lcreteig / thesis

PhD thesis

Neuroplasticity of attention: How brain stimulation and mental fatigue affect attentional performance

These are the source files for the PhD thesis of Leon Reteig. View the html and pdf version at https://lcreteig.github.io/thesis.

• Institution: Department of Psychology, University of Amsterdam
• Advisors:
  1. Prof. Dr. Heleen A. Slagter
  2. Prof. Dr. K. Richard Ridderinkhof
• Defense date: 20 November 2019

Summary

Attention allows us to focus on what is relevant and to ignore what is not. While we call upon attention at every waking moment, it is not static: we cannot sustain attention indefinitely, and often fall prey to distractions. This PhD thesis is a study of the short-term neuroplasticity of attentional processes: how susceptible is attention to change, and what processes in the brain (neuro-) give rise to changes in attention (-plasticity)? In Chapters 2–5, I examined whether attention can be improved with electrical stimulation of the brain, in the form of transcranial Direct Current Stimulation (tDCS). Previous studies that attempted to use tDCS to enhance attention have yielded promising, but inconsistent results (reviewed in Chapter 2). My attempt to enhance spatial attention with tDCS (Chapter 3) was unsuccessful, as stimulation of the frontal eye fields did not lead to changes in eye movements. Applying tDCS over the dorsolateral prefrontal cortex also did not enhance temporal attention (Chapters 4 and 5), as participants’ performance on an attentional blink task remained unchanged. In Chapter 6, I investigated the opposite effect: decreases in attention, when attention has to be sustained for a long time. Using EEG, I tracked whether similar decreases occurred in different attention-related signals in the brain. tDCS may one day be used to counteract these declines, or to relieve other deficits in attention. However, barring a deeper understanding of the technique and more large-scale studies of its efficacy, such practical applications of tDCS are not yet feasible.

Chapters

Chapter 2

Reteig, L. C., Talsma, L. J., van Schouwenburg, M. R., & Slagter, H. A. (2017). Transcranial Electrical Stimulation as a Tool to Enhance Attention. Journal of Cognitive Enhancement, 1, 10–25. https://doi.org/10.1007/s41465-017-0010-y

Materials	Open Science Framework

Chapter 3

Reteig, L. C., Knapen, T., Roelofs, F. J. F. W., Ridderinkhof, K. R., & Slagter, H. A. (2018). No evidence that frontal eye field tDCS affects latency or accuracy of prosaccades. Frontiers in Neuroscience 12:617. https://doi.org/10.3389/fnins.2018.00617

Project website	https://lcreteig.github.io/sacc-tDCS
Data	figshare
Code	GitHub
Materials	OSF

Chapter 4

Reteig, L. C., Newman, L. A., Ridderinkhof, K. R., & Slagter, H. A. (n.d.). Effects of tDCS on the attentional blink revisited: A statistical evaluation of a replication attempt.

Project website	https://lcreteig.github.io/AB-tDCS
Behavioral data	OSF
EEG data	OpenNeuro
Code	GitHub
Materials	OSF

Chapter 5

Reteig, L. C., Newman, L. A., Ridderinkhof, K. R., & Slagter, H. A. (n.d.). Spontaneous eye blink rate does not predict attentional blink size, nor the effects of tDCS on attentional blink size.

Project website	https://lcreteig.github.io/AB_tDCS-sEBR
Data	OSF
Code	OSF
Materials	OSF

Chapter 6

Reteig, L. C., van den Brink, R. L., Prinssen, S., Cohen, M. X., & Slagter, H. A. (2019). Sustaining attention for a prolonged period of time increases temporal variability in cortical responses. Cortex, 117, 16–32. https://doi.org/10.1016/j.cortex.2019.02.016

Project website	https://lcreteig.github.io/MFBrain
Data	OSF
Code	OSF
Materials	OSF

Usage

Setup

1. Click on Clone or download > Download ZIP and download and unzip the files. Or just clone the repository:

git clone https://github.com/lcreteig/thesis

2. I’d recommend to open the thesis.Rproj file using RStudio. If you’re not using RStudio, you’ll need another means to run the R code, set your working directory to the root of the /thesis folder, and you’ll also need an installation of pandoc

3. Install the required R packages if you don’t have them:

# from CRAN
install.packages(c("tidyverse", "pander", "kableExtra"))

# from GitHub
if (!require("devtools")) install.packages("devtools", repos = "http://cran.rstudio.org")
remotes::install_github("rstudio/bookdown")
remotes::install_github("crsh/papaja")

4. If you want to recreate the pdf version of the thesis, you’ll also need a LaTeX distribution. If you don’t have one yet, I recommend TinyTex. It’s quite a miminal distribution, but while rendering the book it will automatically install any extra LaTeX packages you might need. To install TinyTex through R:

install.packages('tinytex')
tinytex::install_tinytex()
tinytex:::is_tinytex() # after restarting RStudio, confirm that the LaTeX distribution is now available:
tinytex::tlmgr_install("hyphen-dutch") # install package to work with Dutch text (tinytex will not auto-detect this)

The pdf is typeset with the “Helvetica” and “Minion Pro” typefaces. They are commercial fonts, and so cannot be distributed here. If you don’t have these fonts installed on your system, make sure to delete lines 27–32 in tex/preamble.tex:

%% Typefaces
\usepackage{fontspec}
\setmainfont{Minion Pro}
\setsansfont[Ligatures=TeX]{Helvetica}
\setmathsfont(Digits,Greek,Latin)[Numbers={Proportional}]{Minion Pro}
\setmathrm{Minion Pro}

Building the thesis

5. If using RStudio, click “Build Book” from the “Build” pane. Select bookdown::gitbook to create the html version, bookdown::pdf_book to create the pdf version, or “All Formats” to build both. If not using RStudio, run the following code:

bookdown::render_book("index.Rmd", "bookdown::gitbook") # html version
bookdown::render_book("index.Rmd", "bookdown::pdf_book") # PDF version

6. If not done automatically, navigate to the newly created _book folder, and open the index.html file in a browser to view the html version, or thesis.pdf to view the pdf version.

Contents of this repository

root

.
├── 01-introduction.Rmd
├── 02-review.Rmd
├── 03-sacc_tDCS.Rmd
├── 04-AB_tDCS.Rmd
├── 05-AB_sEBR.Rmd
├── 06-MFBrain.Rmd
├── 07-summary_discussion.Rmd
├── 08-sacc_tDCS_supplement.Rmd
├── 09-AB_tDCS_supplement.Rmd
├── 10-MFBrain-supplement.Rmd
├── 11-resources-supplement.Rmd
├── 12-references.Rmd
├── 13-contributions.Rmd
├── 14-publications.Rmd
├── 15-dutch_summary.Rmd
├── 16-acknowledgments.Rmd
├── DESCRIPTION
├── README.md
├── _00-preface.Rmd
├── _README.Rmd
├── _bookdown.yml
├── _output.yml
├── index.Rmd
├── thesis.Rproj
├── thesis.log
└── thesis.rds

• Each .Rmd file contains the content of one thesis chapter, written in (R)Markdown. The chapters are rendered in order according to the number the file starts with (_00-preface.Rmd is an exception; it’s included only in the html version of the thesis, before the introduction)
• DESCRIPTION lists the R packages that are required to build the thesis (under Imports:)
• _bookdown.yml, index.Rmd, and _output.yml contain parameters in the YAML header for bookdown to render the book
• thesis.Rproj can be used to open the project in R Studio

/_bookdown_files folder

_bookdown_files
├── AB_sEBR_files
│   ├── AB_sEBR.RData
│   └── figures
├── AB_tDCS_files
│   ├── AB_tDCS.RData
│   ├── AB_tDCS_supplement.RData
│   └── figures
├── CC-BY.png
├── MFBrain_files
│   └── figures
├── introduction_files
│   └── figures
├── sacc_tDCS_files
│   ├── FEF_coords_MNI_excl.csv
│   ├── figures
│   └── tdcs_sensations.csv
└── tDCS_att_review_files
    ├── other.csv
    ├── spatial_bias.csv
    ├── spatial_orienting.csv
    ├── sustained_attention.csv
    └── visual_search.csv

Chapters 1–6 (as well as the supplements that correspond to these chapters) contain more than just prose, but also tables, figures, and statistical results. The files necessary to create these live here.

• .csv files are read in to produce tables
• the /figures folders contains the figures in pdf (for pdf version of the thesis) and png (for html version of the thesis) format.
• the .Rdata files contain variables from the scripts that produced the statistical results. Their values are inserted into the text in the apppropriate place

other folders

.
├── bib
│   ├── apa.csl
│   ├── r-packages.bib
│   └── thesis.bib
├── cover
│   ├── thesis_cover.jpg
│   └── thesis_cover.pdf
├── css
│   └── style.css
└── tex
    ├── front_matter.tex
    └── preamble.tex

• /bib contains everything needed to rendered the bibliopgraphy: information on the cited works (thesis.bib) and R packages (r-packages.bib), as well as a style file to format the biblipgraphy in APA style (apa.csl)
• /cover contains the book cover
• /css contains a style file to render the html version of the thesis
• /tex contains two files with LaTeX commands, used to set options (preamble.tex) and create everything prior to the first chapter (front_matter.tex) for the pdf version of the thesis

License

All the text and figures are licensed under a Creative Commons Attribution 4.0 International License (CC-BY 4.0), except for the art on the cover, which is by Alicia Martin Lopez ©. There’s barely any code in this repository, other than some html and LaTeX formatting; feel free to use those however you see fit.