Llamanade: an open-source computational pipeline for robust nanobody humanization

Nanobodies (Nbs) have recently emerged as a promising class of antibody fragments for biomedical and therapeutic applications. Despite having marked physicochemical properties, Nbs are derived from camelids and may require "humanization" to improve translational potentials for clinical trials. Here we have systematically analyzed the sequence and structural properties of Nbs based on NGS (next-generation sequencing) databases and high-resolution structures. Our analysis reveals substantial framework diversities and underscores the key differences between Nbs and human Immunoglobulin G (IgG) antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen-binding, providing insights into Nb humanization. Based on big data analysis, we developed "Llamanade", a user-friendly, open-source to facilitate rational humanization of Nbs. Using Nb sequence as input, Llamanade provides information on the sequence features, model structures, and optimizes solutions to humanize Nbs. The full analysis for a given Nb takes less than a minute on a local computer. To demonstrate the robustness of this tool, we applied it to successfully humanize a cohort of structurally diverse and highly potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a web server to support the development of a rapidly expanding repertoire of therapeutic Nbs into safe and effective trials.

Electronic educational resource "Entertaining Informatics"

The article describes the electronic educational resource "Entertaining Informatics" for secondary schools, the use of which is aimed at implementing a system activity approach in the educational process to achieve students not only subject results, but also metasubject and personal ones.The resource can be used both by teachers in the educational process and by students for independent work. The use of the application in the classroom and outside the classroom allows to increase the efficiency of learning, create a productive atmosphere and interest of students in the studied material, helps to increase cognitive interest, the formation of universal educational actions of students, is aimed at personality oriented and individual learning.The application does not require special installation on a local computer; to work with the application, you only need a modern browser and Internet access. The student can work with the resource both at school and at home, both on a personal computer and on smartphone and tablet. You can complete assignments on the interactive whiteboard. The teacher can include resource elements in their courses in the Learning Management System Moodle by adding them as an external application.

Internet Based Control System Design

The thesis presents a novel Internet-based controller designed with the remote controller computer synchronizing its clock with the local computer. An observer-based state feedback control strategy is proposed to compensate the Internet delay and improve the system performance. Asymptotic stability of the closed-loop system is achieved without the assumption of reliable transmission from the controller computer to the local computer, which reduces the requirement for high performance Internet access. Computer simulations are conducted to evaluate the proposed control strategy, and the results have confirmed its effectiveness. The experimental result have demonstrated the supreme performance of the proposed control strategy.

Internet Based Control System Design

The thesis presents a novel Internet-based controller designed with the remote controller computer synchronizing its clock with the local computer. An observer-based state feedback control strategy is proposed to compensate the Internet delay and improve the system performance. Asymptotic stability of the closed-loop system is achieved without the assumption of reliable transmission from the controller computer to the local computer, which reduces the requirement for high performance Internet access. Computer simulations are conducted to evaluate the proposed control strategy, and the results have confirmed its effectiveness. The experimental result have demonstrated the supreme performance of the proposed control strategy.

Cloud-Native Repositories for Big Scientific Data

Scientific data has traditionally been distributed via downloads from data server to local computer. This way of working suffers from limitations as scientific datasets grow towards the petabyte scale. A “cloud-native data repository,” as defined in this paper, offers several advantages over traditional data repositories—performance, reliability, cost-effectiveness, collaboration, reproducibility, creativity, downstream impacts, and access & inclusion. These objectives motivate a set of best practices for cloud-native data repositories: analysis-ready data, cloud-optimized (ARCO) formats, and loose coupling with data-proximate computing. The Pangeo Project has developed a prototype implementation of these principles by using open-source scientific Python tools. By providing an ARCO data catalog together with on-demand, scalable distributed computing, Pangeo enables users to process big data at rates exceeding 10 GB/s. Several challenges must be resolved in order to realize cloud computing’s full potential for scientific research, such as organizing funding, training users, and enforcing data privacy requirements.