![]() ![]() Regenerative medicine aims to repair organs or tissues that have congenital abnormalities, or that have been damaged by disease, aging, or trauma, and to restore or at least improve their native function. In the present systematic review, we highlight the potential therapeutic effects of exosomes in the context of NDDs and neurological diseases by targeting the PI3K/Akt/mTOR signaling pathway. Due to their ability to cross the blood-brain barrier, these nano-sized structures have been introduced as proper vehicles for central nervous system drug delivery by multiple studies. Exosomes significantly take part in the intercellular communications due to their specific features including low immunogenicity, flexibility, and great tissue/cell penetration capabilities. Exosomes are nanoscale membrane-bound carriers that can be secreted by cells and carry several cargoes, including proteins, nucleic acids, lipids, and metabolites. Considering the functional and structural aspects of the blood-brain barrier, drug delivery to the central nervous system is relatively challenging. During the aforementioned inflammatory/apoptotic/oxidative stress procedures, the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) pathway plays a crucial role. Recent studies have indicated that apoptosis, inflammation, and oxidative stress are the main players of NDDs and have critical roles in neurodegenerative processes. Neurological diseases affect millions of people worldwide. We intend that readers be able to quickly and economically incorporate Cytoscape app functionality as reproducible workflows that scale independently to large data sets and production runs.As major public health concerns associated with a rapidly growing aging population, neurodegenerative diseases (NDDs) and neurological diseases are important causes of disability and mortality. They are written by the app authors themselves according to a template that calls for explaining newly available functions, how they can be called, and with real world examples. This collection of Cytoscape app articles at F1000Research is intended to serve as a resource to researchers (as workflow authors) and app developers to understand the features and interfaces exposed by automation-enabled apps. As of March, 2018, app authors upgraded and released 22 apps. For an app to be callable, it must be upgraded to support automation via either a Commands or Functions interface. In 2018, Cytoscape Automation was created to enable external workflows to also call functionality in apps. ![]() Finally, external workflows enable reproducibility not available using Cytoscape’s standard mouse/keyboard/display interaction mode. Furthermore, such workflows can more easily integrate external applications (e.g., GenePattern and iGraph) and multiple large datasets. By authoring such workflows in common languages (such as R and Python), users can combine the best features of Cytoscape with those available in language-specific libraries, thus creating new value much more quickly and cheaply than writing conventional Cytoscape apps. In 2014, the CyREST app 3 was created to allow external programs to exercise core Cytoscape functionality as part of custom workflows. To date, Cytoscape users can choose among over 330 apps written by over 550 authors. Most importantly, it also enables and encourages users to add extensions (called apps) that deliver custom features important for specific workflows (e.g., ClueGO 2 for enrichment analysis relative to various ontologies). ![]() At heart, Cytoscape provides basic network analysis functionality (e.g., network import/export, network data analysis, visualization and layout) in a menu-driven desktop format. Cytoscape is an open source software platform for interactive analysis, integration and visualization of networks and network data 1.
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