codingarchitect

LLM Wiki

A pattern for building personal knowledge bases using LLMs.

This is an idea file, it is designed to be copy pasted to your own LLM Agent (e.g. OpenAI Codex, Claude Code, OpenCode / Pi, or etc.). Its goal is to communicate the high level idea, but your agent will build out the specifics in collaboration with you.

The core idea

Most people's experience with LLMs and documents looks like RAG: you upload a collection of files, the LLM retrieves relevant chunks at query time, and generates an answer. This works, but the LLM is rediscovering knowledge from scratch on every question. There's no accumulation. Ask a subtle question that requires synthesizing five documents, and the LLM has to find and piece together the relevant fragments every time. Nothing is built up. NotebookLM, ChatGPT file uploads, and most RAG systems work this way.

codingarchitect

- The Remedy creates a Medicinal Disease which Replaces the Natural Disease (Primary Action)
- Vital force's curative response to the medicinal disease (Secondary Action)
![Primary and Seondary Actions in Orthodox systems of medicine and homeopathy](https://private-user-images.githubusercontent.com/1906866/558795443-1e05d9cb-f9d2-45d0-8ca9-a402735780f9.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.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.IZclPU8TTVazfvpELZSxuP-A3QAc5X8lJ_a5Ul4tB

codingarchitect

• Reversing gut dysbiosis
  Butyrate (tributyrin) supplementation

  • Antibiotics wipe out butyrate producers, putting significant stress on the cells that line the large intestine. If we can support epithelial metabolism with supplemental butyrate until our butyrate-producers can recover, theoretically, we may be able to prevent an environment that favors opportunistic pathogens.
  Glutamine supplementation

  • (Likewise, supplementing with glutamine may prevent antibiotic-induced dysbiosis in the small intestine.)

codingarchitect

• Fiber Paradox:
  • for people who have a damaged gut adding more fiber to their diet can be challenging and
  • it's because your gut is not in a good place and we actually need a healthy gut to break down and process our fiber but the paradox of it is not that it's that these are the people who need the fiber the most
  • fiber is the most powerful way to heal and enhance the health of your gut microbiome
  • when you reduce your fiber you are in no way moving yourself towards a more healthy gut microbiome
  • from: https://youtu.be/pxbS5HkaWa8?t=3120

• You Need to START LOW and GO SLOW
• The GROWTH strategy doesn’t work for every single food sensitivity
  • Celiac disease
• Food allergies (as opposed to intolerances)

codingarchitect

Tips for eating fiber when you cannot tolerate fiber

• Select foods that are
  • low viscosity and
    • Pectin
    • Inulin
    • Partially Hydrolyzed Guar Gum (PHGG)
    • Oats
    • Acacia Fiber
  • naturally high in digestive enzymes
• Sprouted lentils

codingarchitect

• [[sibo]] [[treatment-protocol]] [[rajsree-nambudripad]] Dr. Rajsree's Herbal Protocol for SIBO: Treat Your Gas, Bloating, and IBS! collapsed:: true
  • Four Phase Protocol:
    • Phase 1: Promote Motility
    • Phase 2: Reduce Gas Levels
    • Phase 3: Reduce Inflammation
    • Phase 4: Kill Bacteria
  • Types
    • Hydrogen SIBO - Diarrhea, IBS-D
• Methane SIBO / Intestinal Methanogen Overgrowth IMO - Constipation, IBS-C

codingarchitect

Summarized from New subtyping of insomnia disorder and Insomnia disorder subtypes derived from life history and traits of affect and personality

• Highly Distressed
• Moderately Distressed
  • Reward-Sensitive
  • Reward-Insensitive
• Slightly Distressed
  • Low Reactive
• High Reactive

codingarchitect

Summary of The gut Microbiome Associates with Phenotypic Manifestations of Post-Acute COVID-19 Syndrome

Source and Special thanks to Reddit User kwil2

• ENTEROTYPE 1
  • gut-biome characteristics
    • a low count of
      • Bifidobacterium adolescentis and
• high count of

codingarchitect

TLDR Version

• Long COVID is associated with reduced circulating serotonin levels
• Serotonin depletion is driven by viral RNA-induced type I interferons (IFNs)
• IFNs reduce serotonin through diminished tryptophan uptake and hypercoagulability
• Peripheral serotonin deficiency impairs cognition via reduced vagal signaling

Graphical Abstract

codingarchitect

• Etiopathogenic theories about long COVID, Del Carpio-Orantes L. Etiopathogenic theories about long COVID. World J Virol 2023; 12(3): 204-208 [PMID: 37396704 DOI: 10.5501/wjv.v12.i3.204]
  • Theory of viral persistence or viral particles:
    • There is evidence that after an acute episode of COVID-19, there is persistence of viral particles in various organs up to one year after the episode and the organs mainly affected are: Brain, Gastrointestinal and Hemolymphatic; Similarly, they have been detected in blood, feces and urine
  • Theory of endothelial dysfunction:
    • This theory deals with the damage to the vascular endothelium that leads to endothelitis which, in turn, will favor platelet increase and activation, increased risk of thrombus formation with subsequent damage to organs and tissues by a mechanism of tissue ischemia that can affect the main organs and systems of the human body
  • **Theory of plat