Brohl, F. | bioRxiv Science

bioRxiv2024

NERVE 2.0: boosting the New Enhanced Reverse Vaccinology Environment via artificial intelligence and a user-friendly web interface

BackgroundVaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills. ResultsWe report here on the development and release of NERVE 2.0 (available at: https://nerve-bio.org) which keeps the original integrative and modular approach of NERVE, while showing higher predictive performance than its previous version and other web-RV programs (Vaxign and Vaxijen). We renewed some of its modules and added innovative ones, such as Loop Razor, to recover fragments of promising vaccine candidates or epitopepredict for the epitope prediction binding affinities and population coverage. Along with two newly built AI (Artificial Intelligence)-based models: ESPAAN and Virulent. To improve user-friendliness, NERVE was shifted to a tutored, web-based interface, with a noSQL-database to consent the user to submit, obtain and retrieve analysis results at any moment. ConclusionsWith its redesigned and updated environment, NERVE 2.0 allows customisable and refinable bacterial protein vaccine analyses to all different kinds of users.

bioinformatics↗

bioRxiv2023

Detection of spatially-localized sounds is robust to saccades and concurrent eye movement-related eardrum oscillations (EMREOs)

Hearing is an active process and recent studies show that even the ear is affected by cognitive states or motor actions. One example are movements of the eardrum induced by saccadic eye movements - known as "eye movement-related eardrum oscillations" (EMREOs). While these are systematically shaped by the direction and size of saccades, the consequences of saccadic eye movements and their resulting EMREOs for hearing remain unclear. We here studied their implications for the detection of near-threshold clicks in human participants. Across three experiments sound detection was not affected by their time of presentation relative to saccade onset, by saccade amplitude or direction. While the EMREOs were shaped by the direction and amplitude of the saccadic movement, inducing covert shifts in spatial attention did not affect the EMREO, suggesting that this signature of active sensing is restricted to overt changes in visual focus. Importantly, in our experiments fluctuations in the EMREO amplitude were not related to detection performance, at least when monaural cues are sufficient. Hence while eye movements may shape the transduction of acoustic information the behavioral implications remain unclear.

neuroscience↗