#+startup: beamer #+TITLE: Striatal volume and functional connectivity predict weight gain #+TITLE: in early-phase psychosis * Preamble :ignore: ** General comments :ignore: # ---------------------------------------------------------------------- # - Turn on synonyms by starting synosaurus-mode # - Look up words using C-c sr # - Turn on dictionary by starting flyspell-mode # - Count words by section using org-wc-display # ---------------------------------------------------------------------- ** Specific comments for this manuscript :ignore: # ---------------------------------------------------------------------- ** org specific settings :ignore: # ---------------------------------------------------------------------- #+OPTIONS: email:nil toc:nil num:nil author:nil date:t tex:t title:nil #+STARTUP: align fold #+SEQ_TODO: TODO(t) | DONE(d) #+TAGS: figure(f) check(c) noexport(n) ignore(i) #+LANGUAGE: en #+EXCLUDE_TAGS: noexport TODO #+DATE: {{{time(%Y-%m-%d %H:%M)}}} # ---------------------------------------------------------------------- ** Latex header :ignore: # ---------------------------------------------------------------------- #+LATEX_CLASS: mybeamerposter #+LATEX_HEADER: \setlength{\paperwidth}{36in} #+LATEX_HEADER: \setlength{\paperheight}{48in} # LATEX_HEADER: \setlength{\textwidth}{0.98\paperwidth} # LATEX_HEADER: \setlength{\textheight}{0.98\paperheight} # LATEX_HEADER: \usepackage[absolute,overlay]{textpos} #+LATEX_HEADER: \graphicspath{{../output/figures/}{../lib/}} #+LATEX_HEADER: \usepackage[export]{adjustbox} #+LATEX_HEADER: \usepackage{graphicx,caption} #+LATEX_HEADER: \usepackage{eurosym} #+LATEX_HEADER: \usepackage{textcomp} #+LATEX_HEADER: \usepackage{bibentry} # LATEX_HEADER: \setlength{\TPVertModule}{1cm} # LATEX_HEADER: \setlength{\oddsidemargin}{0.1in} # LATEX_HEADER: \title{The demise of the spotted swamp frog} # LATEX_HEADER: \author{Rob J Hyndman} # LATEX_HEADER: \footer{ # LATEX_HEADER: \textbf{Philipp Homan, MD, PhD}\\ # LATEX_HEADER: phoman1@northwell.edu\\ # LATEX_HEADER: github.com/philipphoman} #+LATEX_HEADER: \date{} # ---------------------------------------------------------------------- ** Latex macros :ignore: # ---------------------------------------------------------------------- #+LATEX_HEADER: \newcommand{\auth}{$^{\ast}$Philipp Homan, MD, PhD} #+LATEX_HEADER: \newcommand{\authemail}{phoman1@northwell.edu} #+LATEX_HEADER: \newcommand{\authtwitter}{@philipphoman} #+LATEX_HEADER: \newcommand{\authgithub}{github.com/philipphoman} # ---------------------------------------------------------------------- ** Authors and affiliations :ignore: # ---------------------------------------------------------------------- #+LATEX_HEADER: \author{ #+LATEX_HEADER: Philipp Homan$^{1\ast}$, #+LATEX_HEADER: Christina Fales$^{1}$, #+LATEX_HEADER: Pamela DeRosse$^{1}$, #+LATEX_HEADER: Philip Szeszko$^{1}$, #+LATEX_HEADER: Delbert Robinson$^{1}$, #+LATEX_HEADER: Todd Lencz$^{1}$, #+LATEX_HEADER: Anil K. Malhotra$^{1}$ #+LATEX_HEADER: \\ #+LATEX_HEADER: \vspace{5mm} #+LATEX_HEADER: \normalsize{$^{1}$Department of Psychiatry,} #+LATEX_HEADER: \normalsize{The Donald and Barbara Zucker} #+LATEX_HEADER: \normalsize{School of Medicine at Northwell/Hofstra,} #+LATEX_HEADER: \normalsize{Hempstead, NY}\\ #+LATEX_HEADER: } # ---------------------------------------------------------------------- ** Buffer-wide source code blocks :ignore: # ---------------------------------------------------------------------- # Set elisp variables need for nice formatting We want no new lines in # inline results and a paragraph size of 80 characters Important: this # has to be evaluated witch C-c C-c in order to work in the current # buffer #+BEGIN_SRC emacs-lisp :exports none :results silent ; set timestamp format ;(setq org-export-date-timestamp-format "%FT%T%z") (require 'org-wc) (flyspell-mode t) ;(evil-declare-change-repeat 'company-complete) (setq synosaurus-choose-method 'popup) (synosaurus-mode t) (auto-complete-mode t) ;(ac-config-default) ;(add-to-list 'ac-modes 'org-mode) (linum-mode t) (whitespace-mode t) (setq org-babel-inline-result-wrap "%s") (setq org-export-with-broken-links "mark") (setq fill-column 72) (setq whitespace-line-column 72) ;(setq org-latex-caption-above '(table image)) (setq org-latex-caption-above nil) (org-toggle-link-display) ; don't remove logfiles at export (setq org-latex-remove-logfiles nil) ; Keybindings ; (global-set-key (kbd " c") "#+CAPTION: ") (defun setfillcolumn72 () (interactive) (setq fill-column 72) ) (defun setfillcolumn42 () (interactive) (setq fill-column 42) ) (define-key org-mode-map (kbd "C-c c #") "#+CAPTION: ") (define-key org-mode-map (kbd "C-c l #") "#+LATEX_HEADER: ") (define-key org-mode-map (kbd "C-c f c 4 2") 'setfillcolumn42) (define-key org-mode-map (kbd "C-c f c 7 2") 'setfillcolumn72) (setq org-odt-category-map-alist '(("__Figure__" "*Figure*" "value" "Figure" org-odt--enumerable-image-p))) ; let ess not ask for starting directory (setq ess-ask-for-ess-directory nil) ;(setq org-latex-pdf-process '("latexmk -pdflatex='xelatex ;-output-directory=../output/tex/ -interaction nonstopmode' -pdf ;-bibtex -f %f")) (setq org-latex-logfiles-extensions (quote("bcf" "blg" "fdb_latexmk" "fls" "figlist" "idx" "log" "nav" "out" "ptc" "run.xml" "snm" "toc" "vrb" "xdv"))) ; deactivate link resolving (setq org-activate-links nil) ; set tags identation (setq org-tags-column -72) #+END_SRC # # # # ---------------------------------------------------------------------- ** End preamble :ignore: # ---------------------------------------------------------------------- * References :ignore: \bibliographystyle{nature} \nobibliography{master} * The poster :PROPERTIES: :BEGIN: :BEAMER_env: fullframe :END: ** Code :ignore: # First, make sure all variables are availabe #+HEADER: :exports none #+BEGIN_SRC R :results silent :session if (!(grepl("src", getwd()))) setwd("../../../../src") source("fe_func.R") source("bmi_load.R") # R version rvers <- version$version.string # Python version # pyvers <- system("python --version") # pysurfvers <- system("pip freeze | grep pysurf") #pyvers <- "2.7.13" #pysurfvers <- "0.7" pyplusvers <- system("pyv=$(python -V 2>&1); echo $pyv", intern=TRUE) pysurfplusvers <- system("pip list | grep pysurf", intern=TRUE) #+END_SRC ** Left column :BMCOL: :PROPERTIES: :BEAMER_col: 0.45 :BEAMER_opt: [t] :END: *** Background :B_block: :PROPERTIES: :BEAMER_env: block :END: - Schizophrenia has long been considered a disorder of dysconnectivity in the brain - Using graph theory, we computed statistical similarity networks for each individual (Fig [[figflowchart]], [[figshrinkage]]) in two early-phase schizophrenia cohorts src_R[:session]{parse_n("sz")} {{{results((/N/ = 82))}}} and in healthy controls src_R[:session]{parse_n("hc")} {{{results((/N/ = 77))}}} and tested whether network architecture predicted treatment response *** Methods: Structural similarity networks :B_block: :PROPERTIES: :BEAMER_env: block :END: \captionsetup{justification=justified,width=.85\linewidth} #+NAME: figflowchart #+CAPTION: *Analysis flow chart.* #+CAPTION: The similarity between any pair of region was #+CAPTION: estimated by calculating the #+CAPTION: Kullback-Leibler (KL) divergence of their #+CAPTION: probability distributions, resulting in #+CAPTION: a similarity matrix. #+CAPTION: The similarity matrix #+CAPTION: was then thresholded into a binary matrix to #+CAPTION: create a network graph. Graph-based #+CAPTION: degree (or hubness) for each node was then #+CAPTION: calculated for each individual participant. #+CAPTION: Nodal degrees were then entered as #+CAPTION: predictors into a partial #+CAPTION: least squares regression, using individual #+CAPTION: treatment response slopes as outcome #+CAPTION: measure. #+ATTR_LATEX: :width 0.85\textwidth [[file:fe_freesurfer_flowchart.pdf]] *** Methods: Individual treatment response :B_block: :PROPERTIES: :BEAMER_env: block :END: \captionsetup{justification=justified,width=.85\linewidth} #+NAME: figshrinkage #+CAPTION: *Partial pooling to regularize individual response slopes.* #+CAPTION: *A.* *Individual time courses for all participants* #+CAPTION: *from the first schizophrenia cohort.* #+CAPTION: Partial pooling regularized #+CAPTION: the individual slopes, i.e., the influence #+CAPTION: of outliers with only few assessments was attenuated. #+CAPTION: *B.* *The partial pooling effect* #+CAPTION: *is demonstrated by the individual responses being* #+CAPTION: *pulled toward the average treatment effect.* #+CAPTION: As a consequence, outliers are less influential. #+CAPTION: *C, D. The same is shown for the second schizophrenia* #+CAPTION: *cohort.* #+CAPTION: Dotted ellipses indicate confidence regions for the #+CAPTION: average treatment effect. #+ATTR_LATEX: :width 0.85\textwidth [[file:fe_freesurfer_shrinkage.pdf]] ** Right column :BMCOL: :PROPERTIES: :BEAMER_col: 0.45 :BEAMER_opt: [t] :END: *** Results: Partial least squares regression :B_block: :PROPERTIES: :BEAMER_env: block :END: - Individual differences in the configuration of structural similarity networks explained a significant proportion of variance in treatment response (Fig. [[figplsbrains]]) - Exploratory analysis: increased clustering and decreased network integration in patients compared to controls (Fig. [[figge]]) \captionsetup{justification=justified,width=.8\linewidth} #+NAME: figplsbrains #+CAPTION: *PLS scores with individual treatment* #+CAPTION: *response and contribution of cortical nodes* #+CAPTION: *in the schizophrenia cohort* #+CAPTION: Nodal degree for each of #+CAPTION: the src_R[:session]{n_nodes} {{{results(68)}}} #+CAPTION: was entered into a partial least squares (PLS) #+CAPTION: regression, with individual treatment response #+CAPTION: slopes as outcome measure. The first two #+CAPTION: PLS components explained a significant proportion #+CAPTION: of variance in treatment response. *A, B. The first* #+CAPTION: *PLS component correlated most strongly with* #+CAPTION: *nodal degree of orbito- and prefrontal cortices* #+CAPTION: *and posterior cingulate cortex.* Note that #+CAPTION: more negative slopes meant better #+CAPTION: treatment response. #+CAPTION: *B, C. The second PLS component correlated most* #+CAPTION: *most strongly with superior temporal, precentral,* #+CAPTION: *and middle cingulate brain areas.* #+ATTR_LATEX: :width 0.8\textwidth [[file:fe_freesurfer_plsbrains.pdf]] *** Results: Increased clustering in patients :B_block: :PROPERTIES: :BEAMER_env: block :END: \captionsetup{justification=justified,width=0.8\linewidth} #+NAME: figge #+CAPTION: *A. Decreased network integration in* #+CAPTION: *schizophrenia patients compared to controls.* #+CAPTION: Means with error bands #+CAPTION: are shown. #+CAPTION: *B. Increased clustering in schizophrenia patients* #+CAPTION: *compared to controls.* #+CAPTION: Means with error bands are shown. #+CAPTION: Non-overlapping error bands #+CAPTION: indicate significant group differences (/P/ < 0.05). #+ATTR_LATEX: :width 0.8\textwidth [[file:fe_freesurfer_graphsum_individual_2plots.pdf]] *** Conclusions :B_block: :PROPERTIES: :BEAMER_env: block :END: - These data suggest a potential link between brain network morphology and clinical outcome in early-phase schizophrenia *** Disclosure :B_block: :PROPERTIES: :BEAMER_env: block :END: \tiny Dr. Robinson has served as a consultant for Asubio, Otsuka, and Shire and has received grants from Bristol-Myers Squibb, Janssen, and Otsuka. Dr. Kane has served as a consultant for Alkermes, Eli Lilly, Forest, Forum, Genentech, Intracellular Therapies, Janssen, Johnson & Johnson, Lundbeck, Otsuka, Reviva, Roche, Sunovion, and Teva; he has received honoraria for lectures from Genentech, Janssen, Lundbeck, and Otsuka; and he is a shareholder in MedAvante and Vanguard Research Group. Dr. Lencz is a consultant for Genomind. Dr. Malhotra has served as a consultant for Forum Pharmaceuticals and has served on a scientific advisory board for Genomind. The other authors report no financial relationships with commercial interests.