SUMO-MCP: Leveraging the Model Context Protocol for Autonomous Traffic Simulation and Optimization [PDF]
arXivTraffic simulation tools, such as SUMO, are essential for urban mobility research. However, such tools remain challenging for users due to complex manual workflows involving network download, demand generation, simulation setup, and result analysis. In this paper, we introduce SUMO-MCP, a novel platform that not only wraps SUMO' s core utilities into a
arxiv
New Phytologist, Volume 247, Issue 2, Page 504-517, July 2025.Summary Repetitive DNA is a feature of all organisms, ranging from archaea and plants to humans. DNA repeats can be seen both in coding and in noncoding regions of the genome. Due to the recurring nature of the sequences, simple DNA repeats tend to be more prone to errors during replication and repair, resulting in variability in their unit length ...
Sridevi Sureshkumar +3 more
wiley +1 more source
Recent advances in proteomic workflows to interrogate the SUMOylome in plants
New Phytologist, Volume 247, Issue 1, Page 90-96, July 2025.Summary Protein posttranslational modifications (PTMs) are vital for regulating protein functions. SUMOylation, a PTM essential for plant survival, involves attaching a Small Ubiquitin‐like MOdifier (SUMO) to lysine residues of target proteins. SUMOylation influences stress tolerance, cell proliferation, protein stability, and gene expression.
Kishor D. Ingole +3 more
wiley +1 more source
New Phytologist, Volume 247, Issue 1, Page 233-248, July 2025.Summary Pathogenesis‐related (PR) proteins are diverse stress‐ or pathogen‐induced proteins. Some are associated with specialised metabolism, including proposed functions for anthocyanin biosynthesis. However, data are limited to a few angiosperm species, and the mode(s) of action are uncertain.
Yanfei Zhou +8 more
wiley +1 more source
SUMO: Search-Based Uncertainty Estimation for Model-Based Offline Reinforcement Learning [PDF]
arXivThe performance of offline reinforcement learning (RL) suffers from the limited size and quality of static datasets. Model-based offline RL addresses this issue by generating synthetic samples through a dynamics model to enhance overall performance. To evaluate the reliability of the generated samples, uncertainty estimation methods are often employed.
arxiv
Light Quantity Impacts Early Response to Cold and Cold Acclimation in Young Leaves of Arabidopsis
Plant, Cell &Environment, Volume 48, Issue 7, Page 5030-5052, July 2025.ABSTRACT Plant reactions to stress vary with development stage and fitness. This study assessed the relationship between light and chilling stress in Arabidopsis acclimation. By analysing the transcriptome and proteome responses of expanding leaves subjected to varying light intensity and cold, 2251 and 2064 early response genes and proteins were ...
Markéta Luklová +14 more
wiley +1 more source
Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks? [PDF]
arXiv, 2006 In protein-protein interaction networks certain topological properties appear to be recurrent: networks maps are considered scale-free. It is possible that this topology is reflected in the protein structure. In this paper we investigate the role of protein disorder in the network topology.
arxiv
Structural attributes in the conjugation of Ubiquitin, SUMO and RUB to protein substrates [PDF]
, 2002 Sandra Goettsch, Peter Bayer
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A Synergy Control Motif within the Attenuator Domain of CCAAT/Enhancer-binding Protein α Inhibits Transcriptional Synergy through Its PIASy-enhanced Modification by SUMO-1 or SUMO-3 [PDF]
, 2003 Lalitha Subramanian +2 more
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Lactylation: From Homeostasis to Pathological Implications and Therapeutic Strategies
MedComm, Volume 6, Issue 6, June 2025.Lactylation, a novel post‐translational modification derived from lactate metabolism, plays a critical role in cellular homeostasis and disease pathogenesis. Under physiological conditions, lactylation regulates gene expression, immune responses, and metabolic adaptation. However, dysregulated lactylation is implicated in various pathological processes,
Xi Chen +6 more
wiley +1 more source