global brain talk monday

# misha ahrens: multimodal imaging studies.
five modality imaging
multimodal imaging. gaba voltage glu calcium
Computational correlation framework: optical imaging corelation functional
Radial astrocytes. transition between active and passive behaviral state
glibal imaging Mu cell 2019
noredrenalergic cells. fiber. medula oblongata. glial calcium transients.
Tze Koh from Byron Yu lab.

# Maneesh Sahani. UCL.
population analysis and theory

Gaussian Process Factor Analysis (GPFA) is a method for inferring latent structure that is shared across a population of neurons from single trials [2]. … Thus, inter-trial variability in neural firing that is shared across the population is modelled via the evolution of the latent processes on a given trial.May 27, 2018Temporal alignment and latent Gaussian process … – bioRxiv
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temporal variability. time warping. additive varition. point process observation
http://papers.neurips.cc/paper/8245-temporal-alignment-and-latent-gaussian-process-factor-inference-in-population-spike-trains

neuron x time x condition: neuronXfactor, conditionXdrive, factorXdriveXtime. Factorization of regression tensor. Soldado-Magraner

DIstribution representation of neural code
A. averaging.

B. Distributed distributional code (DDC). encodes distribution.
– expected value int(p(x)x)
– probablistic computations. beliefe propagation. decidsion making (reward expectation), variational learning (latent statistics expected value)
– so neural firing rate is the coefficient of the basis function

Easy to learn, representative power, …
Helmholtz machine: unsupervised learning by bootstrapping generation and recognition
adversarial? generative and recognition network.
wake phase and sleep phase.

Infrerence in time-postdiction (wenliang & sahani 2019 NIPS) same as NeurIPS
carry belief from the past. dynamical DDC


# Session dinner
Ahrens and Ziquin. voltron imaging.
https://www.biorxiv.org/content/10.1101/436840v1

certain behaviors are phased locked to other behaviors. this is related to the behavioral hierarchy. distributed CPG. this sets the mechanism of multi-timescale behavioral hierarchy (Mark Zimmer)
impute corrupted behavior. probablistic genrative model
Scott Linderman biorxiv, behavioral decoding work.
https://web.stanford.edu/~swl1/#publications

NeuroPAL. deterministic brainbow. neuralID and connectome.

# Svoboda Mesoscale activity project (MAP)
memory guided flexible mbehavior. Jorge Jaramillo
David Lui. Susu Chen. premotor circuits in the medulla. medulla delay period firing rate increases. ALM and basal ganglia.
in-cage training setup. track localization. ALM projection to either thalamic or medulla projection types. differentiate those two. basal ganglia disinhibition. release movement. disinhibition. movement initiation

# Mante (ETH zurich)
dynamics attractor can be modelled by different combination of potential landscape + input dynamics combination. compare saddle point, line attractor, point attractor types.
compare residuals to compare likelihood of model correctness
eigenvalue, singular values. point attractor is stable. 2D dimensional projeciton. see how the system responds to the perturbation.

# Sussilo
Interpretable neural dynamics: GOLD. goal oriented learning of dynamics
Encoder RNN. stimulus to behavior to Neural. Encoder RNN.
dynamical mechanism.
C. Chandrasekeran. PMd neuropixels task.

# xiao-jing Wang. distributed persistent acivity in multi-regional brain circuits
persistent activity. can’t be stimulated directly.
mouse model whole brain. Allen institute Julie Harris
https://www.nature.com/articles/s41593-019-0417-0
keeping track of information. mechanism of short term memory.
long firing or firing chain?
sequential activation

Mom’s kidney problem

enoxaparin can damage kidney and CrCl

Over-anticoagulation can occur in patients with moderate (CrCl 30–50 mL/min) to severe renal dysfunction (CrCl <30 mL/min)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379338/

Thus, an LMWH with a lower molecular weight are is more dependent on renal clearance and therefore may accumulate in patients with renal dysfunction and may be more pronounced with the smaller LMWH [29].

reduce to 1mg/kg once a day if eGFR < 30mL/min . now she gets 1.5 mg twice a day. 3x of the recommended dose if her CrCl is low.

Cockcroft and Gault equation should be used for low therapeutic index and high-risk drugs. In other cases, eGFR is an adequate estimate of the CrCl.

https://academic.oup.com/ndt/article/32/12/1967/3091492

CKD patients have higher risks of bleeding

https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2141.2003.04196.x

Differences between LMWH.

Enoxaparin has 4300 dalton and tin ape run has 5800.

Use of low doses of low‐molecular‐weight heparin (< 3500 anti‐FXa units/d) is associated with equal efficacy and better safety compared with low‐dose unfractionated heparin, whereas use of higher doses of low‐molecular‐weight heparin is associated with significantly greater bleeding (Koch et al, 2001; Mismetti et al, 2001).

action items

1. extent of her kidney damage

2. choice of her anticoagulation regimen

3. her housing situation when discharged

Sep 2 Mon Labor day @ Flatiron

Learning React. why? it ties model view controller framework. Imagine what I can do if I can expose the controls through the web. My work will be completely visible and usable by the users through the web interface. react is the fastest way to get the scientific tools to the users. JSX + react allows easy integration with the python backend. this is why I must learn react. it’s tied to Jeremy’s new visualization effort (reactopya) and it’s a very scalable way to design scientific visualization. Combined with kb-snapshot (model), spikeforest (controller), reactopya (view) it allows full integration of the flatiron pipeline. Now it’s time to build a strong well integrated system.

The ultimate goal is to implement all neural processing routines on the web and work with Jeremy to realize this dream. Break the boundary and make the data available anywhere everywhere. Let the web technology transform the way science is conducted. I bet CZI has similar vision.

Built-in Javascript functions

  • setInterval(fh, milliseconds)
  • new Date().toLocaleTimeString()

Built-in react functions

  • ReactDOM.render(element, document.getElementById(‘root’))
  • const element = (); #declare
  • React.Component doc

Canada health research government grants and contracts inurl:gc.ca

Canada trade commissioner services
Canada start business (startup)
Can export innovation (going global funding)
Application
Canada innovation funding support
SBIR like programs in Canada
CSA funding opportunities and grants

Partners
Reza Khanbabaie google scholar

Life sciences research bodies
Genome Canada
http://www.genomecanada.ca
Offers primary funding and an information resource for genomics and proteomics in Canada.

Health Canada
http://www.hc-sc.gc.ca
Provides national leadership in enhancing healthy living, responding to the changing nature of health issues, and promoting disease prevention.

International Development Research Centre (IDRC)
http://www.idrc.ca
Supports research in developing countries to promote growth and development.

National Research Council Canada (NRC)
http://www.nrc-cnrc.gc.ca
NRC institutes in the field of life sciences specialize in the development of biopharmaceutical and medical devices and foster international research linkages.

Funding Programs
Canadian Institutes of Health Research (CIHR)
http://www.cihr-irsc.gc.ca
Support over 14,000 researchers and trainees in the creation of new health research knowledge and its translation into improved health for Canadians.

Canada Foundation for Innovation (CFI)
http://www.innovation.ca
Supports more than 7,000 projects across Canada that lead to breakthroughs in areas such as health.

Going Global Innovation (GGI)
http://www.tradecommissioner.gc.ca/eng/science/going_global.jsp
Promotes Canada’s innovation efforts by supporting Canadian researchers to solidify partnerships with international key players for science-based research and development projects that have commercial potential.

Natural Sciences and Engineering Research Council of Canada (NSERC)
http://www.nserc-crsng.gc.ca
Supports some 30,000 post-secondary students and post-doctoral fellows and 12,000 professors every year.

Social Sciences and Humanities Research Council of Canada (SSHRC)
http://www.sshrc-crsh.gc.ca
Promotes and supports post-secondary based research and training in the humanities and social sciences to enhance our understanding of modern social, cultural, technological, environmental, economic, and wellness issues.

Explore the Possibilities
A comprehensive list of programs and information on education in Canada
http://www.educationau-incanada.ca
Partnership opportunities and information on innovation projects
http://www.tradecommissioner.gc.ca/eng/science/home.jsp
Profiles on cutting-edge research at institutions across Canada
http://www.InnovationCanada.ca
http://www.science.gc.ca
International scholarships and fellowships
http://www.scholarships.gc.ca
http://www.nserc-crsng.gc.ca
Association of Universities and Colleges of Canada
http://www.aucc.ca
Association of Community Colleges of Canada
http://www.accc.ca

chalk talk

NSEEC industry.

Bickle foundation. high risk high reward.

NSERC grant. Cross-modal measurement of in-vivo spiking activities from the known cell-types (Neural recoding + analysis)

Aim1. Develop cross-modal electrophysiology recording and stimulation capability combined with optical recording and stimulation at the brain-wide, cellular resolution.

polymer microelectrodes, microLED, transparent glass electrodes, multifunctional probes

Aim2. Generate electro-optical groundtruth recordings by tracking the spiking activities of known cell types over multiple days, and use them to validate existing spike sorting and Ca image analysis algorithms.

Aim3. Develop online analysis software to analyze the electrical and optical recordings in real-time.

Implement algorithms using real-time OS, FPGA, and


NSERC grant. Develop AI-based predicitve neuroinformatics platform for distributed computing environment

Aim 1. Develop web-based platform to benchmark existing neural decoding algorithms using publicly available neural recordings paired with behavioral or sensory recordings.

Based on SpikeForest pipeline in collaboration with Flatiron Institute. Combines calcium imaging analysis, spike sorting analysis, behavioral analysis. Uses IBL and Allen brainobservatory dataset

Aim 2. Develop algorithms to predict voluntary decisions animals make during spatial navigations using existing datasets.

T-maze. W-maze. accuracy and predictive time window evaluation. LFP and spiking information. phase

CIHR grant. Neurodynamics during social functions in normal and autistic brains

I am interested in studying synchronized neurodynamics in a pair of socially interacting animals under naturalistic conditions.
In particular, I want to understand how social behaviours are perceived and generated in distributed brain areas including the auditory and motor cortex, amygdala, and hippocampus.
Mice vocalize at ultrasonic frequencies and I want to investigate how various communication signals play a role in synchronizing neural states in healthy individuals as well as a mouse autism model [6].
The understanding gained from this research may reveal novel biological markers for autism spectrum disorder (ASD) based on key factors distinguishing autistic and healthy brains in perceiving and expressing vocal communication.
In addition, long-term neural recordings in multiple brain regions could reveal a circuit-level action of pharmacological agents such as R-Baclofen, which has been recently developed and clinically evaluated to treat the symptoms of ASD.
One of the hallmarks of ASD is an enhanced ability to recognize fine perceptual details while missing out on a larger context.
By using ultrasonic vocalization as a behavioural assay, I want to measure how various stages of sensory (auditory) information processing are affected by ASD and understand the action of R-Baclofen in inducing neuroplasticity over an extended period.
Recently, functional brain stimulation is beginning to replace pharmacological treatments for various neurological conditions including Parkinson’s disease, epilepsy, and depression to overcome drug resistance and unintended side effects.
Based on understanding the circuit-level mechanism of R-Baclofen, I want to explore targeted neurostimulation to achieve similar effects in the animal models of ASD.
My initial approach would be to apply a machine-learning driven bidirectional neural interface to detect and interfere with pathological neurodynamics as well as to induce neuroplasticity that affects the resting brain state.