Article
Biochemistry & Molecular Biology
Wenxiang Zhang, Bin Liu
Summary: Growing evidence suggests that snoRNAs play important roles in biological processes and their malfunction can contribute to the development of complex diseases. This study introduces a computational method called iSnoDi-LSGT for identifying snoRNA-disease associations, which utilizes snoRNA sequence similarity and disease similarity as local similarity constraints.
Article
Multidisciplinary Sciences
Stuart Oldham, Ben D. Fulcher, Kevin Aquino, Aurina Arnatkeviciute, Casey Paquola, Rosita Shishegar, Alex Fornito
Summary: The complex connectivity of nervous systems is influenced by competitive selection pressures, with the aim of minimizing wiring costs and supporting adaptive function. Recent modeling work suggests that stochastic processes, considering the trade-offs between the cost and value of each connection, can replicate many topological properties of human brain connectomes. However, these models struggle to capture spatial network properties. The findings highlight the significant role of genetics in shaping macroscopic brain connectivity and suggest that stochastic models can provide only a partial explanation of connectome organization.
Article
Physics, Multidisciplinary
Carolina Rodriguez-Gallo, Antonio Ortiz-Ambriz, Pietro Tierno
Summary: The study demonstrated that boundaries can be engineered to control the bulk behavior in a colloidal artificial ice, with an antiferromagnetic boundary forcing the system to rapidly reach the ground state, and strategically placed defects at corners generating novel bistable states or topological strings. This approach could be extended to other frustrated micro- and nanostructures where boundary conditions can be engineered using lithographic techniques.
PHYSICAL REVIEW LETTERS
(2021)
Article
Materials Science, Ceramics
N. M. Anoop Krishnan, Yann Le Pape, Gaurav Sant, Mathieu Bauchy
Summary: Molecular dynamics simulations show that pristine crystals in silicate phases are topologically overconstrained, leading to internal elastic stress in the network. Disorder-induced breaking of weaker constraints releases this internal stress, explaining the macroscopic expansion exhibited by atomic networks upon disordering.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Computer Science, Information Systems
Xueli Wang, Shangwei Zhao, Xin Wang, Ming Yang, Xiaoming Wu
Summary: This study investigates the data-driven control problem for discrete-time nonlinear systems with state constraints and dynamic quantization. A dynamic quantizer is used to encode the control signal and alleviate quantization errors. By employing three sets of neural networks, a data-based goal representation heuristic dynamic programming algorithm is developed to achieve near-optimal control without requiring a model. The proposed control strategy includes a barrier-based control strategy for generating repulsive control force at constraint boundaries, a new weight updating rule based on historical data, and demonstration of bounded weight estimation errors using the Lyapunov method.
INFORMATION SCIENCES
(2023)
Article
Computer Science, Interdisciplinary Applications
Haitao Han, Yuchen Guo, Shikui Chen, Zhenyu Liu
Summary: This paper proposes an optimization model based on the BESO method, explicitly specifying the allowed maximal number of holes in the designed structure as an additional design constraint, and introduces a hole-filling method to control the existence of holes. Numerical examples demonstrate that this method can limit the maximum number of holes in the optimal structure and alleviate the checkerboard pattern and mesh dependence phenomena.
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2021)
Article
Polymer Science
Aakash Sharma, Margarita Kruteva, Sascha Ehlert, Martin Dulle, Stephan Foerster, Dieter Richter
Summary: Small-angle X-ray scattering is a powerful technique for investigating the spatial arrangements of polymer-grafted nanoparticles in nanocomposites. However, the commonly used hard sphere model fails to accurately describe the density of the grafted polymer, leading to inappropriate quantitative descriptions of nanoparticle assemblies. By analyzing the scattering data and considering the polymer-induced interactions, we are able to establish quantitative relations between the nanoparticle assembly and the polymer structure in the nanocomposites.
Article
Multidisciplinary Sciences
James C. Pang, Kevin M. Aquino, Marianne Oldehinkel, Peter A. Robinson, Ben D. Fulcher, Michael Breakspear, Alex Fornito
Summary: The anatomy of the brain imposes constraints on its function, but how exactly these constraints work is not well understood. The traditional view in neuroscience is that the interaction between different specialized cell populations connected by a complex network of axonal fibers drives neuronal dynamics. However, neural field theory suggests that the geometry of the brain may be a more fundamental constraint than interregional connectivity. In this study, we confirm these predictions by analyzing human MRI data and show that brain activity can be explained by excitations of the brain's geometric modes rather than complex interregional connectivity.
Article
Mathematical & Computational Biology
Gang Zhao, Chang-ping Liu, Qi-sheng Zhao, Min Lin, Ying-bao Yang
Summary: This paper focuses on the controllability of the aviation supply chain network and establishes judgment criteria for the structural controllability of the network. By applying control inputs to different nodes, such as core enterprises, upstream suppliers, and downstream distributors, the control effect is determined. It is observed that applying control inputs to upstream suppliers has a better effect compared to core enterprises, while applying control inputs to core enterprises is more desirable than distributors.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Article
Mechanics
S. Candelaresi, G. Hornig, B. Podger, D. Pontin
Summary: The study focuses on the relaxation of a topologically nontrivial vortex braid with zero net helicity in a barotropic fluid. It investigates how the topology of the vorticity field affects dynamics, particularly the asymptotic behavior during vortex reconnection at high Reynolds numbers. The relaxation of the vortex braid leads to a simplification of topology into large-scale regions of opposite swirl, influenced by a cascade of vortex reconnection events and the existence of positive and negative kinetic helicity regions setting a lower bound for kinetic energy.
Article
Automation & Control Systems
Carla de Souza, Antoine Girard, Sophie Tarbouriech
Summary: This paper investigates the event-triggered control problem for perturbed systems under neural network controllers. A novel event-triggering mechanism is proposed to reduce the computational cost associated with the neural network evaluation. Sufficient conditions in terms of matrix inequalities are established to design the parameters of the event-triggering mechanism and compute an inner-approximation of the region of attraction for the perturbed feedback system.
Article
Engineering, Mechanical
Hai-Peng Ren, Shan-Shan Jiao, Jie Li, Yi Deng
Summary: Efforts in high performance tracking control of pneumatic position servo systems have achieved considerable results, but current methods often do not consider state constraints. This paper aims to improve tracking accuracy by employing RBFNN for unknown models, Nussbaum function for unknown control directions, and BLF for stability while considering state constraints. Experimental results demonstrate the effectiveness and superiority of the proposed method.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2022)
Article
Automation & Control Systems
Ahmad W. Al-Dabbagh, Aryan Saadat Mehr, Tongwen Chen
Summary: This article explores a strategic topological formation for a wireless control system, presenting a modeling framework and design procedure to reduce the use of nodes and communication links, while discussing conditions for node connectivity under different scenarios. It uses a four-tank process system as an example to demonstrate the strategic topological formation.
IEEE TRANSACTIONS ON CYBERNETICS
(2022)
Article
Automation & Control Systems
Hong Cheng, Yongduan Song
Summary: This paper presents a neuroadaptive tracking control method for a class of pure-feedback nonlinear systems in the presence of dynamic constraints and unmodeled dynamics simultaneously. By introducing a nonlinear mapping (NM) and a dynamic compensation signal, the proposed method allows the states to be confined within given regions and handles the unmodeled dynamics effectively. The simulation results demonstrate the effectiveness of the proposed method.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2023)
Article
Biochemical Research Methods
Pietro Cinaglia, Marianna Milano, Mario Cannataro
Summary: DANTEml is a software tool for Pairwise Global Network Alignment (PGNA) of multilayer networks based on topological assessment. It provides effective alignments on both synthetic and real multilayer networks, and the validity of node mappings can be statistically validated.
BMC BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Zeynep Sezen, Ottar N. Bjornstad, Katriona Shea
Summary: The Musk thistle, a major noxious weed, is controlled by the flower head weevil, which responds variably to plant characteristics, impacting its effectiveness in biological control. Larger flower heads provide more oviposition sites but also result in more seed production, offsetting the efficacy of the weevil's control.
BIOLOGICAL CONTROL
(2021)
Article
Ecology
Joseph A. Keller, Katriona Shea
Summary: Climate warming leads to advanced reproductive phenology in an invasive plant, accelerating its life cycle and population growth rate. Rising temperatures increase the average size of reproducing individuals, the proportion of survivors that reproduce, and the fraction of individuals reproducing as annuals, all contributing to the accelerated population growth of invasive species.
Article
Ecology
James N. Sanchirico, Julie C. Blackwood, Ben Fitzpatrick, David M. Kling, Suzanne Lenhart, Michael G. Neubert, Katriona Shea, Charles B. Sims, Michael R. Springborn
Summary: The authority to manage natural capital often follows political boundaries rather than ecological boundaries, which can lead to unsustainable outcomes due to mismatch. The trade-offs between federal vs. state control of renewable resources involve factors such as biological mechanisms, economic mechanisms, flexibility in federal management, spatial and temporal distribution of economic returns. The analysis reveals the complex political economy dimensions of renewable resource federalism.
ECOLOGICAL APPLICATIONS
(2021)
Article
Ecology
Adam D. Miller, Hidetoshi Inamine, Angus Buckling, Stephen H. Roxburgh, Katriona Shea
Summary: Disturbance is a key factor shaping ecological communities, with historical disturbance processes influencing future community structure. Research shows that past differences in disturbance history can affect invasion success and community outcomes.
Correction
Biochemical Research Methods
Ottar N. Bjornstad, Katriona Shea, Martin Krzywinski, Naomi Altman
Article
Biodiversity Conservation
Shou-Li Li, Joseph Keller, Michael C. Runge, Katriona Shea
Summary: The management of biological invasions is hindered by biological and operational uncertainties. However, simultaneously addressing both sources of uncertainty can help optimize control decisions, leading to a reduction in population growth rate of invasive species.
JOURNAL OF APPLIED ECOLOGY
(2021)
Article
Cell Biology
Clara Alcon, Jorge Gomez Tejeda Zanudo, Reka Albert, Nikhil Wagle, Maurizio Scaltriti, Anthony Letai, Josep Samitier, Joan Montero
Summary: Breast cancer, the most frequent type of cancer in women, has seen improved treatment outcomes with the rapid development of therapeutic options, but some patients still relapse due to cancer cell acquired resistance. Research has identified the crucial role of anti-apoptotic proteins BCL-xL and MCL-1 in the resistance of ER+ breast cancer cells to therapy, leading to the proposal of sequential inhibition using BH3 mimetics as a new treatment option.
Article
Ecology
Hidetoshi Inamine, Adam Miller, Stephen Roxburgh, Angus Buckling, Katriona Shea
Summary: This study examines the effects of disturbances on species diversity and proposes a classification method for pulse and press disturbances. The research found that the two types of disturbances have different impacts on coexistence mechanisms, although their asymptotic diversity patterns are similar. Furthermore, the study emphasizes the importance of using theoretical modeling to guide and interpret empirical research.
AMERICAN NATURALIST
(2022)
Article
Ecology
Joseph A. Keller, Katriona Shea
Summary: Climate change affects weed performance and may impact management practices to control pests. A field experiment on musk thistle showed that under elevated temperatures, thistles were more likely to survive mowing, flowered earlier, grew taller, and produced more flowers. Proportional reductions in height and flower production caused by mowing were smaller under warming. Warming increased population growth rate for all mowing treatments. To achieve similar outcomes in the future, supplemental management may be needed.
ECOLOGICAL APPLICATIONS
(2022)
Article
Ecology
Luke Lear, Daniel Padfield, Hidetoshi Inamine, Katriona Shea, Angus Buckling
Summary: The interactive effects of disturbance regime and resource abundance play a crucial role in determining the success of biological invasions. The study found that disturbance frequency and resource abundance have different impacts on different types of invaders. The life history of invaders and changes in community resource abundance also affect invasion outcomes.
Article
Multidisciplinary Sciences
William J. M. Probert, Sam Nicol, Matthew J. Ferrari, Shou-Li Li, Katriona Shea, Michael J. Tildesley, Michael C. Runge
Summary: This study investigates the methods of comparing control interventions during disease outbreaks using mathematical modelling. Existing methods have limitations, and this study proposes a new approach of combining rankings of interventions instead of model projections. The results suggest that this method provides similar recommendations with fewer assumptions about model comparability.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Biochemical Research Methods
Colin Campbell, Laura Russo, Reka Albert, Angus Buckling, Katriona Shea
Summary: The invasion of non-native species can have a significant impact on the function and structure of ecological communities. Whole community invasion leads to more stable communities with a higher retention of native species and smaller changes in topological measures. Mutualistic interactions act as a buffer against disruptions to the native community.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Jose L. Herrera-Diestra, Michael Tildesley, Katriona Shea, Matthew J. Ferrari
Summary: The structure of contact networks plays a crucial role in the spread of diseases. By analyzing records of cattle transportation among farms in Turkey, this study investigates the correlation between network properties and the risk of foot-and-mouth disease (FMD) infection. The results show that the degree, centrality, and recipient status of nodes are associated with the risk of infection.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Fatemeh Sadat Fatemi Nasrollahi, Jorge Gomez Tejeda Zanudo, Colin Campbell, Reka Albert
Summary: This study examines mutualistic communities of plant and pollinator species using Boolean threshold functions, proposing a novel method to identify attractors based on positive feedback loops. The relationships between these loops determine how stable subcommunities trap the system in specific regions of the state space, leading to diverse community outcomes. The timing of species influx or outflux does not impact the number of attractors, but it may affect their basins of attraction.