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Jamie Ducharme

3 years ago

How monkeypox spreads (and doesn't spread)

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Daniel Clery

3 years ago

Twisted device investigates fusion alternatives

German stellarator revamped to run longer, hotter, compete with tokamaks

Wendelstein 7-X’s complex geometry was a nightmare to build but, when fired up, worked from the start.

Tokamaks have dominated the search for fusion energy for decades. Just as ITER, the world's largest and most expensive tokamak, nears completion in southern France, a smaller, twistier testbed will start up in Germany.

If the 16-meter-wide stellarator can match or outperform similar-size tokamaks, fusion experts may rethink their future. Stellarators can keep their superhot gases stable enough to fuse nuclei and produce energy. They can theoretically run forever, but tokamaks must pause to reset their magnet coils.

The €1 billion German machine, Wendelstein 7-X (W7-X), is already getting "tokamak-like performance" in short runs, claims plasma physicist David Gates, preventing particles and heat from escaping the superhot gas. If W7-X can go long, "it will be ahead," he says. "Stellarators excel" Eindhoven University of Technology theorist Josefine Proll says, "Stellarators are back in the game." A few of startup companies, including one that Gates is leaving Princeton Plasma Physics Laboratory, are developing their own stellarators.

W7-X has been running at the Max Planck Institute for Plasma Physics (IPP) in Greifswald, Germany, since 2015, albeit only at low power and for brief runs. W7-X's developers took it down and replaced all inner walls and fittings with water-cooled equivalents, allowing for longer, hotter runs. The team reported at a W7-X board meeting last week that the revised plasma vessel has no leaks. It's expected to restart later this month to show if it can get plasma to fusion-igniting conditions.

Wendelstein 7-X’s twisting inner surface is now water cooled, enabling longer runs

Wendelstein 7-X's water-cooled inner surface allows for longer runs.

HOSAN/IPP

Both stellarators and tokamaks create magnetic gas cages hot enough to melt metal. Microwaves or particle beams heat. Extreme temperatures create a plasma, a seething mix of separated nuclei and electrons, and cause the nuclei to fuse, releasing energy. A fusion power plant would use deuterium and tritium, which react quickly. Non-energy-generating research machines like W7-X avoid tritium and use hydrogen or deuterium instead.

Tokamaks and stellarators use electromagnetic coils to create plasma-confining magnetic fields. A greater field near the hole causes plasma to drift to the reactor's wall.

Tokamaks control drift by circulating plasma around a ring. Streaming creates a magnetic field that twists and stabilizes ionized plasma. Stellarators employ magnetic coils to twist, not plasma. Once plasma physicists got powerful enough supercomputers, they could optimize stellarator magnets to improve plasma confinement.

W7-X is the first large, optimized stellarator with 50 6- ton superconducting coils. Its construction began in the mid-1990s and cost roughly twice the €550 million originally budgeted.

The wait hasn't disappointed researchers. W7-X director Thomas Klinger: "The machine operated immediately." "It's a friendly machine." It did everything we asked." Tokamaks are prone to "instabilities" (plasma bulging or wobbling) or strong "disruptions," sometimes associated to halted plasma flow. IPP theorist Sophia Henneberg believes stellarators don't employ plasma current, which "removes an entire branch" of instabilities.

In early stellarators, the magnetic field geometry drove slower particles to follow banana-shaped orbits until they collided with other particles and leaked energy. Gates believes W7-X's ability to suppress this effect implies its optimization works.

W7-X loses heat through different forms of turbulence, which push particles toward the wall. Theorists have only lately mastered simulating turbulence. W7-X's forthcoming campaign will test simulations and turbulence-fighting techniques.

A stellarator can run constantly, unlike a tokamak, which pulses. W7-X has run 100 seconds—long by tokamak standards—at low power. The device's uncooled microwave and particle heating systems only produced 11.5 megawatts. The update doubles heating power. High temperature, high plasma density, and extensive runs will test stellarators' fusion power potential. Klinger wants to heat ions to 50 million degrees Celsius for 100 seconds. That would make W7-X "a world-class machine," he argues. The team will push for 30 minutes. "We'll move step-by-step," he says.

W7-X's success has inspired VCs to finance entrepreneurs creating commercial stellarators. Startups must simplify magnet production.

Princeton Stellarators, created by Gates and colleagues this year, has $3 million to build a prototype reactor without W7-X's twisted magnet coils. Instead, it will use a mosaic of 1000 HTS square coils on the plasma vessel's outside. By adjusting each coil's magnetic field, operators can change the applied field's form. Gates: "It moves coil complexity to the control system." The company intends to construct a reactor that can fuse cheap, abundant deuterium to produce neutrons for radioisotopes. If successful, the company will build a reactor.

Renaissance Fusion, situated in Grenoble, France, raised €16 million and wants to coat plasma vessel segments in HTS. Using a laser, engineers will burn off superconductor tracks to carve magnet coils. They want to build a meter-long test segment in 2 years and a full prototype by 2027.

Type One Energy in Madison, Wisconsin, won DOE money to bend HTS cables for stellarator magnets. The business carved twisting grooves in metal with computer-controlled etching equipment to coil cables. David Anderson of the University of Wisconsin, Madison, claims advanced manufacturing technology enables the stellarator.

Anderson said W7-X's next phase will boost stellarator work. “Half-hour discharges are steady-state,” he says. “This is a big deal.”

Will Lockett

Will Lockett

3 years ago

The Unlocking Of The Ultimate Clean Energy

Terrestrial space-solar terminals could look like radio telescopes — Photo by Donald Giannatti on Unsplash

The company seeking 24/7 ultra-powerful solar electricity.

We're rushing to adopt low-carbon energy to prevent a self-made doomsday. We're using solar, wind, and wave energy. These low-carbon sources aren't perfect. They consume large areas of land, causing habitat loss. They don't produce power reliably, necessitating large grid-level batteries, an environmental nightmare. We can and must do better than fossil fuels. Longi, one of the world's top solar panel producers, is creating a low-carbon energy source. Solar-powered spacecraft. But how does it work? Why is it so environmentally harmonious? And how can Longi unlock it?

Space-based solar makes sense. Satellites above Medium Earth Orbit (MEO) enjoy 24/7 daylight. Outer space has no atmosphere or ozone layer to block the Sun's high-energy UV radiation. Solar panels can create more energy in space than on Earth due to these two factors. Solar panels in orbit can create 40 times more power than those on Earth, according to estimates.

How can we utilize this immense power? Launch a geostationary satellite with solar panels, then beam power to Earth. Such a technology could be our most eco-friendly energy source. (Better than fusion power!) How?

Solar panels create more energy in space, as I've said. Solar panel manufacture and grid batteries emit the most carbon. This indicates that a space-solar farm's carbon footprint (which doesn't need a battery because it's a constant power source) might be over 40 times smaller than a terrestrial one. Combine that with carbon-neutral launch vehicles like Starship, and you have a low-carbon power source. Solar power has one of the lowest emissions per kWh at 6g/kWh, so space-based solar could approach net-zero emissions.

Space solar is versatile because it doesn't require enormous infrastructure. A space-solar farm could power New York and Dallas with the same efficiency, without cables. The satellite will transmit power to a nearby terminal. This allows an energy system to evolve and adapt as the society it powers changes. Building and maintaining infrastructure can be carbon-intensive, thus less infrastructure means less emissions.

Space-based solar doesn't destroy habitats, either. Solar and wind power can be engineered to reduce habitat loss, but they still harm ecosystems, which must be restored. Space solar requires almost no land, therefore it's easier on Mother Nature.

Space solar power could be the ultimate energy source. So why haven’t we done it yet?

Well, for two reasons: the cost of launch and the efficiency of wireless energy transmission.

Advances in rocket construction and reusable rocket technology have lowered orbital launch costs. In the early 2000s, the Space Shuttle cost $60,000 per kg launched into LEO, but a SpaceX Falcon 9 costs only $3,205. 95% drop! Even at these low prices, launching a space-based solar farm is commercially questionable.

Energy transmission efficiency is half of its commercial viability. Space-based solar farms must be in geostationary orbit to get 24/7 daylight, 22,300 miles above Earth's surface. It's a long way to wirelessly transmit energy. Most laser and microwave systems are below 20% efficient.

Space-based solar power is uneconomical due to low efficiency and high deployment costs.

Longi wants to create this ultimate power. But how?

They'll send solar panels into space to develop space-based solar power that can be beamed to Earth. This mission will help them design solar panels tough enough for space while remaining efficient.

Longi is a Chinese company, and China's space program and universities are developing space-based solar power and seeking commercial partners. Xidian University has built a 98%-efficient microwave-based wireless energy transmission system for space-based solar power. The Long March 5B is China's super-cheap (but not carbon-offset) launch vehicle.

Longi fills the gap. They have the commercial know-how and ability to build solar satellites and terrestrial terminals at scale. Universities and the Chinese government have transmission technology and low-cost launch vehicles to launch this technology.

It may take a decade to develop and refine this energy solution. This could spark a clean energy revolution. Once operational, Longi and the Chinese government could offer the world a flexible, environmentally friendly, rapidly deployable energy source.

Should the world adopt this technology and let China control its energy? I'm not very political, so you decide. This seems to be the beginning of tapping into this planet-saving energy source. Forget fusion reactors. Carbon-neutral energy is coming soon.

Michael Hunter, MD

Michael Hunter, MD

3 years ago

5 Drugs That May Increase Your Risk of Dementia

Photo by danilo.alvesd on Unsplash

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)

Photo by Towfiqu barbhuiya on Unsplash

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.

Photo by Wengang Zhai on Unsplash

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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Keagan Stokoe

Keagan Stokoe

3 years ago

Generalists Create Startups; Specialists Scale Them

There’s a funny part of ‘Steve Jobs’ by Walter Isaacson where Jobs says that Bill Gates was more a copier than an innovator:

“Bill is basically unimaginative and has never invented anything, which is why I think he’s more comfortable now in philanthropy than technology. He just shamelessly ripped off other people’s ideas….He’d be a broader guy if he had dropped acid once or gone off to an ashram when he was younger.”

Gates lacked flavor. Nobody ever got excited about a Microsoft launch, despite their good products. Jobs had the world's best product taste. Apple vs. Microsoft.

A CEO's core job functions are all driven by taste: recruiting, vision, and company culture all require good taste. Depending on the type of company you want to build, know where you stand between Microsoft and Apple.

How can you improve your product judgment? How to acquire taste?

Test and refine

Product development follows two parallel paths: the ‘customer obsession’ path and the ‘taste and iterate’ path.

The customer obsession path involves solving customer problems. Lean Startup frameworks show you what to build at each step.

Taste-and-iterate doesn't involve the customer. You iterate internally and rely on product leaders' taste and judgment.

Creative Selection by Ken Kocienda explains this method. In Creative Selection, demos are iterated and presented to product leaders. Your boss presents to their boss, and so on up to Steve Jobs. If you have good product taste, you can be a panelist.

The iPhone follows this path. Before seeing an iPhone, consumers couldn't want one. Customer obsession wouldn't have gotten you far because iPhone buyers didn't know they wanted one.

In The Hard Thing About Hard Things, Ben Horowitz writes:

“It turns out that is exactly what product strategy is all about — figuring out the right product is the innovator’s job, not the customer’s job. The customer only knows what she thinks she wants based on her experience with the current product. The innovator can take into account everything that’s possible, but often must go against what she knows to be true. As a result, innovation requires a combination of knowledge, skill, and courage.“

One path solves a problem the customer knows they have, and the other doesn't. Instead of asking a person what they want, observe them and give them something they didn't know they needed.

It's much harder. Apple is the world's most valuable company because it's more valuable. It changes industries permanently.

If you want to build superior products, use the iPhone of your industry.

How to Improve Your Taste

I. Work for a company that has taste.

People with the best taste in products, markets, and people are rewarded for building great companies. Tasteful people know quality even when they can't describe it. Taste isn't writable. It's feel-based.

Moving into a community that's already doing what you want to do may be the best way to develop entrepreneurial taste. Most company-building knowledge is tacit.

Joining a company you want to emulate allows you to learn its inner workings. It reveals internal patterns intuitively. Many successful founders come from successful companies.

Consumption determines taste. Excellence will refine you. This is why restauranteurs visit the world's best restaurants and serious painters visit Paris or New York. Joining a company with good taste is beneficial.

2. Possess a wide range of interests

“Edwin Land of Polaroid talked about the intersection of the humanities and science. I like that intersection. There’s something magical about that place… The reason Apple resonates with people is that there’s a deep current of humanity in our innovation. I think great artists and great engineers are similar, in that they both have a desire to express themselves.” — Steve Jobs

I recently discovered Edwin Land. Jobs modeled much of his career after Land's. It makes sense that Apple was inspired by Land.

A Triumph of Genius: Edwin Land, Polaroid, and the Kodak Patent War notes:

“Land was introverted in person, but supremely confident when he came to his ideas… Alongside his scientific passions, lay knowledge of art, music, and literature. He was a cultured person growing even more so as he got older, and his interests filtered into the ethos of Polaroid.”

Founders' philosophies shape companies. Jobs and Land were invested. It showed in the products their companies made. Different. His obsession was spreading Microsoft software worldwide. Microsoft's success is why their products are bland and boring.

Experience is important. It's probably why startups are built by generalists and scaled by specialists.

Jobs combined design, typography, storytelling, and product taste at Apple. Some of the best original Mac developers were poets and musicians. Edwin Land liked broad-minded people, according to his biography. Physicist-musicians or physicist-photographers.

Da Vinci was a master of art, engineering, architecture, anatomy, and more. He wrote and drew at the same desk. His genius is remembered centuries after his death. Da Vinci's statue would stand at the intersection of humanities and science.

We find incredibly creative people here. Superhumans. Designers, creators, and world-improvers. These are the people we need to navigate technology and lead world-changing companies. Generalists lead.

Leonardo Castorina

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:

  1. 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.
  2. Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
  3. 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:

  1. It had to be private, and nobody had to be able to read the entries.
  2. 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

Hector de Isidro

Hector de Isidro

3 years ago

Why can't you speak English fluently even though you understand it?

Many of us have struggled for years to master a second language (in my case, English). Because (at least in my situation) we've always used an input-based system or method.

I'll explain in detail, but briefly: We can understand some conversations or sentences (since we've trained), but we can't give sophisticated answers or speak fluently (because we have NOT trained at all).

What exactly is input-based learning?

Reading, listening, writing, and speaking are key language abilities (if you look closely at that list, it seems that people tend to order them in this way: inadvertently giving more priority to the first ones than to the last ones).

These talents fall under two learning styles:

  • Reading and listening are input-based activities (sometimes referred to as receptive skills or passive learning).

  • Writing and speaking are output-based tasks (also known as the productive skills and/or active learning).

by Anson Wong

What's the best learning style? To learn a language, we must master four interconnected skills. The difficulty is how much time and effort we give each.

According to Shion Kabasawa's books The Power of Input: How to Maximize Learning and The Power of Output: How to Change Learning to Outcome (available only in Japanese), we spend 7:3 more time on Input Based skills than Output Based skills when we should be doing the opposite, leaning more towards Output (Input: Output->3:7).

I can't tell you how he got those numbers, but I think he's not far off because, for example, think of how many people say they're learning a second language and are satisfied bragging about it by only watching TV, series, or movies in VO (and/or reading a book or whatever) their Input is: 7:0 output!

You can't be good at a sport by watching TikTok videos about it; you must play.

“being pushed to produce language puts learners in a better position to notice the ‘gaps’ in their language knowledge”, encouraging them to ‘upgrade’ their existing interlanguage system. And, as they are pushed to produce language in real time and thereby forced to automate low-level operations by incorporating them into higher-level routines, it may also contribute to the development of fluency. — Scott Thornbury (P is for Push)

How may I practice output-based learning more?

I know that listening or reading is easy and convenient because we can do it on our own in a wide range of situations, even during another activity (although, as you know, it's not ideal), writing can be tedious/boring (it's funny that we almost always excuse ourselves in the lack of ideas), and speaking requires an interlocutor. But we must leave our comfort zone and modify our thinking to go from 3:7 to 7:3. (or at least balance it better to something closer). Gradually.

“You don’t have to do a lot every day, but you have to do something. Something. Every day.” — Callie Oettinger (Do this every day)

We can practice speaking like boxers shadow box.

Speaking out loud strengthens the mind-mouth link (otherwise, you will still speak fluently in your mind but you will choke when speaking out loud). This doesn't mean we should talk to ourselves on the way to work, while strolling, or on public transportation. We should try to do it without disturbing others, such as explaining what we've heard, read, or seen (the list is endless: you can TALK about what happened yesterday, your bedtime book, stories you heard at the office, that new kitten video you saw on Instagram, an experience you had, some new fact, that new boring episode you watched on Netflix, what you ate, what you're going to do next, your upcoming vacation, what’s trending, the news of the day)

Who will correct my grammar, vocabulary, or pronunciation with an imagined friend? We can't have everything, but tools and services can help [1].

Lack of bravery

Fear of speaking a language different than one's mother tongue in front of native speakers is global. It's easier said than done, because strangers, not your friends, will always make fun of your accent or faults. Accept it and try again. Karma will prevail.

Perfectionism is a trap. Stop self-sabotaging. Communication is key (and for that you have to practice the Output too ).

“Don’t forget to have fun and enjoy the process.” — Ruri Ohama

[1] Grammarly, Deepl, Google Translate, etc.