[PhD] November 2024 Updates

Storing papers, reducing screen time and data visualisation.

Top Learnings

1. Storing and organising your papers is challenging (very much a work in progress)

2. How to budget enough time for submitting data in academic settings

3. Reading papers twice helps me retain content better

4. Using an app blocker on my phone helps me focus

5. Visualising data well is an art

A bit more about each of them

1. Storing and organising your papers is challenging (very much a work in progress)

   1. I am working towards my first milestone exam (coming up in December) of my PhD. Oxford has three checkpoints: Transfer of Status, Confirmation of Status and the final Viva. For this, I’ve had to get my papers a bit more organised.

   2. Currently, I have a folder in Zotero (desktop app) for each chapter in my thesis and sub-folders of themes within it. I also use Research Rabbit to find related papers and authors.

      

      This helps me see how popular a research topic has been over the years

   3. When writing a paper, I create a new subsection with the respective title. Currently, I have been writing in Google Docs with the Zotero plug-in, but I am likely to switch to Overleaf next year. Thanks, Laura and Qijing for the suggestion.

      

   4. What programs do you use for your papers and for writing? Please reply to this post in a comment or through DM. I’d love to know.

2. How to budget enough time for submitting data in academic settings

   1. This one I am still not well-calibrated on this. I think that’s normal and takes academics a while (I think!!) Getting author permissions is tricky and budgeting enough time for revisions and reviews.

3. Reading papers twice helps me retain content better

   1. I read it first with a quick glace and take some notes and then I come back to it a few weeks or months later and read it again in a chunk with the other papers of that topic. Eg I am currently re-reading all the codon usage papers (see the screenshot above) and seeing if I can form any new connections.

   2. Maybe once I have enough context knowledge this re-read won’t be necessary, but for now it has proved instrumental. The second re-read makes me only choose the relevant papers, which also helps me cut down on the volume.

4. Using an app blocker on my phone helps me focus.

   1. I use Opal. I block my phone 10:30pm to 7:00am and block Whatsapp from 7:00am to 9:30am. I also do 2hr or 1.5hr focus blocks during the day and they really help me. I think I can I try to be more consistent with them too.

   2. You can try it for 30 days free.

   3. I also use OneSec they have a free version and this is for social media specifically.

5. Visualising data well is an art

   1. I went to a workshop with Charlie from OWID and got some really useful tips on making effective visualisations. If I get permission I will write up a public version of the notes that I took during the session. They were super useful.

   2. I am a HUGE fan of OWID and their mission: Research and data to make progress against the world’s largest problems.

      

   3. Look at the use of the descriptive title, colour, white space and annotations! Read the article here.

Paper Corner

1. Probabilistic weather forecasting with machine learning (link)

   1. GDM released a new model for better weather prediction

   2. I was just thinking about how possibly we haven’t progressed in that area as much recently and then BAM!

2. The Effect of Yoga Practice on Labor Pain: A Systematic Review and Meta-Analysis (link)

   1. 660 pregnant women (average ages of 25–35).

   2. 7 RCTs, 1 non-randomised CT and 1 observational study

   3. Pain intensity was measured using a visual analogue scale.

   4. There seems to have been a reduction in labour pain, but the variation in methodology in the studies is quite high.

3. Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage (link)

   1. A paper by one of the people assessing my Transfer of Status.

   2. RNA viruses have distinct nucleotide signatures.

   3. The bias was particularly enriched in unpaired, single-stranded regions of the RNA genome. This could be due to:

      1. RNA stability - eg A and U destabilise the paring, leading to more loops

      2. Immune evasion: maybe the nt composition in those regions helps the virus evade detection by pattern recognition receptors (PRRs)

   4. This is relevant to my research as the virus that I am studying also might have some similar trends.

As always if you have issues with accessing a paper DM me or send me an email.

Counter Update

Papers are up! Coding is going steady. No complaints this month.

Thank you for reading!

Sofya