Midterm 1 Material (start to Jan 24th)

How many neurons do human brains have?

roughly 100 billion

What is structural homology? What is it important?

because all animals emerged from a common evolutionary ancestor, evidence of our common heritage is still visible in the similar shapes of our bodies and brains (despite animals continually evolving and becoming different from one another)

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The existence of homologous brain structures in non-human animals can be helpful to psychologists, neuroscientists, and other researchers, because these animals can provide an approximate model of the human brain when research hypotheses cannot be directly tested on human participants.

* e.g. rodent models to investigate brain injuries

What is the vertebrate nervous system composed of? What are these divisions composed of?

1. Central NS (CNS)


1. brain
2. spinal cord
2. Peripheral NS (PNS)


1. somatic NS
2. autonomic NS


1. efferent nerves:


1. sympathetic NS
2. parasympathetic NS

What are the roles of the somatic NS and the autonomic NS? What types of nerves do both have?

SNS: interacts with the external environment

* afferent nerves: carries sensory signals in from the skin, skeletal muscles, joints, eyes, ears, etc into the CNS
* efferent nerves carrying motor signal from the CNS out to the skeletal muscles

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ANS: participates in the regulation of the internal environment

* afferent nerves carrying sensory signals from the internal organs to the CNS
* efferent nerves carrying motor signals from the CNS to internal organs

Generally, what do the words efferent and afferent mean?

afferent: towards

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efferent: away from

What role do sympathetic nerves play in the sympathetic NS? Parasympathetic nerves in the parasympathetic NS? How do they interact with one another?

sympathetic nerves: mobilise energy resources in threatening situations, usually via the adrenal glands

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parasympathetic nerves: act to conserve energy

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there is a balance between PS and S NS activity, both systems are active simultaneously

What is the law of bilateral symmetry?

law dictating that we have a left half of our bodies, and a mirror opposite right half of our bodies

How does the brain relate to the law of bilateral symmetry?

our brain is made up of 2 almost symmetrical halves called hemispheres, connected by a tract of neurons called the corpus callosum

What is ***contralaterality***? Is it seen in our brains?

for instance that the left side of your body is mostly controlled by the right side of your brain (and vice versa)

\-many of our brain’s functions exhibit this property

What is the telencephalon? What is its largest constituent?

it is the largest division of the brain

* contains the cerebral cortex

What does lissencephalic mean?

smooth brained

Define fissures/sulci and gyri

large furrows in the cortex

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gyri: ridges between the fissures

What is the largest of all fissues?

longitudinal fissure, separating the hemispheres

What connects the cerebral hemispheres?

a few tracts called the cerebral commissures

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largest: corpus callosum

how is the cerebral cortex usually divided?

4 lobes defined by 2 major landmarks

* central fissure
* separates the frontal from the parietal lobe
* lateral fissure
* separates the frontal and parietal lobes from the temporal lobe

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Name 3 major components of the limbic system

1. hypothalamus
2. amygdala
3. hypothalamus

Is it correct to refer to the limbic system as a true system?

no, based on an archaic view of the structures comprising it

What are the specialities of the lobes?

1. occipital lobe


1. vision
2. temporal lobe


1. hearing
2. learning
3. memory
3. parietal lobe


1. bodily sensations (touch, temperature, and pain)
4. frontal lobe


1. movement, planning, and motivation

Define the following anatomical directional terms:


1. anterior/posterior
2. dorsal/ventral
3. medial/lateral
4. ipsilatera/contralateral

1. **Anterior** – from *Ante* (before). Towards front. Synonymous with **rostral** (means beak)


1. **Posterior** – from *Post* (after). Towards back. Synonymous with **caudal** (means tail)
2. **Dorsal** – from *Dorsum* (back). Think of a shark’s dorsal fin.  Up or on top of. Synonymous with **superior**


1. **Ventral – from Venter (belly).  Down, below, or on the bottom. Synonymous with inferior**
3. **Medial** – from *Medius* (middle).  Towards the midline. Synonymous with **nasal** (means nose)


1. Lateral – from Latus (side).  Away from midline. Synonymous with temporal (means temple)
4. Ipsilateral – from Ipsi (same). On the same side of the body (e.g., right eye and right ear)


1. Contralateral – from Contra (against, opposite to) on opposite sides of the body (e.g., right eye and left eye)

What is the thalamus often defined as a relay system?

because much of the information sent to the cerebral cortex stops in the thalamus before being sent on to its destination

What comprises the thalamus? What does this indicate?

over 50 distinct nuclei, all having several functions

* indicates that the thalamus is much more than the sensory relay station it has traditionally been considered to be

What is the thalamus thought to play a role in high level cognitive functions?

this is indicated by it receiving most of its information from the cortex

Describe the name basal ganglia

basal: located at the base of the brain

ganglia: plural of ganglion, meaning cluster of nerve cells

What comprises the basal ganglia?

1. caudate


1. referred together with the putamen as the striatum
2. putamen
3. globus pallidus


1. made up of multiple nuclei
4. subthalamic nucleus


1. made up of multiple nuclei
5. substantia nigra

What main function do the structures in the basal ganglia conduct? is this their only role?

best known for their role in facilitating movement

* they do other things though!

What do the words striatum, caudate, and putamen mean?

striatum: means striped

caudate: means having a tail

putamen: means shell or shell like covering

Where is the nucleus accumbens found?

located in the basal forebrain, which is located near the front and bottom of the brain

What is the nucleus accumbens the major component of? Where is it situated in relation to other structures?

major component of the ventral striatum, situated between the caudate and the putamen

What is the nucleus accumbens usually divided into? What is a caveat to this?

1. outer shell


1. more associated with limbic system
2. central core


1. more strongly connected to the motor system

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\*NOTE this distinction is clearly seen in rodents, though is less evident in humans

What major function is the nucleus accumbens thought to be involved in? Where is this reflected

major function: reward system

* more complex than simple reward processing, functions still unknown

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connection to reward seen in its connections with the ventral tegmental area (VTA)

* dopamine neurons project from the VTA to the NA as part of the mesolimbic dopamine pathway
* pathway activated in association with rewards
* do not know the exact role NA plays in this, thought to play a role in learning about the rewards and stimuli associated with them
* also seems important for the pursuit of rewards and the selection of actions most likely to result in the attainment of rewards (and suppression of actions less likely to be useful)
* also seems to be important in processing aversive experiences, and learning to move away from an aversive stimuli
* thus: NA seems to be relevant for responding for all kinds of motivationally-relevant stimuli, whether rewarding or aversive

What does accumbens mean?

reclining or lying down

Discuss the role that the hippocampus plays in cognitive mapping

involved in navigation and memory (i.e. can navigate both time and space) has led to the suggesting that it allows for a more general kind of cognitive mapping by which we locate ourselves in time and space

\-memory tool: seahorse navigating space and time

What is the amygdala and where is it found?

collection of nuclei found in the temporal lobe

What is a common scheme for anatomically organising the amygdala?

1. basolateral region

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2. cortico-medial region

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there are other ways of dividing the amygdala as well!

What larger system is the amygdala part of?

limbic system

What functions is the amygdala thought to play?

* fear and threat detection
* when a threatening stimulus is present, involved in identifying it as a threat and activating a fight or flight response to it
* processing of positive stimuli
* challenges the idea of the amygdala as a threat detector
* may be involved with assigning positive or negative value to stimuli and assigning the emotional value to memories
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* it is also being investigated for a variety of other functions - e.g., addiction and social interaction

Describe how the amygdala is a key hub of memory systems

involved with memory alongside the hippocampus - associating events and places with good or bad things that happen

where is the primary somatosensory cortex located?

in a ridge of cortex called the postcentral gyrus, just posterior to the central sulcus

What is the primary somatosensory cortex responsible for? How does it do this generally?

processing somatic sensations (sensations from the body)

* touch
* proprioception- location of body in space
* nociception - pain reception
* temperature

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when a receptor detects one of these stimuli, the information is sent to the thalamus, and then to the somatosensory cortex

Describe the somatotopic arrangement of the somatosensory cortex

arranged so that each location receives information from a particular part of the body

\-more sensitive areas take a differentially large amount of space in the somatotopic arrangement

What is the motor cortex? Where is it located?

region of cortex in the frontal lobe involved with voluntary movement

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located anteriorly from the central sulcus

What are the 2 regions of the motor cortex?

1. primary motor cortex


1. found in the strip of cortex called the precentral gyrus (anterior to the central sulcus)
2. arranged such that different parts of the region are associated with motor control of different parts of the body - contain a motor map of the body (homunculus)
2. nonprimary motor cortex

Signals regarding movement will enter which pathways?

one of 2 pathways


1. corticospinal tract


1. carries movement related signals to the spinal cord to cause movement
2. corticobulbar tract


1. carries signals to the brainstem to control movement of the head, neck, and face

What is the nonprimary motor cortex divided into?

1. supplementary motor cortex


1. involved with the execution of sequences of movement
2. attainment of motor skills
3. selection of movements based on entering sensory information
2. premotor cortex


1. contributes about 30% of neurons
2. seems to be more active during the planning of rather than the execution of movements

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functions not well understood

What do association areas do? What are they?

associate simpler elements of cognition allowing for more complex ones, tuning our sensory experience to our needs (i.e. makes us not like frogs where we see a fly and then catch it)

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include:


1. regions of temporal and parietal lobes
2. prefrontal cortex

What is the prefrontal cortex thought to be important for?

1. planning
2. voluntary behaviour
3. inhibition of inappropriate thoughts and actions

Define executive function

Generally refers to exerting cognitive effort or controlling impulsive behaviour for immediate ends in order to act with a longer-term goal in mind

Where is the prefrontal cortex located?

part of the frontal lobe anterior to the motor cortex

What are the PFC subregions?

no universally agreed upon conception, though there are some reoccuring players

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1. dorsomedial PFC
2. ventromedial PFC
3. orbitofrontal PFC
4. dorsolateral PFC
5. ventrolateral PFC

What is the PFC most commonly associated with? How about it subregions?

executive functions

\-e.g. self control, planning, decision making, problem solving, etc

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we are not at the point where we can confidently assign specific roles to the PFC regions

* evidence suggests that the executive functions of the PFC are accomplished through the interaction of the subregions with one another and communication with other regions outside the PFC

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general model: receives sensory info, use it to plan responses, then communicates with other areas of the brain to enact a response

What is the PFC crucial for generally?

much of the conscious and active and intentional consideration that happens between stimulus and response

* planning, reasoning, rule based action, if-then logic, directing attention, calling up information when you are mad, inhibition, deferring gradification, etc

What is one of the OFC’s (orbitofrontal cortex) key function? What happens to those who suffer damage to this region?

key function: allow us to understand the relationship between a particular course of action and a particular outcome or result in a particular place or type of situation

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damage: can reason perfectly well but have a hard time applying that reason to their actions and making good or appropriate decisions

What is the ventrolateral PFC used for?

1. important for inhibiting inappropriate actions


1. inhibits thoughts that may not be helpful in a given situation

What is the dorsolateral PFC crucial for?

1. working memory - being able to hold and manipulate multiple things in mind


1. keeping track of a stream of names you are hearing
2. doing simple arithmetic
3. maintaining complex sets of rules
4. abstract thought

What brain region is important for understanding the consequences of sleeping through an exam, and trying to develop better sleep habits to be sure it doesn’t happen?

OFC

Which region is important for holding in mind the items on your shopping list , updating it as you put items in the cart, and choosing the specific item from the list that is our goal, depending on what aisle you are in?

DLPFC

What cortical region directs movement by controlling muscle contractions?

primary motor cortex

Describe how the way we conceptualise brain function has always been constrained by the methods available to study it

1. 19th century only had access to focal brain lesion studies, leading to the view that the brain is a collection of focal centers specialised for a particular set of cognitive abilities (e.g. Broca’s area)
2. 20th century developed neurophysiological recording techniques, leading to the neuron doctrine (idea that the functions of individual neurons can be extrapolated to explain the function of a brain as a whole)
3. 1980s had cognitive neuroimaging studies focusing on subtractive comparisons between cognitive tasks: led to the modular view of brain function involving localised and separable regions

Recreate P and F’s table 1 separating the different human neuroscience methods across the dimensions of strength of causal evidence and level of mechanism

jan 19th page 1

Evaluate the criticism that these correlative methods (e.g. functional neuroimaging) are purely correlative and uninformative about mechanism

* Only partly accurate
* When psychological processes are experimental manipulated, and result in a consistent measure of brain activity, we can infer that the brain activity was caused by the psychological processes
* We CANNOT though infer that the observed brain activity is causally responsible for the psychological process under study

What is TES? What is its most common variation?

* Transcranial electric stimulation (TES): current is delivered using external electrodes
* Most common variation: transcranial direct current stimulation (tDCS)

Contrast DBS to non-invasive brain stimulation

Non invasive brain stimulation affects larger and more superficial areas of the brain (compared to DBS), but researchers are seeking to improve spatial resolution with new magnetic coil shapes for TMS and electrode configurations for tDCS

* Pharmacological antagonist and agonists of particular NTsystems can also be used for experimental manipulation, though have imperfect specificity

What are some limitations with the fMRI signal?

1. We know a lot about the biological mechanism underlying the BOLD signal, but still much remains to be understood
* E.g. roles of specific glial and neuronal cell types in the coupling of neuronal activity to blood flow
* Lack of physiological understanding poses problems for fMRI interpretation
2. fMRI signals often correlate strongly with both action potentials (spikes) and local field potentials, though are largely reflective of post synaptic processes 
* This sensitivity to post synaptic processes as opposed to spiking has been seen as a drawback by some viewing spikes as the essence of brain function

briefly outline 3 examples of new approaches to understanding human brain function with fMRI that address questions of representation, computational processes, and network interactions across the brain

1. representational analyses


1. multi-voxel pattern analysis (MVPA)
2. representational similarity analysis (RSA)
2. integration of computational modeling and fMRI
3. functional connectivity analysis and resting state fMRI

What aspect lacking in neuroscience can be filled with representational analysis?

* Early neuroimaging focused on brain mapping: identifying regions based on the mental processes that cause them to be activated
* Provided a large body of associations between function and structure, but is lacking in answering how psychological functions are implemented

Describe MVPA

MVPA: involves the use of methods from the field of machine learning to decode or predict psychological states from patterns of brain activation across voxels

* E.g. reconstruction of visual scenes and faces from BOLD activity patterns
* MVPA also provides insights into neural organisation of cognitive functions
* E.g. attention changes both the representation of stimuli across regions of the visual cortex as well as the mutual information between regions

Describe RSA in contrast to MVPA

RSA: while MVPA is used to decode individual psychological states, RSA instead asks how the patterns of brain activity evoked by different stimuli are related to one another, provides means to answer questions of how mental representations are implemented in the brain

* Psychological theories often make predictions regarding the similarity of different stimuli, and RSA has enabled the directed testing of these theories
* E.g. how are categories represented

How are RSA and MVPA similar?

RSA and MVPA are equally useful for assessing representations spread across the brian (as well as representations in localised brain regions)

List some concerns with representational analysis

1. Interpretation of multivariate analysis
2. Electrophysiology and fMRI in non human primates has demonstrated that the sensitivity of MVPA is limited by the spatial characteristics of the neuronal representations that code for particular features (such that some kinds of neuronal patterns may be more difficult to decode using MVPA than others)
3. Cannot inform about causal mechanisms

Describe the advantage that integration of fMRI and computational modelling brings

Make assumptions explicit, enabling direct testing of theories as well as linking computations at the neuronal level switch higher order functions

What does P and F consider to be the most revolutionary development arising from human neuroimaging?

 realisation that the resting brain is far from quiescent, and that important insights into brain function can be gained by studying the correlated fluctuations of signals across the brain at rest

What insights have resting state neuroimaging brought?

1. Non-human mammals have shown similar activation during rest, suggesting a fundamental principle of mammalian brain organisation
2. Importance of these networks in brain disorders (e.g., default mode network playing a role in the memory deficits observed in alzheimer disease)
3. Resting state providing insights into border functional organisation of the brain
* Components extracted from resting state data show a high degree of concordance with those extracted from task based data

What are some limitations with network connectivity analysis and resting state scanning?

1. Concerns over head motion and other physiological fluctuations influencing estimates of resting state connectivity
2. Concerns whether common data analytic methods may induce systemic artefacts
3. Light sleep may drive differences in resting state signals
* Unconstrained nature of resting state is a double edged sword

Broadly list some applications of human neuroscience

1. brain disorders
2. prediction of behaviour
3. human neuroscience in the courtroom

Specifically describe the applications of human neuroscience in brain disorders

1. psychiatric disorders
* Psychiatric disorders are exclusively diagnosed by behaviours signs and symptoms, which do not have clear relations to the biological processes that would be targeted by new medical treatments
* Alternative way of systematising psychiatric disorders has been developed: NIMH research domain criteria (RDoC), describing disorders according to impairments in specific functional systems of the brain and at different levels of mechanism (e.g. molecules or circuits)
2. Genetic association studies to identify sets of genes associated with a disorder, together may indicate particular molecular pathways underlying the disorder
3. Biomarkers for neurological diseases

Specifically describe the applications of human neuroscience in predicting behaviour

1. Neuromarketing: using brain activity as an indicator of what consumers want over verb al reports
* Also can be used for public service announcements (e.g. brain responses to an anti-smoking ad were predictive of subsequent call volume to an anti smoking hotline)
2. Neuroimaging predicting educational outcomes, academic skills, criminal recidivism, etc
* Enable more appropriate interventions to address individual children's reading and math difficulties?

Specifically describe the applications of human neuroscience in the courtroom

1. Criminal responsibility: proving that a criminal act may have had a neural cause is not itself exculpatory, as every human act is caused by the brain
* Neuroscience can provide evidence of mental dysfunction (e.g. tumour), immaturity, or other psychological grounds for reduced criminal responsibility
2. Determining degree of responsibility
* E.g. lie detection
* Has not been admitted yet into US courts, yet to establish validity
* E.g. brain based biomarkers for pain, helping to discriminate real suffering from malingering
* Admitted in at least one US case

What are some new imaging and manipulation technologies?

1. fMRI will probably remain the principle neuroimaging method in humans for the foreseeable future, but ongoing BRAIN initiative in the US is providing substantial funding to develop entirely new techniques for imaging of brain function
2. New developments of fMRI have increased the utility of standard MRI systems

* E.g. multiband imaging techniques increased temporal resolution
* E.g. higher MRI field strengths increase spatial resolution


1. Study of postmortem brains
* New techniques have enhanced the ability to visualise the structure of human brain tissue
* E.g. optical coherence tomography has been used to image ex vivo human cortical tissue
2. Connectomics:
* Human connectome project: providing a rich database for the modelling of functional and anatomical connectivity of the human brain
* Fundamental challenges remain
* E.g. diffusion MRI tracks white matter pathways, but has inherent biases limiting its ability to accurately track connections across the entire brain

What about neuroimaging research makes reproducibility especially important?

1. High dimensionality of the data
2. Relatively low statistical power for many studies
3. High degree of analytic flexibility in data analysis procedures
4. Potential for questionable research practices

What specific types of questions can the use of MVPA and RSA address?

discussion question, write out an appropriate response

What role can computational modeling play in our understanding of the relationship between cognitive and brain functions?

discussion question, write out an appropriate response

Deficits in a cognitive function observed in a patient or group of patients with brain damage to a network/region allow us to infer that the network region is _________ the cognitive function.

necessary for

Lesion network mapping allows researchers to identify networks from individual patients, each with a lesion in one of a set of ______________ regions.

functionally linked

In studies of lesions either found or made, we measure _________ to assess the function of parts of ________

behaviour, the brain

EEG waves measured at the scalp reflect the output of

large columns of cortical neurons

Event-related potentials are EEG waves that are:

Averaged signal across many trials

ERPs are useful for telling you

When in time a process occurs

Breaking the EEG signal down into different frequency bands allows us to measure

Whether cells in distant regions are communicating by oscillating in synchrony

MEG is somewhat better for modeling the sources of the activity you measure at the scalp than EEG because

Magnetic signal is not distorted by the skull

Which is not a strength of intracranial EEG?

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* non-invasive
* spatial resolution
* temporal resolution
* no distortion by skull and scalp

spatial resolution

What causation can you infer while brain imaging?

experimental manipulation causes brain activation

* but you cannot say that brain activation causes psychological process

How does a structural MRI work?

* protons in nuclei of hydrogen atoms in water naturally ‘vibrate’ (resonate) when the direction of a magnetic field is suddenly changed
* different tissues alter the resonance to produce images of white and gray matter, and CSF
* able to produce very good spatial resolution anatomical or structural images

How does a functional MRI work?

* when a part of the brain is active, it requires more oxygen, and thus more oxygenated blood is delivered
* this affects the blood’s magnetic properties, which affects the brain’s magnetic signal
* this difference in magnetic signal is measured by fMRI
* BOLD: magnetic properties associated with changes in the ratio of oxygenated to deoxygenated blood

What is the BOLD response?

blood oxygen level dependent response

* DV of an fMRI study
* NOT a direct measure of neurons firing

What are the strengths/limitations of fMRI

strengths

* good spatial precision
* non invasive

limitations

* expensive
* poor temporal precision
* indirect measure of brain activity
* correlational relationship between activation and cognition

Contrast encoding and decoding in fMRI analysis.

encoding (standard analysis): ‘brain mapping’, using a stimulus or experimental task and measure activity that is evoked

* e.g., voxel wise analysis
* ALWAYS a contrast of activity between conditions

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decoding (representational): look at the brain activity to predict what the stimulus or cognitive process producing it is

What is a voxel? How large are they?

voxel: volumetric pixel

* these are the units composing MRI and fMRI images
* voxels can be different sizes, though \~150,000 in a whole brain

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Describe how BOLD data is related to voxels

BOLD data is collected in slices and volumes

* these are chopped further into cubes or voxels
* fMRI: BOLD activation level for every brain voxel

What is the focus of the standard fMRI analysis (encoding)? What question does it ask

focuses on discovering regions responsible for basic mental processes

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question: what regions of the brain are involved in a given cognitive process

What is voxel wise analysis? What does it give you?What type of fMRI analysis approach is it?

where you:

* look at every voxel in the brain and run a statistical analysis (regression) for every voxel
* this produces a map of voxels with BOLD activation over statistical threshold
* that’s up to 150,000 statistical analyses!

gives you:

* average BOLD activation for each voxel across trials in each condition
* measures the difference between conditions (e.g., voxel activation when seeing faces versus houses)