Replaced examples with case study

src/cognition-and-neuroscience/module1/sections/_instrumental_learning.tex

@@ -90,13 +90,13 @@ There are two types of learning:
 \end{descriptionlist}
 
 \begin{minipage}{0.55\linewidth}
-    \begin{example}[Aplysia Californica]
+    \begin{casestudy}[Aplysia Californica]
         An Aplysia Californica will withdraw its gill upon stimulating the siphon.
         \begin{itemize}
             \item Repeated mild stimulations will induce a habituation of the reflex.
             \item Repeated intense stimulations will induce a sensitization of the reflex.
         \end{itemize}
-    \end{example}
+    \end{casestudy}
 \end{minipage}
 \begin{minipage}{0.4\linewidth}
     \centering
@@ -114,27 +114,23 @@ There is evidence that dopamine is involved in learning action-outcome associati
         When an unexpected event happens, there is a change in the activity of the striatum.
         There is an increase in response when the feedback is positive and a decrease when negative.
 
-        \begin{@empty}
+        \begin{casestudy}[Microelectrodes in substantia nigra]
-            \small
+            \phantom{}\\
-            \begin{example}[Microelectrodes in substantia nigra]
+            \begin{minipage}{0.7\linewidth}
                 The activity of the substantia nigra of patients with Parkinson's disease is measured during a probabilistic instrumental learning task.
                 The task consists of repeatedly drawing a card from two decks, followed by positive or negative feedback depending on the deck.
+            \end{minipage}
+            \begin{minipage}{0.3\linewidth}
+                \centering
+                \includegraphics[width=0.95\linewidth]{./img/instrumental_dopamine_sn1.png}
+            \end{minipage}
 
-                \begin{figure}[H]
+            The increase and decrease in striatal activity can be clearly seen when the feedback is unexpected.
-                    \centering
+            \begin{figure}[H]
-                    \begin{subfigure}{0.25\linewidth}
+                \centering
-                        \centering
+                \includegraphics[width=\linewidth]{./img/instrumental_dopamine_sn2.png}
-                        \includegraphics[width=\linewidth]{./img/instrumental_dopamine_sn1.png}
+            \end{figure}
-                    \end{subfigure}
+        \end{casestudy}
-                    \begin{subfigure}{0.55\linewidth}
-                        \centering
-                        \includegraphics[width=\linewidth]{./img/instrumental_dopamine_sn2.png}
-                    \end{subfigure}
-                \end{figure}
-
-                The increase and decrease in striatal activity can be clearly seen when the feedback is unexpected.
-            \end{example}
-        \end{@empty}
 
     \item[Dopamine effect on behavior] \marginnote{Dopamine effect on behavior}
         The amount of dopamine changes the learning behavior:
@@ -146,68 +142,62 @@ There is evidence that dopamine is involved in learning action-outcome associati
                 This happens because negative prediction errors cannot occur.
         \end{itemize}
 
-        \begin{@empty}
+        \begin{casestudy}[Probabilistic selection task]
-            \small
+            This instrumental learning task has two phases:
-            \begin{example}[Probabilistic selection task]
+            \begin{descriptionlist}
-                This instrumental learning task has two phases:
+                \item[Learning]
-                \begin{descriptionlist}
+                    There are three pairs of stimuli (symbols) and, at each trial, a pair is presented to the participant who selects one.
-                    \item[Learning]
+                    For each pair, a symbol has a higher probability of providing positive feedback while the other is more likely to be negative.
-                        There are three pairs of stimuli (symbols) and, at each trial, a pair is presented to the participant who selects one.
+                    Moreover, the probabilities are different among the three pairs.
-                        For each pair, a symbol has a higher probability of providing positive feedback while the other is more likely to be negative.
-                        Moreover, the probabilities are different among the three pairs.
 
-                        \begin{center}
+                    \begin{center}
-                            \includegraphics[width=0.55\linewidth]{./img/instrumental_dopamine_selection1.png}
+                        \includegraphics[width=0.55\linewidth]{./img/instrumental_dopamine_selection1.png}
-                        \end{center}
+                    \end{center}
 
-                        Participants are required to learn by trial and error the stimulus in each pair that leads to a positive reward.
+                    Participants are required to learn by trial and error the stimulus in each pair that leads to a positive reward.
-                        Note that learning could be accomplished by:
+                    Note that learning could be accomplished by:
-                        \begin{itemize}
+                    \begin{itemize}
-                            \item Recognizing the more rewarding stimulus.
+                        \item Recognizing the more rewarding stimulus.
-                            \item Recognizing the less rewarding stimulus.
+                        \item Recognizing the less rewarding stimulus.
-                            \item Both.
+                        \item Both.
-                        \end{itemize}
+                    \end{itemize}
 
-                    \item[Testing]
+                \item[Testing]
-                        Aims to assess if participants learned to select positive feedback or avoid negative feedback.
+                    Aims to assess if participants learned to select positive feedback or avoid negative feedback.
 
-                        The same task as above is repeated but all combinations of the stimuli among the three pairs are possible.
+                    The same task as above is repeated but all combinations of the stimuli among the three pairs are possible.
-                \end{descriptionlist}
+            \end{descriptionlist}
 
-                Three groups of participants are considered for this experiment:
+            Three groups of participants are considered for this experiment:
-                \begin{enumerate}
+            \begin{enumerate}
-                    \item Those who took the cabergoline drug (dopamine antagonist).
+                \item Those who took the cabergoline drug (dopamine antagonist).
-                    \item Those who took the haloperidol drug (dopamine agonist).
+                \item Those who took the haloperidol drug (dopamine agonist).
-                    \item Those who took a drug without effects (placebo).
+                \item Those who took a drug without effects (placebo).
-                \end{enumerate}
+            \end{enumerate}
 
-                \begin{center}
+            \begin{center}
-                    \includegraphics[width=0.55\linewidth]{./img/instrumental_dopamine_selection2.png}
+                \includegraphics[width=0.55\linewidth]{./img/instrumental_dopamine_selection2.png}
-                \end{center}
+            \end{center}
 
-                Results show that:
+            Results show that:
-                \begin{enumerate}
+            \begin{enumerate}
-                    \item Cabergoline inhibited positive feedback learning.
+                \item Cabergoline inhibited positive feedback learning.
-                    \item Haloperidol enhanced positive feedback learning.
+                \item Haloperidol enhanced positive feedback learning.
-                    \item Placebo learned positive and negative feedback equally.
+                \item Placebo learned positive and negative feedback equally.
-                \end{enumerate}
+            \end{enumerate}
-            \end{example}
+        \end{casestudy}
-        \end{@empty}
         
-        \begin{@empty}
+        \begin{casestudy}
-            \small
+            It has been observed that:
-            \begin{example}
+            \begin{itemize}
-                It has been observed that:
+                \item Reward prediction errors are correlated with activity in the left posterior putamen and left ventral striatum.
-                \begin{itemize}
+                \item Punishment prediction errors are correlated with activity in the right anterior insula.
-                    \item Reward prediction errors are correlated with activity in the left posterior putamen and left ventral striatum.
+            \end{itemize}
-                    \item Punishment prediction errors are correlated with activity in the right anterior insula.
-                \end{itemize}
 
-                \begin{center}
+            \begin{center}
-                    \includegraphics[width=0.5\linewidth]{./img/pe_location.png}
+                \includegraphics[width=0.5\linewidth]{./img/pe_location.png}
-                \end{center}
+            \end{center}
-            \end{example}
+        \end{casestudy}
-        \end{@empty}
 
     \item[Actor-critic model] \marginnote{Actor-critic model}
         Model to correlate Pavlovian and instrumental learning. 
@@ -227,20 +217,17 @@ There is evidence that dopamine is involved in learning action-outcome associati
         \end{itemize}
 \end{description}
 
-\begin{@empty}
+\begin{casestudy}[Food and cocaine]
-    \small
+    \phantom{}
-    \begin{example}[Food and cocaine]
+    \begin{itemize}
-        \phantom{}
+        \item Food-induced dopamine response is modulated by the reward expectations that promote learning until the prediction matches the actual outcome.
-        \begin{itemize}
+        \item Cocaine-induced dopamine response causes a continuous increase in the predicted reward that
-            \item Food-induced dopamine response is modulated by the reward expectations that promote learning until the prediction matches the actual outcome.
+            will eventually surpass all other cues and bias decision-making towards cocaine.
-            \item Cocaine-induced dopamine response causes a continuous increase in the predicted reward that
+    \end{itemize}
-                will eventually surpass all other cues and bias decision-making towards cocaine.
+    \begin{center}
-        \end{itemize}
+        \includegraphics[width=0.8\linewidth]{./img/dopamine_food_cocaine.png}
-        \begin{center}
+    \end{center}
-            \includegraphics[width=0.8\linewidth]{./img/dopamine_food_cocaine.png}
+\end{casestudy}
-        \end{center}
-    \end{example}
-\end{@empty}
 
 
 
@@ -451,7 +438,7 @@ Studied goal-directed and habitual behavior in humans.
     \end{itemize}
     \begin{figure}[H]
         \centering
-        \includegraphics[width=0.95\linewidth]{./img/human_goal_directed_experiment3.png}
+        \includegraphics[width=0.9\linewidth]{./img/human_goal_directed_experiment3.png}
     \end{figure}
 
     During both training and testing, the fRMIs of the candidates were taken.

src/cognition-and-neuroscience/module1/sections/_introduction.tex

@@ -59,7 +59,7 @@
         Study of the relationship between the physical brain and the intangible mind (thoughts, ideas).
         In other words, it studies the relationship between structure and function.
 
-        \begin{example}[Severed Corpus Callosum\footnote{\url{https://www.youtube.com/watch?v=lfGwsAdS9Dc}}]
+        \begin{casestudy}[Severed Corpus Callosum\footnote{\url{https://www.youtube.com/watch?v=lfGwsAdS9Dc}}]
             Normally, the right and left hemispheres of the brain can communicate. 
             Moreover, the left visual field is sent to the right hemisphere and 
             the right visual field is sent to the left hemisphere.
@@ -67,7 +67,7 @@
             In patients where the hemispheres are split, a text shown on the right visual side is recognized as 
             the speech capabilities are located in the left hemisphere,
             while a text shown on the left visual side does not trigger any speech reaction.
-        \end{example}
+        \end{casestudy}
 \end{description}
 
 

src/cognition-and-neuroscience/module1/sections/_nervous_system.tex

@@ -475,7 +475,7 @@ In a neuron, there are four regions that handle signals:
 
 
 
-\begin{example}[Knee-jerk reflex]
+\begin{casestudy}[Knee-jerk reflex]
     By tapping the patellar tendon (below the kneecap), the following happens:
     \begin{enumerate}
         \item The sensory information is conveyed from the muscle to the spinal cord (central nervous system).
@@ -486,7 +486,7 @@ In a neuron, there are four regions that handle signals:
     \begin{center}
         \includegraphics[width=0.8\textwidth]{./img/knee_jerk.png}
     \end{center}
-\end{example}
+\end{casestudy}
 
 
 \section{Neural system}

src/cognition-and-neuroscience/module1/sections/_pavlovian_learning.tex

@@ -90,7 +90,7 @@ There are two types of learning:
         A new stimulus that is similar to a learned \acl{cs} can elicit a \acl{cr}.
 \end{description}
 
-\begin{example}[Aplysia Californica] \phantom{}\\
+\begin{casestudy}[Aplysia Californica] \phantom{}\\
     \begin{minipage}{0.8\linewidth}
         \begin{enumerate}
             \item Before conditioning, a stimulus to the siphon of an aplysia californica results in a weak withdrawal of the gill.
@@ -117,7 +117,7 @@ There are two types of learning:
         \includegraphics[width=0.3\linewidth]{./img/gill_pavlovian_graph.png}
         \caption{Withdrawal response decay}
     \end{figure}
-\end{example}
+\end{casestudy}
 
 \begin{remark} \marginnote{Amygdala in Pavlovian learning}
     In mammals, aversive Pavlovian conditioning involves the amygdala.
@@ -161,10 +161,10 @@ Once reactivated, the subsequent reconsolidation phase might store a modified ve
     On the other hand, a damaged hippocampus results in patients that present a \ac{cr} without recognizing the \ac{cs}.
 \end{remark}
 
-\begin{example}[Reconsolidation disruption]
+\begin{casestudy}[Reconsolidation disruption]
     Propranolol is a drug that disrupts amygdala-specific memory reconsolidation (i.e. the physiological response).
     A possible therapy to suppress a phobia is to trigger the fear memory and then administer propranolol to prevent its reconsolidation.
-\end{example}
+\end{casestudy}
 
 
 
@@ -195,7 +195,7 @@ Depending on when the \ac{cs} and \ac{us} are presented, conditioning can be:
     \end{figure}
 \end{descriptionlist}
 
-\begin{example}
+\begin{casestudy}
     Two groups of rats were exposed to a 6 seconds tone (\ac{cs}) followed by food delivery (\ac{us}) with a delay of: 
     \begin{itemize}
         \item 6 seconds (red).
@@ -207,7 +207,7 @@ Depending on when the \ac{cs} and \ac{us} are presented, conditioning can be:
         \includegraphics[width=0.55\linewidth]{./img/contiguity_rats.png}
         \caption{Number of entries (i.e. the rat checks the food tray) per second}
     \end{figure}
-\end{example}
+\end{casestudy}
 
 
 \subsection{Contingency}
@@ -227,7 +227,7 @@ Causal relationship between the \acl{cs} and the \acl{us}.
     \caption{Example of contingent and random group}
 \end{figure}
 
-\begin{example}
+\begin{casestudy}
     Two groups of rats are exposed to a shock paired with a bell ring.
     Contiguity is the same but contingency differs.
 
@@ -238,7 +238,7 @@ Causal relationship between the \acl{cs} and the \acl{us}.
         \includegraphics[width=0.8\linewidth]{./img/contingency_rats.png}
         \caption{Representation of the experiment}
     \end{figure}
-\end{example}
+\end{casestudy}
 
 
 \subsection{Surprise}
@@ -258,7 +258,7 @@ Causal relationship between the \acl{cs} and the \acl{us}.
     \caption{Learning outcome due to surprise}
 \end{figure}
 
-\begin{example}[Blocking effect]
+\begin{casestudy}[Blocking effect]
     \phantom{} \label{ex:blocking} \\
     \begin{minipage}{0.65\linewidth}
         \begin{enumerate}
@@ -275,7 +275,7 @@ Causal relationship between the \acl{cs} and the \acl{us}.
             \includegraphics[width=\linewidth]{./img/surprise_rats.png}
         \end{figure}
     \end{minipage}
-\end{example}
+\end{casestudy}
 
 
 
@@ -353,7 +353,7 @@ The prediction error is computed as follows\footnote{\url{https://pubmed.ncbi.nl
 
 In other words, the value signal produced by the reward (\ac{us}) is transferred back to an event (\ac{cs}) that predicts the reward.
 
-\begin{example}[Second-order conditioning]
+\begin{casestudy}[Second-order conditioning]
     Pairing a new \ac{cs} to an existing \ac{cs}.
 
     \begin{center}
@@ -364,7 +364,7 @@ In other words, the value signal produced by the reward (\ac{us}) is transferred
         The Rescorla-Wagner model is not capable of modeling second-order conditioning while 
         the temporal difference model is.
     \end{remark}
-\end{example}
+\end{casestudy}
 
 
 
@@ -376,70 +376,55 @@ There is strong evidence that the dopaminergic system is the major neural mechan
     \item[Response to unexpected rewards] \marginnote{Dopamine response to unexpected rewards}
         Dopaminergic neurons exhibit a strong phasic response in the presence of an unexpected reward.
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey that touches food]
-            \small
+            Some food is put in a box with a hole to reach its content.
-            \begin{example}[Monkey that touches food]
+            In the absence of any other stimuli predicting the reward, 
-                Some food is put in a box with a hole to reach its content.
+            a monkey presents a high dopaminergic response when it touches the food.
-                In the absence of any other stimuli predicting the reward, 
+            \begin{center}
-                a monkey presents a high dopaminergic response when it touches the food.
+                \includegraphics[width=0.55\linewidth]{./img/dopamine_monkey1.png}    
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.55\linewidth]{./img/dopamine_monkey1.png}    
+        \end{casestudy}
-                \end{center}
-            \end{example}
-        \end{@empty}
 
     \item[Reward discrimination] \marginnote{Dopamine reward discrimination}
         Dopamine neurons respond differently depending on the actual presence of a reward.
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey that touches food]
-            \small
+            The dopaminergic response of a monkey that touches an apple attached to a wire in a box is different 
-            \begin{example}[Monkey that touches food]
+            from the response of only touching the wire.
-                The dopaminergic response of a monkey that touches an apple attached to a wire in a box is different 
+            \begin{center}
-                from the response of only touching the wire.
+                \includegraphics[width=0.5\linewidth]{./img/dopamine_monkey2.png}    
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.5\linewidth]{./img/dopamine_monkey2.png}    
+        \end{casestudy}
-                \end{center}
-            \end{example}
-        \end{@empty}
 
     \item[Magnitude discrimination] \marginnote{Dopamine magnitude discrimination}
         Dopamine neurons respond differently depending on the amount of reward received.
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey that drinks]
-            \small
+            By giving a monkey different amounts of fruit juice in a pseudorandom order,
-            \begin{example}[Monkey that drinks]
+            its dopaminergic response is stronger for the highest volume and weaker for the lowest volume.
-                By giving a monkey different amounts of fruit juice in a pseudorandom order,
+            \begin{center}
-                its dopaminergic response is stronger for the highest volume and weaker for the lowest volume.
+                \includegraphics[width=0.7\linewidth]{./img/dopamine_monkey3.png}    
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.7\linewidth]{./img/dopamine_monkey3.png}    
+        \end{casestudy}
-                \end{center}
-            \end{example}
-        \end{@empty}
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey with juice and images]
-            \small
+            Using different \acp{cs}, it can be seen that the dopaminergic response differs based on the amount of reward.
-            \begin{example}[Monkey with juice and images]
+            \begin{center}
-                Using different \acp{cs}, it can be seen that the dopaminergic response differs based on the amount of reward.
+                \includegraphics[width=0.55\linewidth]{./img/dopamine_expected.png}
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.55\linewidth]{./img/dopamine_expected.png}
+        \end{casestudy}
-                \end{center}
-            \end{example}
-        \end{@empty}
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey with juice and images]
-            \small
+            After learning the association between a \ac{cs} and \ac{us} (middle graph), a change in the amount of the reward changes the dopaminergic response.
-            \begin{example}[Monkey with juice and images]
+            \begin{center}
-                After learning the association between a \ac{cs} and \ac{us} (middle graph), a change in the amount of the reward changes the dopaminergic response.
+                \includegraphics[width=0.6\linewidth]{./img/dopamine_expected2.png}
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.6\linewidth]{./img/dopamine_expected2.png}
-                \end{center}
 
-                This behavior also involves the context (i.e. the \ac{cs} image that is shown).
+            This behavior also involves the context (i.e. the \ac{cs} image that is shown).
-                \begin{center}
+            \begin{center}
-                    \includegraphics[width=0.6\linewidth]{./img/dopamine_expected3.png}
+                \includegraphics[width=0.6\linewidth]{./img/dopamine_expected3.png}
-                \end{center}
+            \end{center}
-            \end{example}
+        \end{casestudy}
-        \end{@empty}
 \end{description}
 
 \begin{remark}
@@ -464,20 +449,17 @@ There is strong evidence that the dopaminergic system is the major neural mechan
     \item[Response to blocking] \marginnote{Dopamine response to blocking}
         Dopaminergic response is in line with the blocking effect.
 
-        \begin{@empty}
+        \begin{casestudy}[Monkey with food and images]
-            \small
+            \phantom{}\\
-            \begin{example}[Monkey with food and images]
+            \begin{minipage}{0.7\linewidth}
-                \phantom{}\\
+                A monkey is taught to associate images with food.
-                \begin{minipage}{0.7\linewidth}
+                A new \ac{cs} alongside an existing \ac{cs} will not be learned.
-                    A monkey is taught to associate images with food.
+            \end{minipage}
-                    A new \ac{cs} alongside an existing \ac{cs} will not be learned.
+            \begin{minipage}{0.28\linewidth}
-                \end{minipage}
+                \centering
-                \begin{minipage}{0.28\linewidth}
+                \includegraphics[width=\linewidth]{./img/dopamine_blocking.png}
-                    \centering
+            \end{minipage}
-                    \includegraphics[width=\linewidth]{./img/dopamine_blocking.png}
+        \end{casestudy}
-                \end{minipage}
-            \end{example}
-        \end{@empty}
 
     \item[Probability encoding] \marginnote{Dopamine probability encoding}
         The phasic activation of dopamine neurons varies monotonically with the reward probability
@@ -489,16 +471,13 @@ There is strong evidence that the dopaminergic system is the major neural mechan
         Dopamine response to unexpectedness also involves timing.
         A dopaminergic response occurs when a reward is given earlier or later than expected.
 
-        \begin{@empty}
+        \begin{casestudy}
-            \small
+            After learning that a reward occurs 1 second after the end of the \ac{cs}, 
-            \begin{example}
+            dopamine neurons fire if the timing changes.
-                After learning that a reward occurs 1 second after the end of the \ac{cs}, 
+            \begin{center}
-                dopamine neurons fire if the timing changes.
+                \includegraphics[width=0.5\linewidth]{./img/dopamine_timing.png}
-                \begin{center}
+            \end{center}
-                    \includegraphics[width=0.5\linewidth]{./img/dopamine_timing.png}
+        \end{casestudy}
-                \end{center}
-            \end{example}
-        \end{@empty}
 \end{description}
 
 \begin{remark}

src/cognition-and-neuroscience/module1/sections/_rl.tex

@@ -138,10 +138,10 @@
     only useful changes will last.
 \end{remark}
 
-\begin{example}[Phantom limb pain]
+\begin{casestudy}[Phantom limb pain]
     In amputees, the area of the brain responsible for the missing part of the body is overrun by the neighboring sections.
     In the case of an arm, the area responsible for the face might "conquer" what once was the area of the arm.
-\end{example}
+\end{casestudy}