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At least 109 records · Page 6

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

Game theoretic modeling and optimization of competition and collaboration in dual channel electronic waste supply chains

The rapid growth of electronic waste (e-waste) presents critical challenges for sustainable resource recovery and environmental protection. This study develops a dual-channel closed-loop supply chain (CLSC) model formulated as a hierarchical Stackelberg game, that integrates dynamic pricing and cost-sharing mechanisms to optimize both economic and environmental outcomes. The model explicitly captures strategic interactions between manufacturer-led and third-party recycling channels, accounting for consumer behavior, regulatory incentives, and market competition. Numerical simulations conducted (implemented over a four-iteration horizon using a commercial optimization solver) show that, relative to the baseline equilibrium, manufacturer profit increases from 11.6 thousand USD to 37.9 thousand USD (+226.8%), total recycled volume rises from 7,848 to 7,942 units (+1.2%), and collector profit nearly doubles under cost-sharing, enabling more equitable profit distribution. Furthermore, scenario-based simulations across Sub-Saharan Africa, high-income economies, and emerging Asian industrial countries reveal that infrastructure quality, policy intensity, and labor costs critically shape recycling efficiency and profit allocation. These findings demonstrate that subsidies alone are insufficient to ensure system efficiency. Instead, coordinated strategies that integrate internal incentive alignment with context-sensitive policy support are required. Overall, this study offers a robust framework for designing resilient, efficient, and regionally adaptable e-waste management systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Collaborative energy and land use planning

Energy models make projections for infrastructure, yet struggle to map deployment pathways at the ground level, where risks and benefits to human and natural systems materialize. Furthermore, a study now shows how blending in geospatial science can help to preserve natural capital while allowing for new infrastructure to be built.

Energy and society↗

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

First Limits on Light Dark Matter Interactions in a Low Threshold Two-Channel Athermal Phonon Detector from the TESSERACT Collaboration

We present results of a search for spin-independent dark matter-nucleus interactions in a 1 cm 2 by 1 mm thick (0.233 g) high-resolution silicon athermal phonon detector operated above ground. For interactions in the substrate, this detector achieves an rms baseline energy resolution of 361.5⁢(4) m⁢ eV (statistical error), the best for any athermal phonon detector to date. With an exposure of 0.233 g ×12 hours, we place the most stringent constraints on dark matter masses between 44 and 87 M⁢ eV/c 2 , with the lowest unexplored cross section of 4⁢ × 10 −32 c⁢m 2 at 87 M⁢ eV/c 2 . We employ a conservative salting technique to reach the lowest dark matter mass ever probed via direct detection experiment. This constraint is enabled by two-channel rejection of low energy backgrounds that are coupled to individual sensors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Physics-Informed Graph Neural Networks for Collaborative Dynamic Reconfiguration and Voltage Regulation in Unbalanced Distribution Systems

Network reconfiguration has long been employed as a strategic approach to minimize power distribution system losses and effectively regulate voltage levels. Tap-changing voltage regulators are also critical for controlling bus voltages, especially in accommodating the increasing integration of distributed energy resources (DERs) with intermittent outputs. This paper introduces novel methodologies to address the challenges of dynamic reconfiguration and optimal tap setting in unbalanced three-phase distribution systems. We propose an approximated mixed-integer quadratically constrained program (MIQCP) to model dynamic reconfiguration, along with a pioneering formulation for voltage regulator (VR) tap-setting based on Special Ordered Set type 1 (SOS1). To mitigate computational complexity, we propose a physics-informed spatial-temporal graph convolutional network (STGCN) with an integrated link classifier. The proposed approach enables efficient solution generation by fixing specific variables in the MIQCP instance and solving the simplified sub-MIP using an MIP solver. Numerical studies demonstrate the superior prediction accuracy of our STGCN model compared to baseline neural network models, resulting in reduced DER curtailment and voltage deviation with shorter computation time.

dynamic reconfiguration↗

How to Create, and Sustain, R&D Leadership A blueprint for international collaboration

How the United States can compete in the twenty-first century is one of the most vexing challenges for policy makers and academics today. Many studies have shown that most impactful science and technology advances happen in open and diverse environments, under excellent research conditions, with sufficient funding. Since the end of World War II, the United States has been the most attractive country for open research and commercialization of new discoveries. This strategy—partly articulated in science administrator Vannevar Bush’s Endless Frontier report of 1945—leverages federal government investments in research and development (R&D) to enhance economic competitiveness and national security. The combination of a dynamic, open research ecosystem and world-leading science infrastructure provided an exciting work environment leading to groundbreaking discoveries, and propelled economic growth through the second half of the twentieth century.

99 GENERAL AND MISCELLANEOUS↗

Collaborative Research: Parametric Instabilities of Alfven Waves in Low‐beta Plasmas

Alfven waves are of fundamental importance in magnetized plasmas. This project aims to advance our understanding of the basic physics of the parametric instabilities of Alfven waves using advanced computer simulations. The results will have implications for important processes in the heliosphere involving Alfven waves, such as coronal heating and solar wind heating.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Lab Collaboration Project (LCP) for Marine Energy: Quantifying Collision Risk for Fish and Turbines Final Technical Report (Task 10)

A persistent environmental concern for the widespread deployment of tidal turbines is the potential for fish and marine mammals to collide with rotating blades (Copping et al. 2016, Copping and Hemery 2020). This is a consequence of well-documented bird and bat mortalities around wind turbines (Smallwood 2007, Thompson et al. 2017), as well as fish mortality at conventional hydropower dams (Pracheil et al. 2016) and tidal barrages (Dadswell and Rulifson 1994). However, unlike hydropower dams or barrages, tidal turbines do not involve structures that channel all flow through the turbines. Similarly, while functionally similar to wind turbines, tidal turbines often operate at lower relative velocities and, depending on the end-use application, may be significantly smaller than utility-scale wind turbines. Both of these factors reduce the likelihood and severity of collision, but the knowledge base on this topic remains limited.

13 HYDRO ENERGY↗