Blog on Jin Saeki Ko

Surrogate endpoints in clinical trials

Mon, 29 Jun 2026 00:00:00 +0000

Surrogate endpoints are endpoints that are not directly related to the clinical outcome of interest but are used as a substitute for it. They are often used in clinical trials to assess the efficacy of a treatment when the actual clinical outcome may take a long time to observe or may be difficult to measure. For instance, in a trial for a new drug to treat high blood pressure, the surrogate endpoint may be the reduction in blood pressure rather than the actual clinical outcome of interest: reduction in the risk of heart attack, stroke, or death.

JAMA on how to read clinical trials

Wed, 27 May 2026 00:00:00 +0000

There’s a series from JAMA that goes over how to read clinical trials. The series is written by individuals who are widely recognized in the field of evidence-based medicine. The entire series is a valuable resource for navigating literature in general, but there’s a total of six relevant parts to the series, specifically on how to read clinical trials:

I: how to get started ¹ II-A: validity of therapy/prevention studies ² II-B: results and whether they help your patients ³ XIX-A: surrogate endpoints XIX-B: drug class effect \

Ethical Considerations: Sham Surgeries

Mon, 02 Mar 2026 00:00:00 +0000

Sham surgeries are procedures that mimic real surgeries but do not include the critical therapeutic component. They are often used in clinical trials to serve as one of the controls, allowing researchers to assess efficacy of surgical interventions. These surgeries imply that patients undergo anesthesia and incisions, but the actual surgical procedure is not performed. This obviously raises very interesting questions about the ethical implications of such practices.

Utilitarian Arguments in Favor of Sham Surgeries: My Objections to Abbasi and Cifu’s Paper

Most of the arguments in favor of sham surgeries employ utilitarian reasoning, which is the idea that the best action is the one that maximizes overall happiness or well-being of a population in question. In this case, the argument is that sham surgeries provide more of a benefit to society than they do harm to the individual patients who undergo them. This is what¹ argues. As a evidence-based thinker, I like most of the things Dr. Cifu says, but this is an interesting paper to say the least…

RSS Feeds

Mon, 23 Feb 2026 00:00:00 +0000

So far I’ve subscribed to a couple journals and some blogs. Here’s a partial list:

CDC MMWR
Phase 3 and 4 clinical trials from:
- BMJ
- NEJM
- The Lancet
Blogs from:

The NIH walks you through how to set up filtered RSS feeds for pubmed: NIH RSS Feeds . This is how I obtained the feeds for phase 3 and above.

SPICES Model of Medical Education

Sun, 21 Dec 2025 00:00:00 +0000

What follows is an argument for the more liberal forms of the SPICES model of medical education¹. The paper itself is relatively old, but many medical schools, especially in the States, have still not seriously re-evaluated their curriculum. Even though newer schools tend to be more liberal in their approach, the inertia of older programs makes the framework oddly current, and therefore still relevant.

The SPICES model is a way of describing a curriculum by placing it on six continua. The acronym stands for student-centered versus teacher-centered learning, problem-based versus information-gathering learning, integrated versus discipline-based teaching, community-based versus hospital-based education, electives versus a standard programme, and systematic versus apprenticeship or opportunistic training. The point is not that every school must live at one extreme, but that schools should be honest about where they sit and whether that position makes sense.

Interbacterial Antagonism via Secretion Systems and its Applications

Fri, 19 Dec 2025 00:00:00 +0000

Most antagonism doesn’t need contact. Bacteria just secrete stuff into the environment—for instance, specific bacteriocins and broad antibiotics. These diffuse and hit any nearby cells that don’t have the right resistance or immunity. This is a great example of long-range killing, with no direct contact needed¹.

Type V secretion system: the cell has a huge outer-membrane protein, CdiA, exported by CdiB. The N-terminal part of CdiA binds a specific receptor on the target cell. The C-terminal part (CdiA-CT) is the toxin domain that actually goes into the target and does the damage (DNase, RNase, translation block, etc.). The producing cell makes a small immunity protein, CdiI, that binds its own CdiA-CT and blocks it. So, if you have the matching cdiI gene, you’re safe; if not, you get killed².

Diabetic Ketoacidosis and Non-Ketotic Coma

Wed, 24 Sep 2025 00:00:00 +0000

Robbins pathology¹ and GH medical physiology²

Introduction

Type 1 diabetes mellitus (T1DM) is an autoimmune disease characterized by the destruction of beta cells, leaving patients lacking insulin. Immune effector cells react to self-antigens present on the surface of beta cells. There are a variety of reasons why the effector cells target endogenous antigens (T-cell selection, HLA alleles, etc.), but that discussion would digress from the topic.

Overview Of Sequencing

Fri, 29 Aug 2025 00:00:00 +0000

1st Gen Sequencing

Dideoxy gene sequencing uses what is called “primed synthesis” for sequencing. Primed synthesis works as follows: primers anneal onto a denatured strand of DNA, yielding ssDNA and creating a free 3’-OH group. A DNA polymerase then binds to the oligonucleotide primer, copying the remainder of the template strand. Understanding this mechanism is important for understanding the later stages of sequencing.

How this Website was Made

Thu, 21 Aug 2025 00:00:00 +0000

I used Quarto, which was recommended to me by a friend for its simplicity and ease of management. I could have used any number of other tools to build the website for greater customization, but I don’t sweat the details; the uncouth aesthetics of a website don’t bring me much displeasure. I’m also lazy, which I suppose is the real reason.

What I did to deploy my website is by no means special, so writing about this process is merely a way for me to fully understand it.