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At least 343 records · Page 19

SSRS (Stochastic Soaring Raptor Simulator)

SSRS (Stochastic Soaring Raptor Simulator) is a generalizable, probabilistic, and predictive tool for wind energy developers, ecologists, wildlife managers and industry consultants to estimate the potential for soaring raptors to interact with operating wind turbines, without the need for site-specific data collection. Rapid expansion of wind energy development across the world has exposed the risk of turbine collisions for birds and bats. The risk to obligate soaring raptors such as golden eagles is of particular concern due to their small population and influence on ecological balance. Golden eagles rely heavily on updrafts to subsidize their flight, putting them in direct conflict with operational wind turbines that utilize the same wind resource. Understanding the behavior of soaring raptors with varying atmospheric conditions is crucial for predicting and mitigating the risk of turbine collision. This software contains a predictive movement model that simulates individual flight paths of golden eagles during updraft-subsidized long-distance flight, including migration. For a given set of atmospheric conditions, the model simulates thousands of eagles at turbine-scale spatial resolution (50m) to produce a relative presence density map. The simulated eagles rely on updrafts to pursue uninterrupted directional flight with minimal energy expenditure, following fluid-flow principles. The simulator includes a stochastic model of eagle behavior and a systematic method of accounting for spatiotemporal variations in atmospheric conditions. This framework only requires publicly available atmospheric data to estimate orographic and thermal updrafts, ensuring general usability.

Sandhu, Rimple↗

NEMA-Phase Compliant Traffic Signal Controller Module in SUMO

The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp

Wang, Qichao↗

Data Citation Explorer (DCE) v1.0

Increases in sequencing capacity, combined with rapid accumulation of publications and associated data resources, have increased the complexity of maintaining associations between literature and genomic data. As the volume of literature and data have exceeded the capacity of manual curation, automated approaches to maintaining and confirming associations among these resources have become necessary. Here we present the Data Citation Explorer (DCE), which discovers literature incorporating genomic data whether or not provenance was clearly indicated. This service provides advantages over manual curation methods including consistent resource coverage, metadata enrichment, documentation of new use cases, and identification of conflicting metadata. The service reduces labor costs associated with manual review, improves the quality of genome metadata maintained by the U.S. Department of Energy Joint Genome Institute (JGI), and increases the number of known publications that incorporate its data products. The DCE facilitates an understanding of JGI impact, improves credit attribution for data generators, and can encourage data sharing by allowing scientists to see how reuse amplifies the impact of their original studies.

Parker, Charles↗

EyeON

EyeON: Eye on Operational technology Software Supply Chain attacks have risen drastically over the past few years, none more well-known and impactful than the SolarWinds compromise. Criminal organizations inserted an attack vector into a specific version of the source code, giving themselves an air of credibility. Once news broke on SolarWinds, identifying compromised sites was very difficult, even knowing the culprit update. Software Bills of Materials (SBOM) have been touted as the solution to reclaiming control of your software supply chain. Deployment of SBOMs has been slow, however, due to conflicting standards, opaque storage requirements, and vendor adoption. Additionally, the path from obtaining an SBOM and securing your supply chain is unclear; how can an SBOM library be leveraged to provide insight to your attack surface? The EyeON tool, sponsored by Department of Energy Cybersecurity, Energy Security, and Emergency Response (DoE CESER), aims to address these gaps by providing an encapsulated solution to tracking which updates have been installed in an enterprise, and alerting system administrators to vulnerabilities as they become known. Similar to a virus scanner, EyeON is a command line tool to parse either a single file, nested directory structure, or filesystem. It collects data such as signature (hashes), version information, VirusTotal tags, compiler, compilation date, and code signing information. Users will anonymously submit scan data periodically to DoE CESER, who will then compile a database of known software products employed by Critical Infrastructure and broadcast alerts based on discovered flaws as they arise.

Tenzing, Wangmo↗

VerifyIO: Verifying Adherence to Parallel I/O Consistency Semantics

VerifyIO is a tool designed for verifying I/O consistency semantics in High-Performance Computing (HPC) applications. It addresses the challenges of ensuring correctness and portability across different I/O consistency models, such as POSIX, Commit, Session, and MPI-IO. By analyzing execution traces, detecting conflicts, and verifying synchronization adherence, VerifyIO provides actionable insights for both application developers and I/O library designers.

Wang, Chen [Lawrence Livermore National Laboratory↗

py-boomer v0.1.0

Py-BOOMER (Python Bayesian OWL Ontology MErgER in Python) is a probabilistic reasoning system for knowledge representation and ontological reasoning with uncertainty. Itnables reasoning over probabilistic facts and taxonomic relationships, finding the most likely consistent interpretation of potentially conflicting assertions. It uses a combination of graph-based reasoning and Bayesian probabilistic inference. Key features: Represent probabilistic ontological statements Reason over class subsumption hierarchies Evaluate class equivalence relationships Detect and resolve logical inconsistencies Calculate posterior probabilities for each assertion

Mungall, Chris [Lawrence Berkeley National Laborat↗

AQDrop Quantum Service (AQDrop) v1.0

AQDrop is a job management system designed to streamline access to the Advanced Quantum Testbed (AQT) at NERSC (National Energy Research Scientific Computing Center). It serves as a centralized middleware layer between researchers and quantum processing hardware. Key Features: AQDrop provides a FastAPI-based server backed by PostgreSQL for job submission, queue management, and role-based access control (members, operators, and administrators). Users submit Qiskit circuits via JSON payloads, which are queued, dispatched to the QPU through the Qubic API, and returned as measurement counts. A Python client library and web dashboard round out the interface options. Primary Use: Researchers submit quantum circuit jobs from a laptop or login node; an operator client executes those jobs on the AQT's physical QPU and returns results — all coordinated through the central API. Advantages: Compared to ad-hoc or direct hardware access, AQDrop adds structured queue management, auditable job-status tracking and OAuth2 authentication — reducing scheduling conflicts and unauthorized access. Its containerized deployment also improves reproducibility and scalability. Overall, AQDrop functions as a purpose-built quantum job broker tailored to NERSC's specific hardware and institutional access requirements.

Caplinger, Evan [Lawrence Berkeley National Labora↗

Lightfall v0.0.1

Lightfall is a desktop application for synchrotron beamline instrument control, data acquisition, and live analysis at the Advanced Light Source (ALS). Built on Python and Qt, it provides a native graphical interface for operating beamline hardware, configuring and executing experimental scans, and visualizing results in real time. Key features include direct integration with EPICS control systems, a built-in electronic logbook, remote beamline access over secure tunnels, and an interprocess communication (IPC) architecture that coordinates with external analysis applications via ZMQ and EPICS process variables. This IPC approach allows Lightfall to orchestrate specialized analysis tools—including GPU-accelerated streaming correlators—without embedding them, avoiding the dependency conflicts common in monolithic scientific software platforms. Compared to prior approaches such as Xi-CAM's plugin-based architecture, Lightfall's design cleanly separates instrument control from domain-specific analysis, enabling feedback-driven acquisition where live analysis results can adjust scan parameters during an experiment. Its native Qt interface provides responsive performance for real-time data visualization that web-based alternatives struggle to match. Lightfall is designed for use by beamline scientists and staff operating synchrotron instruments at national user facilities.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

Contrasting Trends in Colorado Fire Weather Index from Reanalysis and Observations

Recent wildfires in Colorado raise the question of whether rising global temperatures have increased fire weather occurrences in Colorado. The U.S. National Weather Service defines fire weather as when “forecast weather conditions will result in a significant threat for the ignition and/or spread of wildfires.” We use two datasets to address the question: “How has the occurrence of fire weather changed in Colorado?” Using 22 years of observed weather conditions from a meteorological tower at the National Renewable Energy Laboratory and 67 years of ERA5 reanalysis data, we assess changing trends in Colorado fire weather as defined by hot, dry, and windy conditions. Additionally, we explore if the difference in recorded wind speeds between observational data and reanalysis data can be explained by differences in spatial and temporal resolution and what are the implications in the context of quantifying fire weather occurrences. The observational data are limited in temporal extent and spatial representativeness, but they capture exact real-world conditions at a location in complex terrain. The reanalysis data are available for an extended period of time and for the entire state, but the data are of relatively coarse spatial and temporal resolution and may fail to capture extremes. To quantify fire risk, we calculate the hot–dry–windy index (HDWI), which relies on wind speed and vapor pressure deficit. No statistically significant trend in the HDWI appears in the observational dataset. However, according to the reanalysis data, strong increasing trends in HDWI values emerge across all of Colorado. This apparent conflict between observational and reanalysis data suggests that reanalysis data may not be representative. Further, more long-term observational datasets are required to assess fire risk.

17 WIND ENERGY↗

Reliability of Open Public Electric Vehicle Direct Current Fast Chargers

The aim was to systematically evaluate the usability of all public electric vehicles (EV) direct current fast chargers (DCFC) in the San Francisco region. To achieve a rapid transition to EVs, a highly reliable and easy to use charging infrastructure is critical to building confidence among consumers. The functionality and usability of all 182 open, public DCFC charging stations with CCS connectors (combined charging system) in the 9 counties of the Bay Area were tested (655 electric vehicle service equipment (EVSE) ports). An EVSE was classified as functional if it charged an EV for 2 minutes. Overall, 73.3% of the 655 EVSEs were functional. The causes of the nonfunctioning EVSEs (23.5%) were blank or unresponsive screens or error messages; payment system failures; charge initiation failures; network failures; or broken connectors. In addition, the cable was too short to reach the EV inlet for 3.2% of the EVSEs. A random sampling of 10% of the EVSEs, approximately 8 days after the first evaluation, found no overall change in functionality. The level of functionality found with field testing conflicts with the 95–98% uptime reported by the EV service providers (EVSPs) who operate the EV charging stations. There is a need for precise and verifiable definitions of uptime, downtime, and excluded time, as applied to public EV chargers. In conclusion, the level of failure of the existing public EV DCFC charge infrastructure highlights the importance of improving the system design and maintenance to improve adoption of EVs.

33 ADVANCED PROPULSION SYSTEMS↗

Commercial Vehicle Driver Behaviors and Decision Making: Lessons Learned from Urban Ridealongs

As e-commerce and urban deliveries spike, cities grapple with managing urban freight more actively. In order to effectively manage urban deliveries, city planners and policy makers need to better understand driver behaviors and the challenges they experience in performing deliveries. In this study, we collected data on commercial vehicle (CV) driver behaviors by performing ridealongs with various logistics carriers. Ridealongs were performed in Seattle, Washington, covering a range of vehicles (cars, vans, and trucks), goods (parcels, mail, beverages, and printed materials), and customer types (residential, office, large and small retail). Observers collected qualitative observations and quantitative data on trip and dwell times, while also tracking vehicles through GPS devices. The results showed that, on average, urban CVs spent 80 percent of their daily operating time parked. The study also found that, unlike the common belief, drivers (especially those operating heavier vehicles) parked in authorized parking locations, with only less than 5 percent of stops occurring in the travel lane. Dwell times associated with authorized parking locations were significantly longer than those of other parking locations, and mail and heavy goods deliveries generally had longer dwell times. We also identified three main criteria CV drivers used for choosing a parking location: avoiding unsafe maneuvers, minimizing conflicts with other users of the road, and coopetition with other commercial drivers. Here, the results provide estimates for trip times, dwell times, and parking choice types, as well as insights into why those decisions are made and the factors affecting driver choices.

33 ADVANCED PROPULSION SYSTEMS↗

Metatranscriptomic dynamics after Verticillium dahliae infection and root damage in Olea europaea

Background: The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt, which causes substantial economic losses in numerous areas. We analyzed metatranscriptomic samples taken from a previous study conducted on leaves and roots of Olea europaea that were infected with Verticillium dahliae. In addition, we also analyzed mechanically damaged roots. The aim of our approach is to describe the dynamics of the root microbiome after severe perturbations. Results: Our results not only describe the dynamics of the microbial community associated with the disturbance, but also show the high complexity of these systems and explain how this can lead to a conflicting assignment of the various types of parasitism observed in a specific organism. Conclusions: Our findings indicate that this infection, although led by Verticillium, is driven not by a single species, but by a polymicrobial consortium that also includes natural endophytes of the olive tree. This community contains both biotrophic and necrotrophic organisms that alternate and live together during the infection. In addition, opportunistic organisms appear that take profit not from plant tissues, but from new emerging populations of microorganisms. Therefore, this system can be described as a complex biological system composed of different interacting communities. Notably, our work has important considerations when it comes to classifying the type of parasitism of a given species.

Verticillium dahliae↗

Designing a Framework for Solving Multiobjective Simulation Optimization Problems

Multiobjective simulation optimization (MOSO) problems are optimization problems with multiple conflicting objectives, where evaluation of at least one of the objectives depends on a black-box numerical code or real-world experiment, which we refer to as a simulation. Whereas an extensive body of research is dedicated to developing new algorithms and methods for solving these and related problems, it is challenging and time-consuming to integrate these techniques into real-world production-ready solvers. This is partly because of the diversity and complexity of modern state-of-the-art MOSO algorithms and methods and partly because of the complexity and specificity of many real-world problems and their corresponding computing environments. The complexity of this problem is only compounded when introducing potentially complex and/or domain-specific surrogate-modeling techniques, problem formulations, design spaces, and data acquisition functions. Here, this paper carefully surveys the current state of the art in MOSO algorithms, techniques, and solvers, as well as problem types and computational environments where MOSO is commonly applied. We then present several key challenges in the design of a parallel multiobjective simulation optimization framework (ParMOO) and how they have been addressed. Finally, we provide two case studies demonstrating how customized ParMOO solvers can be quickly built and deployed to solve real-world MOSO problems.

engineering design optimization↗

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution

When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F 1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F 1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a “faster male” model for Haldane’s rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a “large-X effect” for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.

59 BASIC BIOLOGICAL SCIENCES↗

COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients

Background: The COVID-19 pandemic remains a significant global threat. However, despite urgent need, there remains uncertainty surrounding best practices for pharmaceutical interventions to treat COVID-19. In particular, conflicting evidence has emerged surrounding the use of hydroxychloroquine and azithromycin, alone or in combination, for COVID-19. The COVID-19 Evidence Accelerator convened by the Reagan-Udall Foundation for the FDA, in collaboration with Friends of Cancer Research, assembled experts from the health systems research, regulatory science, data science, and epidemiology to participate in a large parallel analysis of different data sets to further explore the effectiveness of these treatments. Methods: Electronic health record (EHR) and claims data were extracted from seven separate databases. Parallel analyses were undertaken on data extracted from each source. Each analysis examined time to mortality in hospitalized patients treated with hydroxychloroquine, azithromycin, and the two in combination as compared to patients not treated with either drug. Cox proportional hazards models were used, and propensity score methods were undertaken to adjust for confounding. Frequencies of adverse events in each treatment group were also examined. Results: Neither hydroxychloroquine nor azithromycin, alone or in combination, were significantly associated with time to mortality among hospitalized COVID-19 patients. No treatment groups appeared to have an elevated risk of adverse events. Conclusion: Administration of hydroxychloroquine, azithromycin, and their combination appeared to have no effect on time to mortality in hospitalized COVID-19 patients. Continued research is needed to clarify best practices surrounding treatment of COVID-19.

60 APPLIED LIFE SCIENCES↗

Keep CALM and CRDT On

Despite decades of research and practical experience, developers have few tools for programming reliable distributed applications without resorting to expensive coordination techniques. Conflict-free replicated datatypes (CRDTs) are a promising line of work that enable coordination-free replication and offer certain eventual consistency guarantees in a relatively simple object-oriented API. Yet CRDT guarantees extend only to data updates; observations of CRDT state are unconstrained and unsafe. We propose an agenda that embraces the simplicity of CRDTs, but provides richer, more uniform guarantees. We extend CRDTs with a query model that reasons about which queries are safe without coordination by applying monotonicity results from the CALM Theorem, and lay out a larger agenda for developing CRDT data stores that let developers safely and efficiently interact with replicated application state.

Computer Science↗

What is Considered Reliable Information?

Pre-editorial draft chapter for book titled: "Nano- Safety: What we need to know to Protect Workers" edited by Dr. Dominick Fazarro- University of Texas at Tyler. Chapter 6 addresses two complementary aspects of communicating information related to all things “nano”. The first of these is the general concept of reliable information and its compatible concept of objective evidence. Second we will address the overuse and sometimes conflicting use of the modifier and short-form or prefix “nano”. How these two complementary aspects of communicating information are employed can complicate the usability of information, especially when considering the use of available research and impacts of nanotechnologies on worker safety and health.

information reliability, data integrity, nano-safe↗