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  1. Article ; Online: Friedel-Crafts reactions for biomolecular chemistry.

    Ohata, Jun

    Organic & biomolecular chemistry

    2024  

    Abstract: Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used ... ...

    Abstract Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used synthetic methods for the preparation of small molecules but their use in biological and medical fields is relatively less frequent than the other reactions, possibly owing to the notion of their plausible incompatibility with biological systems. This review demonstrates advances in Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or -assisted processes, these reactions have garnered considerable interest in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated their utility for the construction and functionalization of all the four major biomolecules (
    Language English
    Publishing date 2024-04-16
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2097583-1
    ISSN 1477-0539 ; 1477-0520
    ISSN (online) 1477-0539
    ISSN 1477-0520
    DOI 10.1039/d4ob00406j
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  2. Article ; Online: Incremental Learning of Goal-Directed Actions in a Dynamic Environment by a Robot Using Active Inference.

    Matsumoto, Takazumi / Ohata, Wataru / Tani, Jun

    Entropy (Basel, Switzerland)

    2023  Volume 25, Issue 11

    Abstract: This study investigated how a physical robot can adapt goal-directed actions in dynamically changing environments, in real-time, using an active inference-based approach with incremental learning from human tutoring examples. Using our active inference- ... ...

    Abstract This study investigated how a physical robot can adapt goal-directed actions in dynamically changing environments, in real-time, using an active inference-based approach with incremental learning from human tutoring examples. Using our active inference-based model, while good generalization can be achieved with appropriate parameters, when faced with sudden, large changes in the environment, a human may have to intervene to correct actions of the robot in order to reach the goal, as a caregiver might guide the hands of a child performing an unfamiliar task. In order for the robot to learn from the human tutor, we propose a new scheme to accomplish incremental learning from these proprioceptive-exteroceptive experiences combined with mental rehearsal of past experiences. Our experimental results demonstrate that using only a few tutoring examples, the robot using our model was able to significantly improve its performance on new tasks without catastrophic forgetting of previously learned tasks.
    Language English
    Publishing date 2023-10-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e25111506
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  3. Article: Small-Molecule CO2 Donors Accelerate Three-Component Peptide/Protein Bioconjugation with Alkylazides and Phosphines in Ionic Liquids

    Colella, Brandon M. / Ohata, Jun

    Synlett

    2023  

    Abstract: Development of chemical modification techniques for peptides and proteins has been facilitated by a set of multicomponent reactions to date. This Letter demonstrates the use of small-molecule CO 2 donors to promote reaction efficiency of the coupling of ... ...

    Abstract Development of chemical modification techniques for peptides and proteins has been facilitated by a set of multicomponent reactions to date. This Letter demonstrates the use of small-molecule CO 2 donors to promote reaction efficiency of the coupling of alkylamine on peptides and proteins with azide-derived iminophosphorane and carbon dioxide.
    Keywords multicomponent reaction ; CO ; donor ; peptide ; protein ; amine ; azide ; phosphine
    Language English
    Publishing date 2023-11-16
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 2042012-2
    ISSN 1437-2096 ; 0936-5214
    ISSN (online) 1437-2096
    ISSN 0936-5214
    DOI 10.1055/a-2212-7816
    Database Thieme publisher's database

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  4. Article ; Online: Turn-Taking Mechanisms in Imitative Interaction: Robotic Social Interaction Based on the Free Energy Principle.

    Wirkuttis, Nadine / Ohata, Wataru / Tani, Jun

    Entropy (Basel, Switzerland)

    2023  Volume 25, Issue 2

    Abstract: This study explains how the leader-follower relationship and turn-taking could develop in a dyadic imitative interaction by conducting robotic simulation experiments based on the free energy principle. Our prior study showed that introducing a parameter ... ...

    Abstract This study explains how the leader-follower relationship and turn-taking could develop in a dyadic imitative interaction by conducting robotic simulation experiments based on the free energy principle. Our prior study showed that introducing a parameter during the model training phase can determine leader and follower roles for subsequent imitative interactions. The parameter is defined as w, the so-called meta-prior, and is a weighting factor used to regulate the complexity term versus the accuracy term when minimizing the free energy. This can be read as sensory attenuation, in which the robot's prior beliefs about action are less sensitive to sensory evidence. The current extended study examines the possibility that the leader-follower relationship shifts depending on changes in w during the interaction phase. We identified a phase space structure with three distinct types of behavioral coordination using comprehensive simulation experiments with sweeps of w of both robots during the interaction. Ignoring behavior in which the robots follow their own intention was observed in the region in which both ws were set to large values. One robot leading, followed by the other robot was observed when one w was set larger and the other was set smaller. Spontaneous, random turn-taking between the leader and the follower was observed when both ws were set at smaller or intermediate values. Finally, we examined a case of slowly oscillating w in anti-phase between the two agents during the interaction. The simulation experiment resulted in turn-taking in which the leader-follower relationship switched during determined sequences, accompanied by periodic shifts of ws. An analysis using transfer entropy found that the direction of information flow between the two agents also shifted along with turn-taking. Herein, we discuss qualitative differences between random/spontaneous turn-taking and agreed-upon sequential turn-taking by reviewing both synthetic and empirical studies.
    Language English
    Publishing date 2023-01-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e25020263
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  5. Article ; Online: Iron-sensitive protein conjugates formed with a Wittig reaction precursor in ionic liquid.

    Nizam, Zeinab M / Stowe, Ashton M / Mckinney, Jada K / Ohata, Jun

    Chemical communications (Cambridge, England)

    2023  Volume 59, Issue 81, Page(s) 12160–12163

    Abstract: In this report, formation of protein conjugates with an iron-sensitive enamine linkage is demonstrated through the ionic liquid-based bioconjugation method. ...

    Abstract In this report, formation of protein conjugates with an iron-sensitive enamine linkage is demonstrated through the ionic liquid-based bioconjugation method.
    Language English
    Publishing date 2023-10-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc03825d
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  6. Article ; Online: Comparison of 2,5-dimethyl-4-hydroxy-3(2H)-furanone, a volatile odor compound generated by the Maillard reaction, in cooked meat of various animal species and parts.

    Yokoyama, Issei / Ohata, Motoko / Komiya, Yusuke / Nagasao, Jun / Arihara, Keizo

    Animal science journal = Nihon chikusan Gakkaiho

    2023  Volume 94, Issue 1, Page(s) e13813

    Abstract: 2,5-Dimethyl-4-hydroxy-3(2H)-furanone (DMHF), a compound having a sweet caramel-like odor, is one of the major compounds generated by the Maillard reaction. DMHF could affect the palatability of cooked and processed foods such as meat, while its ... ...

    Abstract 2,5-Dimethyl-4-hydroxy-3(2H)-furanone (DMHF), a compound having a sweet caramel-like odor, is one of the major compounds generated by the Maillard reaction. DMHF could affect the palatability of cooked and processed foods such as meat, while its inhalation induces several physiological functions. However, basic findings of DMHF generation in meat remain unclear. In this study, we compared the amount of DMHF in cooked meat of various animal meat (Japanese black cattle beef, Australian beef, pork, and chicken) and parts (round, loin, thigh, and breast). Meat samples were heated at 230°C, and then the amount of DMHF was measured using the solvent extraction methods. Moreover, the substrates (total free amino acid and glucose) used for the Maillard reaction were also measured to elucidate the relation between DMHF generation and nutrients in meat. DMHF was detected in all cooked meat samples, suggesting that DMHF is generated in meat regardless of animal species and parts. A significant positive correlation was observed between the DMHF generation and glucose content in the round and thigh parts. Our results suggest that DMHF generation during meat cooking would be regulated by the glucose content.
    MeSH term(s) Cattle ; Animals ; Odorants ; Maillard Reaction ; Australia ; Glucose
    Chemical Substances furaneol (3658-77-3) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2023-03-03
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2095161-9
    ISSN 1740-0929 ; 1344-3941
    ISSN (online) 1740-0929
    ISSN 1344-3941
    DOI 10.1111/asj.13813
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  7. Article: Translation of a Phosphine- and Azide-Based Reaction to Chemical Modification of Biomolecules in Ionic Liquid

    Uzoewulu, Chiamaka P. / Ohata, Jun

    Synlett

    2022  Volume 33, Issue 19, Page(s) 1879–1883

    Abstract: The difference of reaction design principles between traditional, small-molecule synthetic chemistry and biomolecular chemical reactions prevented the simple translation of small-molecule chemistry into biomolecular reactions. One of the key challenges ... ...

    Abstract The difference of reaction design principles between traditional, small-molecule synthetic chemistry and biomolecular chemical reactions prevented the simple translation of small-molecule chemistry into biomolecular reactions. One of the key challenges of bioconjugation, or reactions on biomolecules, are the necessity of aqueous solutions as the solvent. In this Synpacts article, we describe our pursuit of using an ionic liquid as a nonaqueous reaction medium to conduct phosphine- and azide-based bioconjugation reactions.
    Keywords bioconjugation ; ionic liquid ; amine ; azide ; phosphine ; phosphazide ; iminophosphorane
    Language English
    Publishing date 2022-07-24
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 2042012-2
    ISSN 1437-2096 ; 0936-5214
    ISSN (online) 1437-2096
    ISSN 0936-5214
    DOI 10.1055/a-1908-2066
    Database Thieme publisher's database

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  8. Article: Investigation of the Sense of Agency in Social Cognition, Based on Frameworks of Predictive Coding and Active Inference: A Simulation Study on Multimodal Imitative Interaction.

    Ohata, Wataru / Tani, Jun

    Frontiers in neurorobotics

    2020  Volume 14, Page(s) 61

    Abstract: When agents interact socially with different intentions (or wills), conflicts are difficult to avoid. Although the means by which social agents can resolve such problems autonomously has not been determined, dynamic characteristics of agency may shed ... ...

    Abstract When agents interact socially with different intentions (or wills), conflicts are difficult to avoid. Although the means by which social agents can resolve such problems autonomously has not been determined, dynamic characteristics of agency may shed light on underlying mechanisms. Therefore, the current study focused on the sense of agency, a specific aspect of agency referring to congruence between the agent's intention in acting and the outcome, especially in social interaction contexts. Employing predictive coding and active inference as theoretical frameworks of perception and action generation, we hypothesize that regulation of complexity in the evidence lower bound of an agent's model should affect the strength of the agent's sense of agency and should have a significant impact on social interactions. To evaluate this hypothesis, we built a computational model of imitative interaction between a robot and a human via visuo-proprioceptive sensation with a variational Bayes recurrent neural network, and simulated the model in the form of pseudo-imitative interaction using recorded human body movement data, which serve as the counterpart in the interactions. A key feature of the model is that the complexity of each modality can be regulated differently by changing the values of a hyperparameter assigned to each local module of the model. We first searched for an optimal setting of hyperparameters that endow the model with appropriate coordination of multimodal sensation. These searches revealed that complexity of the vision module should be more tightly regulated than that of the proprioception module because of greater uncertainty in visual information flow. Using this optimally trained model as a default model, we investigated how changing the tightness of complexity regulation in the entire network after training affects the strength of the sense of agency during imitative interactions. The results showed that with looser regulation of complexity, an agent tends to act more egocentrically, without adapting to the other. In contrast, with tighter regulation, the agent tends to follow the other by adjusting its intention. We conclude that the tightness of complexity regulation significantly affects the strength of the sense of agency and the dynamics of interactions between agents in social settings.
    Language English
    Publishing date 2020-09-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2453002-5
    ISSN 1662-5218
    ISSN 1662-5218
    DOI 10.3389/fnbot.2020.00061
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  9. Article: Correction: Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids.

    Ishizawa, Seiya / Tumurkhuu, Munkhtuya / Gross, Elizabeth J / Ohata, Jun

    Chemical science

    2022  Volume 13, Issue 22, Page(s) 6749–6751

    Abstract: This corrects the article DOI: 10.1039/D1SC05204G.]. ...

    Abstract [This corrects the article DOI: 10.1039/D1SC05204G.].
    Language English
    Publishing date 2022-05-30
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d2sc90102a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Human-Robot Kinaesthetic Interaction Based on Free Energy Principle

    Sawada, Hiroki / Ohata, Wataru / Tani, Jun

    2023  

    Abstract: The current study investigated possible human-robot kinaesthetic interaction using a variational recurrent neural network model, called PV-RNN, which is based on the free energy principle. Our prior robotic studies using PV-RNN showed that the nature of ... ...

    Abstract The current study investigated possible human-robot kinaesthetic interaction using a variational recurrent neural network model, called PV-RNN, which is based on the free energy principle. Our prior robotic studies using PV-RNN showed that the nature of interactions between top-down expectation and bottom-up inference is strongly affected by a parameter, called the meta-prior, which regulates the complexity term in free energy.The study also compares the counter force generated when trained transitions are induced by a human experimenter and when untrained transitions are induced. Our experimental results indicated that (1) the human experimenter needs more/less force to induce trained transitions when $w$ is set with larger/smaller values, (2) the human experimenter needs more force to act on the robot when he attempts to induce untrained as opposed to trained movement pattern transitions. Our analysis of time development of essential variables and values in PV-RNN during bodily interaction clarified the mechanism by which gaps in actional intentions between the human experimenter and the robot can be manifested as reaction forces between them.

    Comment: 12 pages, 8 figures, journal paper
    Keywords Computer Science - Robotics
    Subject code 629
    Publishing date 2023-03-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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