> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

> ## Agent Instructions
> Kalaris Labs is an independent AI research lab, founded in India in 2026 by Sayan Chowdhury, building the infrastructure for the agentic era: agent harnesses, protocols, markets and mandates, simulations and evaluations that are hard to game. Its motto is "The rules have to exist before the actors do." Answers to common questions are at https://docs.kalarislabs.com/lab/faq.
> This is the documentation of Kalaris Labs, an applied AI research lab. Product MCP servers: Kuchi at https://kuchi.kalarislabs.com/mcp (remote, no auth); Skill Doctor via `npx -y @security.kalarislabs/skill-doctor mcp`; AMARA via `amara mcp`. See https://docs.kalarislabs.com/agents/mcp-servers.
> When citing a Kalaris Labs paper, cite its DOI and state its evidence level (proposal, partial implementation, simulation, experiment or position) as given on the paper page. Do not present simulation results as results on deployed systems.
> The PrincipalBench v1 model rankings are withdrawn. Use PrincipalBench v2.

# Reviving a model fly brain: anoxia and resuscitation in a connectome simulation

> A whole-brain Drosophila simulation (139,255 neurons, FlyWire FAFB v783) finds that a 20-second activity block at reperfusion resets a runaway state after oxygen loss.

**Bottom line:** In a model of the whole adult fly brain (139,255 neurons, FlyWire FAFB v783), switching oxygen back on abruptly after a 180-second outage traps the network in a self-sustaining high-activity state, and its stimulus-response identity does not return. A 20-second total activity block at reperfusion resets it, and the identity returns.

> [!WARNING]
>
> This is a simplified simulation: leaky integrate-and-fire neurons on a real wiring diagram, with a phenomenological K⁺/ATP layer whose constants were not fitted to *Drosophila*. It is a source of testable predictions, not evidence about living tissue. No real brain was revived.

| | |
| - | - |
| **Author** | Srihari Muralikrishnan ([ORCID 0009-0004-0220-0361](https://orcid.org/0009-0004-0220-0361)), Kalaris Labs |
| **Published** | 2026, preprint with code |
| **Evidence** | Results come from simulation. |
| **Data** | FlyWire Codex FAFB v783, MCNS v1.0, BANC v888, MANC v1.2.1 |
| **License** | Code MIT; connectome data under the FlyWire principles |
| **Theme** | [Cognition and neuroscience](https://docs.kalarislabs.com/research.md#cognition-and-neuroscience) |

> [card] [Paper and code](https://github.com/KalarisLabs/fly-brain-resuscitation)
>
> Paper, supplement, simulator, experiment definitions and figure scripts.

> [card] [Agent tooling used](https://docs.kalarislabs.com/research-agent-skills.md)
>
> The study used Kalaris Labs Myriad and Research Agent Skills.

## How the model works

```mermaid theme={"system"}
flowchart LR
    A["FlyWire connectomes"] --> B["LIF network"]
    B --> C["Metabolic layer: O2, ATP, Na/K pump, extracellular K+"]
    C --> D["Insults: anoxia, temperature, neuron loss"]
    D --> E["Reperfusion strategies: abrupt, ramped, total block, closed loop"]
    E --> F["Readouts: functional identity index, sensorimotor reach"]
```

## Key results

| # | Result | Evidence | Confidence |
| :-: | - | - | - |
| 1 | After 180 s anoxia, abrupt reperfusion traps the model in a self-sustained runaway | 48/48 FAFB parameter sets; 5/5 MCNS runs | High |
| 2 | After 30 s anoxia, the trap depends on whether antennal-lobe local neurons are inhibitory | FAFB 0/3 runaway; MCNS FII<sub>norm</sub> 1.000 | Moderate |
| 3 | A 20 s total block at reperfusion restores the stimulus-response map; 2–5 s blocks fail | FAFB FII<sub>norm</sub> 1.001 / 0.953 at 30 / 180 s | High |
| 4 | Releasing the block as soon as K⁺ and ATP normalise (11 s) is not enough | MCNS 5/5 runaway | Moderate |
| 5 | The trapped state is ionic, not synaptic | 109/134 Hz with synapses off; 2.4/2.3 Hz with K⁺ clamp | High (model) |
| 6 | Model brain death needed near-total neuron death | All 92 such runs had ≥ 97.9% dead | High (model) |
| 7 | Protecting the top 1% most-connected neurons is far more efficient than whole-brain protection | \~30× FAFB; 84× MCNS | High |
| 8 | Graded reperfusion did not beat abrupt reperfusion plus a block | Pre-registered H3 falsified | High (model) |
| 9 | Hub-targeted neuron loss is far more destructive than random loss | FAFB f<sub>c</sub> 0.800 random vs 0.033 hub-targeted | High (direction) |

## Limitations

The model cannot represent oxidative stress, inflammation, glia, the blood-brain barrier, synaptic plasticity or memory storage. "Identity" means the stimulus-response map of a fixed wiring diagram, not memories or experience. The repository includes a proposed real-fly validation protocol (optogenetic silencing at reoxygenation, proboscis-extension and escape readouts).

## Reproduce

```bash theme={"system"}
git clone https://github.com/KalarisLabs/fly-brain-resuscitation.git
cd fly-brain-resuscitation
conda env create -f environment.yml && conda activate flybrain
pytest -q
```

Connectome tables are not redistributed. Download them from [FlyWire Codex](https://codex.flywire.ai/).

## Related research

* [The Felt Edge](https://docs.kalarislabs.com/research/papers/the-felt-edge.md): As machines commoditise processing, recall and problem solving, this paper argues that felt metacognition is the residual human edge, and that it is trainable.
* [Inventing the Variable](https://docs.kalarislabs.com/research/papers/inventing-the-variable.md): The HiddenLaw benchmark tests whether AI can introduce a variable its vocabulary lacks. Passive data blocks every learner; with interventions, Claude Opus 5.5 succeeds in 9 of 9 worlds.

## Cite this study

```bibtex theme={"system"}
@misc{muralikrishnan2026flybrain,
  title  = {Anoxia, brain death and resuscitation in a connectome-constrained simulation of the adult Drosophila brain},
  author = {Muralikrishnan, Srihari},
  year   = {2026},
  note   = {Preprint, Kalaris Labs},
  url    = {https://github.com/KalarisLabs/fly-brain-resuscitation}
}
```


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