United States Space Force (USSF) Space Systems Command (SSC) and the Department of the Airforce, and foster students’ professional growth. It provides an overview of CHIRP's objectives and strategic focus, establishing the foundation for participant engagement through a network of collaborations with academic institutions, contracted industry partners, training and certification organizations, federal agencies, and community organizations. It states a clear participation strategy for SSC and Pacific Northwest National Laboratory (PNNL) for program execution and successful support for student transition to a career in space cybersecurity.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

AutoSAC-Automated Sample Activation Calculation on VULCAN

AutoSAC is an automated python program to conduct sample activation calculation immediately after neutron scattering experiment on VULCAN. AutoSAC takes account of sample dimensions, compositions, forms, sample environments, neutron beam configurations, neutron scattering history, and proton charged resolved beam power etc., and uses a simplified method to rapidly estimate the radioactivity at end of beam or after. It generates a draft report per sample and repository of radioactivity per measurement and provides feedback of current radioactivity and decay time back to a neutron proposal Slack channel to inform users immediately on sample handling. It also utilizes either the sample note field in EPICS or sample composition or thickness correction and takes slack prompt or command to conduct post-beam SAC by demand. The program can be shared to be used in other beamlines at spallation neutron source with modified instrument configurations including instrument specific characteristic beam fluxes.

An, Ke [Oak Ridge National Laboratory (ORNL), Oak ↗

Graphical User Interface for a Biasing Board for the PSEC6

The PSEC6 is an application-specific integrated circuit (ASIC) designed for a readout system for a large area picosecond photodetector (LAPPD). The PSEC6 is currently in fabrication and pending testing. The testing system for the PSEC5, the previous iteration of the ASIC, required expensive and non-portable equipment, because the ASIC needs twelve adjustable reference voltages. The new testing system consists of an low-cost, open-source, cross-platform graphical user interface (GUI), a digital system, and a biasing board. The digital system is the interface between the GUI and biasing board, and can be implemented on a microcontroller or field-programmable gate array (FPGA). The biasing board contains twelve digital-to-analog converters (DACs) that are configurable via the GUI, which gives users the ability to write voltage values to all or specific DACs. The GUI was developed in C on Linux using the widget library GTK4 and cross-compiled for Windows compatibility. I2C and SPI protocols were implemented on an Adafruit Feather ESP32-S3 microcontroller to write commands to the DACs and PSEC6. A hardware implementation of the I2C protocol is in development on an FPGA. Since LAPPDs will be used by the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) at Fermilab, the PSEC6 testing system in this internship project can potentially benefit future neutrino research. The project is relevant to the Department of Energy’s microelectronics mission, because the PSEC6 is an ASIC that will handle fast time signals arriving from the detector for readout. It also provided experience with building a cross-platform user interface, practicing digital design and implementation in hardware description language (HDL), and using simulations to inform new design iterations.

Guerrero, Sasha Camila [North Central Coll.]↗

Conversational Grid Storage: Bridging Rucio and LLMs with Model Context Protocol

Experiments at Fermilab use Rucio to handle datasets that can be up to exabyte scale. However, navigating through Rucio’s syntax-heavy Command Line Interface (CLI) is a major workflow obstruction for researchers who just want to check quotas, track data identifiers (DIDs), or locate data sets. This project introduces a natural language interface. By building a containerized Model Context Protocol (MCP) server, an AI agent is created that translates plain English queries into data operations.

Akella, Kashyap [Fermilab; Illinois U., Urbana (ma↗

Cyber Halo Innovation Research Program (CHIRP) Student Research Report: Program Analysis

The Cybersecurity and Space Systems Research Program (CHIRP) conducted multi-year, mission-focused research addressing emerging cybersecurity challenges affecting space and ground systems. Students from California State University San Bernardino (CSUSB), University of Texas El Paso (UTEP), and California State University Dominguez Hills (CSUDH) conducted structured research, developed proof-of-concept demonstrations, participated in applied cybersecurity training, and collaborated with Space Systems Command (SSC), academic, and industry partners. This report documents the research questions, methodologies, findings, demonstrations, and student contributions associated with each cohort. It also summarizes the program’s workforce-development outcomes, including applied cybersecurity training, professional certifications, technical credentials, and partnerships with organizations such as CT Cubed, Inc. and ISC2. Collectively, CHIRP strengthened the space-cybersecurity workforce pipeline and produced research and prototype efforts that may inform future cybersecurity assessments, test and evaluation activities, cyber-range development, acquisition planning, operational training, and mission-assurance initiatives.

McKenzie, Penny L.↗

Automated tape-target centering based on template matching for construction measurement tasks using robotic total station

Robotic total stations have transformed surveying and construction mapping through precise, efficient, and automated measurements. These instruments integrate a theodolite, which measures horizontal and vertical angles, with an electronic distance measurement (EDM) unit to determine distances, allowing accurate 3D measurement of observable points. Traditionally, users manually aimed the total station at a target. Recent advancements in robotic motor control and integration of cameras now enable automatic rotation and aiming, typically requiring only a single operator to position the target. Automated aiming is commonly performed using retroreflector prisms, which reflect light back to the source with minimal scattering, enabling high-precision measurements over long distances. However, retroreflectors, especially those designed for 360 degree, can be expensive and impractical for certain applications. This paper presents an algorithm for automating the center detection of low-cost disposable tape targets using the total station's onboard camera and a template matching algorithm. The algorithm identifies the target's center pixel in the image, and the instrument is commanded to aim at that location. We evaluated the performance of this template-matching-based centering method under various distances, angles, lighting conditions, and field environments, comparing its results to both manual aiming and conventional automated aiming of tape targets. Manual aiming was used as the baseline operational reference in the absence of an independent ground-truth measurement. The proposed approach achieves target centering results comparable to the manual baseline. This method provides a cost-effective alternative for high-precision applications where retroreflector targets are constrained by budget or logistics.

Harrington, Joshua [ORNL]↗

Design, Selection, and Evaluation of Reinforcement Learning Single Agents for Ground Target Tracking

Previous approaches for small fixed-wing unmanned air systems that carry strapdown rather than gimbaled cameras achieved satisfactory ground target tracking performance using both standard and deep reinforcement learning algorithms. However, these approaches have significant restrictions and abstractions to the dynamics of the vehicle, such as constant airspeed and constant altitude, because the number of states and actions was necessarily limited. Thus, extensive tuning was required to obtain good tracking performance. The expansion from 4 state–action degrees of freedom to 15 enabled the agent to exploit previous reward functions that produced novel yet undesirable emergent behavior. This paper investigates the causes of and various potential solutions to undesirable emergent behavior in the ground target tracking problem. A combination of changes to the environment, reward structure, action space simplification, command rate, and controller implementation provides insight into obtaining stable tracking results. Consideration is given to reward structure selection and refinement to mitigate undesirable emergent behavior. Results presented in the paper for a simulated environment of a single unmanned air system tracking a randomly moving single ground target show that a soft actor–critic algorithm can produce feasible tracking trajectories without limiting the state space and action space, provided that the environment is properly posed.

Engineering↗

Data for The utility of transfer learning to improve the performance of deep learning in axon segmentation

The utility of transfer learning to improve the performance of deep learning in axon segmentation Data Data: All the input and labeled volumes tf-logs: Tensorflow logs, view with command "tensorboard --logdir [name of folder]" Model Weights: model_weights: the argument list under variable combo indicate 1) no oversampling, 2) no rotation, 3) no learn scheduler, and 4) flipping on all three dimensions, and the additional values indicate 5) elastic deformation percentage, 6) rotate deformation percentage, 7) layer setting , 8) learning rate, and 9) training/validation/test data division suffix (leave '' if not using suffix). Results: Output from inference segment_total_results_validation_final: All validation results and calculations segment_total_results: All test results and calculations Authors The modified code was created for a paper by: Marjolein Oostrom, Michael A. Muniak, Rogene Eichler West, Sarah Akers, Paritosh Pande, Moses Obiri, Wei Wang, Kasey Bowyer, Zhuhao Wu, Lisa Bramer, Tianyi Mao, Bobbie Jo Webb-Robertson The work is adapted from Github TrailMap, which was created by Albert Pun and Drew Friedmann Acknowledgments MO, RMEW, SA, MO, LB, BJWR were supported by the Laboratory Directed Research and Development at Pacific Northwest National Laboratory (PNNL), a Department of Energy facility operated by Battelle under contract DE-AC05-76RLO01830. WW, KB, and ZW were supported in part by a NIH/BRAIN Initiative Grant RF1MH128969. MAM and TM were supported by two NIH/BRAIN Initiative Grants R01NS104944, RF1MH120119 and NIH R01NS081071. This research is affiliated with the Pacific northwest bioMedical Innovation Co-laboratory (PMedIC) collaboration between OHSU and PNNL.

Oostrom, Marjolein T↗

DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface and command-line tool for high-dimensional mass spectrometry data analysis workflows, offering ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation: algorithm implementations utilize all dimensions simultaneously to (i) offer greater separation between features, improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS data, demonstrating the advantages of a multidimensional approach in each data processing step.

Colby, Sean M↗

Management of Digital Equipment in Preproduction by Means of Uniform Numeric Control Language

The requirements on preproduction and the control software for various digital machining systems (numerically controlled machine tools, robot manipulators, additive manufacturing equipment) in flexible production are considered. By analysis of existing programming languages for digital equipment, UNCL (Uniform Numeric Control Language) has been developed for standard representation of control commands. The use of UNCL in verifying program operation on a machining simulator is considered. Software for the translation of control programs (specified in CLDATA formats and in ISO code) to the invariant format of the universal language is described. The postprocessing of control software from the universal language into programs in commonly used digital control systems is also considered.

42 ENGINEERING↗

Controlling the State of Machine Tools

Globally, manufacturers make great efforts to maintain the performance of industrial equipment. Developers and researchers are interested in automated approaches to maintaining the performance of equipment, especially at enterprises with high degrees of computerization and comprehensive information systems. In the present work, a new approach is outlined: an autonomous control system for maintaining the condition of metal-cutting machines. This approach is based on prior work in the field and permits maintenance on the basis of autonomous control of the state of machine tools. The structure of a system with the following generalized control functions is presented: decision making; and the issuing of commands on the basis of built-in resources. The formulation of control decisions employs the theory of fuzzy sets and fuzzy logic. By means of the ANFIS fuzzy network system, the autonomy of state control of the machine tool may be assessed. Criticality assessment of the condition of machine tools and their components is important in making decisions as to the setup of systems controlling the condition of equipment at enterprises, with assessment of their efficiency. In the monitoring subsystem, provision is made for assessment of the diagnostic results, prediction, and the generation of control decisions so as to prevent disruptions of machine-tool operation.

42 ENGINEERING↗

Teaching Computational Reproducibility for Neuroimaging

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MR scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science.

60 APPLIED LIFE SCIENCES↗

Beyond the Toolpath: Site-Specific Melt Pool Size Control Enables Printing of Extra-Toolpath Geometry in Laser Wire-Based Directed Energy Deposition

A variety of techniques have been utilized in metal additive manufacturing (AM) for melt pool size management, including modeling and feed-forward approaches. In a few cases, closed-loop control has been demonstrated. In this research, closed-loop melt pool size control for large-scale, laser wire-based directed energy deposition is demonstrated with a novel modification, i.e., site-specific changes to the controller setpoint were commanded at trigger points, the locations of which were generated by the projection of a secondary geometry onto the primary three-dimensional (3D) printed component geometry. The present work shows that, through this technique, it is possible to print a specific geometry that occurs beyond the actual toolpath of the print head. This is denoted as extra-toolpath geometry and is fundamentally different from other methods of generating component features in metal AM. A proof-of-principle experiment is presented in which a complex oak leaf geometry was embossed on an otherwise ordinary double-bead wall made from Ti-6Al-4V. The process is introduced and characterized primarily from a controls perspective with reports on the performance of the control system, the melt pool size response, and the resulting geometry. The implications of this capability, which extend beyond localized control of bead geometry to the potential mitigations of defects and functional grading of component properties, are discussed.

36 MATERIALS SCIENCE↗

Deep Reinforcement Learning for Autonomous Water Heater Control

Electric water heaters represent 14% of the electricity consumption in residential buildings. An average household in the United States (U.S.) spends about USD 400–600 (0.45 ¢/L–0.68 ¢/L) on water heating every year. In this context, water heaters are often considered as a valuable asset for Demand Response (DR) and building energy management system (BEMS) applications. To this end, this study proposes a model-free deep reinforcement learning (RL) approach that aims to minimize the electricity cost of a water heater under a time-of-use (TOU) electricity pricing policy by only using standard DR commands. In this approach, a set of RL agents, with different look ahead periods, were trained using the deep Q-networks (DQN) algorithm and their performance was tested on an unseen pair of price and hot water usage profiles. The testing results showed that the RL agents can help save electricity cost in the range of 19% to 35% compared to the baseline operation without causing any discomfort to end users. Additionally, the RL agents outperformed rule-based and model predictive control (MPC)-based controllers and achieved comparable performance to optimization-based control.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Study of Integrated Signal and Power Transfer for Compact Isolated SiC MOSFET Gate-Drivers

This work discusses a novel set of alternate implementations of isolated gate driver circuits for power electronic transistors. The proposed topologies for the driver have been designed specifically for SiC power MOSFET. Three different solutions are discussed, all of them providing the required gate turn-on and turn-off command signal with galvanic isolation, but also supplying power to the secondary side of the driver by means of magnetic transformers. The resulting solutions, all of them implemented with simple circuitry, enable the integration of the driver into the power cell, allowing for theoretical higher power density values in the final system. The principle of operation of the different solutions is discussed, and then the main relevant implementation details are presented. After that, the operation of the circuits is demonstrated experimentally, by testing a set of prototypes of these drivers. This provides a comprehensive design example that assesses the feasibility of the proposed solutions. Finally, the main results of the performance of the three gate drivers, on an SiC MOSFET-based prototype are presented and compared.

42 ENGINEERING↗

Development of a Control Platform for a Building-Scale Hybrid Solar PV-Natural Gas Microgrid

Building-scale microgrids are a type of behind-the-meter microgrids where the building operator has control of the distributed energy resources, including, in this case, a natural gas-fired microturbine in addition to solar PV and battery energy storage systems. There is a growing trend in deploying behind-the-meter microgrids due to their benefits including the resiliency of serving critical loads, especially in regions with abundant natural gas. In order to ensure distributed energy resources are dispatched optimally for the desired mode of operation, a hierarchical control platform including a centralized controller was developed and installed. The platform includes communication and control infrastructure that interface with controllers for distributed energy resources and the building automation system of a recently built energy efficient commercial building. Based on desirable outcomes under different grid and building conditions, operational modes were defined for the microgrid controller. The controller is programmed to map each mode to respective operational modes for distributed energy resources controllers. Experimental data for test runs corresponding to two operational modes confirm the communication and control infrastructure can execute hierarchical control commands. Finally, dispatch optimization for a year-long simulation of system operation is presented and the benefits of the hybrid solar PV-natural gas setup are evaluated.

Energy & Fuels↗