Wednesday, February 16, 2022

Deep Nose

Artificial networks learn to smell like the brain
Oct 2021,

We now have an artificial neural network that works like the nose. It's not an electronic nose; that's not the big deal part. 

What's important here is that, first of all, this is from the lab that brought us olfactory receptors. Next, these scientists didn't even model the network on evolution. They made an algorithm to solve an odor categorization task, and let the network run with it. Some might call that artificial evolution, but scientists will call it machine learning. After several iterations, the network found an optimized structure for solving this task -- the network ended up looking just like our olfactory system. Go figure.

The "brains" of a neural network lies in its ability to reduce the dimensionality of the information thereby optimizing computation. This is done using compression layers that learn to accept information from some neurons and not from others. After enough iterations, a pattern emerges between the layers of neurons.

Talking about this pattern, and the number of neurons connected to by each neuron on the compression layer:
"It could have been one, it could have been 50. It could have been anywhere in between," Yang says. "Biology finds six, and our network finds about six as well."

The first part of our nose where the hundreds of olfactory receptors collapse into far less neural nodes, one layer up the network, is very similar to the type of artificial neural network used in this study. It is, apparently now supported by these findings, a very effective way to condense a multi-dimensional information-space of chemical signals. Would it work for other information-spaces? What other Big Data can this deep nose model compute?

The side story: Evolution found this organization through random mutation and natural selection over eons; the artificial network found it through standard machine learning algorithms, in under one minute. 

via  Massachusetts Institute of Technology: Peter Y. Wang et al, Evolving the olfactory system with machine learning, Neuron (2021). DOI: 10.1016/j.neuron.2021.09.010

Image credit: Google's quantum computer, totally unrelated, just for looks

Post Script:
Neural network reveals new insights into how the brain functions
Dec 2021,

"The neural network model approach we have developed in this work presents an 'instruction manual' for other researchers to use to study other areas of the brain or other organs"
-co-author Dr. James Martin, co-author and professor of molecular physiology and biophysics at Baylor College
Their model is called Spatial Transcriptomics cell-types Assignment using Neural Networks (STANN).

via Baylor College of Medicine: Francisco Jose Grisanti Canozo et al, Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain, Cell Systems (2021). DOI: 10.1016/j.cels.2021.09.004

I'm not certain about this, but I think the reason they chose the olfactory system is because they were looking at the interaction of transcription genes and brain cell types, and the olfactory receptor brain cells are the only one's that each get their own gene. So that would make the olfactory bulb an ideal nexus for investigation of this kind. See studies below for further reference:

Marei H.E.S. et. al. Gene expression profile of adult human olfactory bulb and embryonic neural stem cell suggests distinct signaling pathways and epigenetic control. PLoS One. 2012; 7: e33542.

Nagayama S. et. al.  Neuronal organization of olfactory bulb circuits. Front. Neural Circuits. 2014; 8: 98.

Social Deodorization

AKA Life Without Body Odor, Coming Soon

Life in the pits - Scientists identify the key enzyme behind body odor
Aug 2020,

We already knew the bacterium Staphylococcus hominis was the culprit, but these researchers have identified the specific enzyme (C-T lyase) in the bacteria that turns our odorless sweat into body odor, or what scientists call thiolalcohol. So now we can create a model of that enzyme, and figure out how to deactivate it. 

There's not enough science fiction out there looking at a society without body odor. Just kidding, this is already reality. And what happens is, the people who don't smell still use deodorant, because the people who do smell have just enough spending power to sustain a global corporate personal hygiene complex so powerful it can influence you to deodorize yourself even if you have no odor in the first place. 

If you're interested in this sort of thing, soft paywall to the New York Times about Unilever's attempts to sell deodorant in China, "a market with 2.6 billion armpits" (2018).

via University of York and Unilever: The molecular basis of thioalcohol production in human body odour, Scientific Reports (2020). DOI: 10.1038/s41598-020-68860-z

Post Script:
The smell of your breath is a subset of body odor. 
Research reveals details of how salivary glands collectively produce constellation of proteins found in saliva
Nov 2020,

What's in your saliva? Here you go. They don't tell you what it smells like, but with this info you'll be halfway there. Also, "oral biofluid" is science for saliva.

Also, in case you were wondering, "cysteine-rich secretory protein 3 (CRISP3) ... is expressed by human labial glands."

via University at Buffalo: Marie Saitou et al. Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports Volume 33 Issue 7, 108402, Nov 17, 2020. DOI: 10.1016/j.celrep.2020.108402

Tuesday, February 1, 2022

You Don't Know What You're Missing

Attention and memory deficits persist for months after recovery from mild Covid
University of Oxford News, Jan 2022

"Although our Covid-19 survivors did not feel any more symptomatic at the time of testing, they showed degraded attention and memory."
-Dr Sijia Zhao of the Department of Experimental Psychology, University of Oxford
Repasted from above article:
All the participants had previously suffered from Covid-19 but were not significantly different from a control group at the time of testing on factors such as fatigue, forgetfulness, sleep patterns or anxiety.

But, they displayed significantly worse episodic memory and a greater decline in the ability to sustain attention over time than uninfected individuals for 6-9 months.

Note, the COVID-19 survivors in this study were young, mean age around 28, n=136.

How bad was it? Here is a measurements for context: Over the course of the 9-minute experiment, control participants’ accuracy dropped from 78.5% to 75.4%, whilst COVID survivors started with a similar baseline at 75.5%, reducing to 67.8% ... For a 30-minute memory test, COVID-19 survivors showed a significant memory decrement which was larger than in controls by 9.2%.

And to be specific: The larger episodic memory decrement amongst COVID-19 survivors was driven by errors in which the wrong orientation was chosen for a correct item. This difference suggests that the deficit in episodic memory in the COVID group might be associated with a deficit in binding information in memory. 

Interesting: word-memory tasks showed no change. 

How it might happen, if you're interested: One investigation of COVID-19 survivors demonstrated that the most severely cognitively affected patients demonstrated a degree of cognitive impairment accompanied by hypometabolism in the frontoparietal regions. These brain regions are implicated in sustained attention as well as in episodic memory. Reassuringly, the follow-up study of Hosp et al. showed slow but evident improvement after 6 months.

Last thing: The good news is that COVID-19 survivors performed well in most cognitive abilities tested, including working memory, executive function, planning and mental rotation. 

via University of Oxford: Rapid vigilance and episodic memory decrements in COVID-19 survivors. Zhao et al. Brain Communications. Jan 2022.

How Is This Related to Smell?
We already know that changes in our ability to smell were the primary symptom of the initial varieties of covid. Some of us still deal with these changes. But something we also know, regardless of any pandemic, is that smell is tightly linked to episodic memory -- "grandma's attic" or "first boyfriend's cologne" -- and a subset called autobiographical memory. These type of memories tie together people, places, feelings and smells into the olfactory cluster. Chemosensation enabled the first navigation, as primordial protists sniffed their way through the soup of early Earth. Chemosensation enabled the first social experience, when you detected your mother's immunity profile via her amniotic fluid. And chemosensation enabled your primate ancestors to remember where that really ripe fruit tree was. 

So it does seem appropriate that a virus attacking your olfactory neurons would also affect your episodic memory.

Image credit: Just astrocytes, upsplash

Post Script:
For those who haven't heard about this enough already, here's a good reminder of what Long Covid is: People who survive COVID-19 infection present a significantly higher risk of major neurological and psychiatric conditions, particularly if they were hospitalized. These include acute cerebrovascular events such as ischaemic stroke and intracerebral haemorrhage. In addition to severe neurological conditions, there can also be more chronic, longer-term consequences such as fatigue, low motivation, disturbed mood and poor sleep—all commonly reported symptoms amongst survivors, the so-called long-COVID (see recent review). -source