Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies

Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive pr

Neural network analysis identifies scaffold properties necessary for in vitro chondrogenesis in elastin-like polypeptide biopolymer scaffolds.

The successful design of biomaterial scaffolds for articular cartilage tissue engineering requires an understanding of the impact of combinations of material formulation parameters on diverse and competing functional outcomes of biomaterial performance. This study sought to explore the use of a type of unsupervised artificial network, a self-organizing map, to identify relationships between scaffold formulation parameters (crosslink density, molecular weight, and concentration) and 11 such outcomes (including mechanical properties, matrix accumulation, metabolite usage and production, and histological appearance) for scaffolds formed from crosslinked elastin-like polypeptide (ELP) hydrogels. The artificial neural network recognized patterns in functional outcomes and provided a set of relationships between ELP formulation parameters and measured outcomes. Mapping resulted in the best mean separation amongst neurons for mechanical properties and pointed to crosslink density as the strongest predictor of most outcomes, followed by ELP concentration. The map also grouped formulations together that simultaneously resulted in the highest values for matrix production, greatest changes in metabolite consumption or production, and highest histological scores, indicating that the network was able to recognize patterns amongst diverse measurement outcomes. These results demonstrated the utility of artificial neural network tools for recognizing relationships in systems with competing parameters, toward the goal of optimizing and accelerating the design of biomaterial scaffolds for articular cartilage tissue engineering.

Network analysis of 2-mode data

Network analysis is distinguished from traditional social science by the dyadic nature of the standard data set. Whereas in traditional social science we study monadic attributes of individuals, in network analysis we study dyadic attributes of pairs of individuals. These dyadic attributes (e.g. social relations) may be represented in matrix form by a square 1-mode matrix. In contrast, the data in traditional social science are represented as 2-mode matrices. However, network analysis is not completely divorced from traditional social science, and often has occasion to collect and analyze 2-mode matrices. Furthermore, some of the methods developed in network analysis have uses in analysing non-network data. This paper presents and discusses ways of applying and interpreting traditional network analytic techniques to 2-mode data, as well as developing new techniques. Three areas are covered in detail: displaying 2-mode data as networks, detecting clusters and measuring centrality.