Home 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.

AAS Trial 1 / Standard Operating Procedure

Fri, 05 Jun 2026 00:00:00 +0000

Quantification of Iron in E. coli Cells by Atomic Absorption Spectroscopy

Purpose

This protocol describes the use of atomic absorption spectroscopy (AAS) to quantify iron in an E. coli cell sample using an external calibration curve.

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 \

Colony Counting using YOLOv8n

Tue, 12 May 2026 00:00:00 +0000

Model used is YOLOv8n pretrained on colonies¹, but optimized for our use. The process is as follows:

 flowchart TD
 A["Load image"] --> B["Find Petri dish with OpenCV"]
 B --> C["Create inner dish mask"]
 C --> D["Black out area outside dish"]
 D --> E["Run YOLO on masked image"]
 E --> F["Filter YOLO boxes"]
 F --> G["Count accepted colonies"]
 G --> H{"More than 300?"}
 H -->|Yes| I["Report too many to count"]
 H -->|No| J["Report final count"]
 I --> K["Draw, crop, and save output"]
 J --> K
 K --> L["Return result data"]

Flowchart outlines the steps involved in the colony counting process using YOLOv8n. Below are some sample images obtained from using the model to count colonies on our plates/public datasets. Does a pretty good job overall. We can further optimize the model (though this requires labelling of our data) and the filtering process to improve accuracy, but this is a solid starting point for our colony counting needs.

Calculations for AAS

Sun, 12 Apr 2026 00:00:00 +0000

The reported amount of of iron in WT E. coli is around 10^5 to 10^6 atoms per cell ¹.

Converting atoms per cell to micrograms per gram of cells

Using

\[ 10^5 \,\text{atoms Fe/cell} \]

the iron mass per cell is

Revision to the Biofilm Assay: The Bladder Cell Invasion Protocol

Tue, 31 Mar 2026 00:00:00 +0000

Since we were having issues with the biofilm formation, as expounded upon in a previous post, Dr. Yep decided to make some revisions to the protocol. This post will be a brief overview of the changes that were propsed, and the rationale behind them.

Throughout, I’ll be referring to a paper studying decreased expression of fimbriae and its effects on the pathogenesis of CFT073¹. The paper is a good example of the bladder cell invasion protocol, and the rationale behind it.

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.

Iron Quantification using Atomic Absorption Spectroscopy

Sat, 14 Feb 2026 00:00:00 +0000

Since we’re working under the assumption that we have isogenic mutants with varying intracellular iron concentrations, it would only make sense to verify this assumption by quantifying intracellular iron of each strain. I’m planning on working with Dr. Lehr from the Chemistry department to do just this using AAS. This will be a crucial step in our project, as it will allow us to correlate the phenotypic differences we observe with the actual intracellular iron levels, thereby strengthening our conclusions about the role of iron in the observed phenotypes.

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.

ASM 2025

Mon, 10 Nov 2025 00:00:00 +0000

This short informal post is long overdue, but I’ll excuse myself since this website wasn’t up and running in June, when I attended the conference—and besides, I’ve been busy with other things.

I had the chance to attend ASM 2025 in LA back in June. I presented my findings along with my lab partner, and overall I’d say it was a pretty good experience.

Before this, my lab partner and I had attended a smaller research conference in January. That conference was made up mainly of undergraduates. Many disciplines from the biological sciences were represented—everything from ecology to biochemistry. Since we were all undergrads, I found it easier to walk up to posters and ask as many questions as I wanted to satisfy my curiosity, because it was mutually understood that none of us really knew much about each other’s disciplines. It was nice in this way; you could pull the “I’m ignorant just like you, help me out” card, even though any basic lack of knowledge is really my own fault.

Issues with Biofilm Formation

Mon, 27 Oct 2025 00:00:00 +0000

In the lab, Kelsey and I have been running into issues with the biofilm assay. Regardless of the incubation period, the E. coli strains that are supposed to form biofilms aren’t doing so. After a couple of failed attempts, we also tried growing Pseudomonas, which is known for robust biofilm formation, but this trial also resulted in no observable biofilm. By testing these two strains, we could assess whether the problem lies with the E. coli strains we were using or whether it stems from a systemic error in our protocol.

LB, ∆fur, and Stationary Phase

Fri, 03 Oct 2025 00:00:00 +0000

Dr. Yep noticed how ∆fur stalled earlier than the other strains. It’s not necessarily a problem, but I’d like to understand the cause. The paper should also explain this, so we’ll need the rationale anyway.

∆fur entered stationary phase early in Lysogeny Broth (LB). This didn’t happen with any of the other strains or media. Why? I’ll attempt to explain this in a few ways.

ROS Damage

Since this phenomenon was absent in all other media, I think the early stalling most likely reflects a specific interaction between the high intracellular iron characteristic of ∆fur, and some inherent property of LB.

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.

∆waaF and Colanic Acid as a Surfactant

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

Over the summer, I got my hands on Escherchia coli ∆waaF. The researchers at UT Austin were kind enough to consider a collaboration. This strain overproduces colanic acid, which I wanted to take advantage of. I want to test whether external supplemementation can rescue a certain non-swarming strain. The following information will frequently reference their publication, so I will list it here¹. In the subsequent passages, I will attempt to digest their paper in a way I can understand and apply in the lab.

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.

The Yep Lab: Iron and the Motility of CFT073

Sun, 17 Aug 2025 00:00:00 +0000

Preface

After writing a first draft of this page, which came out to a couple thousand words, I decided to break this post up into multiple posts. In this first one, I will explain only one of the several projects I’ve been working on.