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In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a(More)
Identifying molecular connections between developmental processes and disease can lead to new hypotheses about health risks at all stages of life. Here we introduce a new approach to identifying significant connections between gene sets and disease genes, and apply it to several gene sets related to human development. To overcome the limits of incomplete(More)
MOTIVATION It has long been hypothesized that incorporating models of network noise as well as edge directions and known pathway information into the representation of protein-protein interaction (PPI) networks might improve their utility for functional inference. However, a simple way to do this has not been obvious. We find that diffusion state distance(More)
Intensive in vitro studies on the neurotoxicity of amyloid beta have been conducted for decades; however, a three-dimensional neuronal tissue model for Alzheimer's disease has not yet been achieved. In this study, we developed size-controllable networked neurospheres comprised of cerebral cortical neuronal cells that mimics the cytoarchitecture of the(More)
There has been a growing need for in vitro models of neurodegenerative diseases such as Alzheimer's disease that would enable a better understanding of etiology and faster development of treatment strategies. However, meeting this demand has been held back by the limited ability to mimic the in vivo microenvironment in an in vitro system. Here, we developed(More)
Transmembrane protein 39A (TMEM39A) belongs to the TMEM39 family. TMEM39A gene is a susceptibility locus for multiple sclerosis. In addition, TMEM39A seems to be implicated in systemic lupus erythematosus. However, any possible involvement of TMEM39A in cancer remains largely unknown. In the present report, we provide evidence that TMEM39A may play a role(More)
The encapsulation of living cells in a variety of soft polymers or hydrogels is important, particularly, for the rehabilitation of functional tissues capable of repairing or replacing damaged organs. Cellular encapsulation segregates cells from the surrounding tissue to protect the implanted cell from the recipient's immune system after transplantation.(More)
UNLABELLED Alcohol-induced liver injury is the most common liver disease in which fatty acid metabolism is altered. It is thought that altered NAD(+)/NADH redox potential by alcohol in the liver causes fatty liver by inhibiting fatty acid oxidation and the activity of tricarboxylic acid cycle reactions. β-Lapachone (βL), a naturally occurring quinone, has(More)