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Hosaka, T.

Publications and source records attributed to Hosaka, T..

4 recordsLinked to original sources

Graph neural networks for integrated information and major complex estimation

This study investigates the potential of graph neural networks (GNNs) for estimating the system-level integrated information and major complex in integrated information theory (IIT) 3.0. Owing to the hierarchical complexity of IIT 3.0, tasks such as calculating integrated information and identifying major complex are computationally prohibitive for large systems, thereby restricting the applicability of IIT 3.0 to small systems. To overcome this difficulty, we propose a GNN model with transformer convolutional layers characterized by multi-head attention mechanisms for estimating the major complex and its integrated information. In our approach, exact solutions for integrated information and major complex are obtained for systems with 5, 6, and 7 nodes, and two evaluations are conducted: (1) a non-extrapolative setting in which the model is trained and tested on a mixture of systems with 5, 6, and 7 nodes, and (2) an extrapolative setting in which systems with 5 and 6 nodes are used for training and systems with 7 nodes are used for testing. The results indicate that the estimation performance in the extrapolative setting remains comparable to that in the non-extrapolative setting, showing no significant degradation. In an additional experiment, the model is trained on systems with 5, 6, and 7 nodes and tested on a larger system of 100 nodes, composed of two subsystems of 50 nodes each, with limited inter-subsystem connectivity resembling a split-brain configuration. When the connectivity between the subsystems is low, "local integration" emerges, meaning that a single subsystem forms a major complex. As the connectivity increases, local integration rapidly disappears, and the integrated information gradually rises toward "global integration," in which a large portion of the entire system forms a major complex. Overall, our findings suggest that GNNs can potentially be used for estimating integrated information, major complex, and other IIT-related quantities. Author summaryUnderstanding consciousness is one of the most profound challenges in science. Integrated information theory (IIT) provides a solution to this problem by assessing how information is intrinsically unified within a system, suggesting that consciousness emerges from this integrated structure. However, calculating the extent of this integration in large systems, e.g., the brain, is an extraordinarily complex task; such a calculation is currently feasible only in small systems. Our study explores how graph neural networks (GNNs), a type of deep learning model designed for analyzing graph structures, can estimate IIT-related measures without the intricate calculations required by IIT. By training GNNs on small-sized systems and testing them on more complex configurations, we find that GNN models are a promising candidate for approximating the key measures of information integration and identifying regions of high integration, known as "major complex," which is considered essential for consciousness. This study opens possibilities for using artificial intelligence to model larger brain-like networks, potentially offering new insights into the nature of consciousness and the inner workings of complex systems.

neuroscience↗

Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating

Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in proteorhodopsins, proton pump rhodopsins abundant in marine environments. Here, using marine bacterial isolates, we detected energy transfer from a carotenoid (myxol) to retinal not only in proteorhodopsin but also in the chloride ion-pumping rhodopsin. Carotenoid binding improved the light utilization efficiency of the proteorhodopsin by accelerating the photocycle, together with facilitating light-harvesting. The carotenoid-binding ability is conserved in rhodopsins of the phylum Bacteroidota, which are widely transcribed in the photic zone. These findings suggest that the distribution of carotenoid-binding rhodopsins is more taxon-specific than previously thought, thus underscoring the importance of carotenoid-binding rhodopsins that provide an extended light utilization strategy in the environmental adaptation of marine bacteria.

microbiology↗

Unidirectional ion transport mechanism of a light-driven chloride pump revealed using X-ray free electron lasers

Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10 s and 1 ms time-points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied with a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3. SignificanceLight-driven chloride pumps have been identified in various species, including archaea and marine flavobacteria. The function of ion transportation controllable by light is utilized for optogenetics tools in neuroscience. Chloride pumps differ among species, in terms of amino acid homology and structural similarity. Our time-resolved crystallographic studies using X-ray free electron lasers reveal the molecular mechanism of halide ion transfer in a light-driven chloride pump from a marine flavobacterium. Our data indicate a common mechanism in chloride pumping rhodopsins, as compared to previous low temperature trapping studies of chloride pumps. These findings are significant not only for further improvements of optogenetic tools but also for a general understanding of the ion pumping mechanisms of microbial rhodopsins.

molecular biology↗

Assessing the impacts of climate change on reproductive phenology in tropical rainforests of Southeast Asia

In humid forests in Southeast Asia, many species from dozens of plant families flower gregariously and fruit synchronously at irregular multi-year intervals1-4. Little is known about how climate change will impact these community-wide mass reproductive events. Here, we perform a comprehensive analysis of reproductive phenology and its environmental drivers based on a monthly reproductive phenology record from 210 species in 41 families in peninsular Malaysia. We find that the proportion of flowering and fruiting species decreased from 1976 to 2010. Using a phenology model with inputs obtained from general circulation models, we show that low-temperature flowering cues became less available during the monitoring period and will further decrease in the future, leading to decreased flowering opportunities in 57% of species in the Dipterocarpaceae family. Our results highlight the vulnerability of and variability in phenological responses across species in tropical ecosystems that differ from temperate and boreal biomes.

ecology↗