More on Science
Jamie Ducharme
3 years ago
How monkeypox spreads (and doesn't spread)
Monkeypox was rare until recently. In 2005, a research called a cluster of six monkeypox cases in the Republic of Congo "the longest reported chain to date."
That's changed. This year, over 25,000 monkeypox cases have been reported in 83 countries, indicating widespread human-to-human transmission.
What spreads monkeypox? Monkeypox transmission research is ongoing; findings may change. But science says...
Most cases were formerly animal-related.
According to the WHO, monkeypox was first diagnosed in an infant in the DRC in 1970. After that, instances were infrequent and often tied to animals. In 2003, 47 Americans contracted rabies from pet prairie dogs.
In 2017, Nigeria saw a significant outbreak. NPR reported that doctors diagnosed young guys without animal exposure who had genital sores. Nigerian researchers highlighted the idea of sexual transmission in a 2019 study, but the theory didn't catch on. “People tend to cling on to tradition, and the idea is that monkeypox is transmitted from animals to humans,” explains research co-author Dr. Dimie Ogoina.
Most monkeypox cases are sex-related.
Human-to-human transmission of monkeypox occurs, and sexual activity plays a role.
Joseph Osmundson, a clinical assistant professor of biology at NYU, says most transmission occurs in queer and gay sexual networks through sexual or personal contact.
Monkeypox spreads by skin-to-skin contact, especially with its blister-like rash, explains Ogoina. Researchers are exploring whether people can be asymptomatically contagious, but they are infectious until their rash heals and fresh skin forms, according to the CDC.
A July research in the New England Journal of Medicine reported that of more than 500 monkeypox cases in 16 countries as of June, 95% were linked to sexual activity and 98% were among males who have sex with men. WHO Director-General Tedros Adhanom Ghebreyesus encouraged males to temporarily restrict their number of male partners in July.
Is monkeypox a sexually transmitted infection (STI)?
Skin-to-skin contact can spread monkeypox, not simply sexual activities. Dr. Roy Gulick, infectious disease chief at Weill Cornell Medicine and NewYork-Presbyterian, said monkeypox is not a "typical" STI. Monkeypox isn't a STI, claims the CDC.
Most cases in the current outbreak are tied to male sexual behavior, but Osmundson thinks the virus might also spread on sports teams, in spas, or in college dorms.
Can you get monkeypox from surfaces?
Monkeypox can be spread by touching infected clothing or bedding. According to a study, a U.K. health care worker caught monkeypox in 2018 after handling ill patient's bedding.
Angela Rasmussen, a virologist at the University of Saskatchewan in Canada, believes "incidental" contact seldom distributes the virus. “You need enough virus exposure to get infected,” she says. It's conceivable after sharing a bed or towel with an infectious person, but less likely after touching a doorknob, she says.
Dr. Müge evik, a clinical lecturer in infectious diseases at the University of St. Andrews in Scotland, says there is a "spectrum" of risk connected with monkeypox. "Every exposure isn't equal," she explains. "People must know where to be cautious. Reducing [sexual] partners may be more useful than cleaning coffee shop seats.
Is monkeypox airborne?
Exposure to an infectious person's respiratory fluids can cause monkeypox, but the WHO says it needs close, continuous face-to-face contact. CDC researchers are still examining how often this happens.
Under precise laboratory conditions, scientists have shown that monkeypox can spread via aerosols, or tiny airborne particles. But there's no clear evidence that this is happening in the real world, Rasmussen adds. “This is expanding predominantly in communities of males who have sex with men, which suggests skin-to-skin contact,” she explains. If airborne transmission were frequent, she argues, we'd find more occurrences in other demographics.
In the shadow of COVID-19, people are worried about aerosolized monkeypox. Rasmussen believes the epidemiology is different. Different viruses.
Can kids get monkeypox?
More than 80 youngsters have contracted the virus thus far, mainly through household transmission. CDC says pregnant women can spread the illness to their fetus.
Among the 1970s, monkeypox predominantly affected children, but by the 2010s, it was more common in adults, according to a February study. The study's authors say routine smallpox immunization (which protects against monkeypox) halted when smallpox was eradicated. Only toddlers were born after smallpox vaccination halted decades ago. More people are vulnerable now.
Schools and daycares could become monkeypox hotspots, according to pediatric instances. Ogoina adds this hasn't happened in Nigeria's outbreaks, which is encouraging. He says, "I'm not sure if we should worry." We must be careful and seek evidence.
Tomas Pueyo
2 years ago
Soon, a Starship Will Transform Humanity
SpaceX's Starship.
Launched last week.
Four minutes in:
SpaceX will succeed. When it does, its massiveness will matter.
Its payload will revolutionize space economics.
Civilization will shift.
We don't yet understand how this will affect space and Earth culture. Grab it.
The Cost of Space Transportation Has Decreased Exponentially
Space launches have increased dramatically in recent years.
We mostly send items to LEO, the green area below:
SpaceX's reusable rockets can send these things to LEO. Each may launch dozens of payloads into space.
With all these launches, we're sending more than simply things to space. Volume and mass. Since the 1980s, launching a kilogram of payload to LEO has become cheaper:
One kilogram in a large rocket cost over $75,000 in the 1980s. Carrying one astronaut cost nearly $5M! Falcon Heavy's $1,500/kg price is 50 times lower. SpaceX's larger, reusable rockets are amazing.
SpaceX's Starship rocket will continue. It can carry over 100 tons to LEO, 50% more than the current Falcon heavy. Thousands of launches per year. Elon Musk predicts Falcon Heavy's $1,500/kg cost will plummet to $100 in 23 years.
In context:
People underestimate this.
2. The Benefits of Affordable Transportation
Compare Earth's transportation costs:
It's no surprise that the US and Northern Europe are the wealthiest and have the most navigable interior waterways.
So what? since sea transportation is cheaper than land. Inland waterways are even better than sea transportation since weather is less of an issue, currents can be controlled, and rivers serve two banks instead of one for coastal transportation.
In France, because population density follows river systems, rivers are valuable. Cheap transportation brought people and money to rivers, especially their confluences.
How come? Why were humans surrounding rivers?
Imagine selling meat for $10 per kilogram. Transporting one kg one kilometer costs $1. Your margin decreases $1 each kilometer. You can only ship 10 kilometers. For example, you can only trade with four cities:
If instead, your cost of transportation is half, what happens? It costs you $0.5 per km. You now have higher margins with each city you traded with. More importantly, you can reach 20-km markets.
However, 2x distance 4x surface! You can now trade with sixteen cities instead of four! Metcalfe's law states that a network's value increases with its nodes squared. Since now sixteen cities can connect to yours. Each city now has sixteen connections! They get affluent and can afford more meat.
Rivers lower travel costs, connecting many cities, which can trade more, get wealthy, and buy more.
The right network is worth at least an order of magnitude more than the left! The cheaper the transport, the more trade at a lower cost, the more income generated, the more that wealth can be reinvested in better canals, bridges, and roads, and the wealth grows even more.
Throughout history. Rome was established around cheap Mediterranean transit and preoccupied with cutting overland transportation costs with their famous roadways. Communications restricted their empire.
The Egyptians lived around the Nile, the Vikings around the North Sea, early Japan around the Seto Inland Sea, and China started canals in the 5th century BC.
Transportation costs shaped empires.Starship is lowering new-world transit expenses. What's possible?
3. Change Organizations, Change Companies, Change the World
Starship is a conveyor belt to LEO. A new world of opportunity opens up as transportation prices drop 100x in a decade.
Satellite engineers have spent decades shedding milligrams. Weight influenced every decision: pricing structure, volumes to be sent, material selections, power sources, thermal protection, guiding, navigation, and control software. Weight was everything in the mission. To pack as much science into every millimeter, NASA missions had to be miniaturized. Engineers were indoctrinated against mass.
No way.
Starship is not constrained by any space mission, robotic or crewed.
Starship obliterates the mass constraint and every last vestige of cultural baggage it has gouged into the minds of spacecraft designers. A dollar spent on mass optimization no longer buys a dollar saved on launch cost. It buys nothing. It is time to raise the scope of our ambition and think much bigger. — Casey Handmer, Starship is still not understood
A Tesla Roadster in space makes more sense.
It went beyond bad PR. It told the industry: Did you care about every microgram? No more. My rockets are big enough to send a Tesla without noticing. Industry watchers should have noticed.
Most didn’t. Artemis is a global mission to send astronauts to the Moon and build a base. Artemis uses disposable Space Launch System rockets. Instead of sending two or three dinky 10-ton crew habitats over the next decade, Starship might deliver 100x as much cargo and create a base for 1,000 astronauts in a year or two. Why not? Because Artemis remains in a pre-Starship paradigm where each kilogram costs a million dollars and we must aggressively descope our objective.
Space agencies can deliver 100x more payload to space for the same budget with 100x lower costs and 100x higher transportation volumes. How can space economy saturate this new supply?
Before Starship, NASA supplied heavy equipment for Moon base construction. After Starship, Caterpillar and Deere may space-qualify their products with little alterations. Instead than waiting decades for NASA engineers to catch up, we could send people to build a space outpost with John Deere equipment in a few years.
History is littered with the wreckage of former industrial titans that underestimated the impact of new technology and overestimated their ability to adapt: Blockbuster, Motorola, Kodak, Nokia, RIM, Xerox, Yahoo, IBM, Atari, Sears, Hitachi, Polaroid, Toshiba, HP, Palm, Sony, PanAm, Sega, Netscape, Compaq, GM… — Casey Handmer, Starship is still not understood
Everyone saw it coming, but senior management failed to realize that adaption would involve moving beyond their established business practice. Others will if they don't.
4. The Starship Possibilities
It's Starlink.
SpaceX invented affordable cargo space and grasped its implications first. How can we use all this inexpensive cargo nobody knows how to use?
Satellite communications seemed like the best way to capitalize on it. They tried. Starlink, designed by SpaceX, provides fast, dependable Internet worldwide. Beaming information down is often cheaper than cable. Already profitable.
Starlink is one use for all this cheap cargo space. Many more. The longer firms ignore the opportunity, the more SpaceX will acquire.
What are these chances?
Satellite imagery is outdated and lacks detail. We can improve greatly. Synthetic aperture radar can take beautiful shots like this:
Have you ever used Google Maps and thought, "I want to see this in more detail"? What if I could view Earth live? What if we could livestream an infrared image of Earth?
We could launch hundreds of satellites with such mind-blowing visual precision of the Earth that we would dramatically improve the accuracy of our meteorological models; our agriculture; where crime is happening; where poachers are operating in the savannah; climate change; and who is moving military personnel where. Is that useful?
What if we could see Earth in real time? That affects businesses? That changes society?
Michael Hunter, MD
2 years ago
5 Drugs That May Increase Your Risk of Dementia
While our genes can't be changed easily, you can avoid some dementia risk factors. Today we discuss dementia and five drugs that may increase risk.
Memory loss appears to come with age, but we're not talking about forgetfulness. Sometimes losing your car keys isn't an indication of dementia. Dementia impairs the capacity to think, remember, or make judgments. Dementia hinders daily tasks.
Alzheimers is the most common dementia. Dementia is not normal aging, unlike forgetfulness. Aging increases the risk of Alzheimer's and other dementias. A family history of the illness increases your risk, according to the Mayo Clinic (USA).
Given that our genes are difficult to change (I won't get into epigenetics), what are some avoidable dementia risk factors? Certain drugs may cause cognitive deterioration.
Today we look at four drugs that may cause cognitive decline.
Dementia and benzodiazepines
Benzodiazepine sedatives increase brain GABA levels. Example benzodiazepines:
Diazepam (Valium) (Valium)
Alprazolam (Xanax) (Xanax)
Clonazepam (Klonopin) (Klonopin)
Addiction and overdose are benzodiazepine risks. Yes! These medications don't raise dementia risk.
USC study: Benzodiazepines don't increase dementia risk in older adults.
Benzodiazepines can produce short- and long-term amnesia. This memory loss hinders memory formation. Extreme cases can permanently impair learning and memory. Anterograde amnesia is uncommon.
2. Statins and dementia
Statins reduce cholesterol. They prevent a cholesterol-making chemical. Examples:
Atorvastatin (Lipitor) (Lipitor)
Fluvastatin (Lescol XL) (Lescol XL)
Lovastatin (Altoprev) (Altoprev)
Pitavastatin (Livalo, Zypitamag) (Livalo, Zypitamag)
Pravastatin (Pravachol) (Pravachol)
Rosuvastatin (Crestor, Ezallor) (Crestor, Ezallor)
Simvastatin (Zocor) (Zocor)
This finding is contentious. Harvard's Brigham and Womens Hospital's Dr. Joann Manson says:
“I think that the relationship between statins and cognitive function remains controversial. There’s still not a clear conclusion whether they help to prevent dementia or Alzheimer’s disease, have neutral effects, or increase risk.”
This one's off the dementia list.
3. Dementia and anticholinergic drugs
Anticholinergic drugs treat many conditions, including urine incontinence. Drugs inhibit acetylcholine (a brain chemical that helps send messages between cells). Acetylcholine blockers cause drowsiness, disorientation, and memory loss.
First-generation antihistamines, tricyclic antidepressants, and overactive bladder antimuscarinics are common anticholinergics among the elderly.
Anticholinergic drugs may cause dementia. One study found that taking anticholinergics for three years or more increased the risk of dementia by 1.54 times compared to three months or less. After stopping the medicine, the danger may continue.
4. Drugs for Parkinson's disease and dementia
Cleveland Clinic (USA) on Parkinson's:
Parkinson's disease causes age-related brain degeneration. It causes delayed movements, tremors, and balance issues. Some are inherited, but most are unknown. There are various treatment options, but no cure.
Parkinson's medications can cause memory loss, confusion, delusions, and obsessive behaviors. The drug's effects on dopamine cause these issues.
A 2019 JAMA Internal Medicine study found powerful anticholinergic medications enhance dementia risk.
Those who took anticholinergics had a 1.5 times higher chance of dementia. Individuals taking antidepressants, antipsychotic drugs, anti-Parkinson’s drugs, overactive bladder drugs, and anti-epileptic drugs had the greatest risk of dementia.
Anticholinergic medicines can lessen Parkinson's-related tremors, but they slow cognitive ability. Anticholinergics can cause disorientation and hallucinations in those over 70.
5. Antiepileptic drugs and dementia
The risk of dementia from anti-seizure drugs varies with drugs. Levetiracetam (Keppra) improves Alzheimer's cognition.
One study linked different anti-seizure medications to dementia. Anti-epileptic medicines increased the risk of Alzheimer's disease by 1.15 times in the Finnish sample and 1.3 times in the German population. Depakote, Topamax are drugs.
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Leonardo Castorina
3 years ago
How to Use Obsidian to Boost Research Productivity
Tools for managing your PhD projects, reading lists, notes, and inspiration.
As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.
The article has three parts:
- What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.
This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.
1. Philosophy: Taking and organizing notes
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/
Notes
We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:
- Deep Learning
- Recurrent Neural Networks
- Convolutional Neural Networks
Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:
#Tags and [[Links]] over /Folders/
The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:
- /Proteins/
- Protein Folding
- /Deep Learning/
- /Proteins/
Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).
You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.
My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.
My Knowledge Graph and the note “Backrpropagation” and its links.
Backpropagation note and all its links
Why use Folders?
Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:
My Zettelkasten's 5 folders
They usually gather data from various sources:
MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.
Keeping images separate from other files can help keep your main folders clean.
I will elaborate on these in the Workflow Section.
My general recommendation is to use tags and links instead of folders.
Maps of Content (MOC)
Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:
An example of a Machine Learning MOC generated with Dataview.
As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
2. Tools: Knowing Obsidian
Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/
Obsidian interface.
Obsidian is highly customizable, so here is my preferred interface:
The theme is customized from https://github.com/colineckert/obsidian-things
Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).
My interface is organized as follows:
How my Obsidian Interface is organized.
Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.
Tags:
I use nested tags and look into each one to find specific notes to link.
cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)
Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.
Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.
Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.
Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.
Plugins
An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.
Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)
Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.
Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.
Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.
3. Workflows: Cool stuff
Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary
3.1 Using Templates to Structure Notes
Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:
An example of a note using a template.
### [[YOUR MOC]]
# Note Title of your note
**Tags**::
**Links**::
The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:
### [[Books MOC]]
# Title
**Author**::
**Date::
**Tags::
**Links::
A book template example.
Using a simple query, I can hook Dataview to it.
dataview
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”
from “4. Books”
SORT grade DESCENDING
using Dataview to query templates.
3.2 Free Note Syncing (Laptop, Phone, Tablet)
No plugins used.
One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).
Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).
For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).
3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers
My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.
My Zotero library is tagged as follows:
My reference manager's tags
For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:
An example of my citations template.
Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.
Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144
You can then convert your notes to digital. I found that transcribing helped me retain information better.
3.4 Projects and Lab Books
Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:
- One folder for all my projects
- One file for each project
I use a template to create each project
### [[Projects MOC]]
# <% tp.file.title %>
**Tags**::
**Links**::
**URL**::
**Project Description**::## Notes:
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>
#### Done:
#### TODO:
#### Notes
You can insert a template into a new note with CMD + P and looking for the Templater option.
I then keep adding new days with another template:
### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>
#### Done:
#### TODO:
#### Notes:
This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:
Example of project note with timestamped notes.
3.5 Private Encrypted Diary
This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:
- It had to be private, and nobody had to be able to read the entries.
- Cloud syncing was required for editing on multiple devices.
Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:
Conclusion
So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)
Read original post here
Andy Murphy
2 years ago
Activating Your Vagus Nerve
11 science-backed ways to improve health, happiness, healing, relaxation, and mental clarity.
Vagus nerve is the main parasympathetic nervous system component.
It helps us rest and digest by slowing and stabilizing a resting heart rate, slowing and stabilizing the breath, promoting digestion, improving recovery and healing times, producing saliva, releasing endorphins and hormones like dopamine, oxytocin, and serotonin, and boosting the immune, digestive, and cardiovascular systems.
The vagus nerve sends anti-inflammatory signals to other parts of the body and is located behind the tongue, in the throat, neck, heart, lungs, abdomen, and brainstem.
Vagus means wandering in Latin. So, it's bold.
Here are 11 proven ways to boost health, happiness, and the vagus nerve.
1. Extend
“Yoga stimulates different nerves in your body, especially the vagus nerve that carries information from the brain to most of the body’s major organs, slows everything down and allows self-regulation. It’s the nerve that is associated with the parasympathetic system and emotions like love, joy, and compassion.” — Deepak Chopra
Stretching doesn't require a yoga background.
Listen to your body and ease into simple poses. This connects the mind and body.
If you're new to yoga or don't have access to an in-person class, try Yoga with Adrienne. Over 600 YouTube videos give her plenty of material.
2. Inhale
Because inhaling and exhaling activate the autonomic nervous system, we can breathe to relax.
Exhaling activates the parasympathetic nervous system (rest and digest). One inhales stress, the other exhales it.
So, faster or more intense breathing increases stress. Slower breathing relaxes us.
Breathe slowly, smoothly, and less.
Rhythmic breathing helps me relax.
What to do is as follows:
1. Take 4 smooth, forceless nose breaths.
2. Exhale smoothly and forcefully for 4 seconds
3. Don't pause at the inhale or exhale.
4. Continue for 5 minutes/40 breaths
5. Hold your breath as long as comfortable.
6. Breathe normally.
If four seconds is too long, try breathing in and out for two seconds, or in and out for three seconds, until your breath naturally relaxes. Once calmer, extend your breath.
Any consistent rhythm without force is good. Your heart will follow your lead and become coherent.
3. Chant/Hum
Singing, chanting, or humming activate the vagus nerve through the back of the throat.
Humming emits nitric oxide.
Nitric oxide improves blood circulation, blood flow, heart health, and blood pressure.
Antiviral, antibacterial, anti-inflammatory, antioxidant, and antimicrobial properties kill viruses and bacteria in the nose and throat.
Gargling water stimulates the vagus nerve.
Simple ways to heal, boost energy, and boost mood are often the healthiest. They're free and can be done anywhere.
4. Have more fun
Laughing stimulates the throat muscles, activating the vagus nerve. What's not to like? It releases dopamine.
Take time to enjoy life. Maybe it's a book, podcast, movie, socializing with friends, or laughing yoga.
Follow your bliss, as Joseph Campbell says.
Laugh at yourself
Actually. Really.
Gagging activates vagus nerve-connected muscles. Some doctors use the gag reflex to test the vagus nerve.
Grossness isn't required. While brushing, gag quickly. My girlfriend's brother always does it.
I'm done brushing when I gag, he says.
6. Take in the outdoors
Nature relaxes body and mind. Better if you can walk barefoot.
Earthing is associated with hippies dancing in daisies.
Science now supports hippies.
7. Enter some chilly water.
The diving reflex activates the vagus nerve when exposed to cold water.
The diving reflex involves holding your breath in cold water. Cold showers work best.
Within minutes of being in cold water, parasympathetic nervous system activity, which calms the body, increases.
8. Workout
Exercise increases dopamine, blood circulation, and breathing. So we feel energized, calm, and well-rested.
After resting, the parasympathetic nervous system engages.
It's worth waiting for, though.
9. Play music with brainwaves
Brainwave music harmonizes brainwave activity, boosts productivity and mental clarity, and promotes peace and relaxation by stimulating the vagus nerve.
Simply play a song.
My favorite.
10. Make gentle eyes
Eyes, like breath, often reflect inner state. Sharp, dilated, focused eyes indicate alertness.
Soft, open eyes reflect relaxation and ease. Soft eyes relax the nervous system.
This practice reduces stress, anxiety, and body tension. It's a quick and effective way to enter a calm, peaceful state.
Wild animals can be hunted one minute and graze the next.
Put it into action:
Relax while seated.
Gaze at a distant object
Use peripheral vision while looking straight ahead
Without moving your eyes, look up and down. Connect side spaces to your vision.
Focus on everything as your eyes soften.
Keep breathing
Stay as long as you like
11. Be intimate
We kiss, moan, and breathe deeper during love. We get dopamine, oxytocin, serotonin, and vagus nerve stimulation.
Why not?
To sum up
Here are 11 vagus nerve resets:
Stretch
Breathe
Hum/Chant
More humor
Amuse yourself
Spend time outdoors
Leap into chilly water
Exercise
Play music with brainwaves.
Make gentle eyes.
Be intimate
If these words have inspired you, try my favorite breathwork technique. Combining breathing, chanting, and brainwave music. Win-win-win :)
Aldric Chen
3 years ago
Jack Dorsey's Meeting Best Practice was something I tried. It Performs Exceptionally Well in Consulting Engagements.
Yes, client meetings are difficult. Especially when I'm alone.
Clients must tell us their problems so we can help.
In-meeting challenges contribute nothing to our work. Consider this:
Clients are unprepared.
Clients are distracted.
Clients are confused.
Introducing Jack Dorsey's Google Doc approach
I endorse his approach to meetings.
Not Google Doc-related. Jack uses it for meetings.
This is what his meetings look like.
Prior to the meeting, the Chair creates the agenda, structure, and information using Google Doc.
Participants in the meeting would have 5-10 minutes to read the Google Doc.
They have 5-10 minutes to type their comments on the document.
In-depth discussion begins
There is elegance in simplicity. Here's how Jack's approach is fantastic.
Unprepared clients are given time to read.
During the meeting, they think and work on it.
They can see real-time remarks from others.
Discussion ensues.
Three months ago, I fell for this strategy. After trying it with a client, I got good results.
I conducted social control experiments in a few client workshops.
Context matters.
I am sure Jack Dorsey’s method works well in meetings. What about client workshops?
So, I tested Enterprise of the Future with a consulting client.
I sent multiple emails to client stakeholders describing the new approach.
No PowerPoints that day. I spent the night setting up the Google Doc with conversation topics, critical thinking questions, and a Before and After section.
The client was shocked. First, a Google Doc was projected. Second surprise was a verbal feedback.
“No pre-meeting materials?”
“Don’t worry. I know you are not reading it before our meeting, anyway.”
We laughed. The experiment started.
Observations throughout a 90-minute engagement workshop from beginning to end
For 10 minutes, the workshop was silent.
People read the Google Doc. For some, the silence was unnerving.
“Are you not going to present anything to us?”
I said everything's in Google Doc. I asked them to read, remark, and add relevant paragraphs.
As they unlocked their laptops, they were annoyed.
Ten client stakeholders are typing on the Google Doc. My laptop displays comment bubbles, red lines, new paragraphs, and strikethroughs.
The first 10 minutes were productive. Everyone has seen and contributed to the document.
I was silent.
The move to a classical workshop was smooth. I didn't stimulate dialogue. They did.
Stephanie asked Joe why a blended workforce hinders company productivity. She questioned his comments and additional paragraphs.
That is when a light bulb hit my head. Yes, you want to speak to the right person to resolve issues!
Not only that was discussed. Others discussed their remark bubbles with neighbors. Debate circles sprung up one after the other.
The best part? I asked everyone to add their post-discussion thoughts on a Google Doc.
After the workshop, I have:
An agreement-based working document
A post-discussion minutes that are prepared for publication
A record of the discussion points that were brought up, argued, and evaluated critically
It showed me how stakeholders viewed their Enterprise of the Future. It allowed me to align with them.
Finale Keynotes
Client meetings are a hit-or-miss. I know that.
Jack Dorsey's meeting strategy works for consulting. It promotes session alignment.
It relieves clients of preparation.
I get the necessary information to advance this consulting engagement.
It is brilliant.