![]() Interestingly, EMT triggered by TGF-β was found to be associated with cytostasis and altered cellular metabolism. Therefore, as part of this study, we treated HCC cells with TGF-β and characterized the cellular processes associated with EMT. In spite of its clinical relevance, the cellular events associated with TGF-β-induced EMT and its molecular regulation is poorly elucidated. One of its classical functions involve facilitation of epithelial to mesenchymal transition (EMT), in tumour cells, promoting an invasive phenotype. In this context, one of the major cytokines present in the HCC tumour milieu is the transforming growth factor-β (TGF-β). A better understanding of the cytokine functions and their contributions to disease development is key to design of future therapeutic strategies and reduction of global HCC burden. Which will be interesting for people wanting to implement this kind of workflow (beyond this somewhat narrow – albeit super-fun – scenario :-).Hepatocellular carcinoma (HCC) frequently unfolds under an inflammatory condition, which is a hub for a plethora of cytokines. It’s unlikely I’ll go the extra step to make the code create associative geometry, but it will certainly show you how it’s possible to bring a snapshot of data across from a graph layout system such Cytoscape into an AutoCAD drawing. The code is basically ready to share but I’m going to finish up the “Export to AutoCAD” capability before I post it here. Here’s a static image of a more extensive graph I mapped over an additional minute or so: When you come to a location that already exists in the graph, its node will get highlighted and subsequent new nodes will be positioned relative to that. The graph is mostly laid out relative to the points of the compass, but you can position nodes manually as you go. Right now it’s launched using a separate command – ZMAP – but could also be launched by the ZORK command directly. Here’s the palette in action – expanded to the extent of the video recording so it’s nicely visible. It ended up being straightforward to integrate Cytoscape into AutoCAD: I chose to use a palette, rather than a document window, as this sets us up nicely for bringing the geometry across into AutoCAD (something we’ll see in another post). We’ll see whether it makes sense to use Cola, too, or something else. I’d thought Cola.js might be a candidate but ended up settling on Cytoscape.js: Cola.js is just one higher-level layout library that works with Cytoscape.js. I knew I wanted to use a JavaScript library for the graph management. This proved to be straightforward to do and worked a treat, but meant I also then had to tackle the bigger problem of getting the rest of it to work. When I chatted this over with Christer – who had spent many years playing and mapping Zork, as a teenager – he suggested hacking the Z-Machine VM to expose a unique identifier (which certainly exists in the file format) for the current location. I’d already decided I needed to use a graph – rather than a grid – to map Zork, but had stalled when I realised I didn’t have a way to identify locations uniquely: many have the same names and some also get described differently if you’ve been there before. My original, abortive attempts at mapping Zork automatically were based on the assumption that Zork’s map was perfectly recto-linear (which it absolutely isn’t). While I didn’t expect to recreate anything as beautiful as this, I did want to let people capture the essence of the games they play, and provide them some flexibility to control the layout of the map. My favourite is from the mainframe version ( by all accounts it may well be the only that exists from that era): You can find a number of Zork maps online. Something I mentioned in a recent blog post but was reminded of last Thursday while catching up with Christer Janson in San Rafael. These days I typically find jetlag to be a bit of a curse, but this weekend I ended up using it to tackle a fun challenge: generating maps for Z-machine games such as Zork inside AutoCAD. I remember some great trips to Asia, waking up at strange times to experience the dawn, walking the streets and seeing everyday life starting up around me. I mostly despise jetlag but once in a while manage to harness it for something positive.
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