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Public health, data analysis, and generative AI
Notes on public health, mental health, disasters, data analysis, and AI.
English articles
Using Gemini Notebook from the terminal: Introducing the "notebooklm" skill
An introduction to the "notebooklm" skill for operating Gemini Notebook (formerly NotebookLM) from the terminal, complete with installation steps and command examples.
[Video released] Using generative AI to improve clinical quality
Watch my talk on using generative AI safely in clinical practice and find out how to get the handouts.
Using generative AI to prepare grant applications
Introduces two generative AI agents that expand research ideas and narrow down analysis using relevant literature when preparing research grant applications.
The ethics and potential of writing academic papers with generative AI
What does responsible AI use look like before you start writing a paper? I discuss developing a study idea, planning the research, and checking references.
How to add references in Gemini (Part 2): Gem and prompt released
I share the setup and instructions for Clinical Evidence Mapper, a custom Gem for finding and checking clinical references in Gemini.
How to include references in Gemini
How to prompt standard Gemini to cite sources using Google Search and unique identifiers like PMID and DOI without hallucinating URLs.
Using generative AI in healthcare settings: Turning off model training is not always enough
Three clinical examples show what Japanese privacy and security rules require when handling medical information with generative AI.
OpenEvidence Search Helper: systematic reviews, GRADE, and Japanese input
OpenEvidence Search Helper prioritizes systematic reviews, drafts GRADE assessments, and prevents accidental sends while typing Japanese.
The role of secondary sources (UpToDate) and search/general-purpose AI in answering clinical questions
I outline how to balance UpToDate and AI search tools when researching clinical questions, and introduce a Chrome extension for OpenEvidence that prioritizes reviews.
Building a Chrome extension to get more out of OpenEvidence
Why I built a Chrome extension to prioritize systematic reviews in OpenEvidence, and how to install it manually.
"Verify, then trust" — Fostering critical thinking in medical education in the AI era
Drawing on NEJM Medical Education, I look at how to teach clinicians and trainees to verify generative AI output.
What healthcare professionals should know first when using generative AI
Outlines key precautions for using generative AI in healthcare and education, with guides on OpenEvidence and a lecture video.
Guide to using image-generating AI tools in educational institutions
A guide for educators on copyright, exceptions for teaching, and the ethics of using image-generating AI tools.
Generative AI and critical thinking: Implications for university education
A dialogue for university teachers about a 2025 study of generative AI, confidence, and critical thinking at work.
Zotero setup for researchers (Zotero 7 edition)
Set up Zotero 7 to save references from your browser, store PDFs externally, manage citation keys, and translate papers.
Personal notes on using Quarto in R
Getting started with Quarto in RStudio, from document settings and editing modes to inserting an R code chunk.
Scheduling on-call shifts with GPT and mathematical optimization
I built a custom GPT that collects availability through Chouseisan and uses mathematical optimization to make a duty roster.
Smooth audio file transcription! Noise reduction and volume normalization in Python (Google Colab)
Learn how to automate noise reduction and volume normalization for audio files before transcription using Python and Google Colab, explained clearly for beginners.
Batch-correcting typos using an Excel table (Google Colab)
How to automate batch typo correction in meeting minutes and transcripts using an Excel replacement table and Google Colaboratory (Colab).
For those whose UMIN server WordPress sites stopped displaying after the PHP update
What to check when a WordPress site on UMIN PLAZA stops working after the server moves to PHP 8.1.
Life career workbook for medical students and physicians
Reading the Life Career Workbook for Medical Students and Physicians got me thinking about choice, teaching ethics, and burnout.
For those feeling unsettled by the #NotoPeninsulaEarthquake news coverage
Advice for anyone distressed by news of the Noto Peninsula earthquake, drawing on psychological first aid.
Changes to how reasons for suicide are tallied starting in January 2022
Our JAMA Network Open research letter examines how a January 2022 change in Japan’s reporting of reasons for suicide affects comparisons over time.
Batch-highlighting revised text in Word
How to use a Word macro to automatically highlight all revised text in an academic manuscript after peer review.
Ethical use of ChatGPT for writing a first draft
My notes on using ChatGPT to turn rough notes into a first draft while following journal guidance on authorship and disclosure.
Publication bias in psychiatry and the rate of English-language journal publication following conference presentations
Kazuo Yoshida and I discuss what we learned from using online tools to write a paper on publication bias in Japanese psychiatry.
Recommended books for psychiatry residents: Surveying psychiatrists
I surveyed psychiatrists about books they recommend for residents. Browse the results by topic.
When asked for audio/video presentation slides at an academic conference: Compressing .mp4 file sizes with FFmpeg
How to use FFmpeg to reduce the size of an MP4 file for an academic conference or online workshop.
[Quick review] Literature list on suicide in Japan during the COVID-19 pandemic (Updated April 13)
A reading list on suicide in Japan during the COVID-19 pandemic, with abstracts and limitations where available.
[Abstract translations] J EPIDEMIOL, 31(4); 2021
The January 2021 issue of the Journal of Epidemiology at a glance, based on my Japanese translations of the abstracts.
Introduction to epidemiology for clinicians
A reading list for clinicians covering epidemiologic terms, research hypotheses and DAGs, bias, and the role of statistics.
Books for senior psychiatry residency
Browse Dr. Irito Akiisa’s book recommendations for senior psychiatry residency, grouped by clinical topic.
Book review: What Data Visualization by Kieran Healy teaches beyond the code
My review of Kieran Healy’s Data Visualization, including what the book teaches about reading plots and working with geographic data.
Using Zotero in RStudio 1.4
How to configure Zotero integration with the visual markdown editor in RStudio 1.4, including setup steps for RStudio Server and the Zotero Web API.
Installing RStudio ver. 1.4 with Docker
Use Zotero to insert citations and build bibliographies in the RStudio 1.4 visual editor.
[Abstract translation] J Epidemiol, 31(1); 2021
The April 2021 issue of the Journal of Epidemiology at a glance, based on my Japanese translations of the abstracts.
How to display Japanese text while typing in a popped-out RStudio editor
A workaround for Japanese text disappearing while you type in a popped-out RStudio editor.
Frequently used R tips and tricks (updated regularly)
A regularly updated collection of handy R tips and tricks for data wrangling, visualization, and analysis that I find myself looking up repeatedly.
Manual templates for arranging online visits using only phone numbers
Ways to arrange remote hospital visits for patients and families using their phone numbers.
Stop Dropbox from syncing .git and .Rproj.user in RStudio project folders
Exclude temporary Git and RStudio files when Dropbox gets stuck syncing an RStudio project.
Setting the default path for R Markdown files managed in subdirectories
How to set the default working directory to the project root when managing R Markdown (.Rmd) files in subdirectories.
Configuring citation keys in Zotero (zotero-better-bibtex)
How to configure citation keys in Zotero using the zotero-better-bibtex extension to match the Google Scholar format.
Managing RStudio with Docker Compose
Set up RStudio Server with Docker Compose so you can bring it up without retyping a long docker run command.
Managing RStudio with GitHub and project templates
Use GitHub and RStudio project templates to keep scripts, data, and outputs organized across projects.
Standardizing boilerplate R code: Using {pacman}, clearing the environment, and freeing memory
Use {pacman} to install and load R packages, clear the working environment, and free memory at the start of a script.
Notes on preventing garbled characters in RStudio on Docker and sharing filesystems between host and container
Set up RStudio in Docker so Japanese text displays correctly and your host and container can share files.
Installing WordPress on a UMIN server
Notes on compiling MySQL from source and installing WordPress on a UMIN PLAZA server.