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Comments

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Ultrasound Technique Provides a New Radiation Free Way To Visualize Tumors

macklin01 Re:'Radiation Free' (35 comments)

I suspect the real story here is likely finding a good target (SFRP2), more so than the microbubbles. Finding a specific enough target always seems to be the limiting factor in immunotherapy, nanoparticle-based drug delivery, GNP-based radiothermal therapy, etc.

Now if they could find a good target for more cancers (I definitely agree on breast as a good target--elastography ultrasound is already a big topic of interest there), it could have a nice impact on treatment options. Since you can't really image too frequently by MRI, CT, etc. due to exposure limits, you can't do high-frequency watchful waiting, which biases clinicians and patients towards intervention when they detect something.

In breast cancer, this is a pretty hot topic: all these frequent / early mammograms are detecting lots of DCIS, and the standard thing to do is lumpectomy. But there's growing evidence that these are likely being overtreated, and many if left alone would likely not progress to invasive carcinoma for a long time. But since there's no great way to know on a patient-by-patient basis, and since you can't really keep a close eye on them by frequent imaging, it's tough to do otherwise.

But if you could image the breast cancer really well by ultrasound, you could do such a watchful waiting: image frequently, and so long as there's no change, keep monitoring. (Not sure if this would have have the resolution to detect an in situ cancer like DCIS, though. Will have to read the article.) It would be nice to see such watchful waiting options open up for other cancers where treatment choices are perhaps otherwise unclear.

I've also seen early work attempting to use interference patterns in ultrasound (putting a few piezoelectric membranes at the right spacing, etc.) to induce apoptosis at specific spots. It would be interesting to see if this work could help enhance that ...

about 3 months ago
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3D Printing of Human Tissue To Spark Ethics Debate

macklin01 Re:3D Printing is too complex. There is an easier (234 comments)

I disagree with a lot of the parent's post, but this part is reasonably solved. When you decellularize an ECM, the vessel walls remain intact. Then you reseed with HUVECs (an endothelial cell line), and they tend to find their way back onto the old vessel walls to form a vasculature.

But you are absolutely right that the microarchitecture of the tissue is very, very significant to proper function.

about 3 months ago
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3D Printing of Human Tissue To Spark Ethics Debate

macklin01 Re:3D Printing is too complex. There is an easier (234 comments)

While the ECM molecular components are conserved as you point out in another post, their distribution (e.g., how much collagen IV, matrix-embedded glycoproteins, etc.), stiffness, and microarchitecture vary quite a bit from species to species, organ to organ, and even individual to individual. And this radically affects the phenotype of the cells that you transplant on them. Both cancer and "normal" epithelial cells are known to change their motility, proliferation, and even polarization characteristics based upon the stiffness of the tissue, for example.

And take a look at livers: pig livers have a very thick membrane between hepatic lobules, making them great for textbooks, as you can very clearly see portal triads and central veins and the overall lobular outlines. Human tissue, by contrast, has very thin membranes between lobules that can scarcely be seen in H&E pathology. This makes pig liver ECM a very poor starting point for growing a human organ replacement. When our collaborators build bioengineered liver tissue, they actually start with decellularized ferret livers because their structures are closer to humans than pigs.

This is why a mix of 3-D printing and seeding progenitor cells could be promising in the future. If you could 3-D print the ECM to have the correct spatial distribution and mechanical properties, you'd have a much better starting point when you seed them with progenitor cells to grow the epithelium / parenchyme, HUVECs to grow the vessels, etc.

Aside: I have yet to see XCM in 10+ years of cancer research and tissue biomechanics work. It's ECM.

about 3 months ago
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Stephen Wolfram Developing New Programming Language

macklin01 Re:His next project is interesting (168 comments)

Wolfram announced his latest idea - that there needed to be some kind of pliable material available next to toilets with which to clean one's bum. This material, he said, is going to be really soft, probably a couple of layers thick, and needed to be on some kind of continuous dispenser mechanism which he is developing.

And naturally, he'll call it Wolfram paper. :-)

about 5 months ago
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Google: Our Robot Cars Are Better Drivers Than You

macklin01 Re:Data will get you jailed (722 comments)

I figure there needs to be something similar to the National Vaccine Injury Compensation Program: here, something that makes society safer overall (vaccines) is promoted by reducing the risk of an individual harm (a rare side effect). This says: "Pay in and help make society safer, and if it individually harms you, we've got your back."

So, why not something for driverless cars? You opt into a driverless car with the societal benefit of reduced accidents, and if your driverless car harms you individually (physically or legally), the national defense fund takes over.

about 6 months ago
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NHTSA and DOT Want Your Car To Be Able To Disable Your Cellphone Functions

macklin01 Re:Driver not the only one in the car (405 comments)

Furthermore, the passenger might be helping with the navigation, answering those critical emails, etc ... to help the driver keep focused on the road.

about 10 months ago
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The Balkanization of Chatting

macklin01 Re:iPhone and "txt" messages (242 comments)

this and this are pretty similar. I see this most frequently in multi-person text messages from iPhone, and indeed, in the default txt message client, these often appear as attachments / multimedia instead of text.

about a year ago
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The Balkanization of Chatting

macklin01 Re:iPhone and "txt" messages (242 comments)

Good point. Since I've seen this issue sporadically with multiple iPhones sending messages to Android, I had figured it was more on the iPhone end with a standards-breaking or standards-bending SMS behavior.

about a year ago
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The Balkanization of Chatting

macklin01 Re:iPhone and "txt" messages (242 comments)

BitZtream (692029) wrote: That doesn't happen on iPhones, perhaps its your end thats the problem.

theurge14 (820596) wrote: Sounds like it might be a problem on your phone. I haven't seen this problem at all on iPhones.

[snark]Of course the standards-breaking message sender renders its standards-breaking messages correctly.[/snark]

More seriously, we have:

  • iPhone -> iPhone : no problem
  • non-iPhone -> iPhone : no problem
  • non-iPhone -> Android : no problem
  • iPhone -> Android : textual messages appearing like multimedia attachments

This suggests that iPhone is using iChat or similar to "txt" with other phones and encoding outgoing info in some sort of multimedia or attachment tags within the SMS format.

about a year ago
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The Balkanization of Chatting

macklin01 iPhone and "txt" messages (242 comments)

I can't stress enough how much it drives me up the wall to get text messages on my Android phone from iPhones. Far too often, they show as "multimedia" messages requiring a data connection just to download 5-7 words of text.

Or when an iPhone user sends a txt message to several people, and each "reply to all" response appears as a separate, disjoint SMS thread without the full conversation or context.

about a year ago
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Developers Begin Hunt For a Killer App For Google Glass

macklin01 Re:Privacy and etiquette (155 comments)

The "universal translator" idea had crossed my mind, too. ;-)

about a year ago
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Developers Begin Hunt For a Killer App For Google Glass

macklin01 Re:Privacy and etiquette (155 comments)

Personally, as a guy with hearing loss that's really cutting into those handy consonant sounds above 2000 Hz, I'm thrilled at the idea of real-time "closed captioning" placed under each speaker. Right now, noisy restaurants and lectures can be a bit of a nightmare, even with top-of-the-line hearing aids.

about a year ago
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Programming Immune Cells To Treat Disease

macklin01 Re:Immunology works... (32 comments)

Great answer to this type of comment. :-)

about a year ago
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Programming Immune Cells To Treat Disease

macklin01 Re:Immunology works... (32 comments)

Many thanks from another member of the cancer community. So glad this has shown such tremendous results for you. Hope we can some day understand this better and help more people! All the best wishes for continued health! -- Paul

about a year ago
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International Challenge To Computationally Interpret Protein Function

macklin01 Re:How does it work? (59 comments)

I am not a biologist so forgive me my ignorance but when people say that DNA is the blueprint for an organism I never understand how a bunch of proteins can determine an organism's shape and behavior. Aren't there more factors that determine those things, like the surroundings in which the DNA is used, like chemicals that the growing organism is surrounded with, temperature, etc?

You're absolutely right. Microenvironment -- the cell's chemical, mechanical, and physical environment, determines which genes are switched on, whether those proteins get made, and how and whether they interact with other proteins to alter cell behavior.

This has been a challenge (and perhaps even a failure) of many current genome projects, which are often reductionist to the point of ignoring much of these features, whereas "context" may well be more important than the genome.

There was a big splashy paper in the New England Journal of Medicine last year, where multiple regions of a single tumor were sequenced. It was found that while there were significant differences in the genome across a single tumor, the cell phenotypes (their behavior) was much more convergent. That is, even with significantly different genes, these cells found a way to function similarly when presented a similar environmental context.

about a year ago
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GoDaddy Goes Down, Anonymous Claims Responsibility

macklin01 Re:You think this is a Game? (483 comments)

It's affecting a lot more than commerce.

My cancer research website is down, too. (Only works on computers that had cached the DNS entries.) So much for inviting seminar speakers today.

I'm an academic. I set my site up years ago (before all the SOPA business) and don't have time to muck with moving my site around, hosting DNS here and content there, and the like. I barely have time to maintain content in the middle of a busy research career. I suppose I'm now supposed to be an expert on mathematical modeling + cancer + hosting my own DNS?

It's always worth keeping in mind that these things affect far more than business sites.

about a year and a half ago
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How Long Is Your Morning Commute?

macklin01 The joys of a one-car family (353 comments)

My commute itself is 20-30 minutes.

But as a one-car family, it's 20-30 minutes to get my wife to the bus stop, another 20-30 minutes to get my daughter to day care, and then my own commute.

I'm not honestly sure if this comes out net positive for the environment vs. two cars: two cars would probably cut 10-20 minutes of driving twice daily, but of course adds extra environmental impact of maintaining a second car. It certainly is a net positive on the budget for now, though.

about a year and a half ago
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Software Emulates Organism's Entire Lifespan

macklin01 Re:OO vs real life (86 comments)

Simplified answer:

These models tend to be object-oriented in the sense that a genetics "module" interacts with a protein signaling module, etc. In each module, you'd have the member data (say, a list of all proteins) and member functions (say, a model of the reaction network that discretizes the massive system of ODEs).

The objects then interact. You have well-defined interfaces between these modules to codify currently known (or hypothesized!) biology. For example, members of the proteins module activate certain genes in the genetics module to (eventually) drive synthesis of more proteins.

You write the rules based upon our current state-of-the-art in understanding cell biology, simulate, and see what happens. To the extent that it quantitatively matches experiments, we can assess the underlying hypotheses, refine them, or toss them out.

In this work, it looks like they pulled information from 900 papers on this species of bacterium to simulate 525 genes, God knows how many proteins (genes can encode multiple proteins), and 28 processes.

Notably, there is no spatial component (e.g., transport of proteins, RNAs, cell volume changes, cell mechanics, etc.), but it's an incredible set of work. And to be able to predict phenotype solely based upon the emergent behavior of this network is pretty incredible.

about a year and a half ago
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Ask Slashdot: What To Do With a Math Degree?

macklin01 Re:Research scientist / research assistant ... (416 comments)

(replying to myself): Also, if her statistics are good, she might consider joining the biostatistics core at a med school or medical company. There will be no shortage of clinical trials or other biological experiments where they really need a statistician (or mathematician) to help with experimental design and statistical analysis / hypothesis testing.

about 2 years ago

Submissions

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Sept 14 is red letter day: Black Mesa Half-Life rewrite to be released!

macklin01 macklin01 writes  |  about a year and a half ago

macklin01 writes "Sep. 14 is red letter day: after 8 years of development, the third-party "Black Mesa" rewrite of Half-Life is finally going to be released. This re-writes the original Half-Life with the HalfLife2 Source engine, along with significant improvements to the graphics and soundtrack. While you're waiting, you can look at recent screenshots (and a few videos here and there, such as here) and download the soundtrack (and donate!) to whet your appetite. So go on: they're waiting for you in the test chamber, Gordon!"
Link to Original Source

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