One of the most widely used biomimicry algorithms is the Particle Swarm Optimization (PSO). Since its introduction in 1995, it has caught the attention of both researchers and academicians as a way of solving various optimization problems, such as in the fields of engineering and medicine, to computer image processing and mission critical operations. PSO has been widely applied in the field of swarm robotics, however, the trend of creating a new variant PSO for each swarm robotic project is alarming. We investigate the basic properties of PSO algorithms relevant to the implementation of swarm robotics and characterize the limitations that promote this trend to manifest. Experiments were conducted to investigate the convergence properties of three PSO variants (original PSO, SPSO and APSO) and the global optimum and local optimal of these PSO algorithms were determined. We were able to validate the existence of premature convergence in these PSO variants by comparing 16 functions implemented alongside the PSO variant. This highlighted the fundamental flaws in most variant PSOs, and signifies the importance of developing a more generalized PSO algorithm to support the implementation of swarm robotics. This is critical in curbing the influx of custom PSO and theoretically addresses the fundamental flaws of the existing PSO algorithm.

A common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins with similar binding sites may bind to similar drugs, the 3D substructure similarity data can be used to identify similar sites in other proteins that are not known targets. The Drug ReposER (DRug REPOSitioning Exploration Resource) web server is designed to identify potential targets for drug repurposing based on sub-structural similarity to the binding interfaces of known drug binding sites. The application has pre-computed amino acid arrangements from protein structures in the Protein Data Bank that are similar to the 3D arrangements of known drug binding sites thus allowing users to explore them as alternative targets. Users can annotate new structures for sites that are similarly arranged to the residues found in known drug binding interfaces. The search results are presented as mappings of matched sidechain superpositions. The results of the searches can be visualized using an integrated NGL viewer. The Drug ReposER server has no access restrictions and is available at http://mfrlab.org/drugreposer/.

A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database—http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.

The applicability of machine learning-based analysis in the field of biomedical field has been very beneficial in determining the biological mechanism and validation for a wide range of biological scenarios. This approach is also gaining momentum in various stem cells research activities, specifically for stem cells characterization and differentiation pattern. The adoption of similar computational approaches to study and assess biosafety and bioefficacy risks of stem cells for clinical application is the next progression. In particular where tumorigenicity has been one of the major concerns in stem cells therapy. There are many factors influencing tumorigenicity in stem cells which may be difficult to capture under conventional laboratory settings. In addition, given the possible multifactorial etiology of tumorigenicity, defining a one-size-fits-all strategy to test such risk in stem cells might not be feasible and may compromise stem cells safety and effectiveness in therapy. Given the increase in biological datasets (which is no longer limited to genomic data) and the advancement of health informatics powered by state-of-the-art machine learning algorithms, there exists a potential for practical application in biosafety and bioefficacy of stem cells therapy. Here, we identified relevant machine learning approaches and suggested protocols intended for stem cells research focusing on the possibility of its usage for stem cells biosafety and bioefficacy assessment. Ultimately, generating models that may assist healthcare professionals to make a better-informed decision in stem cell therapy.

Large-scale companies across various sectors maintain substantial IT infrastructure to support their operations and provide quality services for their customers and employees. These IT operations are managed by teams who deal directly with incident reports (i.e., those generated automatically through autonomous systems or human operators). (1) Background: Early identification of major incidents can provide a significant advantage for reducing the disruption to normal business operations, especially for preventing catastrophic disruptions, such as a complete system shutdown. (2) Methods: This study conducted an empirical analysis of eleven (11) state-of-the-art models to predict the severity of these incidents using an industry-led use-case composed of 500,000 records collected over one year. (3) Results: The datasets were generated from three stakeholders (i.e., agency, customer, and employee). Separately, the bidirectional encoder representations from transformers (BERT), the robustly optimized BERT pre-training approach (RoBERTa), the enhanced representation through knowledge integration (ERNIE 2.0), and the extreme gradient boosting (XGBoost) methods performed the best for the agency records (93% AUC), while the convolutional neural network (CNN) was the best model for the rest (employee records at 95% AUC and customer records at 74% AUC, respectively). The average prediction horizon was approximately 150 min, which was significant for real-time deployment. (4) Conclusions: The study provided a comprehensive analysis that supported the deployment of artificial intelligence for IT operations (AIOps), specifically for incident management within large-scale organizations.

The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.