Reproduction: Kim & Kim (2022) | UCSD PSYC201A

written by Jinwoo Lee (jil527@ucsd.edu)

Note

• original paper: https://doi.org/10.1073/pnas.2205162119
• preregistration: https://doi.org/10.17605/OSF.IO/38WV4
• final reproduction report: https://psyc-201.github.io/kim2022/

This repository serves as a workspace for the Reproduction Project in UCSD PSYC201A. The goal of this project is to reproduce the following key findings reported in Kim & Kim (2022, PNAS):

Younger adults: “Mantel tests revealed that the left amygdala-ventral PFC tract-morphology dissimilarity matrix was significantly correlated with the trait-anxiety dissimilarity matrix.”
Older adults: “Tests on the older adult sample also depicted a significant correlation between the trait-anxiety dissimilarity matrix and the left amygdala-ventral PFC tract-morphology dissimilarity matrix.”

Code Availability

All dependencies required to run the code are stored in a Pixi-based virtual environment named ‘kim2024’ (note: “2024” is a typo of “2022” in the original naming). To set up and use the environment, please follow the steps below:

1. Clone the GitHub repository: git clone https://github.com/psyc-201/kim2022.git.
2. Activate the Pixi-based virtual environment in your local machine: pixi shell.
3. When using Jupyter, select the kernel named “Python (kim2024)” or "R".

Caution

Also, the key analytic package - DIM is on-going project in UCSD SciMinds Research Studio. For this reason, the directory of DIM was not shared in this repository. For the sharing request, please contact the project lead: Jinwoo Lee (jil527@ucsd.edu).

Data Availability

This project assumes the presence of two datasets:

• Preprocessed data for confirmatory analysis: This data includes metadata, STAI-G-X2 self-report total scores, and tractgraphy-based imaging driven phenotypes. To request access to the data, please contact Dr. Justin Minue Kim (minuekim@skku.edu), the corresponding author of Kim & Kim (2022 PNAS). Once you receive the data, place it in a folder named data-from-authors located in the top-level directory of this project.

• Raw data for exploratory analysis: Exploratory analysis uses additional self-report scores - Emotion Regulation Questionnaire (ERQ), NEO Five-Factor Inventory (NEO-FFI), and Impulsive Behavior Scale (UPPS). You can download the full dataset at the official website of LEMON dataset. Once you download the data, place it in a folder named Behavioural_Data_MPILMBB_LEMON located in the top-level directory of this project.

Contact

For inquiries regarding this reproducibility project, please contact the project lead: Jinwoo Lee (jil527@ucsd.edu).

References

Kim, W., & Kim, M. J. (2022). Morphological similarity of amygdala-ventral prefrontal pathways represents trait anxiety in younger and older adults. Proceedings of the National Academy of Sciences, 119(42), e2205162119.