Whole brain radiation dose: think about it.

I have always wondered about the tolerance of brain tissue to radiation. Whole brain radiation can be “safely” given up to 54-60 Gy (in the previous protocols for glioblastoma- NO LONGER used). Brainstem dose, in the current QUANTEC era, is not exceeded to 54Gy as a point dose (disregard the 10cc volume for a minute).

The whole brain mean dose is preferably not exceeded beyond a mean dose of 28Gy which we are propagating in the post-hippocampal era (so as to say).

It brings me back to the original question. Why is a focused radiation dose exceeding 60Gy (for example) more injurious than whole brain dose to the same effect? And why brainstem isn’t affected in that scenario?

Another question. If a phased plan is executed, is it sufficient to only add up the mean doses? This is because both the phases have used different calculation subsets; radiation delivery is also going to be markedly different.

Well, no easy answers!

Scientific elitism, failure and research.

Dwight D. Eisenhower Source: Wikipedia

I was alerted to an interesting discussion on effects of federally funded research- the rise of scientific elite and “military-industrial complexes“. The thought process was initiated with a compelling article on what President Dwight D. Eisenhower had mentioned in his address about 50 years back.

I quote:

“Today, the solitary inventor, tinkering in his shop, has been overshadowed by task forces of scientists in laboratories and testing fields… ,” Eisenhower warned. “Partly because of the huge costs involved, a government contract becomes a substitute for intellectual curiosity virtually.”

While continuing to respect discovery and scientific research, he said, “We must also be alert to the equal and opposite danger that public policy could itself become the captive of a scientific-technological elite.”

There’s been enough debate in the knowledge circles about the exact import of this. But these words ring real as the years have passed. “Military-Industrial” complex has grown in stature, causing havoc, while the new upstarts in the scientific research world are increasingly elbowing their way in this cosy club from China.

This isn’t a geopolitically nuanced post. It only serves to reflect my concerns about wastage of research efforts and how much it is held hostage to scientific committees. It is a good thing to keep a rein on how the dollars are being invested, but this also comes with the riders on how difficult it is to fail.

All of this has come at the cost of progress and reward to the scientific thought and tinkering.

It is true that the advent of “atomic bomb” spurred on research in the US, but there was defined anxiety to achieve the goals. In Asia, we grapple with the income inequalities and access to equitable healthcare, while in western democracies, they are floundering to create the next breakthrough. Hence, the likes of “project moonshot” because it is recognised that something is required.

It leads us to another question: Has the scientific process and the research methodology gone too bureaucratic in its approach?

Likewise, the cost of publishing the research has become beholden to the established interests. The scientific cabal controls access to literature pushing vanity metrics (which in turn determines means to get further funding). It transpires that if the research isn’t published in a “high impact journal”, it isn’t meritorious enough. The unstated pressure to achieve publications in high impact journals breaks most people resolve to push through them. It only leads to either cronyism, cooking lab results to dress them up and an established PR machinery to impress the charities backing the research efforts.

Who loses out?

The patients. It is because the bulk of published research can neither be reproduced nor translated in clinical domains efficiently.

The spinoff from this has also led to an arms race to find the next big molecular target. The idea is to of course, “sell” it to the pharma company to patent it. While not inherently evil but it feeds the same demon wherein we know how equitable access worsens.

Rinse and repeat.

What are the implications for developing countries?

Herein, lies the rub. It is sad that bulk of doctors have turned away from scientific research because what they see in the patients is not meaningfully communicated in the lab. Dr Ronald Ross discovered the malarial parasite while actively practising medicine. Leannec invented the stethoscope because he needed an efficient way to auscultate the patients presenting to him. He went stumbling from various kind of tubes to something resembling a stethoscope that we now know as- universally ubiquitous.

Ideally, we should be researching the hows and whys of radiation effects on cells, the way it breaks DNA, the downstream effects, minimising the impact on healthy tissues, exploiting the fractionation schedules and a better mathematical modelling. Instead, we are going agog about Amazon and JP Morgan’s of the world stepping in healthcare, ferreting away the precious human health data to their data centres, feeding algorithms and fuelling the hype cycle about AI in healthcare as the next breakthrough. It only reflects how faith in the system has broken down.

Clinician-scientist is a moniker. What we lack is a comprehensive roadmap to what we want to achieve- not concerning survival but a meaningful continuation. As the world celebrates cancer day, it is a call for the radiation oncology community (and the medical profession) to evaluate its priorities and work towards alleviating what we are supposed to do.

What is the way forward?

The way out, forward, is to break shackles of our minds and allow ideas to fail. If I were to have my lab (someday!), I would dedicate a portion of funding only to tinker with the possibilities. Involve people from different fields to brainstorm on what all possible directions the idea can go. Involve mathematics, for example, with probabilities on what can go wrong or right. These are not the core competencies of clinicians but opening up dialogue and communicating with teams looking at the same problem with a different perspective can help enlarge the idea.

“Cure” will not be hope but a purpose and an end all.

Is research wasted?

How far is this true?

I would dispute the numbers but the questions raised here are extremely pertinent.

  • As always, we need to ask the right question. Design appropriate methodology.
  • Put it out in public domain.
  • And make the research accessible.

These are desirable goals but not the end points that we see in practise. Things have to change for meaningful outcomes.

How to deliver a scientific talk: Or not kill your audience

 

I stumbled on this gem from Twitter! I am sharing this in entirety because I feel that it needs to be shared to a wider audience.

I am not having any claim to fame as far as the public speaking is concerned but I have had my fair share of run ins. The author is right about being able to engage the mental attention and it is a difficult task. Nevertheless, there are some common sensical pointers here that I’d like to share from the embedded document (please feel free to download and share) Thats one reason I usually dread going to the conferences. Its only because of the boring presentations (and sometimes tasteless food).

Be visual!

I prefer to have the pictures do the talking but if they are done to death, it makes for a disaster.

The goal is to have a visually streamlined talk where the audience is so engaged with your presentation that they forget you’re standing in front of them speaking.

Highlight the points and learn to do it!

The bulleted points! They should be banned.

Kill clutter. Remove text. Complete sentences are to be banished from your talk.

Be nice to your audience!

Many times I have seen the speaker pointing the laser as if to highlight the importance of a bullet. The pointer goes up and down and this makes for a perfect recipe for disaster because subconsciously, the audience is following the pointer.

Try not to use a laser pointer. They’re a crutch for you and are distracting to your audience. More to the point, there’s no need for one if your slides are properly designed (uncrowded).

No suspense! This is self explanatory

People really don’t like suspense if they’re not already invested in your talk, and they have bad memories. So tell them the main answer before going into the details. Rather than try to figure out where you’re going, they’ll be able to concentrate on the finer details of your talk.

Keep it brief!

Really! This helps.

Keep methods brief. Most don’t care about methods, it’s a distraction from the story. Provide enough detail that they know what you did and have some confidence that you know what you are doing.

Finally; last but not the least!

Knowing your audience is the most important thing. You need to be able to tailor your talk depending on who is going to listen to what.

Know your audience. Present something that they will enjoy, for scientists this usually means tailoring the level of technical detail (and amount of introductory material) to your audience.

I hope this little list helps!

How I have refined my academic workflow?

(Estimated reading time: around 8 minutes).

I have been trying to establish an academic workflow for quite some time now. Writing about it helps me to organise my thoughts better. I’ll highlight what I have found useful. This list is by no means exhaustive. This is also in line with my idea of documenting everything as I hurtle towards the goal of academia. Its an ongoing struggle but I am hoping that someone more knowledgeable than me would take time out to point any obvious flaws. I also hope to spur on discussion about their own workflows.

Mind Map and how ideas could flow

Created in scapple; a basic mind map

Step 1: Creating a mind map.

I use Scapple for it. There are other alternatives available but I haven’t explored them. Stare at a blank canvas and start writing randomly. Identify the thoughts as they come to you. They help in brainstorming. This involves identifying the parameters that I have to use/cover, all the ideas I have to write about and how I need to be able to distinguish my write up from other published ones.

That, I believe, is the most important part, since the first part of any research is identifying the question and being able to coherently frame it. This is followed by supportive evidence (if any) and the strength of the protocol that you are out to write. If you don’t want to use Scapple from the outset, you can always write it down; see all the ideas that form a feedback loop, if any, and then take it forward.

Key takeaway: Identify the idea first!

Step 2: Pubmed

Once I have done it, I hit Pubmed. The search on Pubmed has improved vastly although a compelling use case exists for Quertle as well. Previously, Quertle had a free tier but its a paid option now. I haven’t used it recently though. Nevertheless, I use advanced search and booleans to drill down to the specifics on pubmed. Once I have identified my key words that give me adequate results, the fun starts.

A specific keyword is likely to give a river of publications. Most of them are usually contextually related and Pubmed has complex algorithms to sort them out. I prefer to subscribe the whole list by RSS feeds (which I covered recently). These RSS feeds then pipe into Inoreader. Few people might prefer to get email for it but this is easily lost in the sea of email that we get (I hit on a specific actionable inbox zero protocol long time back and its serving me very well). Email is a bad idea.

Step 3: Inoreader for RSS feeds

Inoreader is a fantastic resource. Apart from the specific Twitter searches, I can filter out the feeds.

Lets say, if the feed is showing up keywords for canine oligodendroglioma (which is irrelevant for me), it can be filtered out. Once its done, I can set up several other rules in conjunction with IFTTT.

Inoreader and IFTTT (If This, Then That) allows you to create applets that links various services. For example, I pipe articles related to specific keywords, IFTTT can be triggered each time the article comes in. I add specific hashtags to it and viola! All articles that are of relevance (from specific keywords/filtered) are pushed out to Twitter. A bit of human curation also occurs in this river of articles. I usually “star” the articles (things I have to follow) and IFTTT appends separate hash tag to it and pushes out to Twitter.

In this, specific write ups that are relevant to my work (starred articles, for example), are saved and downloaded (usually from Sci-Hub or through institutional paywalls).

Step 4: HighlightsApp on Mac

I use Highlights App on Mac (I think it was created by a PhD student himself). The coolest thing about it is the annotations come as a note (which now happens in Bookends as well). These notes are exported as TextBundle and opened up via Ulysses. I add meaning to these notes (needed to learn a little Markdown; enough for me to get going) and Ulysses pushes it to my publishing website on word press.com

Step 5: Using Ulysses to craft your ideas

The beauty about Ulysses (apart from the simplicity, writing long form, ability to preview in various formats etc) is stellar customer support. I faced an issue with Highlights app and Ulysses and it was addressed by the developer himself. They moved towards a subscription based model and I think it was a wise sensible decision.

Step 6: Always use a Bibliography manager for your papers!

Nevertheless, I have found peace with using Bookends. It is (I think) a one man show (Sonny Software) and is one of the most comprehensive solutions. Sente/Papers 3 are gasping but Bookends has thrived on a payment model (upgrade every 2 years) with stellar support; both on forums and email. Bookends serves as a bibliography tool (this deserves another blog post some day).

Step 7: Scrivener for writing papers. A must have and a life saver!

After annotations/note taking, I prefer to write using Scrivener; especially the long form. I break up the article in several parts and I can work on them at different intervals. This also requires another blog post!

Scrivener pipes out the output in rtf (for example) where Bookends can scan it, add the citations which then requires some more formatting to be pushed to journals for submission (and then hope that the anonymous reviewer would be nice to you!)

Starting from Pubmed, this train of thought may sound complex (but it isn’t) and is straightforward. Each one of them serves a specific purpose.

Ulysses works perfectly to write these blog posts since I prefer to use a distraction free environment. I use Vivaldi browser as my preferred software; has tons of shortcuts and muscle thats absolutely amazing.

Don’t forget cups of tea/coffee and some Spotify lists to keep things interesting! (meditative music helps me :))

Disclosure: None of them are affiliate links and I have paid for the software in full. They deserve to be highlighted! 

 

How to use Telegram chat app for academics

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This post is prompted by a discussion I had with a few people on Twitter recently.

Instant messaging applications abound; the most popular amongst them is WhatsApp. It relies on phone numbers to get the work done. By being dead simple, WhatsApp became the most popular application for majority of the users. I believe that it is only a SMS replacement and nothing else. Furthermore, other reason I don’t use it is because its now completely owned by Facebook. The wealth of data related to our social interactions is more important for the company (and thats the reason why its free). Nevertheless, I’ll come straight to the point. How I found Telegram to be better than any chat application and how I use it effectively.

  1. The most important aspect: Bots. They are small nifty software programs that run on the application and automate things. For example, in a group, a Group Butler bot will assist the administrator in welcoming users, make them aware about the rules, limit the media (from pre-arranged rules) and prevent users from flooding. There is a classical music bot that works like Spotify 🙂 The possibilities with bots are endless. Payment bots are maturing on the platform as well.
    bots
  2. Notifications: This is the biggest bane of chat applications and serves to distract us most of the time. As a result, we are hooked to the devices. In Telegram, I have muted all users/groups/channels. The group notifies me only when someone mentions me by my screen name (like Twitter). This indeed is a life saver!
  3. Instant view for articles. It loads up the article (for example from New York Times) inside the app itself. This ensures that I don’t have to jump to the browser.
    instant-view-telegram-updated
  4. Channels serve as a mechanism for one way flow of information. Channel owners can post in media (file limits of 1.5 GB are pretty generous); videos, files, pictures etc but the subscribers cannot comment on it. This avoids the hassles with comment moderation. Channels can have unlimited number of subscribers while groups can accommodate upto 50,000 users (easily managed by bots!) Channels with companion groups can serve as a decent platform for two way communication between users. I manage couple of channels (which are automated) and serve as an admin for several groups without breaking into a sweat.
    Telegram-Channels-List
  5. Last but the not the least. It is a cloud based platform which ensures complete cross platform availability. I can start the conversation on my desktop and continue the same on my mobile device. It can also be accessed via browser. A personal cloud storage comes with it that can store my files indefinitely. Numerous granular privacy controls ensure that I can restrict users from adding me to groups or controlling who can initiate voice calls with me.
    telegram-two-step-verification

Publishers should explore Telegram channels; they can have dedicated systems for payments for premium content (which is invite only link); instant view from the app can ensure filtered information. This app can serve as a distribution hub for media. Bots can be used to link Telegram channel with Twitter, for example. The possibilities, actually are endless! Better still, you get to control access to your busy schedules (Personal chats, except family, groups and channels are all muted).

I really hope academicians and fellow professionals explore this application in right earnestness!

5 ways how Twitter helps: How I embraced Twitter (and learned to stop worrying)

I had been social media averse because of privacy concerns. I am much happier to pay for a service than have a company muck around with my personal data. I had been on Twitter way before “fake news” became a phenomenon and much before presidential tweets became the new normal.

As an individual, its easier to get lost in the stream of work, cynicism and unmet goals. This plays out in professional domain as well since its impossible to keep personal life segregated completely. However, those seeking care from us require more emergent solutions that requires us to “divorce” our personal problems, cast them aside and have a smiling face. Social awkwardness has its own set of limitations though; it becomes difficult to open up to a colleague , at times, to discuss issues like marriage or issues with boss etc (problems which are universal).

As a result, we wear a thick coat of cynicism. We look at the issues (as they are happening) through a narrow perspective. While we are attending to patients, it appears as if we are merely going through the motions of it; almost like a robot. This needed a change.

Much has changed over the past few years (ever since I quit Twitter in the first instance). I have matured, become more patient and accommodating. However, I couldn’t feel the inner connect with my drive; I knew I am capable of far better output!

Twitter, as a platform, has become better than previous iteration. I discovered a whole community of very interesting people and indeed a revelation! In no specific order, Twitter interactions with them definitely helped me both personally and professionally (and I have just started!) by helping me to see what people are doing; what they have achieved and what I can aim at.

  1. First and foremost is the patient advocacy. This is extremely important because patients need a voice of their own and they need to look up to their clinicians. I have always been empathic to this cause and realised early on that their individual voices need to be channelised. Many organisations are now harnessing the power of social media and its important to amplify this good cause. Once I got used to the interface, I made a specific twitter list for various patient advocates. There’s a whole community out there which touches the lives of individuals in a profound way; makes them one of their own. This is important aspect in their recovery and coping up mechanisms.

2.Overcoming my “writers block”. I have always been blogging and writing about everything else except my own profession! This step was important and I owe it to some individuals who are prolific writers in their own right! The breath of ideas and thoughts has deeply impacted me and motivated me to get on with my own writing.

3. I have always been interested about technology and how deeply it impacts our day to day lives. I am more keen for the privacy aspect; especially the deluge of data being analysed by unknown entities. Big data has entered our lexicon that brings forth new set of challenges for professionals. “Shape up or ship out” is the new mantra; healthcare professionals are being tasked with administrative issues which requires this domain expertise. The inter-connectedness of diverse health care streams and cross pollination of ideas is bound to affect the rich heterogeneity of radiation oncology community. I was very happy to find people with similar interests there!

4. I was extremely happy to learn about other disciplines; especially Pathology! It was something that I dread during med school days but it is only because I couldn’t appreciate or go beyond the routine “stains”. However, much water has flowed since then! Molecular diagnostics has made a roaring presence and “clinico-radio-pathological” diagnosis (as part of the comprehensive joint neuro-oncology meet ups) is the new norm. Nothing beats the thrill of a diagnosis and a debate between diverse fields! I have a renewed respect for my colleagues pursuing it! (Bonus tip: I love the #pathart so much!)

5. Last but not the least. Its an amazing community to be with. Ignore the “politics” and you’ll find more meaning in it. I did some things to automate tweets, use RSS feeds to push new updates (which in turn have been sliced and diced using complex rules), follow timeline with muted words and hashtags (to improve signal from the noise) and created multiple private lists to avoid being overwhelmed with information. Its worthwhile intellectually fulfilling exercise!

More importantly, it has become a go-to place to see whats being discussed and I get more ideas to write about; blogging is actively being shaped by my Twitter experience in order to get my voice out. I owe to each one of them!

Thats how I embraced Twitter and stopped worrying about it!