From 819c8a251c8bdb879c0680dc946d650e781ab1f5 Mon Sep 17 00:00:00 2001 From: Ankur Sinha (Ankur Sinha Gmail) Date: Sep 05 2019 17:53:29 +0000 Subject: initial commit --- diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a67ac67 --- /dev/null +++ b/.gitignore @@ -0,0 +1,61 @@ +*.acn +*.lol +*.acr +*.alg +*.aux +*.bbl +*.blg +*.brf +*.dvi +*.fdb_latexmk +*.glg +*.glo +*.gls +*.idx +*.ilg +*.ind +*.ist +*.lof +*.log +*.lot +*.maf +*.mtc +*.mtc0 +*.nav +*.nlo +*.out +*.pdfsync +*.ps +*.snm +*.synctex.gz* +*.toc +*.vrb +*.xdy +*.tdo +*blx.bib +*.fls +*.equ + +# +#dia +*.dia~ + +*.swp +*.swo + +comment.cut +.ropeproject + +*.pyg +*.pygtex +_minted* + +*.synctex.gz + +*.~* + +tags +tags.* + +*.run.xml +*.bcf diff --git a/20190909_neurofedora.tex b/20190909_neurofedora.tex new file mode 100644 index 0000000..8620ebb --- /dev/null +++ b/20190909_neurofedora.tex @@ -0,0 +1,496 @@ +%% 2019 NeuroFedora contributors + +%% packages %% +% support for coloured text +\usepackage{xcolor} +\definecolor{FedoraBlue}{cmyk}{1.0,0.46,0.0,0.0} +\definecolor{FedoraDarkBlue}{cmyk}{1.0,0.57,0.0,0.38} +\definecolor{FriendsMagenta}{cmyk}{0.0,0.8,0.4,0.0} +\definecolor{FeaturesOrange}{cmyk}{0.0,0.5,1.0,0.0} +\definecolor{FirstGreen}{cmyk}{0.5,0.0,1.0,0.0} +\definecolor{FreedomPurple}{cmyk}{0.57,0.46,0.0,0.0} + +% IPA +\usepackage{tipa} +\usepackage[scale=2]{ccicons} +\usepackage{amssymb} +\usepackage{tikz} +\usetikzlibrary{arrows.meta, arrows, positioning} +\usepackage{jneurosci} +\usepackage{subfig} +\usepackage[T1]{fontenc} +\usepackage[utf8]{inputenc} +\usepackage[style=verbose,backend=biber,autocite=footnote]{biblatex} +\addbibresource{masterbib.bib} +% Use opensans +\usepackage[default,osfigures,scale=0.95]{opensans} +% for strike through +\usepackage[normalem]{ulem} +% links, urls, refs +\usepackage{hyperref} +\hypersetup{colorlinks,linkcolor=FreedomPurple,urlcolor=FreedomPurple} +% graphics +\usepackage{graphicx} +% algorithm +\usepackage{algorithmic} +\usepackage{textcomp} +\usepackage{wrapfig} +\usepackage{textgreek} +\usepackage{euler} +% \usepackage{minted} + +% beamer theme +\usetheme[numbering=fraction]{metropolis} +\usefonttheme[onlymath]{serif} +\setbeamerfont{footnote}{size=\tiny} +\setbeamerfont{caption}{size=\tiny} +\setbeamercolor{alerted text}{fg=FeaturesOrange} +\setbeamercolor{progress bar}{fg=FriendsMagenta} +\setbeamercolor{title separator}{fg=FriendsMagenta} +\setbeamercolor{frametitle}{bg=FedoraDarkBlue} + +\renewcommand{\figurename}{} + +% Not needed in metropolis, but in general footnote citation fixes: https://tex.stackexchange.com/questions/44217/how-can-i-stop-footcite-from-hijacking-my-beamer-columns +% how to use multiple references to the same footnote: https://tex.stackexchange.com/questions/27763/beamer-multiple-references-to-the-same-footnote + +%% title %% +\title[NeuroFedora]{\includegraphics[keepaspectratio,width=.25\textwidth]{images/NeuroFedoraLogo01.png}\\NeuroFedora} +\subtitle{FOSS and Free/Open (neuro) Science} +\author{NeuroFedora contributors} +\date[]{} +%% document begins %% +\begin{document} + +% title frame %% +\begin{frame} + \titlepage{} +\end{frame} + +%% Three slides for 5 minutes, so 25--30 for 50 minutes. + +%% First we define the problem statement. What is it that neuroscience is trying to achieve? +%% Added advantage is that this bit has lots of nice pictures, so it helps to gain the audience's attention. +\section{Problem statement: the brain} +\begin{frame}[c]{The brain: neurons} + \begin{figure}[h] + \centering + \includegraphics[width=\linewidth]{images/Neurons.jpg} + \end{figure} + \note[item]{The brain is composed of specialised cells that enable it to process information by the use of electrical impulses} + \note[item]{As the figure shows, these cells, neurons, have specialised into many many types. They serve different functions, include different proteins and markers, and can be classified in many different ways.} +\end{frame} +\begin{frame}[c]{The brain: in numbers: neurons} + \begin{columns} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \includegraphics[width=\textwidth]{images/brain-sizes.jpg} + \end{figure} + \end{column} + \begin{column}{0.5\textwidth} + \begin{itemize} + \item \alert{86B} neurons\footnotemark{}. + \end{itemize} + \end{column} + \end{columns} + \vspace{0.2cm} + \footnotetext[1]{\fullcite{Herculano-Houzel2009}} + \note[item]{The most recent estimate puts the number of neurons in the human brain at 86B.} +\end{frame} +\begin{frame}[c]{The brain: in numbers: synapses} + \begin{columns} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \includegraphics[width=\textwidth]{images/reconstruction.jpg} + \end{figure} + \end{column} + \begin{column}{0.5\textwidth} + \begin{itemize} + \item \alert{Thousands} of connections between neurons \alert{(synapses)}\footnotemark[2]. + \item Synapses are also of different types, and serve different functions. + \pause{} + \item Synapses underlie \alert{learning}\footnotemark[3]. + \end{itemize} + \end{column} + \end{columns} + \vspace{0.2cm} + \footnotetext[2]{\href{https://drexel.edu/medicine/about/departments/neurobiology-anatomy/research/gao-lab/images/}{Image from The Gao lab, College of Medicine, Drexel University.}} + \footnotetext[3]{\fullcite{Hebb1949}} + \note[item]{Each neuron connects with thousands of other neurons, forming a massive network.} + \note[item]{So, the brain can be thought of as a massively parallel processor.} +\end{frame} +\begin{frame}[c]{So, we want to know (among other things)} + \begin{itemize} + \item how the brain functions (\alert{physiology}), + \item how it is structured (\alert{anatomy}), + \item about its chemicals (\alert{pharmacology, biochemistry}), + \item \ldots{} + \pause{} + \item how it processes information (\alert{computational}), + \item about behaviours, and cognition (\alert{behavioural, cognitive}), + \item \ldots{} + \end{itemize} +\end{frame} +\begin{frame}[c]{with the aim of applying this knowledge to} + \begin{itemize} + \item \alert{disease} prevention and treatment, + \item \ldots{} + \pause{} + \item brain inspired \alert{computing}, + \item \ldots{} + \pause{} + \item philosophy and consciousness, + \end{itemize} + \note[item]{To take applications from the extreme ends of the spectrum: immediate clinical applications, immediate technological applications.} +\end{frame} +\section{How: research pipeline} +\begin{frame}[c]{General workflow} + \begin{figure}[h] + \centering + \only<1>{\input{images/Neuroscience-cycle}}% + \only<2>{\input{images/Neuroscience-cycle-complex}} + \note[item]{A simplified diagram. Actually a lot more complex} + \end{figure} +\end{frame} +\begin{frame}[c]{Tools of the trade} + \textcolor{FedoraBlue}{Experimental:} + \begin{itemize} + \item EEG, ECoG, intracellular and extracellular single and multi neuron recording, + \item CT, DOI, MRI, f-MRI, MEG, PET, + \end{itemize} + \pause{} + \textcolor{FriendsMagenta}{Data analysis:} + \begin{itemize} + \item Statistics, + \item Machine Learning, Big Data, Deep learning, + \end{itemize} + \pause{} + \textcolor{FeaturesOrange}{Theory} and \textcolor{FirstGreen}{modelling:} + \begin{itemize} + \item Simulators of all kinds, + \end{itemize} + \note[item]{Lots of hardware and software is required for basic neuroscience research.} +\end{frame} +\begin{frame}[c]{Tools of the trade:\ II} + \textcolor{FedoraDarkBlue}{Tools for the dissemination of knowledge\footnotemark[4]:} + \begin{itemize} + \item visualisation, + \item academic writing, + \item non academic writing: blogging \ldots, + \item podcasting, + \item video making, + \item creating teaching materials, + \end{itemize} + \pause{} + \textcolor{FirstGreen}{Collaborative tools and utilities.} + \footnotetext[4]{also to a non-specialist audience.} + \note[item]{Often ignored, but not less important} +\end{frame} +\section{Free/Open (neuro) Science?} +\begin{frame}[c]{A familiar ideal} + Free/Open science:\\\alert{Everyone} should have the freedom to \alert{share, study, and modify} scientific material.\\ + \note[item]{This includes all research related activities, tools, and output, not only source code.} + \pause{} + \vspace{0.5cm} + FOSS\@:\\\alert{Everyone} should have the freedom to \alert{share, study, and modify} software\footnotemark[5].\\ + \pause{} + \vspace{0.5cm} + \alert{Free/Open Science implicitly includes, and relies heavily on FOSS.}\\ + \footnotetext[5]{\href{https://u.fsf.org/user-liberation}{Free software foundation}} +\end{frame} +\begin{frame}[c]{Now,} + \alert{FOSS is becoming the standard in research\footnotemark[6].} + \begin{figure}[htpb] + \centering + \includegraphics[width=\linewidth]{images/open-source-paper.png} + \end{figure} + \footnotetext[6]{\href{http://opensourceforneuroscience.org/}{Open source for neuroscience}} +\end{frame} +\section{What can we, Fedora, do to help?} +\begin{frame}[c]{Neuroscience community: highly multidisciplinary} + \begin{itemize} + \item \alert{various specialities:} biologists, mathematicians, physicists, chemists, psychologists, \ldots, + \pause{} + \item \alert{small proportion of trained software developers}, + \end{itemize} +\end{frame} +\begin{frame}[c]{(Anecdotal) notes on development of research software} + \begin{itemize} + \item often \alert{single developer}, or small development teams, + \pause{} + \item limited \alert{access to hardware/resources}, + \pause{} + \item limited \alert{code quality}, + \pause{} + \item limited \alert{use of established best practices}, + \pause{} + \item limited \alert{testing for correctness (!)}, + \pause{} + \item limited \alert{maintenance, short-lived projects}, + \pause{} + \item \alert{complex dependency chains}, + \pause{} + \item lack of \alert{documentation and support}, + \pause{} + \item lack of \alert{community development know-how}, + \end{itemize} + \note[item]{Give how interdisciplinary neuroscience is, most researchers are NOT trained in development} + \note[item]{This implies, and this is based on anecdotal evidence, that the software used in research is not of the best quality} +\end{frame} +\begin{frame}[c]{(Anecdotal) notes on users of research software} + \begin{itemize} + \item \alert{waste time and effort} installing (and reinstalling) their software stacks, + \pause{} + \item are \alert{unaware of helpful development tools}, + \pause{} + \item \alert{rarely run test suites (!)}, + \pause{} + \item \alert{rarely report bugs} upstream, + \pause{} + \item \alert{rarely send improvements} upstream, + \end{itemize} + \note[item]{The other side of the bridge is the users} + \note[item]{Because they aren't trained, they have a hard time setting up and using the software} + \note[item]{If correctness of a tool cannot be verified, how can the correctness of the scientific result be claimed?} +\end{frame} +\begin{frame}[c]{We, at Fedora, are in a unique position} + \begin{itemize} + \item we \alert{liaison between upstream and users} already, + \pause{} + \item we \alert{follow best practices} in software development, + \pause{} + \item we have the \alert{infrastructure}, + \pause{} + \item we constantly \alert{work to grow the community}, + \pause{} + \item we \alert{learn from one another}---train as we work, + \pause{} + \item we \alert{disseminate} information to end-users, + \end{itemize} +\end{frame} +\begin{frame}[c]{So, we started NeuroFedora} + \textcolor{FedoraBlue}{Primary goal:} + \begin{itemize} + \item Provide a \alert{ready to use, integrated FOSS platform} for neuroscientists\footnotemark[7]. + \end{itemize} + \pause{} + \textcolor{FirstGreen}{Secondary/collateral goals:} + \pause{} + \begin{itemize} + \item help \alert{improve the standard and maintenance} of tools, + \item help users \alert{develop software development skills}, + \item \alert{make neuroscience accessible} to non-specialists, + \pause{} + \item \textcolor{FriendsMagenta}{make Fedora the go-to distribution for neuroscience}. + \end{itemize} + \footnotetext[7]{Researchers, academics, hobbyists, anyone!} +\end{frame} +\begin{frame}[c]{In essence,} + \textcolor{FedoraBlue}{NeuroFedora is:\\} + \begin{itemize} + \item \textcolor{FriendsMagenta}{merely leveraging pre-existing community resources to a new domain of software.}\\ + \pause{} + \item \textcolor{FeaturesOrange}{taking the community model of FOSS to neuroscience research,} + \end{itemize} +\end{frame} +\begin{frame}[c]{NeuroFedora: current metrics} + \begin{itemize} + \item \alert{less than a year old\footnotemark[8],} + \pause{} + \item \textcolor{FirstGreen}{15 active contributors:} + \begin{itemize} + \item 10 package maintainers, + \item 5 designers, newcomers, + \item only 5 from a neuroscience background, + \end{itemize} + \pause{} + \item \textcolor{FriendsMagenta}{software:} + \begin{itemize} + \item 105 packages ready to install\footnotemark[9]. + \item \textasciitilde{}160 in queue\footnotemark[10]. + \end{itemize} + \pause{} + \item \textcolor{FedoraBlue}{poster presented at annual Computational Neuroscience Conference (CNS), 2019\footnotemark[11].} + \end{itemize} + \footnotetext[8]{in its second iteration} + \footnotetext[9]{\href{https://src.fedoraproject.org/group/neuro-sig}{src.fedoraproject.org: Neuro-SIG}} + \footnotetext[10]{\href{https://pagure.io/neuro-sig/NeuroFedora/issues?status=Open&tags=T\%3A+Software}{Pagure.io: Neuro-SIG: issues}} + \footnotetext[11]{\href{https://neurofedora.github.io/2019/07/11/neurofedora-poster-at-cns-2019.html}{NeuroFedora blog: poster at CNS*2019}} +\end{frame} +\begin{frame}[c]{NeuroFedora: future plans} + \begin{itemize} + \item \alert{make more software available,} + \begin{itemize} + \item \alert{via modularity,} + \item \alert{via containers,} + \end{itemize} + \pause{} + \item \textcolor{FirstGreen}{improve documentation, and support,} + \pause{} + \item \textcolor{FriendsMagenta}{increase community,} + \begin{itemize} + \item \textcolor{FriendsMagenta}{convert research user base into FOSS contributors,} + \item \textcolor{FriendsMagenta}{convert FOSS contributor base into users,} + \end{itemize} + \end{itemize} +\end{frame} +\begin{frame}[c]{NeuroFedora: what you can do} + \textcolor{FriendsMagenta}{Anything! It's just more of Fedora!} + \pause{} + \begin{columns} + \begin{column}{0.5\textwidth} + \begin{itemize} + \item packaging, + \item testing + \item containers, + \item documentation, + \item evangelism, + \item marketing, + \item design, + \item \ldots, + \end{itemize} + \end{column} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \includegraphics[width=0.8\linewidth]{images/NeuroFedoraBadge.png} + \end{figure} + \end{column} + \end{columns} +\end{frame} +\section{So!} +\begin{frame}[c]{There's so much more to talk about} + \textcolor{FedoraBlue}{Mailing list:\ neuro-sig@lists.fedoraproject.org}\\ + \textcolor{FirstGreen}{IRC:\ \#fedora-neuro}\\ + \textcolor{FeaturesOrange}{Telegram:\ t.me/NeuroFedora}\\ + \textcolor{FriendsMagenta}{Docs:\ neuro.fedoraproject.org}\\ + \textcolor{FirstGreen}{Blog:\ neurofedora.github.io}\\ + \textcolor{FeaturesOrange}{Pagure:\ neuro-sig/NeuroFedora} +\end{frame} +\begin{frame}[c]{Fedora \ensuremath\heartsuit{} Science} + \textcolor{FreedomPurple}{There's more science in Fedora! Come to the HACKATHON!} + \begin{itemize} + \item \textcolor{FedoraBlue}{Astronomy SIG} + \item \textcolor{FirstGreen}{Bigdata SIG} + \item \textcolor{FeaturesOrange}{Machine Learning} + \item \textcolor{FriendsMagenta}{Electronic Lab} + \item \textcolor{FedoraBlue}{Medical} + \item \textcolor{FirstGreen}{Sci-tech} + \end{itemize} + \pause{} + \textcolor{FreedomPurple}{Is your interest not listed? Start your own!} + \note[item]{All the resources are already available in the community---all one needs to do is find others who share interests and start working!} +\end{frame} +% If time permits, and the audience looks interested +\section{Myths} +\begin{frame}[c]{Myth 1} + \textcolor{FriendsMagenta}{(Neuro) science is all about working on \enquote{core research}.}\\ + \vspace{0.5cm} + \pause{} + \textcolor{FirstGreen}{Wrong! There is more to (neuro) science!}\\ + \note[item]{The learning curve is similar to what non-techies experience when they try to join FOSS\@. It takes similar effort to gain the required domain specific knowledge.} +\end{frame} +\begin{frame}[c]{Myth buster example: Open Source Brain} + \begin{figure}[h] + \centering + \includegraphics[width=\linewidth]{images/OSB.png} + \end{figure} + \footnotetext[12]{\href{https://opensourcebrain.org}{opensourcebrain.org}} +\end{frame} +\begin{frame}[c]{Myth buster example: OpenWorm } + \begin{figure}[h] + \centering + \includegraphics[width=\linewidth]{images/openworm.png} + \end{figure} + \footnotetext[13]{\href{https://openworm.org}{openworm.org}} +\end{frame} +\begin{frame}[c]{Myth buster example: Science art} + \begin{columns} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \includegraphics[height=0.6\textheight]{images/rebeccaivatts-dementia.jpg} + \caption{Snail: related to Dementia} + \end{figure} + \end{column} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \includegraphics[height=0.6\textheight]{images/rebeccaivatts-pieces-of-mind.jpg} + \caption{Pieces of the Mind (2014)} + \end{figure} + \end{column} + \end{columns} + \footnotetext[14]{\href{https://rebeccaivatts.com}{rebeccaivatts.com}, \textcopyright{} Rebecca Ivatts 2019} +\end{frame} +\begin{frame}[c]{Myth 2} + \textcolor{FriendsMagenta}{Only researchers can do (neuro) science. It's too hard.}\\ + \vspace{0.5cm} + \pause{} + \textcolor{FirstGreen}{Wrong! Everyone can do (neuro) science!}\\ + \note[item]{The learning curve is similar to what non-techies experience when they try to join FOSS\@. It takes similar effort to gain the required domain specific knowledge.} +\end{frame} +\begin{frame}[c]{Myth buster example: understanding learning} + \note[item]{We learn when synapses change in the brain} + \note[item]{As an example, let's say we have a neuron that was activated by a smell.} + \note[item]{Later, we found out that that was the smell of some food, say curry.} + \note[item]{Because these neurons fired one after the other here, this synapse is strengthened.} + \note[item]{When this happens repeatedly, the synapse is strengthened again and again.} + \note[item]{Until, the faintest whiff of the smell reminds you of the food!} + \begin{columns} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \only<1>{\input{images/ltp-schematic-1.tex}} + \only<2>{\input{images/ltp-schematic-2.tex}} + \only<3>{\input{images/ltp-schematic-3.tex}} + \only<4>{\input{images/ltp-schematic-4.tex}} + \only<5>{\input{images/ltp-schematic-5.tex}} + \end{figure} + \end{column} + \begin{column}{0.5\textwidth} + \begin{figure}[h] + \centering + \input{images/spike-train.tex} + \end{figure} + \end{column} + \end{columns} + \footnotetext[15]{Spike-timing dependent plasticity (STDP): underlies learning in the Brain.} + \note[item]{Of course, the more you look at it, the more information you find, but that doesn't mean that we can't study or apply it.} +\end{frame} +\begin{frame}[fragile]{Myth buster example: an example simulation in NEST} + \tiny{ + \begin{verbatim} +# sudo dnf install python3-nest +import pylab +import nest +import nest.voltage_trace + +weight = 20.0 +delay = 1.0 +stim = 1000.0 + +# create two neurons and a voltmeter +neuron1 = nest.Create("iaf_psc_alpha") +neuron2 = nest.Create("iaf_psc_alpha") +voltmeter = nest.Create("voltmeter") + +# give the first neuron a stimulus, connect it to the second one, watch the second spike +nest.SetStatus(neuron1, {"I_e": stim}) +nest.Connect(neuron1, neuron2, syn_spec={'weight': weight, 'delay': delay}) +nest.Connect(voltmeter, neuron2) + +nest.Simulate(100.0) + +nest.voltage_trace.from_device(voltmeter) +nest.voltage_trace.show() + \end{verbatim} +} + + \note[item]{This is all it takes to simulate two neurons that are connected through a synapse.} + \note[item]{Of course, this is a simple example, but the point is---it's just programming with a little bit of domain knowledge.} + \footnotetext[16]{\href{https://nest-simulator.org}{nest-simulator.org}} +\end{frame} +\end{document} diff --git a/20190909_neurofedora_handouts.pdf b/20190909_neurofedora_handouts.pdf new file mode 100644 index 0000000..30dc23f Binary files /dev/null and b/20190909_neurofedora_handouts.pdf differ diff --git a/20190909_neurofedora_handouts.tex b/20190909_neurofedora_handouts.tex new file mode 100644 index 0000000..d6473b7 --- /dev/null +++ b/20190909_neurofedora_handouts.tex @@ -0,0 +1,2 @@ +\documentclass[usenames,dvipsnames,handout]{beamer} +\input{20190723_neurofedora.tex} diff --git 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new file mode 100644 index 0000000..3af1fec Binary files /dev/null and b/20190909_neurofedora_notes_only_print.pdf differ diff --git a/20190909_neurofedora_notes_only_print.tex b/20190909_neurofedora_notes_only_print.tex new file mode 100644 index 0000000..c343566 --- /dev/null +++ b/20190909_neurofedora_notes_only_print.tex @@ -0,0 +1,7 @@ +\documentclass[a4paper]{article} +\usepackage{pdfpages} +\begin{document} +\includepdf[pages=1-last,nup=2x4,landscape=false,frame=true, + noautoscale=true,scale=0.6,delta=0mm 5mm]{20190723_neurofedora_notes_only.pdf} +\end{document} + diff --git a/20190909_neurofedora_presentation.pdf b/20190909_neurofedora_presentation.pdf new file mode 100644 index 0000000..8d80cb8 Binary files /dev/null and b/20190909_neurofedora_presentation.pdf differ diff --git a/20190909_neurofedora_presentation.tex b/20190909_neurofedora_presentation.tex new file mode 100644 index 0000000..826b828 --- /dev/null +++ b/20190909_neurofedora_presentation.tex @@ -0,0 +1,2 @@ +\documentclass[usenames,dvipsnames]{beamer} +\input{20190723_neurofedora.tex} diff --git a/20190909_neurofedora_presentation.tex.latexmain b/20190909_neurofedora_presentation.tex.latexmain new file mode 100644 index 0000000..963550c --- /dev/null +++ b/20190909_neurofedora_presentation.tex.latexmain @@ -0,0 +1 @@ +Main ppt for vimtex diff --git a/20190909_neurofedora_presentation_notes.pdf b/20190909_neurofedora_presentation_notes.pdf new file mode 100644 index 0000000..c6f82df Binary files /dev/null and b/20190909_neurofedora_presentation_notes.pdf differ diff --git a/20190909_neurofedora_presentation_notes.tex b/20190909_neurofedora_presentation_notes.tex new file mode 100644 index 0000000..5fa610f --- /dev/null +++ b/20190909_neurofedora_presentation_notes.tex @@ -0,0 +1,7 @@ +\documentclass[usenames,dvipsnames]{beamer} +\usepackage{pgfpages} +\setbeameroption{show notes on second screen} +%\setbeamertemplate{note page}[plain] +\input{20190723_neurofedora.tex} + + diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..0417c7c --- /dev/null +++ b/Makefile @@ -0,0 +1,33 @@ +.PHONY: pdf + +all: pdf with_notes notes_only notes_only_print handouts handouts_print handouts_space +# all: pdf with_notes handouts handouts_print handouts_space clean + +pdf: 20190723_neurofedora.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make 20190723_neurofedora_presentation.tex + +with_notes: 20190723_neurofedora_presentation_notes.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make 20190723_neurofedora_presentation_notes.tex + +notes_only: 20190723_neurofedora_notes_only.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make -bibtex- 20190723_neurofedora_notes_only.tex + +notes_only_print: notes_only 20190723_neurofedora_notes_only_print.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make -bibtex- 20190723_neurofedora_notes_only_print.tex + +handouts: 20190723_neurofedora_handouts.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make 20190723_neurofedora_handouts.tex + +handouts_print: handouts 20190723_neurofedora_handouts_print.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make 20190723_neurofedora_handouts_print.tex + +handouts_space: 20190723_neurofedora_handouts_with_space.tex + latexmk -pdf -pdflatex="pdflatex -interactive=nonstopmode" -use-make 20190723_neurofedora_handouts_with_space.tex + +deps: + sudo dnf install 'tex(pgfpages.sty)' 'tex(pdfpages.sty)' 'tex(handoutWithNotes.sty)' 'tex(pdfpages.sty)' 'tex(pgfpages.sty)' 'tex(xcolor.sty)' 'tex(tipa.sty)' 'tex(ccicons.sty)' 'tex(amssymb.sty)' 'tex(tikz.sty)' 'tex(jneurosci.sty)' 'tex(subfig.sty)' 'tex(fontenc.sty)' 'tex(inputenc.sty)' 'tex(biblatex.sty)' 'tex(opensans.sty)' 'tex(ulem.sty)' 'tex(hyperref.sty)' 'tex(graphicx.sty)' 'tex(algorithmic.sty)' 'tex(textcomp.sty)' 'tex(wrapfig.sty)' 'tex(textgreek.sty)' 'tex(euler.sty)' 'tex(minted.sty)' 'tex(import.sty)' --setopt=strict=0 + + +clean: + rm -fv *.aux *.bbl *.blg *.log *.nav *.out *.snm *.toc *.dvi *.vrb *.bcf *.run.xml *.cut *.lo* + latexmk -c diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..ab0cec3 --- /dev/null +++ b/README.rst @@ -0,0 +1,21 @@ +20190723 NeuroFedora +--------------------- + +These are the slides for our talk on NeuroFedora_ at Flock 2019. + +All the text is in :code:`20190723_neurofedora.tex`. The other files are merely +used to generate different outputs. Generally, it is enough to modify the main +file and then use the Makefile to generate all the outputs. + +Dependencies +============= + +On a Fedora system, please :code:`make deps` to install the required TeXlive +packages from the repositories using :code:`dnf`. + +License +======== + +Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) + +.. _NeuroFedora: https://fedoraproject.org/wiki/SIGs/NeuroFedora diff --git a/handoutWithNotes.sty b/handoutWithNotes.sty new file mode 100644 index 0000000..a8898d0 --- /dev/null +++ b/handoutWithNotes.sty @@ -0,0 +1,466 @@ +% Copyright 2009 by Guido Diepen +% Parts provided by Edson Valle +% +% This file may be distributed and/or modified +% +% 1. under the LaTeX Project Public License and/or +% 2. under the GNU Public License. +% +% Changelog +% 20091202 - Added "1 on 1 with notes" layout, provided by Harald Welte +% 20091108 - Added "2 on 1 with notes landscape" layout, provided by Edson Valle +% 20091104 - Added "3 on 1 with notes" layout +% 20091104 - Added "2 on 1 with notes" layout +% 20091104 - Added "1 on 1 with notes landscape" layout, provided by Edson Valle +% 20090101 - Initial Version + +\RequirePackage{pgfpages} + \pgfpagesdeclarelayout{1 on 1 with notes landscape} { + \edef\pgfpageoptionheight{\the\paperwidth} + \edef\pgfpageoptionwidth{\the\paperheight} + \edef\pgfpageoptionborder{0pt} + } + { + \setkeys{pgfpagesuselayoutoption}{landscape} + \pgfpagesphysicalpageoptions + {% + logical pages=2,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=1% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=1.2, + center=\pgfpoint{.3\pgfphysicalwidth}{.5\pgfphysicalheight}% + }% + + + + \pgfpageslogicalpageoptions{2} + {% + border shrink=\pgfpageoptionborder,% + resized width=.45\pgfphysicalwidth,% + resized height=.45\pgfphysicalheight,% + center=\pgfpoint{.78\pgfphysicalwidth}{.6\pgfphysicalheight},% + copy from=2 + }% + + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{2}\copy\notesbox + + + } + } + + \pgfpagesdeclarelayout{4 on 1 with notes} { + \edef\pgfpageoptionheight{\the\paperheight} + \edef\pgfpageoptionwidth{\the\paperwidth} + \edef\pgfpageoptionborder{0pt} + } + { + \pgfpagesphysicalpageoptions + {% + logical pages=8,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=4% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.875\pgfphysicalheight}% + }% + \pgfpageslogicalpageoptions{2} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.625\pgfphysicalheight}% + }% + + \pgfpageslogicalpageoptions{3} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.375\pgfphysicalheight}% + }% + + \pgfpageslogicalpageoptions{4} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.125\pgfphysicalheight}% + }% + + + + + + + + + \pgfpageslogicalpageoptions{5} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.3333\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.875\pgfphysicalheight},% + copy from=5 + }% + \pgfpageslogicalpageoptions{6} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.3333\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.625\pgfphysicalheight},% + copy from=6 + }% + \pgfpageslogicalpageoptions{7} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.3333\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.375\pgfphysicalheight},% + copy from=7 + }% + \pgfpageslogicalpageoptions{8} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.3333\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.125\pgfphysicalheight},% + copy from=8 + }% + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{5}\copy\notesbox + \pgfpagesshipoutlogicalpage{6}\copy\notesbox + \pgfpagesshipoutlogicalpage{7}\copy\notesbox + \pgfpagesshipoutlogicalpage{8}\copy\notesbox + } + } + + + + \pgfpagesdeclarelayout{2 on 1 with notes} { + \edef\pgfpageoptionheight{\the\paperheight} + \edef\pgfpageoptionwidth{\the\paperwidth} + \edef\pgfpageoptionborder{0pt} + } + { + \pgfpagesphysicalpageoptions + {% + logical pages=4,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=2% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.67\pgfphysicalheight}% + }% + \pgfpageslogicalpageoptions{2} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.33\pgfphysicalheight}% + }% + + + \pgfpageslogicalpageoptions{3} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.5\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.67\pgfphysicalheight},% + copy from=3 + }% + \pgfpageslogicalpageoptions{4} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.5\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.33\pgfphysicalheight},% + copy from=4 + }% + + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{3}\copy\notesbox + \pgfpagesshipoutlogicalpage{4}\copy\notesbox + } + } + + + \pgfpagesdeclarelayout{3 on 1 with notes} { + \edef\pgfpageoptionheight{\the\paperheight} + \edef\pgfpageoptionwidth{\the\paperwidth} + \edef\pgfpageoptionborder{0pt} + } + { + \pgfpagesphysicalpageoptions + {% + logical pages=6,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=3% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.82\pgfphysicalheight}% + }% + \pgfpageslogicalpageoptions{2} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.50\pgfphysicalheight}% + }% + \pgfpageslogicalpageoptions{3} + {% + scale=.70, + center=\pgfpoint{.25\pgfphysicalwidth}{.18\pgfphysicalheight}% + }% + + + \pgfpageslogicalpageoptions{4} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.5\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.82\pgfphysicalheight},% + copy from=4 + }% + \pgfpageslogicalpageoptions{5} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.5\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.50\pgfphysicalheight},% + copy from=5 + }% + \pgfpageslogicalpageoptions{6} + {% + border shrink=\pgfpageoptionborder,% + resized width=.5\pgfphysicalwidth,% + resized height=.5\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.18\pgfphysicalheight},% + copy from=6 + }% + + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{4}\copy\notesbox + \pgfpagesshipoutlogicalpage{5}\copy\notesbox + \pgfpagesshipoutlogicalpage{6}\copy\notesbox + } + } + + + + + + \pgfpagesdeclarelayout{2 on 1 with notes landscape} { + \edef\pgfpageoptionheight{\the\paperheight} + \edef\pgfpageoptionwidth{\the\paperwidth} + \edef\pgfpageoptionborder{0pt} + } + { + \setkeys{pgfpagesuselayoutoption}{landscape} + \pgfpagesphysicalpageoptions + {% + logical pages=4,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=2% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=1, + center=\pgfpoint{.3\pgfphysicalwidth}{.75\pgfphysicalheight}% + }% + \pgfpageslogicalpageoptions{2} + {% + scale=1, + center=\pgfpoint{.3\pgfphysicalwidth}{.25\pgfphysicalheight}% + }% + + + + \pgfpageslogicalpageoptions{3} + {% + border shrink=\pgfpageoptionborder,% + resized width=.7\pgfphysicalwidth,% + resized height=.4\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.3\pgfphysicalheight},% + copy from=3 + }% + + \pgfpageslogicalpageoptions{4} + {% + border shrink=\pgfpageoptionborder,% + resized width=.7\pgfphysicalwidth,% + resized height=.4\pgfphysicalheight,% + center=\pgfpoint{.75\pgfphysicalwidth}{.8\pgfphysicalheight},% + copy from=4 + }% + + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + %\hrule width\paperwidth\vskip1cm + %\hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth\vskip1cm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{3}\copy\notesbox + \pgfpagesshipoutlogicalpage{4}\copy\notesbox + + + } + } + + + + \pgfpagesdeclarelayout{1 on 1 with notes} { + \edef\pgfpageoptionheight{\the\paperwidth} + \edef\pgfpageoptionwidth{\the\paperheight} + \edef\pgfpageoptionborder{0pt} + } + { + \setkeys{pgfpagesuselayoutoption}{portrait} + \pgfpagesphysicalpageoptions + {% + logical pages=2,% + physical height=\pgfpageoptionheight,% + physical width=\pgfpageoptionwidth,% +% last logical shipout=3% + last logical shipout=1% + } + + \pgfpageslogicalpageoptions{1} + {% + scale=1.5, + center=\pgfpoint{.5\pgfphysicalwidth}{.73\pgfphysicalheight}% + }% + + + + \pgfpageslogicalpageoptions{2} + {% + border shrink=\pgfpageoptionborder,% + resized width=\pgfphysicalwidth,% + resized height=\pgfphysicalheight,% + center=\pgfpoint{.5\pgfphysicalwidth}{.25\pgfphysicalheight},% + copy from=2 + }% + + \AtBeginDocument{ + \newbox\notesbox + \setbox\notesbox=\vbox{ + \hsize=.85\paperwidth + \vskip-1in\hskip-1in\vbox{ + \vskip1cm + Notes\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth\vskip5mm + \hrule width\paperwidth} + } + \pgfpagesshipoutlogicalpage{2}\copy\notesbox + + + } + } + + + + + diff --git a/images/NeuroFedoraBadge.eps b/images/NeuroFedoraBadge.eps new file mode 100644 index 0000000..e572dc9 --- /dev/null +++ b/images/NeuroFedoraBadge.eps @@ -0,0 +1,740 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%Creator: cairo 1.16.0 (https://cairographics.org) +%%CreationDate: Tue Jul 2 14:22:24 2019 +%%Pages: 1 +%%DocumentData: Clean7Bit +%%LanguageLevel: 3 +%%BoundingBox: 6 5 188 188 +%%EndComments +%%BeginProlog +50 dict begin +/q { gsave } bind def +/Q { grestore } bind def +/cm { 6 array astore concat } bind def +/w { setlinewidth } bind def +/J { setlinecap } bind def +/j { setlinejoin } bind def +/M { setmiterlimit } bind def +/d { setdash } bind def +/m { moveto } bind def +/l { lineto } bind def +/c { curveto } bind def +/h { closepath } bind def +/re { exch dup neg 3 1 roll 5 3 roll moveto 0 rlineto + 0 exch rlineto 0 rlineto closepath } bind def +/S { 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with the `import' package (which may need to be +%% installed) using +%% \usepackage{import} +%% in the preamble, and then including the image with +%% \import{}{.pdf_tex} +%% Alternatively, one can specify +%% \graphicspath{{/}} +%% +%% For more information, please see info/svg-inkscape on CTAN: +%% http://tug.ctan.org/tex-archive/info/svg-inkscape +%% +\begingroup% + \makeatletter% + \providecommand\color[2][]{% + \errmessage{(Inkscape) Color is used for the text in Inkscape, but the package 'color.sty' is not loaded}% + \renewcommand\color[2][]{}% + }% + \providecommand\transparent[1]{% + \errmessage{(Inkscape) Transparency is used (non-zero) for the text in Inkscape, but the package 'transparent.sty' is not loaded}% + \renewcommand\transparent[1]{}% + }% + \providecommand\rotatebox[2]{#2}% + \newcommand*\fsize{\dimexpr\f@size pt\relax}% + \newcommand*\lineheight[1]{\fontsize{\fsize}{#1\fsize}\selectfont}% + \ifx\svgwidth\undefined% + \setlength{\unitlength}{192bp}% + \ifx\svgscale\undefined% + \relax% + \else% + \setlength{\unitlength}{\unitlength * \real{\svgscale}}% + \fi% + \else% + \setlength{\unitlength}{\svgwidth}% + \fi% + \global\let\svgwidth\undefined% + \global\let\svgscale\undefined% + \makeatother% + \begin{picture}(1,1)% + \lineheight{1}% + \setlength\tabcolsep{0pt}% + \put(0,0){\includegraphics[width=\unitlength]{NeuroFedoraBadge.eps}}% + \end{picture}% +\endgroup% diff --git a/images/NeuroFedoraLogo01.png b/images/NeuroFedoraLogo01.png new file mode 100644 index 0000000..5858fa4 Binary files /dev/null and b/images/NeuroFedoraLogo01.png differ diff --git a/images/Neurons.jpg b/images/Neurons.jpg new file mode 100644 index 0000000..b836acf Binary files /dev/null and b/images/Neurons.jpg differ diff --git a/images/Neuroscience-cycle-complex.tex b/images/Neuroscience-cycle-complex.tex new file mode 100644 index 0000000..bbfacd4 --- /dev/null +++ b/images/Neuroscience-cycle-complex.tex @@ -0,0 +1,49 @@ +\tikzset{ + %Define standard arrow tip + >=stealth', + %Define style for boxes + punkt/.style={ + circle, + draw=black, very thick, + text=FedoraDarkBlue, + text width=6em, + minimum height=2em, + text centered}, + % Define arrow style + pil/.style={ + <-, + very thick, + draw=FreedomPurple, + shorten <=2pt, + shorten >=2pt,} +} +\begin{tikzpicture}[node distance=1cm, auto,] + %nodes + \node[punkt, draw=FedoraBlue, text=FedoraBlue] (experiments) {Experimental work}; + \node[punkt, draw=FriendsMagenta, text=FriendsMagenta, above right=of experiments] + (analysis) {Data analysis} + edge[pil, ->, bend left=45, opacity=0.4] (experiments.east) + edge[pil, bend right=45] (experiments.north); + \node[punkt, draw=FeaturesOrange, text=FeaturesOrange, below right=of analysis] + (theory) {Theory} + edge[pil, bend right=45] (analysis.east) + edge[pil, ->, bend left=45, opacity=0.4] (analysis.south); + \node[punkt, draw=FirstGreen, text=FirstGreen, below left=of theory] + (modelling) {Modelling} + edge[pil, bend right=45] (theory.south) + edge[pil, ->, bend left=45] (experiments.south) + edge[pil, ->, bend left=45, opacity=0.4] (theory.west) + edge[pil, <-, bend right=45, opacity=0.4] (experiments.east) + edge[pil, ->, bend left=45, opacity=0.4] (analysis.south) + edge[pil, <-, bend right=45, opacity=0.4] (analysis.south); + % We make a dummy figure to make everything look nice. + % \node[above=of market] (dummy) {}; + % \node[right=of dummy] (t) {Ultimate borrower} + % edge[pil,bend left=45] (market.east) % edges are used to connect two nodes + % edge[pil, bend left=45] (formidler.east); % .east since we want + % % consistent style + % \node[left=of dummy] (g) {Ultimate lender} + % edge[pil, bend right=45] (market.west) + % edge[pil, bend right=45] (formidler.west) + % edge[pil,<->, bend left=45] node[auto] {Direct (a)} (t); +\end{tikzpicture} diff --git a/images/Neuroscience-cycle.tex b/images/Neuroscience-cycle.tex new file mode 100644 index 0000000..82a3590 --- /dev/null +++ b/images/Neuroscience-cycle.tex @@ -0,0 +1,43 @@ +\tikzset{ + %Define standard arrow tip + >=stealth', + %Define style for boxes + punkt/.style={ + circle, + draw=black, very thick, + text=FedoraDarkBlue, + text width=6em, + minimum height=2em, + text centered}, + % Define arrow style + pil/.style={ + <-, + very thick, + draw=FreedomPurple, + shorten <=2pt, + shorten >=2pt,} +} +\begin{tikzpicture}[node distance=1cm, auto,] + %nodes + \node[punkt, draw=FedoraBlue, text=FedoraBlue] (experiments) {Experimental work}; + \node[punkt, draw=FriendsMagenta, text=FriendsMagenta, above right=of experiments] + (analysis) {Data analysis} + edge[pil, bend right=45] (experiments.north); + \node[punkt, draw=FeaturesOrange, text=FeaturesOrange, below right=of analysis] + (theory) {Theory} + edge[pil, bend right=45] (analysis.east); + \node[punkt, draw=FirstGreen, text=FirstGreen, below left=of theory] + (modelling) {Modelling} + edge[pil, bend right=45] (theory.south) + edge[pil, ->, bend left=45] (experiments.south); + % We make a dummy figure to make everything look nice. + % \node[above=of market] (dummy) {}; + % \node[right=of dummy] (t) {Ultimate borrower} + % edge[pil,bend left=45] (market.east) % edges are used to connect two nodes + % edge[pil, bend left=45] (formidler.east); % .east since we want + % % consistent style + % \node[left=of dummy] (g) {Ultimate lender} + % edge[pil, bend right=45] (market.west) + % edge[pil, bend right=45] (formidler.west) + % edge[pil,<->, bend left=45] node[auto] {Direct (a)} (t); +\end{tikzpicture} diff --git a/images/OSB.png b/images/OSB.png new file mode 100644 index 0000000..95e7ad1 Binary files /dev/null and b/images/OSB.png differ diff --git a/images/brain-sizes.jpg b/images/brain-sizes.jpg new file mode 100644 index 0000000..453b4fd Binary files /dev/null and b/images/brain-sizes.jpg differ diff --git a/images/ltp-schematic-1.tex b/images/ltp-schematic-1.tex new file mode 100644 index 0000000..49a83df --- /dev/null +++ b/images/ltp-schematic-1.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.02cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell A}; + \node [FedoraBlue] at (\circlex, 3 + 1.5) {Food: curry!}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/ltp-schematic-2.tex b/images/ltp-schematic-2.tex new file mode 100644 index 0000000..2475a1e --- /dev/null +++ b/images/ltp-schematic-2.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.04cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell A}; + \node [FedoraBlue] at (\circlex, 3 + 1.5) {Food: curry!}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/ltp-schematic-3.tex b/images/ltp-schematic-3.tex new file mode 100644 index 0000000..1ae7fda --- /dev/null +++ b/images/ltp-schematic-3.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.06cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell A}; + \node [FedoraBlue] at (\circlex, 3 + 1.5) {Food: curry!}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/ltp-schematic-4.tex b/images/ltp-schematic-4.tex new file mode 100644 index 0000000..9a327d6 --- /dev/null +++ b/images/ltp-schematic-4.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.08cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell A}; + \node [FedoraBlue] at (\circlex, 3 + 1.5) {Food: curry!}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/ltp-schematic-5.tex b/images/ltp-schematic-5.tex new file mode 100644 index 0000000..b9f8b60 --- /dev/null +++ b/images/ltp-schematic-5.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.10cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell A}; + \node [FedoraBlue] at (\circlex, 3 + 1.5) {Food: curry!}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/ltp-schematic.tex b/images/ltp-schematic.tex new file mode 100644 index 0000000..b1e1bad --- /dev/null +++ b/images/ltp-schematic.tex @@ -0,0 +1,27 @@ +\def\radiusneuron{0.2cm} +\def\radiussynapse{0.02cm} +\def\lendens{0.5cm} +\def\lenax{2cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{1.5} + \def\circley{0} + \draw [FriendsMagenta] (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {240, 270,...,360} \draw [FriendsMagenta] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FriendsMagenta, very thick] ([shift=(120:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (-1cm, \lenax); + \node [FriendsMagenta] at (\circlex, \circley - 1.5) {Smell}; + + % Neuron 2 + \def\circlex{1} + \def\circley{3} + \draw (\circlex, \circley) circle (\radiusneuron); + \foreach \angle in {120, 150,...,240} \draw [FedoraBlue] ([shift=(\angle:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\angle:\radiusneuron+\lendens); + \draw [FedoraBlue, very thick] ([shift=(0:\radiusneuron + 0.1cm )] \circlex, \circley) -- ++ (\lenax, 0); + \node [FedoraBlue] at (\circlex + 0.5, \circley + 1) {Food}; + + % Synapse + \def\circlex{0.47} + \def\circley{2.11} + \draw [FirstGreen, fill=FirstGreen] (\circlex, \circley) circle (\radiussynapse); +\end{tikzpicture} + diff --git a/images/neurofedora-team.png b/images/neurofedora-team.png new file mode 100644 index 0000000..60de005 Binary files /dev/null and b/images/neurofedora-team.png differ diff --git a/images/open-source-paper.png b/images/open-source-paper.png new file mode 100644 index 0000000..31d192e Binary files /dev/null and b/images/open-source-paper.png differ diff --git a/images/openworm.png b/images/openworm.png new file mode 100644 index 0000000..dd5f307 Binary files /dev/null and b/images/openworm.png differ diff --git a/images/rebeccaivatts-dementia.jpg b/images/rebeccaivatts-dementia.jpg new file mode 100644 index 0000000..6e432a8 Binary files /dev/null and b/images/rebeccaivatts-dementia.jpg differ diff --git a/images/rebeccaivatts-pieces-of-mind.jpg b/images/rebeccaivatts-pieces-of-mind.jpg new file mode 100644 index 0000000..663c011 Binary files /dev/null and b/images/rebeccaivatts-pieces-of-mind.jpg differ diff --git a/images/reconstruction.jpg b/images/reconstruction.jpg new file mode 100644 index 0000000..d5bfce6 Binary files /dev/null and b/images/reconstruction.jpg differ diff --git a/images/spike-train.tex b/images/spike-train.tex new file mode 100644 index 0000000..c2b055d --- /dev/null +++ b/images/spike-train.tex @@ -0,0 +1,20 @@ +\def\lenspike{0.5cm} +\begin{tikzpicture}[scale=1, transform shape] + % Neuron 1 + \def\circlex{0} + \def\circley{0} + \draw [FriendsMagenta, thick, ->] (\circlex, \circley) -- ++ (3cm, 0); + \draw [FriendsMagenta, thick] (\circlex + 1cm, \circley) -- ++ (0, \lenspike); + + \draw [FirstGreen, thick, ->] (\circlex + 1cm, \circley + 0.75) -- ++ (\circlex + 1cm, 2); + + % Neuron 2 + \def\circlex{0} + \def\circley{3} + \draw [FedoraBlue, thick, ->] (\circlex, \circley) -- ++ (3cm, 0); + \draw [FedoraBlue, thick] (\circlex + 2cm, \circley) -- ++ (0, \lenspike); + + +\end{tikzpicture} + + diff --git a/masterbib.bib b/masterbib.bib new file mode 100644 index 0000000..c8828fb --- /dev/null +++ b/masterbib.bib @@ -0,0 +1,12011 @@ +% Encoding: UTF-8 + +@Article{Lohmann2005a, + author = {Lohmann, Christian and Wong, Rachel O. L.}, + title = {Regulation of dendritic growth and plasticity by local and global calcium dynamics}, + journal = {Cell calcium}, + year = {2005}, + volume = {37}, + number = {5}, + pages = {403--409}, + doi = {10.1016/j.ceca.2005.01.008}, + file = {:Lohmann2005a - Regulation of dendritic growth and plasticity by local and global calcium dynamics.pdf:PDF}, + timestamp = {2018-09-07}, +} + +@Article{Goodman2009, + author = {Goodman, Dan F. M. and Brette, Romain}, + title = {The brian simulator}, + journal = {Frontiers in neuroscience}, + year = {2009}, + volume = {3}, + number = {2}, + pages = {192}, +} + +@Article{Topalidou2015, + author = {Topalidou, Meropi and Leblois, Arthur and Boraud, Thomas and Rougier, Nicolas P.}, + title = {A long journey into reproducible computational neuroscience}, + journal = {Frontiers in Computational Neuroscience}, + year = {2015}, + volume = {9}, +} + +@Article{Seyed-allaei2013, + author = {Seyed-allaei, Hamed}, + title = {Phase Diagram of Spiking Neural Networks}, + journal = {arXiv preprint arXiv:1312.0125}, + year = {2013}, +} + +@Article{DeFelipe2015, + author = {DeFelipe, Javier}, + title = {The dendritic spine story: an intriguing process of discovery}, + journal = {Frontiers in Neuroanatomy}, + year = {2015}, + volume = {9}, + number = {14}, + issn = {1662-5129}, + doi = {10.3389/fnana.2015.00014}, +} + +@Article{Bendor2015, + author = {Bendor, Daniel}, + title = {The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information}, + year = {2015}, + doi = {10.1371/journal.pcbi.1004197}, +} + +@Article{Bik2015, + author = {Bik, Holly M. and Dove, Alistair D. M. and Goldstein, Miriam C. and Helm, Rebecca R. and MacPherson, Rick and Martini, Kim and Warneke, Alexandria and McClain, Craig}, + title = {Ten Simple Rules for Effective Online Outreach}, + year = {2015}, +} + +@Article{Karunanithi2015, + author = {Karunanithi, Shanker and Brown, Ian R.}, + title = {Heat shock response and homeostatic plasticity}, + journal = {Frontiers in Cellular Neuroscience}, + year = {2015}, + volume = {9}, +} + +@Article{Casson2012, + author = {Casson, Robert J. and Chidlow, Glyn and Ebneter, Andreas and Wood, John P. M. and Crowston, Jonathan and Goldberg, Ivan}, + title = {Translational neuroprotection research in glaucoma: a review of definitions and principles}, + journal = {Clinical \& experimental ophthalmology}, + year = {2012}, + volume = {40}, + number = {4}, + pages = {350--357}, +} + +@Article{Turrigiano2000, + author = {Turrigiano, Gina G. and Nelson, Sacha B.}, + title = {Hebb and homeostasis in neuronal plasticity}, + journal = {Current opinion in neurobiology}, + journaltitle = {Current opinion in neurobiology}, + year = {2000}, + volume = {10}, + number = {3}, + pages = {358--364}, + doi = {10.1016/s0959-4388(00)00091-x}, + file = {:Turrigiano2000 - Hebb and homeostasis in neuronal plasticity.pdf:PDF}, + groups = {Sinha2018a}, +} + +@Article{Desai2003, + author = {Desai, Niraj S.}, + title = {Homeostatic plasticity in the CNS: synaptic and intrinsic forms}, + journal = {Journal of Physiology-Paris}, + year = {2003}, + volume = {97}, + number = {4}, + pages = {391--402}, + doi = {10.1016/j.jphysparis.2004.01.005}, + file = {:Desai2003 - Homeostatic plasticity in the CNS_ synaptic and intrinsic forms.pdf:PDF}, + timestamp = {2018-09-03}, +} + +@Article{Davis2013, + author = {Davis, Graeme W.}, + title = {Homeostatic signaling and the stabilization of neural function}, + journal = {Neuron}, + journaltitle = {Neuron}, + year = {2013}, + volume = {80}, + number = {3}, + pages = {718--728}, + doi = {10.1016/j.neuron.2013.09.044}, + file = {:Davis2013 - Homeostatic signaling and the stabilization of neural function.pdf:PDF}, + groups = {Sinha2018a}, +} + +@Article{Keck2013, + author = {Keck, Tara and Keller, Georg B. and Jacobsen, R. 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Homeostatic synaptic plasticity as a metaplasticity mechanism ---a molecular and cellular perspective.pdf:PDF}, + timestamp = {2018-09-24}, +} + +@Article{Boldog2018, + author = {Boldog, Eszter and Bakken, Trygve E. and Hodge, Rebecca D. and Novotny, Mark and Aevermann, Brian D. and Baka, Judith and Bordé, Sándor and Close, Jennie L. and Diez-Fuertes, Francisco and Ding, Song-Lin and Faragó, Nóra and Kocsis, Ágnes K. and Kovács, Balázs and Maltzer, Zoe and McCorrison, Jamison M. and Miller, Jeremy A. and Molnár, Gábor and Oláh, Gáspár and Ozsvár, Attila and Rózsa, Márton and Shehata, Soraya I. and Smith, Kimberly A. and Sunkin, Susan M. and Tran, Danny N. and Venepally, Pratap and Wall, Abby and Puskás, László G. and Barzó, Pál and Steemers, Frank J. and Schork, Nicholas J. and Scheuermann, Richard H. and Lasken, Roger S. and Lein, Ed S. and Tamás, Gábor}, + title = {Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type}, + journal = {Nature Neuroscience}, + year = {2018}, + volume = {21}, + number = {9}, + month = sep, + pages = {1185--1195}, + issn = {1546-1726}, + doi = {10.1038/s41593-018-0205-2}, + refid = {Boldog2018}, + timestamp = {2018-11-05}, +} + +@Article{Nakahata2018, + author = {Nakahata, Yoshihisa and Yasuda, Ryohei}, + title = {Plasticity of Spine Structure: Local Signaling, Translation and Cytoskeletal Reorganization}, + journal = {Frontiers in Synaptic Neuroscience}, + year = {2018}, + volume = {10}, + pages = {29}, + issn = {1663-3563}, + doi = {10.3389/fnsyn.2018.00029}, + file = {:Nakahata2018 - Plasticity of Spine Structure_ Local Signaling, Translation and Cytoskeletal Reorganization.pdf:PDF}, + timestamp = {2018-09-24}, +} + +@Article{Rich2018, + author = {Rich, Shannon K. and Terman, Jonathan R.}, + title = {Axon formation, extension, and navigation: only a neuroscience phenomenon?}, + journal = {Current Opinion in Neurobiology}, + year = {2018}, + volume = {53}, + pages = {174--182}, + note = {Developmental Neuroscience}, + issn = {0959-4388}, + doi = {10.1016/j.conb.2018.08.004}, + url = {http://www.sciencedirect.com/science/article/pii/S0959438818301363}, + file = {:Rich2018 - Axon formation, extension, and navigation_ only a neuroscience phenomenon_.pdf:PDF}, + timestamp = {2018-09-24}, +} + +@Article{Kodangattil2013, + author = {Kodangattil, Jayaraj N. and Dacher, Matthieu and Authement, Michael E. and Nugent, Fereshteh S.}, + title = {Spike timing-dependent plasticity at GABAergic synapses in the ventral tegmental area}, + journal = {The Journal of Physiology}, + year = {2013}, + volume = {591}, + number = {19}, + pages = {4699--4710}, + doi = {10.1113/jphysiol.2013.257873}, + eprint = {https://physoc.onlinelibrary.wiley.com/doi/pdf/10.1113/jphysiol.2013.257873}, + file = {:Kodangattil2013 - Spike timing-dependent plasticity at GABAergic synapses in the ventral tegmental area.pdf:PDF}, + timestamp = {2018-09-24}, +} + +@Article{Mariano2018, + author = {Mariano, Vittoria and Domínguez-Iturza, Nuria and Neukomm, Lukas J. and Bagni, Claudia}, + title = {Maintenance mechanisms of circuit-integrated axons}, + journal = {Current Opinion in Neurobiology}, + year = {2018}, + volume = {53}, + pages = {162--173}, + note = {Developmental Neuroscience}, + issn = {0959-4388}, + doi = {10.1016/j.conb.2018.08.007}, + url = {http://www.sciencedirect.com/science/article/pii/S0959438818300345}, + file = {:Mariano2018 - Maintenance mechanisms of circuit-integrated axons.pdf:PDF}, + timestamp = {2018-09-24}, +} + +@Article{Micheva2018, + author = {Micheva, Kristina D. and Chang, Edward F. and Nana, Alissa L. and Seeley, William W. and Ting, Jonathan T. and Cobbs, Charles and Lein, Ed and Smith, Stephen J. and Weinberg, Richard J. and Madison, Daniel V.}, + title = {Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex}, + journal = {eNeuro}, + year = {2018}, + doi = {10.1523/ENEURO.0297-18.2018}, + eprint = {http://www.eneuro.org/content/early/2018/09/19/ENEURO.0297-18.2018.full.pdf}, + url = {http://www.eneuro.org/content/early/2018/09/19/ENEURO.0297-18.2018}, + file = {:Micheva2018 - Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex.pdf:PDF}, + publisher = {Society for Neuroscience}, + timestamp = {2018-09-24}, +} + +@Article{Brette2018, + author = {Brette, Romain}, + title = {Is coding a relevant metaphor for the brain?}, + journal = {bioRxiv}, + year = {2018}, + doi = {10.1101/168237}, + eprint = {https://www.biorxiv.org/content/early/2018/07/13/168237.full.pdf}, + url = {https://www.biorxiv.org/content/early/2018/07/13/168237}, + file = {:Brette2018 - Is coding a relevant metaphor for the brain_.pdf:PDF}, + publisher = {Cold Spring Harbor Laboratory}, + timestamp = {2018-09-24}, +} + +@Article{Humphries2018, + author = {Humphries, Mark D. and Obeso, Jose Angel and Dreyer, Jakob Kisbye}, + title = {Insights into Parkinson’s disease from computational models of the basal ganglia}, + journal = {J Neurol Neurosurg Psychiatry}, + year = {2018}, + volume = {89}, + number = {11}, + pages = {1181--1188}, + doi = {10.1136/jnnp-2017-315922}, + file = {:Humphries2018 - Insights into Parkinson’s disease from computational models of the basal ganglia.pdf:PDF}, + publisher = {BMJ Publishing Group Ltd}, + timestamp = {2018-11-05}, +} + +@Article{Blundell2018, + author = {Blundell, Inga and Brette, Romain and Cleland, Thomas A. and Close, Thomas G. and Coca, Daniel and Davison, Andrew P. and Diaz-Pier, Sandra and Fernandez Musoles, Carlos and Gleeson, Padraig and Goodman, Dan F. M. and Hines, Michael and Hopkins, Michael W. and Kumbhar, Pramod and Lester, David R. and Marin, Bóris and Morrison, Abigail and Müller, Eric and Nowotny, Thomas and Peyser, Alexander and Plotnikov, Dimitri and Richmond, Paul and Rowley, Andrew and Rumpe, Bernhard and Stimberg, Marcel and Stokes, Alan B. and Tomkins, Adam and Trensch, Guido and Woodman, Marmaduke and Eppler, Jochen Martin}, + title = {Code Generation in Computational Neuroscience: A Review of Tools and Techniques}, + journal = {Frontiers in Neuroinformatics}, + year = {2018}, + volume = {12}, + pages = {68}, + issn = {1662-5196}, + doi = {10.3389/fninf.2018.00068}, + file = {:Blundell2018 - Code Generation in Computational Neuroscience_ A Review of Tools and Techniques.pdf:PDF}, +} + +@Article{Humphries2010, + author = {Humphries, Mark D. and Wood, Ric and Gurney, Kevin}, + title = {Reconstructing the three-dimensional GABAergic microcircuit of the striatum}, + journal = {PLoS computational biology}, + year = {2010}, + volume = {6}, + number = {11}, + pages = {e1001011}, + doi = {10.1371/journal.pcbi.1001011}, + file = {:Humphries2010 - Reconstructing the three-dimensional GABAergic microcircuit of the striatum.pdf:PDF}, + publisher = {Public Library of Science}, + timestamp = {2018-11-05}, +} + +@Article{Humphries2009, + author = {Humphries, Mark D. and Wood, Ric and Gurney, Kevin}, + title = {Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit}, + journal = {Neural Networks}, + year = {2009}, + volume = {22}, + number = {8}, + pages = {1174--1188}, + doi = {10.1016/j.neunet.2009.07.018}, + file = {:Humphries2009 - Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit.pdf:PDF}, + publisher = {Elsevier}, + timestamp = {2018-11-05}, +} + +@Article{Newton2018, + author = {Newton, Adam J. H. and McDougal, Robert A. and Hines, Michael L. and Lytton, William W.}, + title = {Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics.}, + journal = {Frontiers in neuroinformatics}, + year = {2018}, + volume = {12}, + pages = {41}, + issn = {1662-5196}, + doi = {10.3389/fninf.2018.00041}, + country = {Switzerland}, + file = {:Newton2018 - Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics..pdf:PDF}, + issn-linking = {1662-5196}, + keywords = {computer simulation; multiscale modeling; reusability; spreading depression; stroke}, + nlm-id = {101477957}, + owner = {NLM}, + pmc = {PMC6049079}, + pmid = {30042670}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-14}, + timestamp = {2018-11-21}, +} + +@Article{Gallinaro2018, + author = {Gallinaro, J{\'u}lia V. and Rotter, Stefan}, + title = {Associative properties of structural plasticity based on firing rate homeostasis in recurrent neuronal networks}, + journal = {Scientific reports}, + year = {2018}, + volume = {8}, + number = {1}, + pages = {3754}, + doi = {10.1038/s41598-018-22077-3}, + file = {:Gallinaro2018 - Associative properties of structural plasticity based on firing rate homeostasis in recurrent neuronal networks.pdf:PDF}, + publisher = {Nature Publishing Group}, + timestamp = {2018-12-10}, +} + +@Article{Dorman2018, + author = {Dorman, Daniel B. and J{\k{e}}drzejewska-Szmek, Joanna and Blackwell, Kim T.}, + title = {Inhibition enhances spatially-specific calcium encoding of synaptic input patterns in a biologically constrained model}, + journal = {eLife}, + year = {2018}, + volume = {7}, + pages = {e38588}, + doi = {10.7554/elife.38588}, + file = {:Dorman2018 - Inhibition enhances spatially-specific calcium encoding of synaptic input patterns in a biologically constrained model.pdf:PDF}, + publisher = {eLife Sciences Publications Limited}, +} + +@Article{Wolff1992, + author = {Wolff, J. R. and Missler, M.}, + title = {Synaptic reorganization in developing and adult nervous systems}, + journal = {Annals of Anatomy-Anatomischer Anzeiger}, + year = {1992}, + volume = {174}, + number = {5}, + pages = {393--403}, + doi = {10.1016/s0940-9602(11)80257-8}, + file = {:Wolff1992 - Synaptic reorganization in developing and adult nervous systems.pdf:PDF}, + publisher = {Elsevier}, + timestamp = {2019-01-16}, +} + +@Article{Rekart2007, + author = {Rekart, Jerome L. and Sandoval, C. Jimena and Bermudez-Rattoni, Federico and Routtenberg, Aryeh}, + title = {Remodeling of hippocampal mossy fibers is selectively induced seven days after the acquisition of a spatial but not a cued reference memory task}, + journal = {Learning \& Memory}, + year = {2007}, + volume = {14}, + number = {6}, + pages = {416--421}, + doi = {10.1101/lm.516507}, + file = {:Rekart2007 - Remodeling of hippocampal mossy fibers is selectively induced seven days after the acquisition of a spatial but not a cued reference memory task.pdf:PDF}, + publisher = {Cold Spring Harbor Lab}, + timestamp = {2019-01-16}, +} + +@Article{Rekart2007a, + author = {Rekart, Jerome L. and Sandoval, C. Jimena and Routtenberg, Aryeh}, + title = {Learning-induced axonal remodeling: evolutionary divergence and conservation of two components of the mossy fiber system within Rodentia}, + journal = {Neurobiology of learning and memory}, + year = {2007}, + volume = {87}, + number = {2}, + pages = {225--235}, + doi = {10.1016/j.nlm.2006.08.013}, + file = {:Rekart2007a - Learning-induced axonal remodeling_ evolutionary divergence and conservation of two components of the mossy fiber system within Rodentia.pdf:PDF}, + publisher = {Elsevier}, + timestamp = {2019-01-16}, +} + +@Article{Spiess2016, + author = {Spiess, Robin and George, Richard and Cook, Matthew and Diehl, Peter U.}, + title = {Structural Plasticity Denoises Responses and Improves Learning Speed.}, + journal = {Frontiers in computational neuroscience}, + year = {2016}, + volume = {10}, + pages = {93}, + issn = {1662-5188}, + doi = {10.3389/fncom.2016.00093}, + abstract = {Despite an abundance of computational models for learning of synaptic weights, there has been relatively little research on structural plasticity, i.e., the creation and elimination of synapses. Especially, it is not clear how structural plasticity works in concert with spike-timing-dependent plasticity (STDP) and what advantages their combination offers. Here we present a fairly large-scale functional model that uses leaky integrate-and-fire neurons, STDP, homeostasis, recurrent connections, and structural plasticity to learn the input encoding, the relation between inputs, and to infer missing inputs. Using this model, we compare the error and the amount of noise in the network's responses with and without structural plasticity and the influence of structural plasticity on the learning speed of the network. Using structural plasticity during learning shows good results for learning the representation of input values, i.e., structural plasticity strongly reduces the noise of the response by preventing spikes with a high error. For inferring missing inputs we see similar results, with responses having less noise if the network was trained using structural plasticity. Additionally, using structural plasticity with pruning significantly decreased the time to learn weights suitable for inference. Presumably, this is due to the clearer signal containing less spikes that misrepresent the desired value. Therefore, this work shows that structural plasticity is not only able to improve upon the performance using STDP without structural plasticity but also speeds up learning. Additionally, it addresses the practical problem of limited resources for connectivity that is not only apparent in the mammalian neocortex but also in computer hardware or neuromorphic (brain-inspired) hardware by efficiently pruning synapses without losing performance. }, + completed = {2016-09-23}, + country = {Switzerland}, + file = {:Spiess2016 - Structural Plasticity Denoises Responses and Improves Learning Speed..pdf:PDF}, + issn-linking = {1662-5188}, + keywords = {STDP; homoeostasis; learning; spiking neural network; structural plasticity}, + nlm-id = {101477956}, + owner = {NLM}, + pmc = {PMC5014863}, + pmid = {27660610}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-13}, +} + +@Article{LeBe2006, + author = {Le Bé, Jean-Vincent and Markram, Henry}, + title = {Spontaneous and evoked synaptic rewiring in the neonatal neocortex.}, + journal = {Proceedings of the National Academy of Sciences of the United States of America}, + year = {2006}, + volume = {103}, + issue = {35}, + month = aug, + pages = {13214--13219}, + issn = {0027-8424}, + doi = {10.1073/pnas.0604691103}, + abstract = {The local microcircuitry of the neocortex is structurally a tabula rasa, with the axon of each pyramidal neuron having numerous submicrometer appositions with the dendrites of all neighboring pyramidal neurons, but is functionally highly selective, with synapses formed onto only a small proportion of these targets. This design leaves a vast potential for the microcircuit to rewire without extensive axonal or dendritic growth. To examine whether rewiring does take place, we used multineuron patch-clamp recordings on 12- to 14-day-old rat neocortical slices and studied long-term changes in synaptic connectivity within clusters of neurons. We found pyramidal neurons spontaneously connecting and disconnecting from each other and that exciting the slice with glutamate greatly increases the number of new connections established. Evoked emergence of new synaptic connections requires action potential activity and activation of metabotropic glutamate receptor 5, but not NMDA receptor or group II or group III metabotropic glutamate receptor activation. We also found that it is the weaker connections that are selectively eliminated. These results provide direct evidence for spontaneous and evoked rewiring of the neocortical microcircuitry involving entire functional multisynaptic connections. We speculate that this form of microcircuit plasticity enables an evolution of the microcircuit connectivity by natural selection as a function of experience.}, + chemicals = {Receptor, Metabotropic Glutamate 5, Receptors, Metabotropic Glutamate}, + citation-subset = {IM}, + completed = {2006-09-29}, + country = {United States}, + file = {:LeBe2006 - Spontaneous and evoked synaptic rewiring in the neonatal neocortex..pdf:PDF}, + issn-linking = {0027-8424}, + keywords = {Action Potentials, physiology; Animals; Animals, Newborn; Cell Nucleus, metabolism; Excitatory Postsynaptic Potentials, physiology; Long-Term Potentiation, physiology; Neocortex, physiology; Neuronal Plasticity; Pyramidal Cells, cytology; Rats; Rats, Wistar; Receptor, Metabotropic Glutamate 5; Receptors, Metabotropic Glutamate, metabolism; Synapses, metabolism; Synaptic Transmission, physiology}, + nlm-id = {7505876}, + owner = {NLM}, + pii = {0604691103}, + pmc = {PMC1559779}, + pmid = {16924105}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-13}, +} + +@Article{Hobbiss2018, + author = {Hobbiss, Anna Felicity and Ramiro-Cortés, Yazmin and Israely, Inbal}, + title = {Homeostatic Plasticity Scales Dendritic Spine Volumes and Changes the Threshold and Specificity of Hebbian Plasticity.}, + journal = {iScience}, + year = {2018}, + volume = {8}, + month = oct, + pages = {161--174}, + issn = {2589-0042}, + doi = {10.1016/j.isci.2018.09.015}, + abstract = {Information is encoded in neural networks through changes in synaptic weights. Synaptic learning rules involve a combination of rapid Hebbian plasticity and slower homeostatic synaptic plasticity that regulates neuronal activity through global synaptic scaling. Hebbian and homeostatic plasticity have been extensively investigated, whereas much less is known about their interaction. Here we investigated structural and functional consequences of homeostatic plasticity at dendritic spines of mouse hippocampal neurons. We found that prolonged activity blockade induced spine growth, paralleling synaptic strength increases. Following activity blockade, glutamate uncaging-mediated stimulation at single spines led to size-dependent structural potentiation: smaller spines underwent robust growth, whereas larger spines remained unchanged. Moreover, spines near the stimulated spine exhibited volume changes following homeostatic plasticity, indicating that there was a breakdown of input specificity following homeostatic plasticity. Overall, these findings demonstrate that Hebbian and homeostatic plasticity interact to shape neural connectivity through non-uniform structural plasticity at inputs.}, + file = {:Hobbiss2018 - Homeostatic plasticity scales dendritic spine volumes and changes the threshold and specificity of Hebbian plasticity.pdf:PDF}, + issn-linking = {2589-0042}, + keywords = {Cellular Neuroscience; Neuroscience; Optical Imaging}, + nlm-id = {101724038}, + owner = {NLM}, + pii = {S2589-0042(18)30150-0}, + pmc = {PMC6187013}, + pmid = {30317078}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-14}, + timestamp = {2018-05-02}, +} + +@Article{Jungenitz2018, + author = {Jungenitz, Tassilo and Beining, Marcel and Radic, Tijana and Deller, Thomas and Cuntz, Hermann and Jedlicka, Peter and Schwarzacher, Stephan W.}, + title = {Structural homo- and heterosynaptic plasticity in mature and adult newborn rat hippocampal granule cells.}, + journal = {Proceedings of the National Academy of Sciences of the United States of America}, + year = {2018}, + volume = {115}, + issue = {20}, + month = may, + pages = {E4670--E4679}, + issn = {1091-6490}, + doi = {10.1073/pnas.1801889115}, + citation-subset = {IM}, + completed = {2018-08-28}, + country = {United States}, + file = {:Jungenitz2018 - Structural homo- and heterosynaptic plasticity in mature and adult newborn rat hippocampal granule cells..pdf:PDF}, + groups = {Sinha2018a}, + issn-linking = {0027-8424}, + nlm-id = {7505876}, + owner = {NLM}, + pii = {1801889115}, + pmc = {PMC5960324}, + pmid = {29712871}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-15}, +} + +@Article{Deger2018, + author = {Deger, Moritz and Seeholzer, Alexander and Gerstner, Wulfram}, + title = {Multicontact Co-operativity in Spike-Timing-Dependent Structural Plasticity Stabilizes Networks.}, + journal = {Cerebral cortex (New York, N.Y. : 1991)}, + year = {2018}, + volume = {28}, + issue = {4}, + month = apr, + pages = {1396--1415}, + issn = {1460-2199}, + doi = {10.1093/cercor/bhx339}, + abstract = {Excitatory synaptic connections in the adult neocortex consist of multiple synaptic contacts, almost exclusively formed on dendritic spines. Changes of spine volume, a correlate of synaptic strength, can be tracked in vivo for weeks. Here, we present a combined model of structural and spike-timing-dependent plasticity that explains the multicontact configuration of synapses in adult neocortical networks under steady-state and lesion-induced conditions. Our plasticity rule with Hebbian and anti-Hebbian terms stabilizes both the postsynaptic firing rate and correlations between the pre- and postsynaptic activity at an active synaptic contact. Contacts appear spontaneously at a low rate and disappear if their strength approaches zero. Many presynaptic neurons compete to make strong synaptic connections onto a postsynaptic neuron, whereas the synaptic contacts of a given presynaptic neuron co-operate via postsynaptic firing. We find that co-operation of multiple synaptic contacts is crucial for stable, long-term synaptic memories. In simulations of a simplified network model of barrel cortex, our plasticity rule reproduces whisker-trimming-induced rewiring of thalamocortical and recurrent synaptic connectivity on realistic time scales.}, + country = {United States}, + file = {:Deger2018 - Multicontact Co-operativity in Spike-Timing-Dependent Structural Plasticity Stabilizes Networks..pdf:PDF}, + issn-linking = {1047-3211}, + nlm-id = {9110718}, + owner = {NLM}, + pii = {4780821}, + pmc = {PMC6041941}, + pmid = {29300903}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2018-11-13}, +} + +@Article{Knoblauch2016, + author = {Knoblauch, Andreas and Sommer, Friedrich T}, + title = {Structural Plasticity, Effectual Connectivity, and Memory in Cortex.}, + journal = {Frontiers in neuroanatomy}, + year = {2016}, + volume = {10}, + pages = {63}, + issn = {1662-5129}, + doi = {10.3389/fnana.2016.00063}, + abstract = {Learning and memory is commonly attributed to the modification of synaptic strengths in neuronal networks. More recent experiments have also revealed a major role of structural plasticity including elimination and regeneration of synapses, growth and retraction of dendritic spines, and remodeling of axons and dendrites. Here we work out the idea that one likely function of structural plasticity is to increase "effectual connectivity" in order to improve the capacity of sparsely connected networks to store Hebbian cell assemblies that are supposed to represent memories. For this we define effectual connectivity as the fraction of synaptically linked neuron pairs within a cell assembly representing a memory. We show by theory and numerical simulation the close links between effectual connectivity and both information storage capacity of neural networks and effective connectivity as commonly employed in functional brain imaging and connectome analysis. Then, by applying our model to a recently proposed memory model, we can give improved estimates on the number of cell assemblies that can be stored in a cortical macrocolumn assuming realistic connectivity. Finally, we derive a simplified model of structural plasticity to enable large scale simulation of memory phenomena, and apply our model to link ongoing adult structural plasticity to recent behavioral data on the spacing effect of learning. }, + completed = {2016-07-06}, + country = {Switzerland}, + file = {:Knoblauch2016 - Structural Plasticity, Effectual Connectivity, and Memory in Cortex..pdf:PDF}, + issn-linking = {1662-5129}, + keywords = {effective connectivity; learning; memory consolidation; potential synapse; spacing effect; storage capacity; synaptic plasticity; transfer entropy}, + nlm-id = {101477943}, + owner = {NLM}, + pmc = {PMC4909771}, + pmid = {27378861}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-13}, +} + +@Article{Sailor2016, + author = {Sailor, Kurt A and Valley, Matthew T and Wiechert, Martin T and Riecke, Hermann and Sun, Gerald J and Adams, Wayne and Dennis, James C and Sharafi, Shirin and Ming, Guo-Li and Song, Hongjun and Lledo, Pierre-Marie}, + title = {Persistent Structural Plasticity Optimizes Sensory Information Processing in the Olfactory Bulb.}, + journal = {Neuron}, + year = {2016}, + volume = {91}, + issue = {2}, + month = jul, + pages = {384--396}, + issn = {1097-4199}, + doi = {10.1016/j.neuron.2016.06.004}, + abstract = {In the mammalian brain, the anatomical structure of neural circuits changes little during adulthood. As a result, adult learning and memory are thought to result from specific changes in synaptic strength. A possible exception is the olfactory bulb (OB), where activity guides interneuron turnover throughout adulthood. These adult-born granule cell (GC) interneurons form new GABAergic synapses that have little synaptic strength plasticity. In the face of persistent neuronal and synaptic turnover, how does the OB balance flexibility, as is required for adapting to changing sensory environments, with perceptual stability? Here we show that high dendritic spine turnover is a universal feature of GCs, regardless of their developmental origin and age. We find matching dynamics among postsynaptic sites on the principal neurons receiving the new synaptic inputs. We further demonstrate in silico that this coordinated structural plasticity is consistent with stable, yet flexible, decorrelated sensory representations. Together, our study reveals that persistent, coordinated synaptic structural plasticity between interneurons and principal neurons is a major mode of functional plasticity in the OB.}, + citation-subset = {IM}, + completed = {2017-08-22}, + country = {United States}, + file = {:Sailor2016 - Persistent Structural Plasticity Optimizes Sensory Information Processing in the Olfactory Bulb..pdf:PDF}, + issn-linking = {0896-6273}, + keywords = {Animals; Dendritic Spines, metabolism; Interneurons, physiology; Mice; Nerve Net, metabolism; Neurogenesis, physiology; Neuronal Plasticity, physiology; Olfactory Bulb, physiology; Patch-Clamp Techniques; Synapses, metabolism}, + mid = {NIHMS863435}, + nlm-id = {8809320}, + owner = {NLM}, + pii = {S0896-6273(16)30257-4}, + pmc = {PMC5476833}, + pmid = {27373833}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-13}, +} + +@Article{Villa2016, + author = {Villa, Katherine L. and Berry, Kalen P. and Subramanian, Jaichandar and Cha, Jae Won and Oh, Won Chan and Kwon, Hyung-Bae and Kubota, Yoshiyuki and So, Peter T. C. and Nedivi, Elly}, + title = {Inhibitory Synapses Are Repeatedly Assembled and Removed at Persistent Sites In Vivo.}, + journal = {Neuron}, + year = {2016}, + volume = {89}, + issue = {4}, + month = feb, + pages = {756--769}, + issn = {1097-4199}, + doi = {10.1016/j.neuron.2016.01.010}, + abstract = {Older concepts of a hard-wired adult brain have been overturned in recent years by in vivo imaging studies revealing synaptic remodeling, now thought to mediate rearrangements in microcircuit connectivity. Using three-color labeling and spectrally resolved two-photon microscopy, we monitor in parallel the daily structural dynamics (assembly or removal) of excitatory and inhibitory postsynaptic sites on the same neurons in mouse visual cortex in vivo. We find that dynamic inhibitory synapses often disappear and reappear again in the same location. The starkest contrast between excitatory and inhibitory synapse dynamics is on dually innervated spines, where inhibitory synapses frequently recur while excitatory synapses are stable. Monocular deprivation, a model of sensory input-dependent plasticity, shortens inhibitory synapse lifetimes and lengthens intervals to recurrence, resulting in a new dynamic state with reduced inhibitory synaptic presence. Reversible structural dynamics indicate a fundamentally new role for inhibitory synaptic remodeling--flexible, input-specific modulation of stable excitatory connections.}, + chemicals = {Carrier Proteins, Disks Large Homolog 4 Protein, Dlg4 protein, mouse, Luminescent Proteins, Membrane Proteins, gephyrin, gamma-Aminobutyric Acid, Guanylate Kinases}, + citation-subset = {IM}, + completed = {2016-06-28}, + country = {United States}, + file = {:Villa2016 - Inhibitory Synapses Are Repeatedly Assembled and Removed at Persistent Sites In Vivo..pdf:PDF}, + groups = {Sinha2018a}, + issn-linking = {0896-6273}, + keywords = {Animals; Carrier Proteins, metabolism; Disks Large Homolog 4 Protein; Female; Functional Laterality; Guanylate Kinases, genetics, metabolism; Luminescent Proteins, genetics, metabolism; Male; Membrane Proteins, genetics, metabolism; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neural Inhibition, genetics, physiology; Neuronal Plasticity, physiology; Organ Culture Techniques; Pregnancy; Pyramidal Cells, ultrastructure; Sensory Deprivation; Synapses, physiology, ultrastructure; Synaptic Transmission, physiology; Visual Cortex, cytology; gamma-Aminobutyric Acid, pharmacology}, + mid = {NIHMS750739}, + nlm-id = {8809320}, + owner = {NLM}, + pii = {S0896-6273(16)00011-8}, + pmc = {PMC4760889}, + pmid = {26853302}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-13}, + timestamp = {2019-03-14}, +} + +@Article{Connor2019, + author = {Connor, Steven A. and Elegheert, Jonathan and Xie, Yicheng and Craig, Ann Marie}, + title = {Pumping the brakes: suppression of synapse development by MDGA-neuroligin interactions}, + journal = {Current Opinion in Neurobiology}, + year = {2019}, + volume = {57}, + pages = {71 - 80}, + note = {Molecular Neuroscience}, + issn = {0959-4388}, + doi = {https://doi.org/10.1016/j.conb.2019.01.002}, + url = {http://www.sciencedirect.com/science/article/pii/S0959438818302721}, + abstract = {Synapse development depends on a dynamic balance between synapse promoters and suppressors. MDGAs, immunoglobulin superfamily proteins, negatively regulate synapse development through blocking neuroligin–neurexin interactions. Recent analyses of MDGA–neuroligin complexes revealed the structural basis of this activity and indicate that MDGAs interact with all neuroligins with differential affinities. Surprisingly, analyses of mouse mutants revealed a functional divergence, with targeted mutation of Mdga1 and Mdga2 elevating inhibitory and excitatory synapses, respectively, on hippocampal pyramidal neurons. Further research is needed to determine the synapse-specific organizing properties of MDGAs in neural circuits, which may depend on relative levels and subcellular distributions of each MDGA, neuroligin and neurexin. Behavioral deficits in Mdga mutant mice support genetic links to schizophrenia and autism spectrum disorders and raise the possibility of harnessing these interactions for therapeutic purposes.}, +} + +@Article{Stimberg2014, + author = {Stimberg, Marcel and Goodman, Dan F M and Benichoux, Victor and Brette, Romain}, + title = {Equation-oriented specification of neural models for simulations.}, + journal = {Frontiers in neuroinformatics}, + year = {2014}, + volume = {8}, + pages = {6}, + issn = {1662-5196}, + doi = {10.3389/fninf.2014.00006}, + abstract = {Simulating biological neuronal networks is a core method of research in computational neuroscience. A full specification of such a network model includes a description of the dynamics and state changes of neurons and synapses, as well as the synaptic connectivity patterns and the initial values of all parameters. A standard approach in neuronal modeling software is to build network models based on a library of pre-defined components and mechanisms; if a model component does not yet exist, it has to be defined in a special-purpose or general low-level language and potentially be compiled and linked with the simulator. Here we propose an alternative approach that allows flexible definition of models by writing textual descriptions based on mathematical notation. We demonstrate that this approach allows the definition of a wide range of models with minimal syntax. Furthermore, such explicit model descriptions allow the generation of executable code for various target languages and devices, since the description is not tied to an implementation. Finally, this approach also has advantages for readability and reproducibility, because the model description is fully explicit, and because it can be automatically parsed and transformed into formatted descriptions. The presented approach has been implemented in the Brian2 simulator. }, + completed = {2014-02-19}, + country = {Switzerland}, + issn-linking = {1662-5196}, + keywords = {computational neuroscience; neuroscience; python; simulation; software}, + nlm-id = {101477957}, + owner = {NLM}, + pmc = {PMC3912318}, + pmid = {24550820}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-13}, + timestamp = {2019-02-20}, +} + +@Article{Vella2014, + author = {Vella, Michael and Cannon, Robert C and Crook, Sharon and Davison, Andrew P and Ganapathy, Gautham and Robinson, Hugh P C and Silver, R Angus and Gleeson, Padraig}, + title = {libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.}, + journal = {Frontiers in neuroinformatics}, + year = {2014}, + volume = {8}, + pages = {38}, + issn = {1662-5196}, + doi = {10.3389/fninf.2014.00038}, + abstract = {NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. }, + completed = {2014-05-05}, + country = {Switzerland}, + issn-linking = {1662-5196}, + keywords = {API; LEMS; NeuroML; Python; SWC; model specification; modeling; standardization}, + nlm-id = {101477957}, + owner = {NLM}, + pmc = {PMC4005938}, + pmid = {24795618}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-13}, + timestamp = {2019-02-20}, +} + +@Article{Harris2016, + author = {Harris, Leonard A and Hogg, Justin S and Tapia, José-Juan and Sekar, John A P and Gupta, Sanjana and Korsunsky, Ilya and Arora, Arshi and Barua, Dipak and Sheehan, Robert P and Faeder, James R}, + title = {BioNetGen 2.2: advances in rule-based modeling.}, + journal = {Bioinformatics (Oxford, England)}, + year = {2016}, + volume = {32}, + issue = {21}, + month = nov, + pages = {3366--3368}, + issn = {1367-4811}, + doi = {10.1093/bioinformatics/btw469}, + abstract = {: BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation and analysis of larger and more complex models than previously possible. Stable BioNetGen releases (Linux, Mac OS/X and Windows), with documentation, are available at http://bionetgen.org Source code is available at http://github.com/RuleWorld/bionetgen CONTACT: bionetgen.help@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.}, + citation-subset = {IM}, + completed = {2017-08-14}, + country = {England}, + issn-linking = {1367-4803}, + keywords = {Biochemistry; Humans; Models, Theoretical; Programming Languages; Software}, + nlm-id = {9808944}, + owner = {NLM}, + pii = {btw469}, + pmc = {PMC5079481}, + pmid = {27402907}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-12-02}, + timestamp = {2019-02-20}, +} + +@Article{Mendes2009, + author = {Mendes, Pedro and Hoops, Stefan and Sahle, Sven and Gauges, Ralph and Dada, Joseph and Kummer, Ursula}, + title = {Computational modeling of biochemical networks using COPASI.}, + journal = {Methods in molecular biology (Clifton, N.J.)}, + year = {2009}, + volume = {500}, + pages = {17--59}, + issn = {1064-3745}, + doi = {10.1007/978-1-59745-525-1_2}, + abstract = {Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generic software package for modeling and simulation of biochemical networks which provides many of these analyses in convenient ways that do not require the user to program or to have deep knowledge of the numerical algorithms. Here we provide a description of how these modeling techniques can be applied to biochemical models using COPASI. The focus is both on practical aspects of software usage as well as on the utility of these analyses in aiding biological understanding. Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis (including metabolic control analysis), global optimization, parameter estimation, and stochastic simulation. The examples used are all published models that are available in the BioModels database in SBML format.}, + citation-subset = {IM}, + completed = {2009-05-21}, + country = {United States}, + issn-linking = {1064-3745}, + keywords = {Algorithms; Animals; Computer Simulation; Humans; Metabolic Networks and Pathways; Models, Biological; Software; Systems Biology, methods}, + nlm-id = {9214969}, + owner = {NLM}, + pmid = {19399433}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2009-04-28}, + timestamp = {2019-02-20}, +} + +@Article{Dudani2009, + author = {Dudani, Niraj and Ray, Subhasis and George, Siji and Bhalla, Upinder S.}, + title = {Multiscale modeling and interoperability in MOOSE}, + journal = {BMC Neuroscience}, + year = {2009}, + volume = {10}, + number = {1}, + pages = {P54}, + publisher = {BioMed Central}, + timestamp = {2019-02-20}, +} + +@Article{Doron2017, + author = {Doron, Michael and Chindemi, Giuseppe and Muller, Eilif and Markram, Henry and Segev, Idan}, + title = {Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I/O Properties of Cortical Neurons.}, + journal = {Cell reports}, + year = {2017}, + volume = {21}, + issue = {6}, + month = nov, + pages = {1550--1561}, + issn = {2211-1247}, + doi = {10.1016/j.celrep.2017.10.035}, + abstract = {The NMDA spike is a long-lasting nonlinear phenomenon initiated locally in the dendritic branches of a variety of cortical neurons. It plays a key role in synaptic plasticity and in single-neuron computations. Combining dynamic system theory and computational approaches, we now explore how the timing of synaptic inhibition affects the NMDA spike and its associated membrane current. When impinging on its early phase, individual inhibitory synapses strongly, but transiently, dampen the NMDA spike; later inhibition prematurely terminates it. A single inhibitory synapse reduces the NMDA-mediated Ca current, a key player in plasticity, by up to 45%. NMDA spikes in distal dendritic branches/spines are longer-lasting and more resilient to inhibition, enhancing synaptic plasticity at these branches. We conclude that NMDA spikes are highly sensitive to dendritic inhibition; sparse weak inhibition can finely tune synaptic plasticity both locally at the dendritic branch level and globally at the level of the neuron's output.}, + chemicals = {Receptors, GABA-A, Receptors, N-Methyl-D-Aspartate, N-Methylaspartate, Calcium}, + citation-subset = {IM}, + completed = {2018-06-20}, + country = {United States}, + file = {:Doron2017 - Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I_O Properties of Cortical Neurons..pdf:PDF}, + keywords = {Calcium, metabolism; Dendrites, drug effects, physiology; Models, Biological; N-Methylaspartate, pharmacology; Neurons, drug effects, metabolism; Receptors, GABA-A, metabolism; Receptors, N-Methyl-D-Aspartate, antagonists & inhibitors, metabolism; Synapses, drug effects, physiology; NMDA-spike; cortical pyramidal cells; dendritic spines; nonlinear dendrites; synaptic inhibition; synaptic plasticity}, + nlm-id = {101573691}, + owner = {NLM}, + pii = {S2211-1247(17)31467-5}, + pmid = {29117560}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2018-06-20}, + timestamp = {2019-03-14}, +} + +@Article{Muellner2015, + author = {Müllner, Fiona E. and Wierenga, Corette J. and Bonhoeffer, Tobias}, + title = {Precision of Inhibition: Dendritic Inhibition by Individual GABAergic Synapses on Hippocampal Pyramidal Cells Is Confined in Space and Time.}, + journal = {Neuron}, + year = {2015}, + volume = {87}, + issue = {3}, + month = aug, + pages = {576--589}, + issn = {1097-4199}, + doi = {10.1016/j.neuron.2015.07.003}, + abstract = {Inhibition plays a fundamental role in controlling neuronal activity in the brain. While perisomatic inhibition has been studied in detail, the majority of inhibitory synapses are found on dendritic shafts and are less well characterized. Here, we combine paired patch-clamp recordings and two-photon Ca(2+) imaging to quantify inhibition exerted by individual GABAergic contacts on hippocampal pyramidal cell dendrites. We observed that Ca(2+) transients from back-propagating action potentials were significantly reduced during simultaneous activation of individual nearby inhibitory contacts. The inhibition of Ca(2+) transients depended on the precise spike-timing (time constant < 5 ms) and declined steeply in the proximal and distal direction (length constants 23-28 μm). Notably, Ca(2+) amplitudes in spines were inhibited to the same degree as in the shaft. Given the known anatomical distribution of inhibitory synapses, our data suggest that the collective inhibitory input to a pyramidal cell is sufficient to control Ca(2+) levels across the entire dendritic arbor with micrometer and millisecond precision. }, + citation-subset = {IM}, + completed = {2015-10-26}, + country = {United States}, + file = {:Muellner2015 - Precision of Inhibition_ Dendritic Inhibition by Individual GABAergic Synapses on Hippocampal Pyramidal Cells Is Confined in Space and Time..pdf:PDF}, + issn-linking = {0896-6273}, + keywords = {Animals; Dendrites, physiology; GABAergic Neurons, physiology; Hippocampus, cytology, physiology; Mice; Mice, Inbred C57BL; Neural Inhibition, physiology; Organ Culture Techniques; Pyramidal Cells, physiology; Synapses, physiology; Time Factors}, + nlm-id = {8809320}, + owner = {NLM}, + pii = {S0896-6273(15)00625-X}, + pmid = {26247864}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2015-08-07}, + timestamp = {2019-03-14}, +} + +@Article{Nishiyama2015, + author = {Nishiyama, Jun and Yasuda, Ryohei}, + title = {Biochemical Computation for Spine Structural Plasticity.}, + journal = {Neuron}, + year = {2015}, + volume = {87}, + issue = {1}, + month = jul, + pages = {63--75}, + issn = {1097-4199}, + doi = {10.1016/j.neuron.2015.05.043}, + abstract = {The structural plasticity of dendritic spines is considered to be essential for various forms of synaptic plasticity, learning, and memory. The process is mediated by a complex signaling network consisting of numerous species of molecules. Furthermore, the spatiotemporal dynamics of the biochemical signaling are regulated in a complicated manner because of geometrical restrictions from the unique morphology of the dendritic branches and spines. Recent advances in optical techniques have enabled the exploration of the spatiotemporal aspects of the signal regulations in spines and dendrites and have provided many insights into the principle of the biochemical computation that underlies spine structural plasticity. }, + citation-subset = {IM}, + completed = {2015-09-15}, + country = {United States}, + file = {:Nishiyama2015 - Biochemical Computation for Spine Structural Plasticity..pdf:PDF}, + issn-linking = {0896-6273}, + keywords = {Dendrites, physiology; Dendritic Spines, physiology; Humans; Learning, physiology; Long-Term Potentiation; Neuronal Plasticity, physiology; Signal Transduction}, + mid = {NIHMS694893}, + nlm-id = {8809320}, + owner = {NLM}, + pii = {S0896-6273(15)00482-1}, + pmc = {PMC4722820}, + pmid = {26139370}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2018-11-13}, + timestamp = {2019-03-14}, +} + +@Article{Kubota2016, + author = {Kubota, Yoshiyuki and Karube, Fuyuki and Nomura, Masaki and Kawaguchi, Yasuo}, + title = {The Diversity of Cortical Inhibitory Synapses.}, + journal = {Frontiers in neural circuits}, + year = {2016}, + volume = {10}, + pages = {27}, + issn = {1662-5110}, + doi = {10.3389/fncir.2016.00027}, + abstract = {The most typical and well known inhibitory action in the cortical microcircuit is a strong inhibition on the target neuron by axo-somatic synapses. However, it has become clear that synaptic inhibition in the cortex is much more diverse and complicated. Firstly, at least ten or more inhibitory non-pyramidal cell subtypes engage in diverse inhibitory functions to produce the elaborate activity characteristic of the different cortical states. Each distinct non-pyramidal cell subtype has its own independent inhibitory function. Secondly, the inhibitory synapses innervate different neuronal domains, such as axons, spines, dendrites and soma, and their inhibitory postsynaptic potential (IPSP) size is not uniform. Thus, cortical inhibition is highly complex, with a wide variety of anatomical and physiological modes. Moreover, the functional significance of the various inhibitory synapse innervation styles and their unique structural dynamic behaviors differ from those of excitatory synapses. In this review, we summarize our current understanding of the inhibitory mechanisms of the cortical microcircuit. }, + chemicals = {gamma-Aminobutyric Acid}, + citation-subset = {IM}, + completed = {2016-10-31}, + country = {Switzerland}, + file = {:Kubota2016 - The Diversity of Cortical Inhibitory Synapses..pdf:PDF}, + issn-linking = {1662-5110}, + keywords = {Animals; Cerebral Cortex, cytology; Humans; Models, Biological; Neural Inhibition, physiology; Neurons, physiology; Synapses, physiology; gamma-Aminobutyric Acid, metabolism; cortex; dually innervated spine; inhibitory synapse; pyramidal cell; spine; thalamocortical fiber; veto}, + nlm-id = {101477940}, + owner = {NLM}, + pmc = {PMC4842771}, + pmid = {27199670}, + pubmodel = {Electronic-eCollection}, + pubstatus = {epublish}, + revised = {2018-11-13}, + timestamp = {2019-03-14}, +} + +@Article{Barnes2015, + author = {Barnes, Samuel J and Sammons, Rosanna P and Jacobsen, R Irene and Mackie, Jennifer and Keller, Georg B and Keck, Tara}, + title = {Subnetwork-Specific Homeostatic Plasticity in Mouse Visual Cortex In Vivo.}, + journal = {Neuron}, + year = {2015}, + volume = {86}, + issue = {5}, + month = jun, + pages = {1290--1303}, + issn = {1097-4199}, + doi = {10.1016/j.neuron.2015.05.010}, + abstract = {Homeostatic regulation has been shown to restore cortical activity in vivo following sensory deprivation, but it is unclear whether this recovery is uniform across all cells or specific to a subset of the network. To address this issue, we used chronic calcium imaging in behaving adult mice to examine the activity of individual excitatory and inhibitory neurons in the same region of the layer 2/3 monocular visual cortex following enucleation. We found that only a fraction of excitatory neurons homeostatically recover activity after deprivation and inhibitory neurons show no recovery. Prior to deprivation, excitatory cells that did recover were more likely to have significantly correlated activity with other recovering excitatory neurons, thus forming a subnetwork of recovering neurons. These network level changes are accompanied by a reduction in synaptic inhibition onto all excitatory neurons, suggesting that both synaptic mechanisms and subnetwork activity are important for homeostatic recovery of activity after deprivation. }, + citation-subset = {IM}, + completed = {2015-08-24}, + country = {United States}, + file = {:Barnes2015 - Subnetwork-Specific Homeostatic Plasticity in Mouse Visual Cortex In Vivo..pdf:PDF}, + groups = {Sinha2018a}, + issn-linking = {0896-6273}, + keywords = {Animals; Female; Homeostasis, physiology; Male; Mice; Mice, Inbred C57BL; Nerve Net, physiology; Neuronal Plasticity, physiology; Photic Stimulation, methods; Sensory Deprivation, physiology; Visual Cortex, physiology; Visual Pathways, physiology}, + nlm-id = {8809320}, + owner = {NLM}, + pii = {S0896-6273(15)00417-1}, + pmc = {PMC4460189}, + pmid = {26050045}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2018-11-13}, +} + +@Article{Massie2003, + author = {Massie, Ann and Cnops, Lieselotte and Smolders, Ilse and Van Damme, Katrien and Vandenbussche, Erik and Vandesande, Frans and Eysel, Ulf T and Arckens, Lutgarde}, + title = {Extracellular GABA concentrations in area 17 of cat visual cortex during topographic map reorganization following binocular central retinal lesioning.}, + journal = {Brain research}, + year = {2003}, + volume = {976}, + issue = {1}, + month = jun, + pages = {100--108}, + issn = {0006-8993}, + citation-subset = {IM}, + completed = {2003-08-14}, + country = {Netherlands}, + file = {:Massie2003 - Extracellular GABA concentrations in area 17 of cat visual cortex during topographic map reorganization following binocular central retinal lesioning..pdf:PDF}, + groups = {Sinha2018a}, + issn-linking = {0006-8993}, + keywords = {Animals; Cats; Extracellular Space, metabolism; In Situ Hybridization; Microdialysis; Retina, injuries, physiology; Sensory Deprivation; Visual Cortex, metabolism; gamma-Aminobutyric Acid, metabolism}, + nlm-id = {0045503}, + owner = {NLM}, + pii = {S0006899303027173}, + pmid = {12763627}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2006-11-15}, +} + +@Article{Garraghty1991, + author = {Garraghty, P E and LaChica, E A and Kaas, J H}, + title = {Injury-induced reorganization of somatosensory cortex is accompanied by reductions in GABA staining.}, + journal = {Somatosensory \& motor research}, + year = {1991}, + volume = {8}, + issue = {4}, + pages = {347--354}, + issn = {0899-0220}, + abstract = {When a portion of primary somatosensory cortex is deprived of its normal inputs by peripheral nerve transection, intact skin surfaces represented in surrounding cortex come to activate the deprived zone within 2 months. We found that this cortical reorganization was accompanied by a marked decrease in the antibody staining of gamma-aminobutyric acid (GABA) within the deprived sector of cortex in monkeys surviving nerve injury for 2-5 months. In contrast, there were no apparent changes in cytochrome oxidase reactivity in the deprived cortex of these same monkeys. Reduced levels of inhibition could allow previously unexpressed connections to become potent. Thus, the regulation of the expression of GABA appears to be one mechanism for maintaining and altering cortical representations.}, + chemicals = {gamma-Aminobutyric Acid, Electron Transport Complex IV}, + citation-subset = {IM}, + completed = {1992-05-19}, + country = {England}, + groups = {Sinha2018a}, + issn-linking = {0899-0220}, + keywords = {Afferent Pathways, physiology; Animals; Brain Mapping; Dominance, Cerebral, physiology; Electron Transport Complex IV, physiology; Hand, innervation; Immunoenzyme Techniques; Nerve Regeneration, physiology; Neuronal Plasticity, physiology; Peripheral Nerve Injuries; Peripheral Nerves, physiology; Saimiri; Somatosensory Cortex, physiology; gamma-Aminobutyric Acid, physiology}, + nlm-id = {8904127}, + owner = {NLM}, + pmid = {1667058}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2011-11-17}, +} +@Article{Garcia-Lopez2006, + author = {García-López, Pablo and García-Marín, Virginia and Freire, Miguel}, + title = {Three-dimensional reconstruction and quantitative study of a pyramidal cell of a Cajal histological preparation}, + journal = {The journal of neuroscience}, + year = {2006}, + volume = {26}, + number = {44}, + issue = {44}, + month = nov, + pages = {11249--11252}, + issn = {1529-2401}, + doi = {10.1523/JNEUROSCI.3543-06.2006}, + abstract = {The year 2006 marks the centenary of the Nobel Prize for Physiology or Medicine awarded to Santiago Ramón y Cajal and Camilo Golgi. We commemorate this centenary with a three-dimensional reconstruction and a quantitative study of a pyramidal cell of a Cajal's histological preparation. This preparation is one of the 4529 histological preparations personally made by Ramón y Cajal and preserved in the Museum Cajal. The three-dimensional reconstruction of the neuron allows visualizing one important discovery of Ramón y Cajal that constitutes an active field of research in present-day neuroscience: dendritic spines.}, + citation-subset = {IM}, + completed = {2006-11-14}, + country = {United States}, + file = {:Garcia-Lopez2006 - Three Dimensional Reconstruction and Quantitative Study of a Pyramidal Cell of a Cajal Histological Preparation.pdf:PDF}, + issn-linking = {0270-6474}, + keywords = {Animals; Cell Count, methods; Cerebral Cortex, cytology; Histocytological Preparation Techniques, methods; Imaging, Three-Dimensional, methods; Mice; Pyramidal Cells, cytology}, + nlm-id = {8102140}, + owner = {NLM}, + pii = {26/44/11249}, + pmid = {17079652}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2006-11-15}, +} + +@Article{Herculano-Houzel2005, + author = {Herculano-Houzel, Suzana and Lent, Roberto}, + title = {Isotropic fractionator: a simple, rapid method for the quantification of total cell and neuron numbers in the brain.}, + journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, + year = {2005}, + volume = {25}, + issue = {10}, + month = mar, + pages = {2518--2521}, + issn = {1529-2401}, + doi = {10.1523/JNEUROSCI.4526-04.2005}, + abstract = {Stereological techniques that estimate cell numbers must be restricted to well defined structures of isotropic architecture and therefore do not apply to the whole brain or to large neural regions. We developed a novel, fast, and inexpensive method to quantify total numbers of neuronal and non-neuronal cells in the brain or any dissectable regions thereof. It consists of transforming highly anisotropic brain structures into homogeneous, isotropic suspensions of cell nuclei, which can be counted and identified immunocytochemically as neuronal or non-neuronal. Estimates of total cell, neuronal, and non-neuronal numbers can be obtained in 24 h and vary by <10% among animals. Because the estimates obtained are independent of brain volume, they can be used in comparative studies of brain-volume variation among species and in studies of phylogenesis, development, adult neurogenesis, and pathology. Applying this method to the adult rat brain, we show, for example, that it contains approximately 330 million cells, of which 200 million are neurons, and almost 70% of these are located in the cerebellum alone. Moreover, contrary to what is commonly assumed in the literature, we show that glial cells are not the majority in the rat brain.}, + citation-subset = {IM}, + completed = {2006-03-02}, + country = {United States}, + file = {:Herculano-Houzel2005 - Isotropic Fractionator_ a Simple, Rapid Method for the Quantification of Total Cell and Neuron Numbers in the Brain..pdf:PDF}, + issn-linking = {0270-6474}, + keywords = {Animals; Brain, cytology; Cell Count, instrumentation, methods, statistics & numerical data; Cell Fractionation, instrumentation, methods, statistics & numerical data; Cell Nucleus; Neurons, cytology; Rats; Rats, Wistar; Stereotaxic Techniques, instrumentation, statistics & numerical data}, + nlm-id = {8102140}, + owner = {NLM}, + pii = {25/10/2518}, + pmid = {15758160}, + pubmodel = {Print}, + pubstatus = {ppublish}, + revised = {2006-11-15}, +} + +@Article{Azevedo2009, + author = {Azevedo, Frederico AC and Carvalho, Ludmila RB and Grinberg, Lea T and Farfel, Jos{\'e} Marcelo and Ferretti, Renata EL and Leite, Renata EP and Filho, Wilson Jacob and Lent, Roberto and Herculano-Houzel, Suzana}, + title = {Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain}, + journal = {Journal of Comparative Neurology}, + year = {2009}, + volume = {513}, + number = {5}, + pages = {532--541}, + doi = {10.1002/cne.21974}, + url = {https://doi.org/10.1002/cne.21974}, + file = {:Azevedo2009 - Equal Numbers of Neuronal and Nonneuronal Cells Make the Human Brain an Isometrically Scaled up Primate Brain.pdf:PDF}, + publisher = {Wiley Online Library}, +} + +@Article{Herculano-Houzel2009, + author = {Herculano-Houzel, Suzana}, + title = {The human brain in numbers: a linearly scaled-up primate brain}, + journal = {Frontiers in human neuroscience}, + year = {2009}, + volume = {3}, + pages = {31}, + doi = {10.3389/neuro.09.031.2009}, + file = {:Herculano-Houzel2009 - The Human Brain in Numbers_ a Linearly Scaled up Primate Brain.pdf:PDF}, + publisher = {Frontiers}, +} + + +@InProceedings{Mundel1997, + author = {Mundel, Trevor and Dimitrov, Alexander and Cowan, Jack D}, + title = {Visual cortex circuitry and orientation tuning}, + booktitle = {Advances in neural information processing systems}, + year = {1997}, + pages = {887--893}, + file = {:Mundel1997 - Visual cortex circuitry and orientation tuning.pdf:PDF}, + timestamp = {2019-04-01}, +} + +@Article{Stepanyants2009, + author = {Stepanyants, Armen and Martinez, Luis M and Ferecsk{\'o}, Alex S and Kisv{\'a}rday, Zolt{\'a}n F}, + title = {The fractions of short-and long-range connections in the visual cortex}, + journal = {Proceedings of the National Academy of Sciences}, + year = {2009}, + volume = {106}, + number = {9}, + pages = {3555--3560}, + file = {:Stepanyants2009 - The fractions of short-and long-range connections in the visual cortex.pdf:PDF}, + publisher = {National Acad Sciences}, + timestamp = {2019-04-01}, +} + +@Article{Buzas2001, + author = {Buz{\'a}s, P{\'e}ter and Eysel, Ulf T. and Adorj{\'a}n, P{\'e}ter and Kisv{\'a}rday, Zolt{\'a}n F.}, + title = {Axonal topography of cortical basket cells in relation to orientation, direction, and ocular dominance maps}, + journal = {Journal of Comparative Neurology}, + year = {2001}, + volume = {437}, + number = {3}, + pages = {259--285}, + file = {:Buzas2001 - Axonal topography of cortical basket cells in relation to orientation, direction, and ocular dominance maps.pdf:PDF}, + publisher = {Wiley Online Library}, + timestamp = {2019-04-01}, +} + +@Article{Haider2013, + author = {Haider, Bilal and H{\"a}usser, Michael and Carandini, Matteo}, + title = {Inhibition dominates sensory responses in the awake cortex}, + journal = {Nature}, + year = {2013}, + volume = {493}, + number = {7430}, + pages = {97}, + file = {:Haider2013 - Inhibition dominates sensory responses in the awake cortex.pdf:PDF}, + publisher = {Nature Publishing Group}, + timestamp = {2019-04-01}, +} + +@Article{Liu2011, + author = {Liu, Bao-hua and Li, Ya-tang and Ma, Wen-pei and Pan, Chen-jie and Zhang, Li I and Tao, Huizhong Whit}, + title = {Broad inhibition sharpens orientation selectivity by expanding input dynamic range in mouse simple cells}, + journal = {Neuron}, + year = {2011}, + volume = {71}, + number = {3}, + pages = {542--554}, + doi = {10.1016/j.neuron.2011.06.017}, + file = {:Liu2011 - Broad inhibition sharpens orientation selectivity by expanding input dynamic range in mouse simple cells.pdf:PDF}, + publisher = {Elsevier}, + timestamp = {2019-04-01}, +} + +@Article{Kang2003, + author = {Kang, Kukjin and Shelley, Michael and Sompolinsky, Haim}, + title = {Mexican hats and pinwheels in visual cortex.}, + journal = {Proceedings of the National Academy of Sciences of the United States of America}, + year = {2003}, + volume = {100}, + issue = {5}, + month = mar, + pages = {2848--2853}, + issn = {0027-8424}, + doi = {10.1073/pnas.0138051100}, + chemicals = {N-Methylaspartate}, + citation-subset = {IM}, + completed = {2003-05-13}, + country = {United States}, + file = {:Kang2003 - Mexican hats and pinwheels in visual cortex..pdf:PDF}, + issn-linking = {0027-8424}, + keywords = {Animals; Cats; Haplorhini; Humans; Models, Statistical; Models, Theoretical; N-Methylaspartate, pharmacology; Nerve Net; Neurons, cytology; Oscillometry; Synapses; Time Factors; Visual Cortex, physiology}, + nlm-id = {7505876}, + owner = {NLM}, + pii = {0138051100}, + pmc = {PMC151429}, + pmid = {12601163}, + pubmodel = {Print-Electronic}, + pubstatus = {ppublish}, + revised = {2018-11-13}, + timestamp = {2019-04-03}, +} + +@Article{Rudiger2013, + author = {Rudiger, Philipp and Law, Judith S. and Antolik, Jan and Bednar, James}, + title = {Developing orientation maps using realistic patterns of lateral connectivity}, + journal = {BMC Neuroscience}, + year = {2013}, + volume = {14}, + number = {1}, + month = {7}, + pages = {P21}, + issn = {1471-2202}, + doi = {10.1186/1471-2202-14-S1-P21}, + url = {https://doi.org/10.1186/1471-2202-14-S1-P21}, + day = {08}, + timestamp = {2019-04-02}, +} + +@Article{Cocchi2017, + author = {Cocchi, Luca and Gollo, Leonardo L. and Zalesky, Andrew and Breakspear, Michael}, + title = {Criticality in the brain: A synthesis of neurobiology, models and cognition}, + journal = {Progress in neurobiology}, + year = {2017}, + volume = {158}, + pages = {132--152}, + doi = {10.1016/j.pneurobio.2017.07.002}, + file = {:Cocchi2017 - Criticality in the Brain_ a Synthesis of Neurobiology, Models and Cognition.pdf:PDF}, + publisher = {Elsevier}, +} + +@Article{Ecker2010, + author = {Ecker, Alexander S and Berens, Philipp and Keliris, Georgios A and Bethge, Matthias and Logothetis, Nikos K and Tolias, Andreas S}, + title = {Decorrelated neuronal firing in cortical microcircuits}, + journal = {science}, + year = {2010}, + volume = {327}, + number = {5965}, + pages = {584--587}, + doi = {10.1126/science.1179867}, + file = {:Ecker2010 - Decorrelated Neuronal Firing in Cortical Microcircuits.pdf:PDF}, + publisher = {American Association for the Advancement of Science}, +} + +@Article{Wilting2018, + author = {Wilting, Jens and Priesemann, Viola}, + title = {Inferring collective dynamical states from widely unobserved systems}, + journal = {Nature communications}, + year = {2018}, + volume = {9}, + number = {1}, + pages = {2325}, + doi = {10.1038/s41467-018-04725-4}, + file = {:Wilting2018 - Inferring Collective Dynamical States from Widely Unobserved Systems.pdf:PDF}, + publisher = {Nature Publishing Group}, +} + +@Article{Kinouchi2006, + author = {Kinouchi, Osame and Copelli, Mauro}, + title = {Optimal dynamical range of excitable networks at criticality}, + journal = {Nature Physics}, + year = {2006}, + volume = {2}, + number = {5}, + month = may, + pages = {348--351}, + issn = {1745-2481}, + doi = {10.1038/nphys289}, + url = {https://doi.org/10.1038/nphys289}, + abstract = {A recurrent idea in the study of complex systems is that optimal information processing is to be found near phase transitions. However, this heuristic hypothesis has few (if any) concrete realizations where a standard and biologically relevant quantity is optimized at criticality. Here we give a clear example of such a phenomenon: a network of excitable elements has its sensitivity and dynamic range maximized at the critical point of a non-equilibrium phase transition. Our results are compatible with the essential role of gap junctions in olfactory glomeruli and retinal ganglionar cell output. Synchronization and global oscillations also emerge from the network dynamics. We propose that the main functional role of electrical coupling is to provide an enhancement of dynamic range, therefore allowing the coding of information spanning several orders of magnitude. The mechanism could provide a microscopic neural basis for psychophysical laws.}, + file = {:Kinouchi2006 - Optimal Dynamical Range of Excitable Networks at Criticality.pdf:PDF}, + refid = {Kinouchi2006}, +} + +@Misc{Jordan2019, + author = {Jordan, Jakob and Mørk, Håkon and Vennemo, Stine Brekke and Terhorst, Dennis and Peyser, Alexander and Ippen, Tammo and Deepu, Rajalekshmi and Eppler, Jochen Martin and van Meegen, Alexander and Kunkel, Susanne and Sinha, Ankur and Fardet, Tanguy and Diaz, Sandra and Morrison, Abigail and Schenck, Wolfram and Dahmen, David and Pronold, Jari and Stapmanns, Jonas and Trensch, Guido and Spreizer, Sebastian and Mitchell, Jessica and Graber, Steffen and Senk, Johanna and Linssen, Charl and Hahne, Jan and Serenko, Alexey and Naoumenko, Daniel and Thomson, Eric and Kitayama, Itaru and Berns, Sebastian and Plesser, Hans Ekkehard}, + title = {NEST 2.18.0}, + year = {2019}, + month = jun, + doi = {10.5281/zenodo.2605422}, + url = {https://doi.org/10.5281/zenodo.2605422}, +} + +@Article{Jedrzejewski-Szmek2016, + author = {Jędrzejewski-Szmek, Zbigniew and Blackwell, Kim T.}, + title = {Asynchronous \(\tau\)-leaping}, + journal = {Journal of Chemical Physics}, + year = {2016}, + volume = {144}, + pages = {125104}, +} + +@Article{Friston2012, + author = {Friston, Karl}, + title = {Ten ironic rules for non-statistical reviewers}, + journal = {Neuroimage}, + year = {2012}, + volume = {61}, + number = {4}, + pages = {1300--1310}, + doi = {10.1016/j.neuroimage.2012.04.018}, + file = {:Friston2012 - Ten Ironic Rules for Non Statistical Reviewers.pdf:PDF}, + publisher = {Elsevier}, +} + +@Comment{jabref-meta: databaseType:biblatex;} + +@Comment{jabref-meta: grouping: +0 AllEntriesGroup:; +1 KeywordGroup:My publications\;0\;author\;Sinha, Ankur\;0\;0\;1\;0x0000ffff\;\;My publications\;; +1 StaticGroup:Sinha2018a\;0\;1\;\;\;Papers referenced in Sinha2017a\;; +}