Thomas Carlson lectures

Question 1

Describe the history of brain measurement methods

Answer 1

Year: Pre 1900
Person: William James
Description: 
-Accidental experiments
---Placement of bullet shots in different parts of the brain determined future abilities if patient survived
-Medicine and philosophy
-Birth of psychology

Year: 1924
Person: Hans Berger
Description: Collects first EEG recording

Year: 1928
Person: Edgar Adrian
Description: First recording of single unit activity

Year: 1968
Person: David Cohen
Description: First MEG recording (direct measure)

Year: 1973
Person: Hoffman, Ter-Pogossian and Phelps
Description: First PET scan

Year: Late 1970s
Person: Lauterbur and Mansfield; and Damadian
Description: Develop MRI technology

Year: 1980
Person: Merton and Morton
Description: Stimulate motor cortex with TMS

Year: 1991
Person: Belliveau et al. + Ogowa et al.
Description: Develop fMRI

Question 2

What are newly developed techniques for measuring brain activity/analysis of this data and how did it come about?

Answer 2

-Brain science is multidisciplinary
•	Cutting edge techniques 
o	Optogenetics
	Shine light onto neurons that have been genetically modified to increase their activity of decrease their activity 
o	Two photon imaging
	Can only be done in animals
	Real time imaging of cellular activity
•	New and upscaled analysis methods have allowed for further learning about the brain 
o	Machine learning
	Reinforcement learning
	Supervised learning
•	Classification
•	Regression 
	Unsupervised learning
•	Clustering
•	Dimensionality reduction

Question 3

Is there a perfect methods to measure the brain? Why/why not?

Answer 3

•	No method is perfect
o	Have to consider spatial and temporal dimensions, as well as invasiveness
o	The right method depends on the scale of the question 
	Components of a neuron
•	E.g. Physiology
	Neurons
•	E.g. Physiology 
	Neural networks
•	E.g. Physiology and arrays 
	Brain areas
•	E.g. fMRI
	Brain networks
•	E.g. fMRI

Question 4

What are the Barlow’s 5 dogmas and what are they arguments for?

Answer 4

• An argument for direct measures and observation of single neurons through single-unit recording- Barlow (perception, 1972)
o To understand nervous function, one needs to look at interactions at a cellular level, rather than either a macroscopic or microscopic level, because behaviour depends upon the organised pattern of these intercellular interactions. This dogma is possible as single neurons have diverse and highly specific responsiveness to sensory stimuli, and are astonishingly reliable
o The sensory system is organised to achieve as complete a representation of the sensory stimulus as possible with the minimum number of active neurons. This dogma is possible as, at higher levels, fewer and fewer cells are active, but each represents a more and more specific happening in the sensory environment.
o Trigger features of sensory neurons are matched to redundant patterns of stimulation by experience as well as by developmental processes (including genetics)
o Perception corresponds to the activity of a small selection from the very numerous high-level neurons, each of which corresponds to a pattern of external events or the order of complexity of the events symbolised by a word. However, not every cortical neuron’s activity has a simple perceptual correlate
o High impulse frequency in a given neuron corresponds to high certainty that the trigger feature is present.

Question 5

What is an argument for measuring neural networks instead of single neurons?

Answer 5

• An argument for neural networks
o Instead of looking at single neurons, scientists should be looking at how neurons interact with each other and their activity
o Avoids the grandmother cell effect
 Don’t need one cell to encode a person- encode a person through a joint activation pattern across multiple neurons

Question 6

What are the two types of brain measures? Define and give examples of technology used for these brain measures

Answer 6

• Direct measures
o Direct measures relate directly to neuronal activity
 E.g. single unit recordings, EMG, EEG
• Indirect measures
o Indirect measures use a conduit to access neural activity
o They are associated with neural activity (although not necessarily linearly) but measure other factors
 E.g. fMRI measures changes in blood oxygenation

Question 7

What techniques are used to measure brain activity?

Answer 7

o	Single unit recordings
o	Electroencephalography (EEG)
o	Magnetoencephalography (MEG)
•	Local field potentials 
•	Optogenetics

Question 8

What are single unit recordings?

Answer 8

 Measures action potentials for individual neurons

Question 9

What are the two types of single unit recordings, and their advantages/disadvantages?

Answer 9

 Types:
• Extracellular-
o Doesn’t penetrate cell body of the neuron: instead, records extracellular fluid properties
o Recordings can occur for months before the cell starts dying
o Reads basic components of an action potential
o High spatial and temporal resolution
• Intracellular-
o Penetration in neural cell body
 However, this means that the cell begins dying as soon as penetration occur, so recording can only occur during a limited time frame
o Records from exactly one neuron
o Can record subthreshold potentials

Question 10

What is the procedure for single unit recordings?

Answer 10

• Record activity for a stimulus
• Identify spikes (spike sorting)
• Measure spiking activity over time
• Repeat for multiple trials

Question 11

What are properties of a good extracellular electrode? Give an example of one

Answer 11

o Properties of a good extracellular electrode
 Ruggedness to pass through neural tissues
 Stability for accurate localisation
 High signal-to-noise ratio (low electrode noise)
 High selectivity
o Examples are platinum black-plated platinum or stainless steel electrodes (which do not require a trade-off between high signal-to-noise ratio and selectivity as other electrodes do)

Question 12

Describe how spikes are produced in single unit recordings, the theoretical recording of an isolated axon (and why it is so) as well as why theoretical values do not always match reality

Answer 12

o The action potential (or spike) recorded with an extracellular microelectrode is produced by currents that are induced to flow in the extracellular space around an active neuron
 Theoretically records a triphasic waveform from the isolated axon
• As the action potential approaches the region underneath the electrode, the electrode sees a positive potential relative to a distant indifferent electrode
• When the action potential reaches the membrane underlying the electrode, the electrode records a negative potential
• As the action potential continues down the axon, the membrane under the electrode once again records a positive potential
 However, as the extracellular space does not have uniform, low resistance, the measured potential is not always accurate

Question 13

Why is there a need to separate and identify spikes in extracellular single cell recordings? How is this done?

Answer 13

o There is a need to separate and identify spikes as extracellular recordings may pick up more than one neuron
 Multidimensional spike sorting allows confident identification of an individual cell, as well as simultaneous recording of ensembles of cells, with on-line and/ or off-line separation based on waveform parameters

Question 14

What is needed if the cell that is recorded during single unit recording is inactive?

Answer 14

o Sometimes need search stimulus activation (electrical of physiological stimulation) of neuron of interest for the extracellular electrode to pick up the spikes

Question 15

Are single unit recordings often done in humans?

Answer 15

 Not easily done in humans- mostly done during epileptic surgery

Question 16

What is electroencephalograhy (EGG) and how does it work?

Answer 16

 EEG measures the summation of electrical activity on the scalp, primarily derived from post-synaptic activity around the dendrites of pyramidal neurons in the cerebral cortex
• Pyramidal neurons are found in the most superficial layer of the brain and are spatially aligned; thus, their activity is synchronous
o This produces a larger signal that can be measured by the EEG
• Summation of the dipoles created by many neurons is what is detected by the EEG
o When the pyramidal neurons fire, they create currents (due to depolarisation and repolarisation at different areas of the pyramidal neuron- follows the action potential)

Question 17

Is EEG safe for humans?

Answer 17

 Safe for humans

• However, electrocorticography and intracranial electroencephalography are invasive

Question 18

What are the similarities between MEGs and EEGs?

Answer 18

 MEGs and EEGs are both direct measures of neural activity and both have excellent temporal resolution (milliseconds).

Question 19

What are the differences between MEGs and EEGs?

Answer 19

 However:
• They measure different signals
• MEG has an advantage in that magnetic fields are not affected by the skull. However, EEGs are affected by skull and tissue interference
o Hence, MEG has slightly better localisation
• Different sensitivity- EEG can measure deep sources in the brain, but MEG is not as sensitive to deep sources (only measures activity at the surface of the brain)
o Electrical signals do not drop out as fast throughout distance compared to magnetic signals
• MEG ($1000) costs a lot more than EEG ($15)
o Sensors in MEG need to be bathed in liquid helium, which is very expensive, and the MEG apparatus needs to be in a room that blocks out interfering magnetic signals

Question 20

What is a common disadvantage of MEGs and EEGs?

Answer 20

 Both have a disadvantage:
• Source localisation can be difficult as, although recordings are done at the scalp (which is a 2D surface), the signals are coming from the brain (which is a 3D object)
• However, there is a tight link between the activity measured by MEG, EEG and single unit recordings, suggesting that spatial and temporal resolution of both techniques is not abysmal

Question 21

What do local field potentials measure?

Answer 21

 Measures electric potential in the extracellular space around neurons- reflects changes in synaptic activity

Question 22

What are the stages of an action potential?

Answer 22

• Stages of an action potential-
o Resting potential
 The voltage across the membrane is about -65 mV at resting potential
o Gets triggered
 Near the terminal bouton, there are voltage-gated calcium channels
 When an action potential fires and gets down to terminal, action potential opens calcium channels which will call the synaptic vesicles to dock and release their neurotransmitters
 Neurotransmitter binds to ligand-binding neurotransmitter receptor which opens up sodium channels which starts making the cell depolarised
 When the threshold is surpassed (-55mV), an action potential occurs
• An action potential is ONLY caused when the depolarization of the membrane is beyond the threshold
• Threshold-the membrane potential at which enough voltage-gated sodium channels open so that the relative ionic permeability of the membrane favors sodium over potassium.
o Rising phase
 Sodium channels open and inside of cell becomes more positive as sodium enters in the cell
o Overshoot
 Voltage is about +35 mV- the part where the inside of the neuron is positively charged with respect to the outside
o Falling phase
 Potassium channels open and inside of cell becomes less positive, returns to negative
 Sodium channels close
o Undershoot
 Rapid depolarisation causes the inside of the membrane to be more negative than the resting potential
o Absolute refractory period
 Sodium channels inactive when the membrane becomes strongly depolarised. They cannot be activated again, and another action potential cannot be generated, until the membrane potential becomes sufficiently negative enough to deinactivate the channels (usually 1msec)
o Relative refractory period
 The membrane potential stays hyperpolarised until the voltage-gated potassium channels close. Therefore, more depolarizing current is required to bring the membrane potential to threshold
o Restoration of the resting potential

Question 23

List indirect measures of measuring/determining brain activity?

Answer 23

•	Brain damaged patients 
o	Often from bullet holes and accidents
o	Stroke, concussions and brain injury 
•	Behavioural approaches
o	Qualitative methods
o	Questionnaires
o	Psychophysics
•	X-rays
•	CT scan
•	MRI
•	Diffusion Tensor Imaging
•	Metabolic methods
o	PET (Positron Emission Tomography) imaging
o	fMRI (functional MRI)
o	Radioactive tracers (only in animals)
•	Optical imaging (Only in animals)
•	Transcranial magnetic stimulation (TMS)
•	Clarity

Question 24

What people are examples of how brain damage and injury can be used to learn about brain functions? Describe what happened to these people and what were learnt from them

Answer 24

 Phineas Gage
• Railroad spike went through frontal lobe- learned that frontal lobe is important for higher cognition/decision making
• Showed lack of ambition and became aggressive
 H.M
• Treated with brain surgery for epilepsy- removed both his hippocampi
• Learned that the hippocampus is critical for forming long term memories
 Victor Leborgne (Tan)
• Had a stroke that affected Brocas area (critical for the production of speech)
• Still understood words and instructions
 NFL players who headbutt each other at full speed often experience depression, high suicide rates
• Tied to repeated concussions that players had (CTE syndrome)

Question 25

What was an initial disadvantage of studying brain functions using brain injury/damage and how was it done?

Answer 25

o Would often have to wait for subjects to die of natural causes before observing their brain  Behaviour+ Anatomy+ Patience= knowledge

Question 26

What is psychophysics? Give examples of such techniques

Answer 26

 Precise manipulations of stimuli to understand how the brain encodes information • Adaptation • Psycho-anatomy • Divided visual field presentation

Question 27

Describe what the disadvantage of X-rays in in elucidating brain function

Answer 27

o Hard to fully observe inside the skull

Question 28

Describe why CT scans were so revolutionary in elucidating brain function

Answer 28

o Can look at the brain in 3D- easy to look at inside structures of the brain o No longer have to wait for patient death to observe their brain anatomy

Question 29

How does MRI work?

Answer 29

o Each atom contains protons which are positively charged and spinning around an axis o This spinning charge creates a small magnetic field o An MRI machine is effectively a large magnet so that when an individual is placed inside the magnet, their magnetic protons line up along the longitudinal axis with the MRI magnetic field o A short strong electromagnetic pulse (radiofrequency pulse) is applied to disturb the spinning protons- this results in less of them spinning in the same axis as the MRI magnetic field and more spinning in a transverse plane o Once the radiofrequency pulse is turned off, the protons return to their original direction along the MRI magnetic field- longitudinal magnetization gradually increases until it reaches the same point where it was before the radiofrequency pulse  The rate of this return is called the longitudinal relaxation time or T1 time  The rate of decrease of the transverse relaxation is called the transverse relaxation time or T2 time  The T1 and T2 relaxation times are different and are independent processes • Rate of decay gives information on different kinds of tissues

Question 30

How does MRI recognise different tissues?

Answer 30

 Different tissues have different T1 and T2 relaxation times  Water has a high T1 and T2 relaxation time whereas fat has lower T1 and T2 relaxation times  By applying a series of radiofrequency pulses the MRI can distinguish between different tissues that have different relaxation rates

Question 31

How are MRI scans prepared for analysis?

Answer 31

 Taking multiple images and averaging them produces greater contrast between gray matter and white matter  Even higher spatial resolution and grey/white differentiation is possible with longer scan times and higher field strengths

Question 32

What is tractography?

Answer 32

tracing tracts by visualising fibres

Question 33

What is the basis of DTI?

Answer 33

o DTI- based on use of diffusion of water molecules to generate different pixel intensities that can contain information about direction of water movement

Question 34

What is mean diffusivity?

Answer 34

o Mean diffusivity-  A measure of the average molecular motion independent of any tissue directionality.  It is affected by cellular size and integrity  Anything that changes the physical structure of the area will alter mean diffusivity

Question 35

What is the concept behind diffusion tensor imaging?

Answer 35

 Diffusion of protons depends on freedom of movement in tissue • Protons move differently in different brain compartments • Membranes restrict movement  In fibre tracts, combination of movement in axonal membrane and surrounding oligodendrocyte membrane (myelin) restricts movement of protons  Restricted proton movement can be discerned in MRI o The diffusion matrix (tensors) can be used to generate a 3D image of the tracts  Outline squares in the matrix where protons can’t move much: these will be the fibre tracts  In the myelin of oligodendrocytes, there is directionality: can tell moving from anterior to posterior/ superior or inferior • Hence, DITs can show which direction the fibres are projecting in and the fibre tracts in an area

Question 36

Describe the properties of protons in CSF that are important in diffusion tensor imaging

Answer 36

o Isotropic  Moves in all directions o Water o High diffusivity

Question 37

Describe the properties of protons in grey matter that are important in diffusion tensor imaging

Answer 37

o Isotropic o Low diffusivity (move in any direction but constrained-in smaller space) o Lots of water in cells but also lipid, cell membranes

Question 38

Describe the properties of protons in white matter that are important in diffusion tensor imaging

Answer 38

o Anisotropic  Constrained direction- can only move in very narrow space along longitudinal axis of axons o High diffusivity o Mostly myelin but also axonal membranes

Question 39

What is fractional anisotropy?

Answer 39

o FA fractional anisotropy- scalar value between zero and one that describes the degree of anisotropy of a diffusion process- a value of zero means that diffusion is unrestricted and value of one means that diffusion is fully restricted

Question 40

What is the basis of positron emission tomography?

Answer 40

 PET measures positrons following injection of a radioactive tracer containing a positron-emitting isotope into the blood stream  More glucose uptake= more gamma radiation= greater image intensity

Question 41

What is the process of PET?

Answer 41

 A commonly used PET tracer is a labelled form of glucose- fluoreoxyglucose (FDG) which is a glucose analogue • Although can also tag water for blood flow or receptors for neurotransmitter release  FDG is taken up by high-glucose-using cells such as neurons, where it is then phosphorylated which prevents the glucose from being released again from the cell  The phosphorylated FDG cannot move out of the cell before its radioactive decay which has a half life of 110 minutes  When radioactive nuclei decay, they emit positrons  These positrons collide with a nearby electron resulting in the emission of 2 gamma rays in opposite directions  Gamma rays are sensed by detectors surrounding the brain  Original gamma ray emission location is then reconstructed • 4-5 minutes

Question 42

What is the principle behind fMRI? Explain

Answer 42

 Most common form of fMRI and relies on the finding that neuronal activity is associated with changes in regional blood flow  T1 relaxation- not related to changes in haemoglobin  T2 relaxation- affected to changes in haemoglobin • Magnetic susceptibility of deoxygenated haemoglobin is about 20% greater than haemoglobin • Magnetic susceptibility of deoxygenated haemoglobin affects rate of T2 relaxation o Magnetic properties of a blood cell (haemoglobin) depends on whether it has an oxygen molecule  With oxygen-> zero magnetic moment  Without oxygen-> sizeable magnetic moment (paramagnetic)

Question 43

What is the process of fMRI and why does this process work?

Answer 43

• fMRI is a relative measure so you need to compare signal changes relative to a baseline period during the same scan o Can only be used to measure evoked activity • When blood vessel is full of deoxyhaemoglobin, disrupts magnetic field • When blood vessel is full of oxygenated haemoglobin, there is no disruption of magnetic field • In a resting neuron, the amount of oxygenated haemoglobin entering the capillary bed is about equal as the amount of deoxygenated haemoglobin leaving the capillary bed • In an activated neuron, there is oversupply of oxygenated haemoglobin and hence leaving capillary body has more oxygenated haemoglobin than it would have at rest o Oversupply results in less overall distortion of magnetic field-> measured as an increase in blood oxygen level dependent signal • However, increased blood flow to meet oxygen demands in activated neurons slightly delayed (4-6 seconds)

Question 44

Explain the shape of the fMRI BOLD response graph

Answer 44

* Initial dip- reduction in the amount of oxygen in that brain area * Positive BOLD response- brain detects that the area of interest is using many resources and rushes new fresh blood to brain area * Negative BOLD response- stimulus is shut down-> blood is not urgently provided to area of interest anymore

Question 45

What are the advantages of fMRI?

Answer 45

- Good spatial resolution | - Non-invasive, not requiring injection of radioactive materials like PET. Subject can be repeatedly scanned

Question 46

What are the disadvantages of fMRI?

Answer 46

- Noisy - Susceptible to motion artefacts - Areas near bone tissue interfaces are susceptible to artefacts - Metal implants can be dangerous - More susceptible to neural inputs than outputs - Bad temporal resolution

Question 47

Describe how imaging using radioactive tracers is done in animals

Answer 47

o Radioactive tracers (only in animals)  Radioactive tracer given  Sacrifice the animal and flatten the desired section  Look at path that the radioactive tracer has gone

Question 48

Describe optical imaging as a way to measure brain activity. Can it be done in humans?

Answer 48

• Optical imaging (Only in animals) o Put a camera directly on surface of the brain and film with a camera o Look at ratio of blue: red light  If a stimulus is shown, the area of the brain activated due to this stimulus will reflect blue light more than red light

Question 49

Describe how transcranial magnetic stimulation (TMS) works and what it allows

Answer 49

• Transcranial magnetic stimulation (TMS) o Uses a magnet in a shape of a coil  Contains a couple of copper windings which passes a strong electrical current, producing a strong magnetic field coming out of the coil o Place coil on top of people’s heads employs magnetic pulse through the skull of the patient, interfering with brain activity directly underneath the coil o By targeting different areas in the brain, can look at different brain activities o Finds if a brain area is causally involved with a function by magnetically interfering with/stimulating that brain area

Question 50

Describe Clarity as a way to image the brain and how it is performed

Answer 50

o Make the brain transparent and use labelling molecules to label areas of interest o Can be done on the whole brain o To make brain transparent, first add a hydrogel mesh (to hold all components together), then remove the fat

Question 51

Who was Claude Shannon and what important contribution did he make?

Answer 51

• Claude Shannon- o Key character in developing and quantifying the concept of information o Worked on missile control systems o Worked for a phone company o Proposed the information theory o Found that compression of information makes for more effective communication o Applied concept of entropy-the amount of disorder- to information processing o Provided framework for thinking about the brain

Question 52

What is the information theory and why was it originally proposed?

Answer 52

o The information theory- studies the quantification, storage and communication of information  Originally proposed by Claude Shannon to find fundamental limits on signal processing and communication operations such as data compression

Question 53

Describe the relationship between entropy and compression. Give an example

Answer 53

 The higher the entropy, the more difficult the compression • E.g. an image of an empty blue sky would compress to an extremely small file whilst an image of static would result in a very big file size o JPEG is such a compression tool

Question 54

How is the information theory applicable to the brain? Which of Barlow's dogmas does this match with?

Answer 54

• Applicable to the brain- the brain wants the smallest number of neurons firing such that it can code important information in an environment without having to use many neurons (which would use a lot of metabolic energy) o Matches with Barlow’s second dogma- The sensory system is organized to achieve as complete a representation of the sensory stimulus as possible with the minimum number of active neurons

Question 55

What is the purpose of the Bayesian framework?

Answer 55

• Bayesian framework | o Allows the use of previously obtained knowledge/beliefs to help the calculate the probability of a related event

Question 56

What percentage of our body weight does the brain consist of?

Answer 56

2%

Question 57

What percentage of our energy does the brain consume?

Answer 57

20%

Question 58

Define the Bayes' theorem and what each letter describes

Answer 58

o Bayes’ theorem is defined as P(HIE)= ((P(EIH)*P(H))/P(E)  Where H is the hypothesis  Where E is the evidence  Where P(HIE) is the conditional probability that hypothesis occurs given the evidence  Where P(EIH) is the likelihood of evidence  Where P(H) is the marginal probability that hypothesis is true

Question 59

What is Bayesian inference?

Answer 59

o Bayesian inference is the process of deducing properties about a population or probability distribution from data using Bayes’ theorem

Question 60

According to the Bayesian framework, what two pieces of information are important in solving ambiguities?

Answer 60

o Two pieces of information important in solving ambiguities  The new event itself  Knowledge of prior information that can be related and used to interpret the new event

Question 61

What are requirements for the information processing system?

Answer 61

• Information processing system takes some form of input and turn it into a useful output

Question 62

What is the information processing system for the brain?

Answer 62

• For the brain: External inputs (sensory information)-> storage and algorithms (memories)-> external outputs

Question 63

What is a representation? How is its usefulness determined?

Answer 63

o Representation- stored information (in a particular format)  Formal system for making explicit certain entities or types of information, together with a specification of how the system does this  Any particular representation makes certain information explicit at the expense of information that is pushed into the background and may be hard to recover  The usefulness of a representation depends upon how well suited it is to the purpose for which it is used

Question 64

What is a process?

Answer 64

o Process- an algorithm that changes the form of the representation

Question 65

Describe Shepard and Metzler (1971)'s representation experiment and its conclusion

Answer 65

o Shepard and Metzler (1971)  Showed subjects either original object or rotated object  The more rotated away from its original orientation the object was, the harder it was to recognise the object as a copy of the original  Suggests that brain is physically rotating the object into the same orientation as the other one to make the comparison

Question 66

What are Marr's (1982) levels of explanation?

Answer 66

• The three levels at which any machine carrying out an information processing task must be understood, but as these concepts are somewhat loosely related, some phenomena may be explained at only one or two of the o Computational theory o Representation and algorithm (most important level of thinking) o Hardware implementation

Question 67

Describe Marr's computational theory, its important features and examples of its accomplishments.

Answer 67

``` o Computational theory  What is the goal of the computation, why is it appropriate, and what is the logic of the strategy by which it can be carried out?  Important features • It contains separate arguments about what is computed and why • Resulting operation is defined uniquely by the constraints it has to satisfy  What and why  What are we trying to accomplish? • Object recognition • Emotion perception • Store memories • Guided action • Etc. ```

Question 68

Describe Marr's representation and algorithm level and examples of such steps

Answer 68

o Representation and algorithm (most important level of thinking)  How can this computational theory be implemented? In particular, what is the representation for the input and output, and what is the algorithm for the transformation?  How  What are the steps we will take to reach this goal? • Inputs (ingredients) • Algorithm (recipe) • Outputs (goal)

Question 69

Describe Marr's hardware implementation level

Answer 69

o Hardware implementation  How can the representation and algorithm be realized physically?  How are we physically going to accomplish this task? • Mechanical system • Biological system

Question 70

What are two examples of smart encoding in the visual system?

Answer 70

* Cone sensitivity-smart encoding example | * Receptor layout- smart encoding example

Question 71

Why is cone sensitivity in humans an example of smart encoding?

Answer 71

o M cone and L cone overlap in wavelength sensitivity allows for increased distinction between red and green- important in our ancestors to distinguish fruit and food in trees- smart encoding

Question 72

What is the sensitivity profile of cones?

Answer 72

o Sensitivity profile demonstrates how much light a cone would absorb, which translates to firing rate, as a function of wavelength

Question 73

What is the peak of the S cone?

Answer 73

 S cone peak- 420 nm

Question 74

What is the peak of the M cone?

Answer 74

 M cone peak- 500 nm

Question 75

What is the peak of the L cone?

Answer 75

 L cone peak- 570 nm

Question 76

Why is receptor layout an example of smart encoding?

Answer 76

• Receptor layout- smart encoding example o Fovea (where light lands) has extremely high sensitivity and is very dense in cone receptors whilst the rest of the retina (periphery) has a high density of rods  Only the fovea sees in colour as it takes a lot more energy to do so • Fovea contains many simple retinal circuits  Rods are extremely sensitive-> makes the periphery extremely sensitive to peripheral light • Periphery contains many convergent retinal circuits

Question 77

How many cone photoreceptors do we have?

Answer 77

5 million

Question 78

How many rod photoreceptors do we have?

Answer 78

120 million

Question 79

How many optic nerve axons do we have?

Answer 79

1.1 million

Question 80

Describe a simple retinal circuit

Answer 80

o Simple retinal circuit- 1 photoreceptor: 1 ganglion cell |  Extremely sensitive localisation

Question 81

Describe a convergent retinal

Answer 81

o Convergent retinal circuit- many photoreceptors converge on one ganglion cell  Sensitivity over large amount of space but poor resolution  Response increases as more of the convergent receptors are activated

Question 82

How can the brain clean up representations?

Answer 82

• Using priors to clean up representations | o The brain can use prior highly reliable information to infer information and representations

Question 83

Are all representations equal? Explain

Answer 83

• Not all representations are equal o The same information can be represented in a variety of ways (encryption is meant to hide information) o Some representation are better for the brain than others

Question 84

How can brain representations be studied?

Answer 84

``` • Reconstructing brain representations from behaviour •fMRI • Magnetoencephalography (EMG) o EEG o Single unit recordings ```

Question 85

How can reconstructing brain representations from behaviour/imaging studies be used to study brain representations?

Answer 85

• Reconstructing brain representations from behaviour o Can look at brain representations in a spatial manner (compare two representations and their distance apart is represents the amount of difference between the two representations- how the brain represents the concepts between one another)  Representational geometry o To characterize the geometry of a representation, we can compare brain-activity patterns representing a set of stimuli to each other or verbally ask the subject the degree of dissimilarity between the two simuli  The dissimilarity of two patterns corresponds to the distance between their points in the representational space  We can then construct the representational dissimilarity matrix, in which we can look up the representational distance for each pair of stimuli

Question 86

What is representational geometry?

Answer 86

 Representational geometry-captures both the information represented in a neuronal population code and the format in which it is represented

Question 87

How can fMRI be used to study brain representations?

Answer 87

o Different brain activity for different types of concepts/images

Question 88

Where are inanimate and animate objects represented on the brain? Who studied this?

Answer 88

 Inanimate and animate objects are represented on separate sides in the inferotemporal cortex (area of the brain dedicated to identifying objects) (Kriegeskorte 2008)

Question 89

How can magnetoencephalography be used to study brain representations?

Answer 89

• Magnetoencephalography (EMG) | o Time varying representational structure

Question 90

What do response patterns elicited by images of the same category form in the ventral-temporal response patterns space? What are these major categories?

Answer 90

• Response patterns elicited by images of the same category form clusters in ventral-temporal response-patterns space o Major categorical divisions are between animates and inanimates and between faces and bodies

Question 91

Is response-pattern dissimilarity significantly correlated with physical distance in the brain?

Answer 91

• However, response-pattern dissimilarity is not significantly correlated with physical distance anywhere in the brain

Question 92

Describe the components of a brain region's representation

Answer 92

• It is the pattern of activity across neurons that represents the content o The many possible combinations of activity states of neurons provide a rich representational space o A brain region’s representation is a multidimensional space  Dimensions of the space correspond to the neurons  Point corresponds to an activity pattern  Set of all possible objects corresponds to av vast set of points in the space  It is the geometry of these points that defines the nature of the representation

Question 93

Describe Marr's 1983 viewer centred steps of hierarchical processing and disentanglement of information for object perception. as well as their purpose and primitives

Answer 93

Name: Image(s) Purpose: Represents intensity Primitives: Intensity value at each point in the image ``` Name: Primal sketch Purpose: Makes explicit important information about the two-dimensional image, primarily the intensity changes there and their geometrical distribution and organization Primitives: Zero-crossings Blobs Terminations and discontinues Edge segments Virtual lines Groups Curvilinear organization Boundaries ``` ``` Name: 2 1/2-D sketch Purpose: Makes explicit the orientation and rough depth of the visible surfaces, and contours of discontinuities in these quantities in a viewer-centred coordinate frame Primitives: Local surface orientation Distance from viewer Discontinuities in depth Discontinuities in surface orientation ```

Question 94

Describe Marr's 1983 object centred step of hierarchical processing and disentanglement of information for object perception. as well as their purpose and primitives

Answer 94

Name: 3-D model representation Purpose: Describes shapes and their spatial organisation in an object-centred coordinate frame, using a modular hierarchical representation that includes volumetric primitives as well as surface primitives Primitives: 3-D models arranged hierarchically, each one based on a spatial configuration of a few sticks of axes, to which volumetric or surface shape primitives are attached

Question 95

What is a receptive field?

Answer 95

• Area covered by receptors in a sensory unit is a receptive field

Question 96

What is acuity?

Answer 96

o Acuity- ability to discriminate two separate stimuli in a sensory system

Question 97

What is needed for high acuity?

Answer 97

o For high acuity, need:  High density of receptors  Small receptive fields  Low convergence

Question 98

What are features?

Answer 98

• Features- physical and cognitive constructs the brain is encoding

Question 99

What features do the visual parts of the brain encode? Give examples for each feature

Answer 99

``` o Vision  Physical features • Spatial frequency and contrast • Motion speed and direction  Higher order features • Face identity • Biological motion  Cognitive features/constructs • Emotions ```

Question 100

What is high spatial frequency?

Answer 100

o High spatial frequency-densely packed stimuli

Question 101

What is low spatial frequency?

Answer 101

o Low spatial frequency- widely spaced stimuli

Question 102

What spatial frequency are humans most sensitive to?

Answer 102

o Most sensitive to frequencies in the medium range

Question 103

Describe how convergent visual circuits work and a disadvantage of such a circuit

Answer 103

• Convergent circuits o Firing rate increases as number of receptors activated increases o Each receptor picks up information from a specific area o Sensory neurons converge on single second order neuron o Receptive field of secondary neuron will be the sum of the receptive field of sensory neurons that converge on it  Hence, secondary neuron cannot discern from which converged sensory neuron the stimulus came from

Question 104

Where are centre-surround circuits found?

Answer 104

o Found in retina and lateral geniculate nucleus

Question 105

What are centre-surround receptive fields used for and how do they work?

Answer 105

o Used to enhance contrast adaptation and accurately locate stimulus o Stimulus-> responses to stimulus-> inhibition of neighbouring cells-> contrast enhancement o Receptors will send signals to respective postsynaptic neurons and circuit postsynaptic to these receptors is arranged in such a way that when a receptor is strongly stimulated, there will be lateral inhibitory interneurons that get stimulated and will inhibit transmission of signals from the receptors not stimulated o Centre of receptive field is excitatory and increases activity of the neuron and outer ring is inhibitory (decreases activity of the neuron)

Question 106

What types of receptor fields/cells are in the primary visual cortex? What are they sensitive to and how are they activated?

Answer 106

o Simple cells acting as edge detectors o Building of V1 elongated receptive fields from circular receptive fields  V1 receptive fields are elongated and rectangular, and are extremely sensitive to direction of bars of light: different cells have different orientation preferences • Orientation preference varies across primary visual cortex areas  Stimulus activation of the neuron- • Bars that are not in a preferred orientation will produce no firing rate for the neuron • If the stimulus is in an angle close to the preferred orientation, a relatively weak response will be produced • If the bar stimulus is in the preferred orientation, it will elicit a strong response

Question 107

Describe Hubel and Wiesel's model of the elongated receptive field in V1

Answer 107

 Hubel and Wiesel model of elongated receptive field • If V1 cortical neurons receive converging input from three or more lateral geniculate nucleus neurons whose receptive fields are aligned on a line in the retina

Question 108

What is neuronal adaptation?

Answer 108

o Neurons can recalibrate their firing rate to their environment

Question 109

How many retinotopic maps are in the visual cortex/frontal cortex?

Answer 109

17-22

Question 110

Why are maps used in the brain?

Answer 110

• Maps are extremely efficient o Minimises axon wiring by mapping connected areas next to each other  Reduces conduction delays

Question 111

What is the relationship between map size on the brain and sensitivity of the area?

Answer 111

• The bigger the map area on the brain, the more sensitive that area is o Neural real estate tells what is important to the brain

Question 112

Describe the conscious vision pathway (include sides)

Answer 112

o Conscious vision optic pathway: Retina-> optic nerve-> decussation at optic chiasm-> lateral geniculate nucleus of the thalamus-> Primary visual cortex  Cells of nasal retina decussate to contralateral side  Cells in temporal half of the retina remain on ipsilateral side o Visual field maps to contralateral cortex  Mapping contains information from both retinae

Question 113

Describe the 6 layers of the LGN and what is in them

Answer 113

o LGN divided into 6 layers:  Three main divisions (functional map) • Top 4 layers (2 for humans)- parvocellular (3-6) • Lower 2 layers- magnocellular (1,2)

Question 114

Compare parvocellular cells and magnocellular cells in terms of: - Cell size - Response length - Input cells - Primary function - Response type - Receptive field size - Contrast sensitivity

Answer 114

``` Parvocellular: Small cells Sustained response Input from midget ganglion cells Responsible for high acuity vision o Carries signals for red-green colour vision (cones) and for high acuity spatial vision On type response Small receptive fields Sensitivity at high contrast Better at detecting higher spatial frequencies ``` ``` Magnocellular: Large cells Transient response Input from parasol ganglion cells Responsible for motion perception On type response Large receptive fields Sensitivity at low contrasts Better at detecting contrast sensitivity ```

Question 115

What are the two mapping types in the LGN?

Answer 115

- Functional map | - Eye of origin information

Question 116

How does the LGN map eye of origin information?

Answer 116

 Retinofugal projection to the lateral geniculate nucleus: segregation of inputs according to eye of origin • Inputs from ipsilateral fibres project to layers 2, 3 and 5 • Inputs from the contralateral fibres project to layers 1,4 and 6 • Neurons in the lateral geniculate nucleus possess very similar receptive field properties to the neurons in the retina

Question 117

Describe the map in the primary visual cortex?

Answer 117

• V1 (primary visual cortex) map- o Faithful input from the lateral geniculate nucleus according to topography, function and laterality o Encodes eye of origin information in alternating column o Has orientation columns distributed across the map  Progressive orientations

Question 118

What is the role of V2 and V3?

Answer 118

Orientation

Question 119

What is the role of V4?

Answer 119

Colour

Question 120

What is the role of V5?

Answer 120

Motion

Question 121

What is the role of ventral visual pathway (lateral occipital complex)?

Answer 121

Object categories

Question 122

What is a brain map?

Answer 122

• Map- a clustering of neurons with similar functional properties that is characterised by a gradual progression of preferred stimulus values across the cortical sheet and has ordinal characteristics

Question 123

What is a brain module?

Answer 123

• Module- a clustering of neurons with similar functional properties that is characterised by discrete regions with clear boundaries across which there is no relation in preferred stimulus values o Progress into modules as cortices increase in complexity

Question 124

What is a rhythm?

Answer 124

• Rhythm- any repeating pattern over time o Simple waveforms o Complex waveforms

Question 125

What is the amplitude of a wave?

Answer 125

o Amplitude- measurement from peak to through

Question 126

What is the phase of a wave?

Answer 126

o Phase- shift forward/backward in time

Question 127

What is the frequency of a wave?

Answer 127

o Frequency- Velocity of wave repeats

Question 128

What is Fourier's theorem, fast fourier transform analysis and its use?

Answer 128

o Complex sounds can be decomposed into a series of pure tones  Fast fourier transform analysis is a mathematical method for transforming a function of time into a function of frequency • Frequency on x axis, amplitude on the y axis o Can be used to calculate energy in waveforms

Question 129

What are biorhythms controlled by the brain?

Answer 129

``` o Biorhythms controlled by brain  Heart rate  Breathing  Sleeping patterns  Hunger patterns ```

Question 130

What is the rhythmic structure of the brain when asleep?

Answer 130

Larger waves and more repetitive

Question 131

What is the rhythmic structure of the brain when awake?

Answer 131

o Rhythmic structure when awake- noisy and small waves: small evidence of rhythmic patterns

Question 132

Describe the brain waves that occur at the boundary between sleep and wakefulness

Answer 132

o Alpha waves at boundary between sleep and wakefulness- caused by lack of visual input and relaxed state  Move closer to sleep-like state  Alpha- 10Hz/sec

Question 133

Describe the brain waves that occur when transitioning to sleep

Answer 133

o Theta waves- transition to sleep |  Slow wave and increase in power

Question 134

What are common brain rhythms studied and their wavelengths? Are they mutually exclusive?

Answer 134

``` o Gamma  30-100 Hz o Beta waves  13-30 Hz o Alpha waves  8-13 Hz o Theta waves  4-8 Hz o Delta waves  0.5-4Hz o These waves are not mutually exclusive- can be combined at a point in time ```

Question 135

Describe the role of the medulla oblongata and how it performs these functions

Answer 135

• Rhythmic core functions- breathing and heart rate o Need the brain stem to survive- essential to rhythmic core functions  Medulla oblongata- controls heart and lungs • Monitors amount of carbon dioxide and oxygen in the bloodstream-> close circuited system • Don’t need to consciously think about this

Question 136

How can the medulla oblongata be fooled?

Answer 136

• Can fool this system by hyperventilating-> brings up oxygen levels in the blood to very high standard-> steal extra seconds underwater o However, has disadvantages-> hyperventilation can lead to passing out

Question 137

How is the binding problem solved by brain rhythms?

Answer 137

• Brain rhythms can solve binding problem- o Neurons fire rhythmically in a way that you can separate two objects  Different visual areas responsible for different properties fire in the same way for a specific object • Unique pattern for a separate object

Question 138

What is the relationship between epilepsy/seizures and brain rhythms? How can this be triggered? What are seizures?

Answer 138

Seizures are large disturbances in brain activity that spread from a focal region of the brain o Epilepsy and seizures  Rhythms get out of control in the brain • Can be triggered by high temperature

Question 139

What is the Jacksonian march?

Answer 139

 Jacksonian march | • Can see seizure moving across body-> move along brain homunculus

Question 140

What substance has good therapeutic properties for some seizures?

Answer 140

 Marijuana has good therapeutic properties for some seizures • THC-hallucinogen • Cannabinoids- reduce seizures

Question 141

What are 4 different types of biorhythms? Define them and their length

Answer 141

o Circannual: about 365 days  Hibernation, reproduction, seasonal depression o Infradian: >24 hours  Estrous and menstrual cycles (multiple days) o Circadian: around 24 hours  Influences alertness levels (highest when awake), core body temperature levels (highest when awake), growth hormone secretion levels (highest when asleep) o Ultradian: <24 hours  90-minute cycles

Question 142

What are biorhythms based on time controlled by? How does this work?

Answer 142

• Biorhythms may be due to environmental or internal influences o Jean-Jacques d’Ortous de Mairan  Something in the genetic code that influences our internal clock  But there are also environmental influence- without environmental influence, internal clock gets distorted • This is as clock gets reset every day when the sun comes up: more precise measurement and calibration

Question 143

What are the two component processes of the circadian sleep cycle?

Answer 143

o Circadian sleep cycle has two component processes  Homeostatic sleep drive • Regulated by hormones • Cortisol decreases, melatonin increases  Circadian rhythm • Driven by suprachiasmatic nucleus • Influenced by light and environmental factors

Question 144

What is homeostasis?

Answer 144

• Homeostasis- the body maintaining balance around a set point o Works through negative feedback loop

Question 145

Describe the neural mechanism of sleep homeostasis

Answer 145

• Sleep homeostasis neural mechanism o Many hours of wakefulness-> Sleep-promoting chemical accumulates-> Sleep-> Sleep-promoting chemical is destroyed during sleep

Question 146

What is adenosine and how does it act? (release, results, effect...)

Answer 146

 Sleep-promoting chemical=adenosine • Adenosine accumulates during wakeful periods and decreases during sleep • Released by glia and neurons when low on fuel • Results in increased blood flow (more fuel) • Increases activity in the ventrolateral preoptic area • Promotes sleep

Question 147

Why does caffeine induce wakefulness?

Answer 147

• Caffeine blocks adenosine receptors (antagonist)

Question 148

How does the structure of mutual inhibition between sleep and wakefulness work? Describe the structures involved

Answer 148

• Mutual inhibition between sleep and wakefulness o Alert waking state activates brainstem and forebrain arousal systems (Ach, NE, 5-HT, Histamine)  Motivation to remain awake comes from orexinergic neurons in the lateral hypothalamus o Inhibited waking state leads to activation of sleep-promoting region in vPOA o vPOA and brainstem/forebrain arousal systems mutually inhibit each other

Question 149

What is the role of the suprachiasmatic nucleus and how does it do so?

Answer 149

• Suprachiasmatic nucleus (SCN) o Master internal clock o Governs circadian rhythms  If structure is damaged, circadian rhythms are impaired o Single-cell rhythmic structure during circadian rhythm  Different cells can run on slightly different cycles (shifted in time/phase) • Govern different processes o Intrinsically reset by projections from photosensitive retinal ganglion cells

Question 150

Are sleep patterns in mammals the same for every mammal?

Answer 150

• Large diversity of sleep patterns in mammals

Question 151

Describe the white-crowned sparrow sleeping patterns

Answer 151

o White-crowned sparrow |  Drop to 1/3 of their normal sleep during migration and catch up afterwards

Question 152

Describe the indus dolphin sleeping patterns

Answer 152

o Indus dolphin |  Will sleep for 7 hours a day but will perform micro sleeps (sleep for a few seconds at a time)

Question 153

Describe the amazonian dolphin sleeping patterns

Answer 153

o Amazonian dolphin |  Hemispheric sleep- sleep one hemisphere at a time

Question 154

What is the important of sleep?

Answer 154

* Sleep as an adaptative state * Hormonal function * Focus and memory * Immune function * Performing maintenance on brain * Emotional balance * Mental health

Question 155

Why is sleep considered to be adaptively important?

Answer 155

o Anticipate difficult periods (scarcity of food, mates, extreme environmental conditions) o Reduced metabolism, energy savings o Avoid risks (injury, predators)

Question 156

Describe an example of how hormonal function is affected by sleep

Answer 156

• Hormonal function | o Insulin action decreases if adequate sleep is not provided

Question 157

Describe an example of a task demonstrating how focus is affected by sleep

Answer 157

• Focus and memory o Psychomotor vigilance task  Reaction time task -how fast people respond to a visual stimulus  Over 2 weeks, there is accumulation of sleep deficit: those who have had little sleep over the two weeks become gradually worse at this task

Question 158

Describe an example showing that immune function is affected by sleep

Answer 158

• Immune function | o Effectiveness of hepatitis vaccine decreased when group denied sleep after vaccine- antibodies not produced as readily

Question 159

Describe an example showing the maintenance of the brain done during sleep

Answer 159

• Performing maintenance on brain | o Beta-amyloid plaque removal (that is linked to Alzheimer’s) during sleep

Question 160

Describe an example showing that lack of sleep disrupts emotional balance

Answer 160

• Emotional balance o Depriving people of sleep decreases memory for all pictures, regardless of emotional affect o However, sleep-deprived people remember negative memories more than positive memories

Question 161

Describe an example showing that mental health is affected by sleep

Answer 161

• Mental health o Depression and apnea are like (if you have apnea, you’re 6x more likely to be depressed)  Helping people get a better night’s sleep with CPAP reduces depression o Great sleep disturbances increase risk of depression

Question 162

Describe REM/non-REM sleep throughout humans' lifespans

Answer 162

• Sleep and types of sleep changes across the lifespan o Firstborns sleep about 16 hours a day, roughly evenly distributed between REM sleep and non-REM sleep o Teens sleep, little REM sleep but a lot of time in non-REM sleep o REM sleep decreases as we get older, but amount of non-REM sleep stays approximately the same

Question 163

What are the two main types of sleep and their main functions?

Answer 163

``` • Types of sleep- o REM sleep-  A part of sleep restorative to the mind o non-REM sleep-  Restorative to the body ```

Question 164

Describe the sleep cycle, its length and the general significance of each stage

Answer 164

• Sleep cycle stages (cycle lasts around 90-120 minutes) o Stage 1  Light transitional sleep (drowsiness begins) o Stage 2  More stable sleep- chemicals block in senses making it difficult to be woken o Stage 3  Deep sleep- growth hormone is released o REM sleep  Revitaliser memory- intense dreams occur

Question 165

What is N1 stage of the sleep cycle, what waves is it characterised by, what bodily changes accompany it and how long is it?

Answer 165

 Stage N1- non-REM sleep • Characterised by theta waves • Body temperature drops, muscles relaxed, eyes slowly pivot side to side • Characterised by slight loss of awareness of surrounding but can be easily awoken • Only a few minutes long

Question 166

What is N2 stage of the sleep cycle, what waves is it characterised by, what bodily changes accompany it and how long is it?

Answer 166

• Slow waves are intermingled with sleep spindles and k complexes o Sleep spindles- brain disconnects from sensory input and related to memory consolidation o K complex-when brain checks on exterior surroundings to ensure its safety  Built in vigilance o Eyes are still and heart rate/breathing continues to slow o Spend 10-20 minutes in this stage

Question 167

What is N3/deep sleep stage of the sleep cycle, what waves is it characterised by, what bodily changes accompany it and how long is it?

Answer 167

* Young people spend about 20% of their time in deep sleep * People over 65 rarely enter deep sleep * After sleep deprivation, people spend a greater proportion of time in deep sleep * Characterised by delta waves * Growth hormones will be released and immune system becomes activated (body maintenance period)

Question 168

What is REM stage of the sleep cycle, what waves is it characterised by, what bodily changes accompany it and how long is it?

Answer 168

 Facilitates learning and memory  People deprived of REM sleep lose these benefits  When deprived of REM sleep, the following night the brain will spend more time in REM (REM-rebound)  All muscles except for eyes flatline in terms of waves-> eyes should be the only muscle movement

Question 169

What is an example of a drug that can be used to avoid sleep? Should it be used?

Answer 169

• Modafinil o Seemingly able to stimulate restorative state  Helps to stay awake  Circumvent sleep o However, danger of addiction and increase of long-term sleeping needs  Need extra time to rest afterwards • Best not to avoid sleep using drug