The relationship between pH and enzyme catalytic activity, as well as the optimal pH (pHopt) at which enzymes function, is crucial for biotechnological applications. Consequently, computational methods that predict pHoptwould significantly benefit enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at a specific pH, and by promoting a better understanding of how sequence affects enzyme function in relation to pH. In this study, we present EpHod (Enzyme pH optimum prediction with deep learning), which is a deep semi-supervised language model for predicting enzyme pHoptdirectly from the protein sequence. By evaluating various machine learning methods with extensive hyperparameter optimization (training over 4,000 models in total), we find that semi-supervised methods that utilize language model embeddings, including EpHod, achieve the lowest error in predicting pHopt. From sequence data alone, EpHod learns structural and biophysical features that relate to pHopt, including proximity of residues to the catalytic center and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pHoptprediction and could potentially speed up the development of improved enzyme technologies.
This article addresses the following question: Is it possible, and if so, to what extent, to draw upon sources from different contexts or disciplines to perform theological research? The first part describes the historical origins and contemporary application of the handmaiden model of theology (“philosophy is the handmaiden of theology,” philosophia ancilla theologiae). In the second section, I consider two closely related objections to this model, namely confirmation bias (or eisegesis) and anachronism. Section three demonstrates that while these objections should be carefully considered, they do not preclude altogether the possibility of engaging with sources across temporal or disciplinary boundaries. Gadamer’s hermeneutical philosophy grounds the possibility of such interaction. The remainder of the article provides a more specific vision of how this model can be practiced. First, I look to the theological tradition itself, in particular Augustine’s interpretive principles as applied to Genesis 1 (Confessiones 12) and Michael Fishbane’s appropriation of the Jewish hermeneutical tradition. Finally, the contemporary scholars William Desmond and Cyril O’Regan exemplify the responsible constructive engagement with the sources. I argue that practitioners of the handmaiden model must take seriously objections to and concerns about their methodology. Nonetheless, once critically adapted to present circumstances, this model is feasible for a contemporary scholarly context. One can respect the integrity of the sources while also interpreting them in ways which apply to present theological interests. A key implication of this research is that for each to function properly, historical theology and systematic theology must consistently interact with each other.
Augustine's understanding of knowledge is grounded in Christ, the eternal wisdom incarnate. Because Christ is the source and summit of knowledge, one's approach to the fullness of truth must pass through prayer, not least of all its highest form, the divine liturgy. With this point established, we proceed to consider Augustine's exegesis of certain key scriptural passages, in particular Matthew 6 and John 17. in the former, Augustine draws from the Pater noster in order to show how he understands the importance of living according to the true meaning of one's prayers, and this with respect to certain key controversies he faced during his episcopate. We conclude by looking at his discussion of Christ's high-Priestly Prayer (John 17), suggesting that Augustine sees here a unique self-disclosure of the inner life of the trinity, which provides the template for transforming oneself in such a way that one does not simply pray but even becomes prayer.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.