T11

Question 1

Neural encoding

Answer 1

Neural encoding is how the brain transforms external stimuli into patterns of neural activity. Goal: To understand how the brain processes sensory information to drive perception, cognition, and behaviour.

Question 2

How do neurons propagate signals?

Answer 2

Neurons propagate signals rapidly over large distances generating characteristic electrical pulses called action potentials->voltage spikes that can travel down axons.

Question 3

Sensory neurons change their activities by

Answer 3

Sensory neurons change their activities by firing sequences of action potentials in various temporal patterns external sensory stimuli-> light, sound, taste, smell, and touch.

Information about the stimulus is encoded in this pattern of action potentials and transmitted into and around the brain

Question 4

In order to describe and analyze neuronal firing,

Answer 4

statistical methods and methods of probability theory and stochastic point processes have been widely applied.

Question 5

With the development of large-scale neural recording and decoding technologies,

Answer 5

researchers have begun to crack the neural code and have already provided the first glimpse into the real-time neural code as memory is formed and recalled in the hippocampus, a brain region known to be central for memory formation.

Question 6

The link between stimulus and response can be studied from two opposite points of view.

Answer 6

Neural Encoding: refers to the map from stimulus to response. The main focus is to understand how neurons respond to a wide variety of stimuli, and to construct models that attempt to predict responses to other stimuli. Neural

Decoding: refers to the reverse map, from response to stimulus, and the challenge is to reconstruct a stimulus, or certain aspects of that stimulus, from the spike sequences it evokes

Question 7

Recording the neural response from a single neuron involves

Answer 7

measuring the electrical activity of that neuron, typically in response to a stimulus.

Question 8

Intracelullar recording

Answer 8

Intracellular Recording: A microelectrode is inserted into the neuron to measure the membrane potential.
Observe the electrical activity, including action potentials and subthreshold potentials High precision in measuring the neuron’s actual membrane potential.
It is invasive and typically works only on cells that are large enough for the electrode insertion without damage.

Question 9

Extracellular recording

Answer 9

Extracellular Recording: The electrode is placed just outside the neuron to detect the flow of ions (usually sodium) when an action potential occurs.
This method primarily records spikes (action potentials) rather than the full membrane potential changes.
Less invasive than intracellular recording, making it more suitable for long-term recordings.
It’s harder to determine the exact neuron that is firing when many neurons are near the electrode.

Question 10

Patch Clamp Technique

Answer 10

Patch Clamp Technique:
A glass pipette electrode forms a tight seal with the membrane of the neuron (patch) to measure current flow through ion channels.
Ion channel activity at a very fine scale, which can be used to study synaptic responses or membrane properties in detail.
High-resolution recording of ionic currents; can record small currents that other methods might miss.
Technically demanding and typically limited to in vitro or ex vivo recordings.

Question 11

Recording Configurations (cell attach)

Answer 11

Cell-attached: The pipette remains attached to the membrane patch without breaking through it-> recording of ion channel activity in the membrane patch itself.

Question 12

Recording Configurations (whole cell)

Answer 12

Whole cell: The membrane patch within the pipette is ruptured, allowing the pipette to access the cell’s interior. This lets researchers measure the entire cell’s ion currents

Question 13

Recording configurations (inside-out and outside-out)

Answer 13

Inside-out and Outside-out: After creating the giga-seal, the membrane patch can be excised (pulled away from the cell). In the inside-out configuration, the cytoplasmic side of the membrane faces outward. In the outside-out configuration, the extracellular side faces outward, which is useful for studying how channels respond to extracellular signals.

Question 14

Recording electrical signals

Answer 14

Recording Electrical Signals: A highly sensitive amplifier detects tiny currents, sometimes as small as a few picoamperes (pA), flowing through the ion channels

Question 15

Neurons respond to stimulus with train of spikes
Response varies from trial to trial:

Answer 15

Arousal, attention
Randomness in the neuron and synapse
Other brain processes

Question 16

Statistical description (stimulus to response)

Answer 16

Fring rate
Correlation function
Spike triggered average
Poisson model

Question 17

Spike analysis

Answer 17

Process for understanding how neurons communicate through action potentials, or “spikes.” This analysis helps to reveal patterns of neural activity, connectivity, and responses to stimuli. Below is an overview of the key concepts, methods, and metrics involved in spike analysis:
This is an active area of study known as neural encoding->Scientists hope to identify neurons that activate specific behaviours, such pain.

Question 18

Using standard electrophysiological techniques,

Answer 18

Using standard electrophysiological techniques, one can record the response of the neuron to each stimulus.

Question 19

Electrophysiology

Answer 19

Electrophysiology is the study of the electrical properties of biological cells and tissues. In neuroscience, it is used to record action potentials. There are fundamental methods to analyze spike trains of single neurons, which aim to characterize their encoding properties.
These techniques are raster plots, peri-stimulus time histograms, and tuning curves
Action Potentials (Spikes): Neurons communicate by generating action potentials, which are brief, rapid changes in voltage across the neuronal membrane.
These “spikes” are the fundamental signals measured in electrophysiological recordings.
Spike Sorting: When recording extracellular signals, the electrode often captures spikes from multiple neurons. Spike sorting is the process of identifying and distinguishing the spikes from different neurons based on their shapes and other characteristics.
Spike Train: A spike train is a series of spikes from a single neuron over time. The timing and pattern of spikes in a train can encode information about stimuli or the neuron’s role in a network.

Question 20

Peristimulus time histogram (PTH)

Answer 20

To analyze the timing and frequency of spikes (action potentials) of neurons relative to a stimulus event. The goal is to determine how neuronal firing rates change over time, typically in response to repeated presentations of a stimulus.
To capture how the average response of the neuron varies with some sensory or motor feature
you can generate a tuning curve that maps the feature value onto the average response of the neuron.
X-Axis (Time Relative to Stimulus): Time is aligned to the onset of the stimulus, and the axis represents the time before, during, and after the stimulus
Y-Axis (Firing Rate): This represents the number of spikes per time bin, averaged across multiple trials or neurons.
The bin size can vary depending on the resolution required.
Stimulus Alignment: All spike times are aligned with respect to when the stimulus occurs. This allows the extraction of patterns or changes in neural activity that correlate with the stimulus.
Averaging Over Trials: By averaging the neuronal responses over several repetitions of the same stimulus, the PSTH helps to smooth out noise and highlight consistent patterns.

Question 21

Time zero

Answer 21

Time zero (0 ms):stimulus is presented. It’s the reference point, and time is measured relative to this moment.

Question 22

negative time values

Answer 22

Negative time values (before the stimulus):Time values that are negative represent the period before the stimulus is applied->to see if the neuron shows any baseline activity or preparation behavior leading up to the stimulus. For example, a negative time of -100 ms means 100 milliseconds before the stimulus onset.

Question 23

positive time values

Answer 23

Positive time values (after the stimulus):After the stimulus is applied (i.e., after time zero), time moves into positive values, and the PSTH shows how the neuron responds to the stimulus over time.
The neural spike times from multiple trials are gathered.
These spike times are binned into time intervals.
The number of spikes in each bin is calculated and averaged across all trials.

Question 24

Histogram and Kernel methods

Answer 24

Histogram and kernel method-> standard tools for capturing the instantaneous rate of
neuronal spike discharges in Neurophysiological community.
These methods are left with one free parameter that determines the smoothness of the estimated rate, namely a binwidth or a bandwidth.
In most of the neurophysiological literature, however, the binwidth or the bandwidth
that critically determines the goodness of the fit of the estimated rate.

Question 25

Tuning curves

Answer 25

a graph of neuronal response (usually measured in action potentials or spikes per unit time) as a function of a continuous stimulus attribute, such as orientation, wavelength, or frequency.
Spikes->langages neurons speak->which information they Covey?

Experiment-> Monkey visual cortex-àspikes->computer that collects the spikes
In front of the mouse, there is another computer that shows images
Systematic way to represent how the stimuli represent a set of spikes
Different stimuli, images-àhigh contrast bars at different angles–àthe parameter is the angle
2 second simply changing the angle of the image, measuring how many spikes 🡪 repeat this many trials stimuli a system

Question 26

Single cell recordings

Answer 26

Single-cell recordings
Single-cell recordings allow to determine what experimental manipulations produce a consistent change in the response rate of an isolated cell:
Does the cell increase its firing rate when the animal moves its arm?
Does the firing rate for that movement depend on the outcome of the action?

Question 27

raster plots / multiunit recordings

Answer 27

Raster plots show the timing of action potentials
Multiunit recordings: recording many neurons simultaneous

Question 28

Electroencephalography (EEG)

Answer 28

test that measures electrical activity in the brain using small, metal discs (electrodes) attached to the scalp
High temporal resolution
Low spatial resolution
Cheap
Non-invasive

Provides a continuous recording of electrical activity of a group of synchronic neurons and not single neurons, primarily at the cortex. It measures post-synaptic potentials

Provides a continuos recording of electrical activity
Frequency
Amplitude Shape
Measures during an event (task) or spontenous

Waves properties:
-Frequency(Hz): number of cycles per time (how fast?)
-Power(Amplitude2): (how strong?)
-Phase(radians): where the wave is in each moment (where?)

Question 29

Frequency tagging (FT) :

Answer 29

Frequency tagging is an EEG method based on the quantification of the steady state visual evoked potential (SSVEP) elicited from stimuli which flicker with a distinctive frequency…

Question 30

Time frequency:

Answer 30

Time-frequency (TF) analyses can better characterize the temporal dynamics of three of the features of oscillations contained in the EEG data: frequency, power, and phase

Advantages
Low cost
Measure brain activity in the order of ms

Disadvantages
Measures big group of neurons, poor spatial resolution
Activity in the cortex but difficult to get deeper into the brain

Clinical applications
Epilepsy 🡪 characterise seizures
Monitor sleep disorders
Other brain disfuctions

Question 31

Magnetoencephalography

Answer 31

MEG provides the same temporal resolution as with ERPs, but it can be used more reliably to localize the source of the signal.
Instead of electrical signal register the magnetic fields that are perpendicular to the current. It has two limitations:
can detect current flow only if that flow is oriented parallel to the surface of the skull
the magnetic fields generated by the brain are extremely weak

All the analysis described for EEG can be done with MEG: ERPs (even related field), time frequency, connectivity…

Question 32

Magnetic Resonance Imaging (MRI)

Answer 32

It applies magnetic fields and radio-frequency pulses to the brain Protons of the hydrogen atoms respond by emitting energy
The MRI machine detects the magnitude and localization of these signals
The final image is reconstructed
Differences between tissues
Applied to every single voxel to characterize itscomposition
Neurons do not have internal reserves of energy in the form of sugar and oxygen 🡪 need constantly a blood supply 🡪 This causes a change of the relative levels of oxyhemoglobin and deoxyhemoglobin (oxygenated or deoxygenated blood) that can be detected on the basis of their differential magnetic susceptibility.
It measures the metabolic demands instead of neural activity directly (oxygen consumption)
- Non-invasive
- High spatial resolution
- Low temporal resolution
- Depends on blood flow
Functional MRI (fMRI) àBold signal (blood oxygenation level-dependent)
Structural MRI (sMRI)
Diffusion tensor imaging (DTI)

Question 33

Functional Magnetic Resonance Imaging (fMRI)

Answer 33

Essence of MRI technique
Functional technique that allows us to measure metabolic changes in the brain 🡪 Infer neural activity changes
fMRI detection of differences between Oxyhemoglobin (O-blood) vs Deoxyhemoglobin (Blood Oxygenated Level Dependent, BOLD)
Reconstruct the image of brain regions being active at every time point

Question 34

Diffusion Tensor Imaging (DTI)

Answer 34

Variant of MRI that is used to study white matter structures of the brain
Water tends to diffuse in all directions randomly over time and equally in all directions (random walk)
Water tends to diffuse more in the direction of the axon than perpendicular to it
Myelin of the axons creates a lipid boundary which accentuates this

Question 35

Positron Emission Tomography (PET)

Answer 35

PET measure local variation in cerebral blood flow related to mental activities. A radioactive tracer is introduced in the bloodstream and is followed with a gamma ray detector.
Tracer injected into the blood stream 🡪 Tracer is a molecule that travels and binds depending on the affinity
Tracer = Isotope 🡪 positron + e- 🡪 gamma ray 🡪 PET scanner Frequent tracer
F-FDG (glucose agonist) 🡪 tumor detection
15O: + presence of tracer = + blood flow = + neural activity

Question 36

Computed tomography (CT)

Answer 36

CT scanning is based in X-rays and allows for the reconstruction of three –dimensional space from compressed two dimensional images
Based on X-rays
Non-invasive
Fast
Cheap
Less spatial resolution than Magnetic Resonance
Very used in clinical cases

Question 37

Transcranial Magnetic Stimulation (TMS)

Answer 37

Is a methodology that allow to stimulate the brain cortex in a non-invasive way
Limitations:
The stimulation is brief
Low spatial resolutio
Restricted to cortex
In repetitive transcranial magnetic stimulation (rTMS), an electromagnetic coil placed against the scalp creates a magnetic field that stimulates certain areas of the brain> activates regions of the brain that have decreased activity during depression
🡪 Cause “temporal virtual lesions”

Question 38

Somatosensory evoked potentials (SSEP)

Answer 38

Presynaptic and postsynaptic responses are recorded over the limbs, spine, and scalp following the stimulation of peripheral nerves
Allow to evaluate the integrity of the pathway and to find where is the lesion
Both sensory and motor evaluation