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ECE410-ECENeuroScience-S22

ECE-410/NE-410 Weekly Schedule Spring 2022

Part I: Lectures, Reading assignments + videos: Calendar Weeks 4-6: Video Index I
WeekMWF
3Martin Luther King Day
L1: Read: \(\ \S \) 1.1 (Preface: pp vii-x; Ch 1: History pp 1-8);
2021 360 Lec 1 (Starts @6:00 mins)
L2: Read: \( \S \) 1.2 (p. 8-11); 2021 360 Lec 2 (Starts @14:00 mins)
4L3: Read: \( \S \) 1.3 (p. 11-19); \(\S\) 9.1 p. 187-104; 2021 360 Lec 3
L4: Read:Scott Ch. 12, \( \S \) 12.1 (p. 293-298); Network Postulates
Assignment: NS1: Due by Lec 11; (NS1.pdf, pp. 150-151
Allen (2020); Solution: (NS1-sol.pdf); 2021 360: Lec 4
L5: Read: 2.1, .2 (p. 25-31, 189, 208); Generic neurons (Scott: Fig. 2.1);
2021 360: Lec 5 (@2:15m)
5L6: Read: 2.2.2-.3 (p. 31-35) Nonlinear Diffusion lines 360 Lec 6
L7: Read: \(\S\) 2.3 (p. 35-40) Synapses & Gap junction;
2021 360 Lec 7 (@1:00m)
L8: Read: \(\S\) 10-.1.2 AI models: (pp. 233-241), Neural Boolean Hilbert-space;
Discuss how solve NS1 problems; 2021 360 Lec 8 (@4:00 m)
6L9: Read: \(\S\) 10.2 (p. 241-248), 2021 360Lec 9 (@0:37m)
L/WDDateDaily lectures
    Part I: Introduction and History
1/3W1/19L1: Introduction to Neuroscience for engineers; The role of H. von Helmholtz; Younger years, Dynamics of a Nerve Impulse,; von Helmholtz; history,
Virtual Rat:, computational models;
Thermodynamics of the Lungs (hypertension): SpO2, CO2 and O2 lung transport models + Basics; A piece of thermodynamic history; Heart Rate vs Mortality Source of Hypertension; Theory of Hypertension; Arterial Pressure model
2F1/21L2: The structure of a nerve cell Brain anatomy; Body, Neuron Glia, DNA and Genetics, Quanta Magazine articles, #1
3/4M1/24L3: Dendritic trees \(\S\) 9.0, p. 187; Organization of the brain; Numbers and density of neurons in the human brain (p. 274); McCullochPitts.43.pdf;
AI and brain waves; The making a brain map
4W1/26L4: The Hierarchical Nature of Brain Dynamics; Integration of the 5 main sensory inputs; Brain fumction and integration Orexin & the Theory of weight gain/loss
Assignment: NS1: Matlab homework on the diffusion and wave equations. Due by Lec 11; (pdf), Postulates
For a discussion of the solution method look at Book; \(\S\) 4.8.3 (pp. 143-147). A detailed example is discussed on pages 149-151;
5F1/28L5: The generic neuron; Action potentials; Voltage-gated membrane channels; Neuron, Body
Σ-∆ codec, png
6/5M1/31L6: Nonlinear diffusion model General solution ;NL-RC Neural Spike model (.cir); , using spice [.asc]; Input & Mylin Voltages
The nonlinear diffusion line and why it acts as a delay line, Diode circuit model of spike propagation, Results from circuit model
Results of LT spice model from William Walters (HW6 4/6/21)
Leading edge models: Chap. 5, p. 95;
NGspice users manual (pdf)
7/5W2/2L7: Chemical synapse, gap junction, Neuron, Body, types of Neurotransmitters; Neuropeptides; oral Ketamine uses
8/-F2/4L8: McCulloch-Pitts (MP) AI neuron (model), \(\S\) 10.1.1-.2: (pp. 235-241) Boolean Hilbert space;
Dendritic Boolean logic;Generalized scalar products (Allen book \( \S \) 3.5.1, Fig 3.4); Just how smart is AI?; AI-Transformers, Basic brain anatomy, (pdf)
(M-P model; pdf); How do AI models work?); Water on Mars (@7:02); The beginning of live on earth
9/6M2/7L9: Deep-learning concepts: STFT and fast convolution; ConvNetJS discussion, Sejnowski.20.pdf
Assignment: NS2 (pdf, (sol), Gscope, Due by Lec 14
Part II: Lectures, Reading assignments + videos: Calendar Weeks 6-11
WeekMWF
6
L10: Read: \( \S \) 3, 3.1 (p. 49-53) 360 Lec10
L11: Read: \( \S \) 3.2 (p. 53-55) Solution: (NS1-sol.pdf) 360 Lec 11
7L12: Read: \( \S \) 3.3 (p. 56-57) 360 Lec 12 (@1:25 min)
L13: Read: \( \S \) 3.3.3 (p. 58-60) 360 Lec 13 (Starts @ 2:30 12:19--13:19)
L14: ''Read: \( \S \) 3.4 (p. 60-63) Membrane models 360 Lec 14 (@1:30); NS2 due; (sol),
8L15: Exam I
L16: Read: \( \S \) 3.5 (p. 63-65) Na & K pumps and Nernst potentials 360 Lec16 (@3:00)
L17: Read: \( \S \) 4.1, (p. 67-69) 360 Lec 17
9L18: Read: \( \S \) 4.1-4.2 (p. 70-74) 360 Lec 18
L19: Read: \( \S \) 4.3 (p. 74-77)
L20: Read: \( \S \) 4.4, 4.5 (p. 77-80) Lec 20 (@2:20)
10L21: Read: \( \S \) 3.4, 4.5.2, 4.6, (p. 80-87) Figs 4.5-4.8 360 L21
L22: Read: \(\S\) 4.7 Matlab similink 2-Diode model, 360 (Topic\(_1\) @0:50, Topic\(_2\) @36:40, T\(3\) @39:00); NS3 due
L23: Moved Exam II to Lec 28
L/WDDateDaily lectures
    Part II: Structure of a Neuron
10/6W2/9L10: Lipid bilayers and their electro/mechanical properties Lipid bilayers, Transport mechanisms, Fun with bubbles, AI and protein folding
11F2/11L11: Electrochemical properties of membranes; hemoglobum and oxyen transport; See Hill Equation in biochemistry;
Blue whale's heart rate
Assignment: NS1 due, Solution: (NS1-sol.pdf)
12/7M2/14L12: Transmembrane currents; Channels & types; Calculating partial pressures (It is an impedance calculation.)
13W2/16L13: Einstein's relation (1905-III) and the derivation Four 1905 papers (@ Princeton.edu), Basic Solutions, Numerical solutions;
System Postulates.pdf
14F2/18L14: Review for Exam I NS2 Due; NS2 Solution
15/8M2/21L15: --NO CLASS-- Exam I: 3--5 PM Rm. 2017 ECEB Next year:Move Exam I to Lec 23;
Compress/combine/reduce Lec 16-22; More on brain Assemblies (Ch 11); eye & ear & touch transduction
16W2/23L16: Ionic currents (conduction, diffusion currents), electrochemistry
Assignment: NS3 pdf, Due by Lec 22 NS3 Solution
17F2/25L17: Redox Resting potentials and pumps HH matlab model; Helmholtz measures velocity of spikes
18/9M2/28L18: Ch. 4,Hodgkin Huxley model: U Mich.s; Fine-tuning the HH model to work off the spike rising onset; HH model (matlab code);
Ion distribution during a spike; Neural oscillators
19W3/2L19: Squid Voltage patch clamp for single cell recording; Adrian and nerve pulses first neural recording from toad eye (1928)
20F3/4L20:Critical point in nonlinear diffusion (cable) equation Muscle dynamics, Neurological disorders, Guillain-Barre syndrom, Demylination disorders; Talk on neural regeneration Jan 25, NSP
21/10M3/7L21: Nodes of Ranvier; Krebs cycle as the energy source;
22W3/9L22: Read:\(\S\)9.1 (187-199, Fig. 9.1) Spike models @3m; Myelin-Sheath @11m; Information processing: \(\S\)9--9.2: @33:40m; @49 bifurcations;
23F3/11L23: Review sol to NS3; Moved Exam II to Lec 28Read: \(\S\)10 (p. 233-241); 360 Lec 25 @2:25; topic II: @38:25
NS3 due, NS3 Solution
-/11MWF3/14Spring Break

Part III: Lectures, Reading assignments + videos: Calendar Weeks 12-17
WeekMWF
12L24: 360 Lec 26 (@1);
Read: Donald Hebb \(\S\)11 (pp. 17-19);
L25: (360 L27 @3:00);Read: Cell-Assembly, \( \S \) 11-.3 (pp. 257-265) of word frequencies;
L26: Cell-Assembly and language hypothesis;
13L27: Zipf's log-linear Law; Brief review for Exam II
L28: Exam II
L29: (360 L28 A(@0:48); B(@11:30);
Read: \( \S \) 10-10.1.1 (233-237), 11-11.2 (256-265)
14L30: Hypertension and its source: 360 L29 (@0)
Read: \( \S \) 9.3.2, 10.1.2, 11.3: Dendritic Boolean logic
L31: L30-360 (2021); Mayfield Brain Anatomy (pdf); cortex anatomy
Read: \( \S \) 10.2.2 (241-248)
L32: Molecular Transport; Protein creation;
L34-360: (2021): Discovery of DNA and RNA;
L33-360: (2022) Thalamus, L32-360: (2021) (@0:25), Hippocampus,
L31-360: (2021) (@4:25) Topic: Brain anatomy;
Read: \( \S \) 9.3, 10.3 (248-252)
15L33: L35-360 S21: The eyes and ears (@3:15m)
Ch 5: Frog vision;
L34: Overview of Sensory systems (Hearing)
L36-360 S21: Hearing (@1:00),
L35: L37-360: Cochlear Transduction
16L36: The inner ear and its function; Cochlear nonlinear processing (@2min),
NL Cochlear processing (pdf), Ashmore Lecture
L37: Organ of CortiL38: Cochlear nonlinearities and its function
17L39: Sensory systems; Vrius; Crisper (360 S21: Audio starts @ 22m)
Read: \( \S \) 8.0-8.3 (165-169));
L40:Last lecture 360 S21 (@1m)
AI's furure, AI darkside; Conscious;
Short term memory
Assignment: NS7 Due
Thur: Reading Day;
Friday: First day of Exams
L/WDDateDaily Lectures
    Part III: Neuronal & Cell Assemblies
24/12M3/21L24: Information processing; Dendritic information processing; Dendritic logic processing (Ch 9; State machines & Branching rules in dendrites); Cell assemblies: Recent Evidence; gap junction disorders, proteins; EM micrographs
Synaptic processing videos: Neural computation power, How brains learn, How networks learn: (Audio podcast 163): (no video) @1:00; Synaptic Information processing (Audio podcast 148): @0:16 (no video),
Backpropagation Methods for machine learning:; Hinton's BackProb Training algorithm;
Assignment: Due by Lec 28; (NS4.pdf; NS4-sol.pdf)
25W3/23L25: (-->L27) Energy sources; mitrohcondrial membrane; Rebooting how cells remember structure: Levin lecture @4:39m; Levin: New Yorker article on his regeneration research:
26F3/25L26: (-->L25) Early Evidence for Cell Assemblies (Hebb) Neural Syntax: Realizations of Hebb's Cell Assemblies: Language Hypothesis; Brain facts
27/13M3/28L27: (-->L26) Zipf-Model, MaxEnt-model; Zipf's log-linear and the Brown Corpus; Zipf's word Brevity-law Raven IQ test
28W3/30L28: Exam II: NS3, NS4, Historical events
29F4/1L29: L29: Hyppocampus and memory; Neurosurgry of the brain; Spatial orientation,
Measures of inntelligence (IQ): Raven's Progressive Matricies
Mental images; Induced love between mice Limbic System
Assignment: NS5, Due on L32 (pdf, NS5-sol)
30/14M4/4L30 Role of vital signs: How the heart rate is regulated by the body (video),
Heart Rate vs Mortality, Source of Hypertension, Kosinski-Theory of Hypertension-I (2018), Kosinski-Theory of Hypertension-II (2018), Arterial Pressure model;
31W4/6L31: A:Brain Anatomy; B:Field Theories for the Neocortex \(\S 9.3\); Models of Brain Anatomy (Dynamics I-II)
Friston Predictive model, claustrum Limits of brain and muscle; Senses of Orientation (NIH); Allen Inst: 12 easy pieces: sentory systems; Allen Inst Brain Atlas;
Allen Inst Home Page; Start @ 6 min; Lung alternatives;, Where does thirst come from? The Chinese room argument
32F4/8L32: Molecular transport: DNA information processing video, comments, RNA information processing video Momecular motors: Now they work,
Switching attention in the brain: Central manimpulation of DNA to enhance memory Michael Halassa: Thalamic Switching, Michael Halassa: Talk @ Allen Inst;
Rubisco: The enzime for life;The makeup of a virus: vurlient DNA, What is a virus;
33/15M4/11L33: Elements of sensory systems:Psychophysics of sound; Associative Network; Information processing;
Assignment: NS6 due on Lec 37 (pdf); NS5 Due
34W4/13L34: Overview on hearing: Speech and hearing science: Loudness and its JND; Sense of Touch and Heat; electronic odor (smell) sensors;
Jeremy Nathans: A complex speech task explained'; Fungi that explodes ants; Metathesis molecular metathesis synthesis
35F4/15L35: Topics on hearing: Speech and hearing science: The middle ear: Window to hearing ;
Effects of Negative Middle Ear Pressure on Wideband Acoustic Immittance in Normal-Hearing Adults, pdf
Otitis Media & hearing loss
36/16M4/18L36: Topics on hearing: Speech and hearing science: The inner ear (cochlea); Cochlear modeling,
37W4/20L37: Auditory systems: the organ of Corti, hair cell transduction, Allen (1980) "Cochlear micromechanics: A physical model of transduction"; Fahey & Allen 1985 (pdf);
Mouse auditory brain map, How we can see with our ears., Speech Development in infants; An example of auditiory (neural) signal processing
38F4/22L38: Topics on hearing: Cochlear nonlinear in the auditory nerve: Transduction & the Organ of Corti, brain map & meaning; circuit1, circuit2, SigmaDelta,
39/17M4/25L39: Virus, bactaeria, antibodies, bacteriophages, organoids and CRISPER (phage, Parasites, Organoids, CRISPER, New studies re weight loss
Assignment: NS6 Due (Octave code that implements spike propagation)
40W4/27L40: Bing-Ze Lin: bzlin2@
41F4/29L41: NO Class (Allen in San Jose for family funeral)
42/18M4/2L42: Allen speech feature research: Techniques and implications (e.g., cell assemblies) for speech recognition and Machine Learning
43W5/4L43: Final Lecture: Koch on consciousness (@1:13), Giulio Tononi on Consciousness

L/WDDate 
-/18W5/4 Instruction Ends
-/18R5/5 Reading Day
-/19T5/10 Final Exam TBD (Official Schedule)

 ||- || F || 5/?? ||  Backup: Exam III TBD+ PM on HW1-HW11atest>><<

L= Lecture #
T= Topic #
W=week of the year, starting from Jan 1
D=day: T is Tue, W Wed, R Thur, S Sat, etc.
Each exam (I, II and Final paper) will count as 30% of your final grade, while the Assignments (NS1-DE3) plus class participation (Prof's Discussion), count for 10%. Please return the final paper by the end of the exam period.


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