Article
Biology
Priscila C. Antonello, Thomas F. Varley, John Beggs, Marimelia Porcionatto, Olaf Sporns, Jean Faber
Summary: Activity-dependent self-organization plays a crucial role in the formation of neural circuits. By studying neuronal cultures and applying methods from network neuroscience and information theory, researchers have gained insights into the emergence and evolution of complex network topology from local neuronal interactions. The findings suggest that the number of connections in the networks increases during development, leading to a shift from a segregated to a more integrated architecture. The networks exhibit small-world and modular topologies, with highly active neurons playing important roles as network nodes and module integrators.
Article
Cell Biology
Richard Boyce, Robin F. Dard, Rosa Cossart
Summary: A study found no difference in the structure of assembly activity in the sensorimotor cortex during awake, non-rapid eye movement sleep (NREMs), or rapid eye movement sleep (REMs), despite the latter two states being associated with reduced consciousness. However, there was a significant coordination between global electroencephalogram (EEG) microstate dynamics and local cortical assembly activity during periods of wakefulness, but not during sleep.
Article
Mathematics, Applied
Jean-Philippe Thivierge, Eloise Giraud, Michael Lynn, Annie Theberge Charbonneau
Summary: This paper proposes a new class of structured reservoir models that incorporate a diversity of cell types and their known connections. Experimental results show that the model has two distinct dynamical regimes and can be used to relay and generate chaotic Lorenz attractors.
Article
Biology
Owen Mackwood, Laura B. Naumann, Henning Sprekeler
Summary: Understanding the connectivity in the brain and how it is influenced by activity-dependent synaptic plasticity is a major challenge in neuroscience. Research in mice's V1 area suggests that connections between excitatory and inhibitory neurons contribute to a stimulus-specific competition among neurons, highlighting the importance of synaptic plasticity in shaping cortical computations.
Article
Chemistry, Multidisciplinary
Antara Reja, Sumit Pal, Kishalay Mahato, Baishakhi Saha, Massimo Delle Piane, Giovanni M. Pavan, Dibyendu Das
Summary: Researchers reported a light-responsive reaction system where the binding sites for C-C bond manipulation were regulated by a photosensitive molecular cofactor. This system achieved a more efficient catalytic state under nonequilibrium conditions with the energy of the light source. Additionally, the binding of a molecular catalyst enhanced activity and facilitated the in situ generation of a light-sensitive cofactor.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Gray Umbach, Ryan Tan, Joshua Jacobs, Brad E. Pfeiffer, Bradley Lega
Summary: This study identifies neuronal assemblies in the human MTL and demonstrates their consistent organization based on gamma phase information. The findings suggest the involvement of neuronal assemblies in human episodic memory and their ability to flexibly adjust based on memory performance.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Aaron D. W. Kennedy, Ray G. DiNardi, Lucy L. Fillbrook, William A. Donald, Jonathon E. Beves
Summary: A study has shown that a photoswitchable ligand and palladium(II) ions can form dynamic metallosupramolecular structures. By irradiating with light, the distribution of isomers in the ligand can be controlled, resulting in selective disassembly and formation of stable structures. This approach provides a new strategy for reversible control of self-assembled structures.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Cell Biology
Belal Shohayeb, Zukhrofi Muzar, Helen M. Cooper
Summary: This review discusses the fundamental molecular and cellular mechanisms regulating neural progenitor function and neuronal diversity generation, as well as the essential structural features of cortical neurons' origin, proliferation, and differentiation. Furthermore, researchers have also explored how individual neuronal identity emerges as a result of exposure to temporally regulated extrinsic cues.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Chandranath Ghosh, Sneha Menon, Subhajit Bal, Surashree Goswami, Jagannath Mondal, Dibyendu Das
Summary: Through evolution, modern enzymes in metabolic pathways have become specialized, unlike their early ancestors which had broader substrate specificities. However, it is still unclear how these early enzymes displayed catalytic versatility without complex three-dimensional structures. This study reports the emergence of promiscuous catalytic triads in short amyloid peptide-based nanofibers that access paracrystalline folds of beta-sheets, allowing them to simultaneously catalyze multiple reactions and contribute to protometabolism and early evolutionary processes.
Article
Mathematics, Interdisciplinary Applications
Adriane S. Reis, Kelly C. Iarosz, Fabiano A. S. Ferrari, Ibere L. Caldas, Antonio M. Batista, Ricardo L. Viana
Summary: The study explores bursting synchronization in a neuronal network model inspired by the human cerebral cortex, which can be partially or completely suppressed using an external signal based on time delay and signal intensity. The findings suggest that bursting synchronization in the network model can be related to pathological rhythms and targeted suppression techniques may have potential applications for mitigating such pathologies.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Chemistry, Multidisciplinary
Jan Bierlmeier, Miguel Alvaro-Benito, Maren Scheffler, Kristina Sturm, Luisa Rehkopf, Christian Freund, Dirk Schwarzer
Summary: Sortase-mediated ligation is a powerful tool in protein chemistry for connecting peptides. By using switchable sortase substrates, multi-fragment SML can be achieved, expanding its applications in protein research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
K. J. Weaver, R. A. Holt, E. Henry, Y. Lyu, S. D. Pletcher
Summary: Hunger state can modulate physiological characteristics in Drosophila, such as increasing lifespan and feeding, through altering neuronal histone acetylation state. Short-term hunger increases feeding through histone variant H3.3, while prolonged hunger decreases the hunger set point, leading to beneficial consequences for aging.
Article
Chemistry, Multidisciplinary
Rongying Liu, Long Li, Shuyu Chen, Zhiwei Yang, Zdravko Kochovski, Shilin Mei, Yan Lu, Lei Zhang, Guosong Chen
Summary: A protein assembly capable of switching interplay modes of multiple driving forces has been successfully achieved by leveraging ligand-ligand interaction and protein-protein interaction. This strategy not only provides a nanoscale understanding on the mechanism underlying the switch of interplay modes in the context of biomacromolecules, but also may enable the fabrication of diverse sophisticated biomacromolecular nanostructures that are historically inaccessible for conventional self-assembly strategies.
Article
Biochemistry & Molecular Biology
Sebastian R. Najle, Xavier Grau-Bove, Anamaria Elek, Cristina Navarrete, Damiano Cianferoni, Cristina Chiva, Didac Canas-Armenteros, Arrate Mallabiabarrena, Kai Kamm, Eduard Sabido, Harald Gruber-Vodicka, Bernd Schierwater, Luis Serrano, Arnau Sebe-Pedros
Summary: The assembly of neuronal and other major cell programs occurred early in animal evolution. Through studying non-bilaterians like placozoans, we can reconstruct this process and understand the affinities of peptidergic cells. Our findings show that key neuronal developmental and effector gene modules evolved before cnidarian/bilaterian neurons, highlighting the importance of paracrine cell signaling.
Article
Chemistry, Inorganic & Nuclear
Pawan Kumar, Jessica Flores Gonzalez, Prem Prakash Sahu, Naushad Ahmed, Joydev Acharya, Vierandra Kumar, Olivier Cador, Fabrice Pointillart, Saurabh Kumar Singh, Vadapalli Chandrasekhar
Summary: The synthesis, structure, and magnetism of four tetranuclear complexes have been reported, with two peroxide ligands assisting in their formation. Weak intramolecular antiferromagnetic interactions were found in three of the complexes, while a structural change in the fourth complex led to a ferromagnetic interaction. The magnetothermal behavior of one complex displayed a magnetocaloric effect with a maximum entropy change close to the calculated value.
INORGANIC CHEMISTRY FRONTIERS
(2022)
Meeting Abstract
Infectious Diseases
A. Myall, J. Price, R. Peach, M. Abbas, S. Mookerjee, I. Ahmad, D. Ming, N. J. Zhu, F. Ramzan, A. Weisse, A. H. Holmes, M. Barahona
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Meeting Abstract
Infectious Diseases
A. Myall, R. Peach, Y. Wan, S. Mookerjee, E. Jauneikaite, F. Bolt, J. Price, F. Davies, A. Weisse, A. H. Holmes, M. Barahona
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Editorial Material
Neurosciences
Christof Koch, Karel Svoboda, Amy Bernard, Michele A. Basso, Anne K. Churchland, Adrienne L. Fairhall, Peter A. Groblewski, Jerome A. Lecoq, Zachary F. Mainen, Mackenzie W. Mathis, Shawn R. Olsen, John W. Phillips, Alexandre Pouget, Shreya Saxena, Josh H. Siegle, Anthony M. Zador
Summary: This article proposes the establishment of centralized brain observatories for large-scale recordings of neural activity in animals, aiming to advance reproducible systems neuroscience and democratize access to advanced tools and data.
Article
Computer Science, Interdisciplinary Applications
Stamatina Lamprinakou, Mauricio Barahona, Seth Flaxman, Sarah Filippi, Axel Gandy, Emma J. McCoy
Summary: This article introduces a BART scheme for estimating the intensity of inhomogeneous Poisson processes, which enables full posterior inference in a non-parametric regression setting. The performance of the new scheme is demonstrated through simulation studies and comparisons with alternative approaches.
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2023)
Editorial Material
Multidisciplinary Sciences
Christof Koch
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Medicine, General & Internal
Thomas Beaney, Jonathan Clarke, David Salman, Thomas Woodcock, Azeem Majeed, Mauricio Barahona, Paul Aylin
Summary: The frequency of diagnostic codes for newly diagnosed LTCs is influenced by factors including patient sociodemographics, disease inclusion in QOF, GP practice, and the impact of the COVID-19 pandemic. Natural language processing or other methods using temporally ordered code sequences should account for these factors to minimise potential bias.
Article
Biology
Leslie D. Claar, Irene Rembado, Jacqulyn R. Kuyat, Simone Russo, Lydia C. Marks, Shawn R. Olsen, Christof Koch
Summary: This study predicts the presence of consciousness in volunteers and patients by stimulating the brain and analyzing the EEG responses. The researchers conducted similar experiments on mice and observed different patterns of cortical and thalamic responses during wakefulness, running, and anesthesia.
Article
Multidisciplinary Sciences
Amadeus Maes, Mauricio Barahona, Claudia Clopath
Summary: The statistical structure of the environment is crucial for decision-making, and the brain represents this structure through various theories. One theory suggests that neural activity samples from probability distributions, spending more time in states encoding high-probability stimuli. By focusing on neural assembly, which is considered the computational unit of the brain, we explore how prior knowledge of the environment can be learned and retrieved. We propose a model based on learning the inverse of the cumulative distribution function, using unsupervised learning with biophysical neurons and biologically plausible rules. This prior knowledge is then used to calculate expectations and signal surprise in downstream networks, and sensory history effects emerge as a result of ongoing learning.
SCIENTIFIC REPORTS
(2023)
Proceedings Paper
Automation & Control Systems
Lilli J. Freischem, Mauricio Barahona, Diego A. Oyarzun
Summary: By applying a machine learning approach, we can directly predict gene essentiality from wild-type flux distributions without assuming that knockout strains optimize the same objectives as the wild-type. We project the wild-type FBA solution onto a mass flow graph and train binary classifiers on the connectivity of graph nodes. Our approach demonstrates high prediction accuracy for essential genes using the most complete metabolic model of Escherichia coli.
Proceedings Paper
Acoustics
T. Mitchell Roddenberry, Florian Frantzen, Michael T. Schaub, Santiago Segarra
Summary: In this paper, we develop wavelet representations for edge-flows on simplicial complexes using ideas from combinatorial Hodge theory and spectral graph wavelets. We demonstrate that the Hodge Laplacian can replace the graph Laplacian to construct a family of wavelets for higher-order signals on simplicial complexes. We then refine this idea to construct wavelets that respect the Hodge-Helmholtz decomposition, preserving familiar concepts of curl-free and divergence-free flows. The representational quality of our Hodgelets for edge flows is characterized in terms of frame bounds, and we show their application in sparse representation of edge flows using real and synthetic data.
2022 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP)
(2022)
Proceedings Paper
Acoustics
T. Mitchell Roddenberry, Michael T. Schaub, Mustafa Hajij
Summary: This research introduces signal processing based on regular cell complexes, which include graphs, simplicial complexes, cubical complexes, and various meshes as special cases. It discusses the derivation of appropriate Hodge Laplacians for these complexes and the construction of convolutional filters for linear and nonlinear filtering.
2022 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP)
(2022)
Proceedings Paper
Acoustics
Michael Scholkemper, Michael T. Schaub
Summary: Finding equitable partitions is closely related to graph symmetries and is of interest in various applications. This work studies blind identification to recover equitable partitions without knowing the network's edges through observations of output from an unknown graph filter. Two settings are considered, each with theoretical error bounds and numerical experiments.
2022 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP)
(2022)
Article
Medical Informatics
Ashleigh Myall, James R. Price, Robert L. Peach, Mohamed Abbas, Sid Mookerjee, Nina Zhu, Isa Ahmad, Damien Ming, Farzan Ramzan, Daniel Teixeira, Christophe Graf, Andrea Y. Weisse, Stephan Harbarth, Alison Holmes, Mauricio Barahona
Summary: This study developed a real-time machine-learning framework that incorporated dynamic patient-contact networks to predict individual hospital-onset COVID-19 infections (HOCIs). The results showed that contact networks are robust predictors of individual patient risk of HOCIs, and their integration in clinical care could enhance individualized infection prevention and early diagnosis.
LANCET DIGITAL HEALTH
(2022)
Article
Environmental Sciences
Felix Laumann, Julius von Kugelgen, Thiago Hector Kanashiro Uehara, Mauricio Barahona
Summary: This study aims to detect and rank the complex interlinkages between objectives of sustainable development. The results show that global partnerships and climate change are highly important in many country groupings. Economic growth is closely related to global partnerships, but if economic growth and trade expansion are repositioned, education and poverty reduction become more central, and urban livelihoods are also important.
LANCET PLANETARY HEALTH
(2022)
Article
Medicine, General & Internal
Manoj Sivan, Trisha Greenhalgh, Julie Lorraine Darbyshire, Ghazala Mir, Rory J. O'Connor, Helen Dawes, Darren Greenwood, Daryl O'Connor, Mike Horton, Stavros Petrou, Simon de Lusignan, Vasa Curcin, Erik Mayer, Alexander Casson, Ruairidh Milne, Clare Rayner, Nikki Smith, Amy Parkin, Nick Preston, Brendan Delaney
Summary: This study aims to optimize the care for Long COVID, including improving access, reducing inequalities, assisting self-management, and providing guidance for primary care. The research will systematically analyze current practices and iteratively improve care pathways to establish a 'gold standard' of care.