{"overview":{"name":"RabbitOS body model","version":"1.0.0","disclaimer":"Educational and research visualisation. Anatomical positions follow standard teaching references and are typical adult values; patterns are textbook-level and illustrative, not measurements from or predictions for any person. Not medical advice and not for diagnosis.","licence":"No licence has been chosen for this model yet; ask the owner before reuse beyond reading it.","frame":{"units":"cm","origin":"jugular notch (top of the breastbone, about T2/T3)","x":"person's right (negative = left)","y":"front (negative = back)","z":"up (negative = below the notch)"},"evidence_levels":{"established":"standard textbook or well replicated","supported":"reported repeatedly but mixed or context dependent","exploratory":"suggestive, not settled"},"sections":["overview","organs","routes","supply","scenarios","systems","genes","layout","physiology","pathways"],"sources":["standard vertebral-level teaching (transpyloric plane at L1; heart T5-T8; diaphragm openings T8, T10, T12)","Wikipedia: Spinal cord, Vagus nerve, Sympathetic nervous system, Thoracic diaphragm, Kidney, Human heart, Lung, Transpyloric plane (checked 2026-10-10)"]},"organs":[{"id":"eyes","name":"Eyes and visual pathway","concepts":{"mesh":{"id":"D005123","label":"Eye","uri":"https://id.nlm.nih.gov/mesh/D005123"},"umls":null},"description":"The retinas send signals through the optic nerves and chiasm to the thalamus (lateral geniculate) and on to the occipital cortex at the back of the brain.","centre_cm":[5.4,16.8,25.5],"routes":["visual"]},{"id":"lungs","name":"Lungs","concepts":{"mesh":{"id":"D008168","label":"Lung","uri":"https://id.nlm.nih.gov/mesh/D008168"},"umls":null},"description":"Three lobes on the right and two on the left (the left has a notch for the heart). Breathing rhythm is set in the brain stem; the brain also adjusts airway width and responds to carbon dioxide.","centre_cm":[9,-1.5,-10],"routes":["vagus","sympathetic","phrenic"]},{"id":"heart","name":"Heart","concepts":{"mesh":{"id":"D006321","label":"Heart","uri":"https://id.nlm.nih.gov/mesh/D006321"},"umls":null},"description":"Four chambers behind the breastbone, tilted so the apex points left. The sinoatrial node starts each beat; the vagus nerve slows it and sympathetic nerves from T1-T4 speed it up.","centre_cm":[-2.2,1.6,-10.5],"routes":["vagus","sympathetic","hpa"]},{"id":"diaphragm","name":"Diaphragm","concepts":{"mesh":{"id":"D003964","label":"Diaphragm","uri":"https://id.nlm.nih.gov/mesh/D003964"},"umls":null},"description":"The dome-shaped breathing muscle under the lungs. The phrenic nerve (C3-C5) drives it; the oesophagus, aorta and vena cava pass through it at T10, T12 and T8.","centre_cm":[0,0,-20],"routes":["phrenic"]},{"id":"esophagus","name":"Oesophagus","concepts":{"mesh":{"id":"D004947","label":"Esophagus","uri":"https://id.nlm.nih.gov/mesh/D004947"},"umls":null},"description":"The swallowing tube behind the windpipe. The vagus nerve and brain stem coordinate each swallow.","centre_cm":[-0.5,-3.4,-12],"routes":["vagus"]},{"id":"liver","name":"Liver","concepts":{"mesh":{"id":"D008099","label":"Liver","uri":"https://id.nlm.nih.gov/mesh/D008099"},"umls":null},"description":"Fills the right upper abdomen under the diaphragm. Releases glucose under stress hormones and breaks down many chemicals, including brain monoamines and drugs.","centre_cm":[4,1.5,-22],"routes":["vagus","sympathetic","hpa"]},{"id":"gallbladder","name":"Gallbladder","concepts":{"mesh":{"id":"D005704","label":"Gallbladder","uri":"https://id.nlm.nih.gov/mesh/D005704"},"umls":null},"description":"Stores bile under the liver; vagal and hormone signals make it contract after a meal.","centre_cm":[8,4,-29],"routes":["vagus"]},{"id":"stomach","name":"Stomach","concepts":{"mesh":{"id":"D013270","label":"Stomach","uri":"https://id.nlm.nih.gov/mesh/D013270"},"umls":null},"description":"A J-shaped bag from the oesophagus (T10-T11) to the pylorus at L1. Controlled by the vagus nerve and its own enteric nerves; stress and emotion change acid release and emptying.","centre_cm":[-4,3,-26],"routes":["vagus","sympathetic","enteric"]},{"id":"pancreas","name":"Pancreas","concepts":{"mesh":{"id":"D010179","label":"Pancreas","uri":"https://id.nlm.nih.gov/mesh/D010179"},"umls":null},"description":"Lies behind the stomach at L1-L2, head in the curve of the duodenum, tail at the spleen. Vagal and sympathetic nerves tune its enzyme and insulin release.","centre_cm":[-1,-2,-31],"routes":["vagus","sympathetic","hpa"]},{"id":"spleen","name":"Spleen and immune system","concepts":{"mesh":{"id":"D013154","label":"Spleen","uri":"https://id.nlm.nih.gov/mesh/D013154"},"umls":null},"description":"Behind the left 9th-11th ribs. Immune cells here respond to nerve signals and to the stress hormone cortisol.","centre_cm":[-12,-4.5,-24.5],"routes":["vagus","sympathetic","hpa"]},{"id":"adrenals","name":"Adrenal glands","concepts":{"mesh":{"id":"D000311","label":"Adrenal Glands","uri":"https://id.nlm.nih.gov/mesh/D000311"},"umls":null},"description":"Caps on top of each kidney. They make cortisol (cortex) and adrenaline and norepinephrine (medulla) when the brain signals stress through the pituitary and sympathetic nerves.","centre_cm":[5.5,-6,-26.5],"routes":["sympathetic","hpa"]},{"id":"kidneys","name":"Kidneys","concepts":{"mesh":{"id":"D007668","label":"Kidney","uri":"https://id.nlm.nih.gov/mesh/D007668"},"umls":null},"description":"T12-L3 on the back wall of the abdomen, the right a little lower. Blood pressure and fluid balance are tuned by brain signals (sympathetic nerves and the hormone vasopressin). Ureters carry urine down to the bladder.","centre_cm":[7.5,-5.5,-33],"routes":["sympathetic","hpa"]},{"id":"gut","name":"Gut (small and large intestine)","concepts":{"mesh":{"id":"D007422","label":"Intestines","uri":"https://id.nlm.nih.gov/mesh/D007422"},"umls":null},"description":"A \"second brain\" of about 500 million neurons. Around 90% of the body's serotonin is made here, and the gut talks to the brain through the vagus nerve (to the splenic flexure) and sacral nerves (beyond).","centre_cm":[0,3,-40],"routes":["vagus","sympathetic","hpa","enteric"]},{"id":"bladder","name":"Bladder","concepts":{"mesh":{"id":"D001743","label":"Urinary Bladder","uri":"https://id.nlm.nih.gov/mesh/D001743"},"umls":null},"description":"Sits in the pelvis behind the pubic bone. Storing and emptying are coordinated by the pons and cortex through the spinal cord (sacral S2-S4).","centre_cm":[0,3.5,-53],"routes":["sympathetic","motor"]},{"id":"muscle","name":"Skeletal muscle (arms and legs)","concepts":{"mesh":{"id":"D018482","label":"Muscle, Skeletal","uri":"https://id.nlm.nih.gov/mesh/D018482"},"umls":null},"description":"Motor cortex and basal ganglia (dopamine) command muscle through the corticospinal tract and cord; acetylcholine is the signal at the nerve-muscle junction.","centre_cm":[22,0,-30],"routes":["motor"]},{"id":"spinalcord","name":"Spinal cord and nerves","concepts":{"mesh":{"id":"D013116","label":"Spinal Cord","uri":"https://id.nlm.nih.gov/mesh/D013116"},"umls":null},"description":"About 45 cm long, ending at L1-L2, with 31 pairs of nerves. The cervical enlargement (C4-T1) serves the arms and the lumbar enlargement the legs. Every brain-to-body signal except the vagus passes through it.","centre_cm":[0,-8.6,-12],"routes":["sympathetic","motor","phrenic"]}],"routes":[{"id":"vagus","name":"Vagus nerve (parasympathetic)","from":"brain stem","evidence":"established","organs":["heart","lungs","esophagus","stomach","gallbladder","pancreas","gut","liver","spleen"],"description":"The longest cranial nerve runs from the brain stem to the chest and abdomen. It slows the heart, drives digestion and carries gut signals back to the brain."},{"id":"sympathetic","name":"Sympathetic nerves (fight or flight)","from":"locus coeruleus, hypothalamus, spinal cord","evidence":"established","organs":["heart","lungs","stomach","pancreas","liver","adrenals","kidneys","gut","bladder","spleen","spinalcord"],"description":"Norepinephrine-driven signals leave through the spinal cord to raise heart rate and blood pressure, widen airways and slow digestion."},{"id":"hpa","name":"Stress hormone axis (HPA)","from":"hypothalamus and pituitary","evidence":"established","organs":["adrenals","liver","heart","gut","spleen","kidneys","pancreas"],"description":"The hypothalamus signals the pituitary, which signals the adrenal glands to release cortisol into the blood, so the effect reaches nearly every organ."},{"id":"motor","name":"Motor pathway (spinal cord)","from":"motor cortex and basal ganglia","evidence":"established","organs":["muscle","bladder","spinalcord"],"description":"Motor cortex fibres cross to the opposite side, run down the spinal cord and reach muscle at the nerve-muscle junction using acetylcholine."},{"id":"enteric","name":"Gut-brain axis (serotonin)","from":"gut and raphe nuclei","evidence":"supported","organs":["gut","stomach"],"description":"Gut serotonin and brain serotonin are made separately but talk through the vagus nerve and the blood. Gut-brain links to mood are an active research area."},{"id":"phrenic","name":"Phrenic nerves (C3-C5)","from":"brain stem breathing centres","evidence":"established","organs":["diaphragm","lungs","spinalcord"],"description":"The breathing centres in the brain stem send signals down the cord to C3-C5, where the phrenic nerves leave to drive the diaphragm. A cord injury above C3 cuts this link."},{"id":"visual","name":"Visual pathway","from":"occipital cortex","evidence":"established","organs":["eyes"],"description":"Retina to thalamus to occipital cortex. Damage at the back of the brain removes part of what the eyes can report."}],"supply":[{"organ":"heart","sympathetic_cord_segments":["T1","T4"],"parasympathetic_or_motor":"vagus (CN X)","sensation":"T1-T4 (angina is felt in the chest, left arm and jaw)","evidence":"established","note":"Sympathetic fibres speed the heart and strengthen each beat; the right vagus slows the sinoatrial node, the left slows the atrioventricular node."},{"organ":"lungs","sympathetic_cord_segments":["T2","T5"],"parasympathetic_or_motor":"vagus (CN X)","sensation":null,"evidence":"established","note":"Sympathetic input widens the airways; vagal input narrows them and increases secretions."},{"organ":"diaphragm","sympathetic_cord_segments":null,"parasympathetic_or_motor":"none (motor: phrenic nerve C3-C5)","sensation":"phrenic C3-C5 centrally, T5-T12 at the edge","evidence":"established","note":"Breathing's main muscle is driven by the phrenic nerve. A cord injury above C3 stops its supply; below C5 it is spared."},{"organ":"stomach","sympathetic_cord_segments":["T5","T9"],"parasympathetic_or_motor":"vagus (CN X)","sensation":"T6-T9","evidence":"established","note":"Greater splanchnic nerves (T5-T9) via the celiac ganglion; the vagal trunks drive acid and emptying."},{"organ":"liver","sympathetic_cord_segments":["T7","T10"],"parasympathetic_or_motor":"vagus (CN X)","sensation":"T7-T9 plus phrenic (shoulder-tip pain)","evidence":"established","note":"Celiac plexus supply; sympathetic input releases glucose."},{"organ":"spleen","sympathetic_cord_segments":["T6","T10"],"parasympathetic_or_motor":"no direct supply shown (vagus acts through the celiac plexus)","sensation":null,"evidence":"supported","note":"Sympathetic nerves follow the splenic artery; the vagus-spleen link is a research topic."},{"organ":"adrenals","sympathetic_cord_segments":["T10","L1"],"parasympathetic_or_motor":"none","sensation":null,"evidence":"established","note":"The only organ whose sympathetic nerves connect straight to its secreting cells: they release adrenaline and norepinephrine into the blood."},{"organ":"kidneys","sympathetic_cord_segments":["T10","L1"],"parasympathetic_or_motor":"vagus (renal branches, role unclear)","sensation":"T10-L1 (loin pain)","evidence":"established","note":"Sympathetic nerves narrow renal vessels and release renin."},{"organ":"gut","sympathetic_cord_segments":["T9","L2"],"parasympathetic_or_motor":"vagus to the splenic flexure, pelvic nerves S2-S4 beyond","sensation":"T9-L2","evidence":"established","note":"Sympathetic input slows movement; parasympathetic input drives it."},{"organ":"bladder","sympathetic_cord_segments":["T10","L2"],"parasympathetic_or_motor":"pelvic nerves S2-S4","sensation":"S2-S4","evidence":"established","note":"Sacral parasympathetic fibres empty the bladder; sympathetic fibres help hold urine."},{"organ":"esophagus","sympathetic_cord_segments":["T4","T6"],"parasympathetic_or_motor":"vagus (CN X) and the brain stem swallowing centre","sensation":"T4-T6 (heartburn is felt behind the breastbone)","evidence":"established","note":"The vagus drives each swallowing wave; the upper third is striated muscle commanded by the brain stem (nucleus ambiguus)."},{"organ":"gallbladder","sympathetic_cord_segments":["T7","T9"],"parasympathetic_or_motor":"vagus (CN X)","sensation":"T7-T9 plus phrenic (right shoulder-tip pain)","evidence":"established","note":"Vagal input and the hormone CCK make it contract after a fatty meal."},{"organ":"pancreas","sympathetic_cord_segments":["T6","T10"],"parasympathetic_or_motor":"vagus (CN X)","sensation":"T6-T10 (felt in the upper back)","evidence":"supported","note":"Vagal input drives enzyme and insulin release; sympathetic input dampens insulin."},{"organ":"muscle","sympathetic_cord_segments":null,"parasympathetic_or_motor":"none (motor: spinal nerves C5-T1 arms, L2-S3 legs)","sensation":null,"evidence":"established","note":"Skeletal muscle is commanded by motor neurons in the cord; the cervical enlargement serves the arms and the lumbar enlargement the legs."}],"scenarios":[{"id":"healthy","name":"Healthy baseline","description":"Typical resting pattern: alpha strongest at the back of the head, with smaller shares of delta, theta, beta and gamma.","typical_eeg":"Alpha strongest at the back.","body_effects":[]},{"id":"stroke","name":"Stroke: left temporal lesion","description":"A blocked or burst vessel damages a patch of tissue. EEG typically shows focal slowing (more delta and theta) and less fast activity over the damaged area, while distant areas look more normal. Fibres that pass through the lesion are interrupted. Brain imaging, not EEG, is what shows the lesion itself.","typical_eeg":"More delta and theta, less alpha and beta, over the lesion.","body_effects":[{"organ":"muscle","evidence":"established","strength":0.7,"description":"If the damage reaches motor pathways, weakness or paralysis appears on the opposite side of the body. A purely temporal lesion mostly affects language and hearing instead."},{"organ":"stomach","evidence":"established","strength":0.5,"description":"Swallowing is often impaired (dysphagia), which raises the risk of choking and chest infection."},{"organ":"heart","evidence":"supported","strength":0.5,"description":"Stroke can disturb heart rhythm and raise heart-muscle injury markers (\"stroke-heart syndrome\"), most clearly with damage near the insula."},{"organ":"lungs","evidence":"supported","strength":0.4,"description":"Chest infection (aspiration pneumonia) is a common complication after stroke."},{"organ":"bladder","evidence":"supported","strength":0.4,"description":"Bladder control is often lost in the first days after a stroke."},{"organ":"esophagus","evidence":"established","strength":0.5,"description":"The swallow is slowed or mistimed, so food and saliva can slip toward the airway."},{"organ":"spinalcord","evidence":"established","strength":0.5,"description":"The motor tract below the damage slowly degenerates (Wallerian degeneration) and the reflexes below it become brisk, which is why weakness turns into stiffness (spasticity)."}]},{"id":"tbi","name":"Traumatic brain injury (diffuse, frontal and temporal)","description":"Frontal and temporal poles are bruised most often, and shearing can injure long fibres everywhere. EEG often shows more theta and delta, less alpha and a slower dominant rhythm, in proportion to severity. Dopamine, acetylcholine and norepinephrine systems are commonly affected.","typical_eeg":"More theta and delta everywhere, less alpha.","body_effects":[{"organ":"heart","evidence":"supported","strength":0.7,"description":"Severe injury can cause surges of sympathetic activity: fast heart rate and high blood pressure (\"paroxysmal sympathetic hyperactivity\")."},{"organ":"lungs","evidence":"supported","strength":0.5,"description":"Breathing rate and rhythm can change, and breathing in is harder when injury is deep in the brain."},{"organ":"adrenals","evidence":"established","strength":0.6,"description":"The pituitary-adrenal axis is disturbed: cortisol can be too high early and too low later if the pituitary is damaged."},{"organ":"muscle","evidence":"established","strength":0.6,"description":"Weakness, stiffness (spasticity) and loss of coordination, depending on which pathways are injured."},{"organ":"gut","evidence":"supported","strength":0.4,"description":"Digestion slows and stress ulcers are more likely in the first days after severe injury."},{"organ":"kidneys","evidence":"supported","strength":0.4,"description":"Water and salt balance can swing (for example diabetes insipidus or salt wasting) when the hypothalamus or pituitary is hurt."},{"organ":"spinalcord","evidence":"supported","strength":0.4,"description":"Diffuse axonal injury can include long tracts running from the brain stem into the cord, so motor and autonomic signals arrive weakened or out of step."},{"organ":"esophagus","evidence":"supported","strength":0.4,"description":"Swallowing coordination is often impaired after moderate to severe injury."},{"organ":"stomach","evidence":"supported","strength":0.4,"description":"Emptying slows in the first days."}]},{"id":"occipital","name":"Occipital lesion","description":"Damage at the back of the brain disrupts the visual pathway. EEG shows the normal posterior alpha rhythm reduced or lost over the damaged side, with slow delta activity there.","typical_eeg":"Posterior alpha reduced or lost, delta increased.","body_effects":[{"organ":"eyes","evidence":"established","strength":0.9,"description":"The eyes themselves are healthy, but part of the visual field is lost on the side opposite the damage (homonymous hemianopia)."}]},{"id":"alz","name":"Alzheimer's-type pattern (illustrative)","description":"Cholinergic neurons of the basal forebrain are lost early, and the cortex thins in temporal and parietal areas. EEG typically shows slowing: more delta and theta, less alpha and beta, most clearly at the back. This pattern is not specific to Alzheimer's disease.","typical_eeg":"More delta and theta, less alpha and beta, most at the back.","body_effects":[{"organ":"stomach","evidence":"supported","strength":0.4,"description":"Swallowing difficulty and weight loss are common as the disease advances."},{"organ":"gut","evidence":"supported","strength":0.3,"description":"Constipation and bowel control problems become more common in later stages."},{"organ":"bladder","evidence":"supported","strength":0.4,"description":"Bladder control is lost in later stages."},{"organ":"muscle","evidence":"supported","strength":0.4,"description":"Movement slows and walking becomes less steady in later stages."},{"organ":"heart","evidence":"exploratory","strength":0.25,"description":"Autonomic (heart-rate and blood-pressure) control may change; findings vary."},{"organ":"esophagus","evidence":"supported","strength":0.35,"description":"The swallow becomes slower and less coordinated as the disease advances."}]},{"id":"epilepsy","name":"Epileptic focus (right frontal)","description":"An irritable patch of cortex fires in bursts. EEG shows brief spikes and sharp waves at the focus, often followed by a slow wave, rather than a lasting change in band power. Weak GABA inhibition or excess glutamate excitation can lower the threshold.","typical_eeg":"Brief spikes and sharp waves at the focus.","body_effects":[{"organ":"muscle","evidence":"established","strength":0.8,"description":"In a generalised convulsive seizure muscles stiffen and jerk. Focal seizures can affect one limb or one side."},{"organ":"heart","evidence":"supported","strength":0.6,"description":"Heart rate usually rises during a seizure and can sometimes slow or stop. Heart-rhythm changes are a leading suspect in sudden unexpected death in epilepsy (SUDEP)."},{"organ":"lungs","evidence":"supported","strength":0.6,"description":"Breathing can pause (apnea) during or after a seizure."},{"organ":"stomach","evidence":"exploratory","strength":0.2,"description":"Nausea or a rising feeling in the stomach can start some temporal-lobe seizures."},{"organ":"bladder","evidence":"established","strength":0.4,"description":"Bladder control can be lost during a convulsive seizure."},{"organ":"diaphragm","evidence":"supported","strength":0.6,"description":"During the tonic phase the breathing muscle is overridden by the convulsion, so breathing stops until the seizure ends."},{"organ":"spinalcord","evidence":"established","strength":0.8,"description":"The cord carries the seizure's motor drive down to the muscles on both sides, and afterwards its signals are briefly reduced."}]}],"systems":[{"id":"dopamine","name":"Dopamine","description":"Three main routes: nigrostriatal (substantia nigra to striatum, movement), mesolimbic (ventral tegmental area to nucleus accumbens, reward and motivation) and mesocortical (to prefrontal cortex, planning and attention). Loss of nigrostriatal neurons causes Parkinson's disease.","body_links":[{"organ":"muscle","evidence":"established","description":"The nigrostriatal route controls movement; losing it causes the tremor and slowness of Parkinson's disease."},{"organ":"gut","evidence":"established","description":"Dopamine slows gut movement, and constipation is an early sign of Parkinson's disease."},{"organ":"kidneys","evidence":"supported","description":"Dopamine made in the kidney itself helps the body excrete salt."}]},{"id":"serotonin","name":"Serotonin","description":"Raphe nuclei in the brainstem send fibres to nearly the whole forebrain: thalamus, hippocampus, amygdala and cortex. It shapes mood, sleep and appetite, and many antidepressants act on it.","body_links":[{"organ":"gut","evidence":"established","description":"Most of the body's serotonin sits in the gut, where it drives movement and digestion."},{"organ":"lungs","evidence":"established","description":"The lung lining clears serotonin from the blood before it can act elsewhere."},{"organ":"heart","evidence":"supported","description":"Serotonin acts on blood vessels and the heart; antidepressants that raise it can slightly change heart rate."}]},{"id":"norepinephrine","name":"Norepinephrine","description":"The locus coeruleus in the pons projects very widely. It raises arousal and attention and drives part of the stress response; firing is high when awake and alert and nearly silent in REM sleep.","body_links":[{"organ":"heart","evidence":"established","description":"Speeds the heart and strengthens each beat."},{"organ":"lungs","evidence":"established","description":"Opens the airways so more air can reach the lungs."},{"organ":"adrenals","evidence":"established","description":"The adrenal medulla releases norepinephrine and adrenaline into the blood."},{"organ":"kidneys","evidence":"established","description":"Raises renin release, which raises blood pressure."},{"organ":"pancreas","evidence":"supported","description":"Dampens insulin release, which helps raise blood sugar during stress."},{"organ":"spinalcord","evidence":"established","description":"Locus coeruleus fibres run down the cord and tune both pain signals and motor neurons."},{"organ":"gut","evidence":"established","description":"Slows digestion during stress."}]},{"id":"acetylcholine","name":"Acetylcholine","description":"The nucleus basalis feeds the neocortex and the medial septum feeds the hippocampus. It supports attention and memory, and these cholinergic neurons are lost early in Alzheimer's disease.","body_links":[{"organ":"muscle","evidence":"established","description":"The signal that makes skeletal muscle contract, at the nerve-muscle junction."},{"organ":"heart","evidence":"established","description":"Vagal acetylcholine slows the heart."},{"organ":"gut","evidence":"established","description":"Drives gut movement and secretions through the vagus and enteric nerves."},{"organ":"diaphragm","evidence":"established","description":"Acetylcholine is the chemical signal from the phrenic nerve to the breathing muscle."},{"organ":"esophagus","evidence":"established","description":"Vagal acetylcholine drives each swallowing wave down the oesophagus."},{"organ":"stomach","evidence":"established","description":"Vagal acetylcholine drives acid release and stomach contractions."},{"organ":"pancreas","evidence":"supported","description":"Vagal acetylcholine tells the pancreas to release enzymes and insulin when food is expected."},{"organ":"spleen","evidence":"supported","description":"Vagus signals can dampen inflammation through the spleen (the \"cholinergic anti-inflammatory pathway\", well shown in animals, still being tested in people)."}]},{"id":"thalamocortical","name":"Thalamocortical loops (glutamate and GABA)","description":"The thalamus and cortex talk in loops. Excitatory (glutamate) fibres carry signals up and down, and the thalamic reticular nucleus applies inhibitory (GABA) control. These loops set the rhythm of the alpha wave and sleep spindles, and the synchronised activity of cortical pyramidal cells is what a scalp electrode picks up.","body_links":[{"organ":"muscle","evidence":"established","description":"Runaway glutamate firing, with too little GABA inhibition, is what drives convulsive seizures."},{"organ":"spinalcord","evidence":"established","description":"Glutamate carries the motor drive down the corticospinal tract; GABA interneurons in the cord keep reflexes in check."}]},{"id":"hpa","name":"Stress axis (HPA, cortisol)","description":"The hypothalamus signals the pituitary, which signals the adrenal glands (outside the brain) to release cortisol. Cortisol feeds back on the hippocampus, prefrontal cortex and hypothalamus through glucocorticoid receptors.","body_links":[{"organ":"adrenals","evidence":"established","description":"Release cortisol when the pituitary signals them."},{"organ":"liver","evidence":"established","description":"Cortisol raises blood sugar by telling the liver to release glucose."},{"organ":"heart","evidence":"supported","description":"Long-term high cortisol is linked to higher blood pressure and heart risk."},{"organ":"spleen","evidence":"established","description":"Cortisol restrains immune cells; long-term stress changes immune responses."},{"organ":"gut","evidence":"supported","description":"Stress hormones change gut movement, sensitivity and the gut lining."}]}],"genes":[{"gene":"SLC6A4","organs":["gut","lungs"],"evidence":"established","description":"The serotonin transporter also works outside the brain: in the gut lining and in the lung lining, where it clears serotonin from the blood.","clinvar_variants":160,"clinvar_pathogenic_or_likely":10,"clinvar_snapshot":"2026-10-09","identifiers":{"name":"solute carrier family 6 member 4 (serotonin transporter)","ncbi_gene_id":"6532","hgnc":"HGNC:11050","omim":"182138","ensembl":"ENSG00000108576","uniprot":"P31645","cytoband":"17q11.2","refseq_transcript":"NM_001045.6","refseq_protein":"NP_001036.1","synonyms":["5-HTT","5HTT","SERT","hSERT","SERT1","HTT","OCD1","5-HTTLPR"],"location":"chromosome 17, NC_000017.11:30,194,319-30,235,697 (minus strand), GRCh38.p14","summary":"This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. It is a target of psychomotor stimulants such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake; results in the literature about any effect on behavior and depression conflict. (NCBI Gene summary, provided by RefSeq, May 2019)","source":"NCBI Datasets package for human SLC6A4 (GRCh38.p14 annotation GCF_000001405.40-RS_2025_08), downloaded 2026-10-10","links":{"ncbi_gene":"https://www.ncbi.nlm.nih.gov/gene/6532","omim":"https://www.omim.org/entry/182138","ensembl":"https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000108576","uniprot":"https://www.uniprot.org/uniprotkb/P31645","hgnc":"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11050"}}},{"gene":"HTR2A","organs":["gut","heart"],"evidence":"supported","description":"The 5-HT2A receptor is also found on blood vessels, platelets and gut muscle.","clinvar_variants":108,"clinvar_pathogenic_or_likely":56,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"MAOA","organs":["liver","gut"],"evidence":"established","description":"The enzyme breaks down monoamines (serotonin, norepinephrine, dopamine) in the gut wall and liver, before they reach the blood.","clinvar_variants":515,"clinvar_pathogenic_or_likely":176,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"COMT","organs":["liver","kidneys"],"evidence":"established","description":"The enzyme is most active in liver and kidney, where it clears dopamine, norepinephrine and adrenaline.","clinvar_variants":662,"clinvar_pathogenic_or_likely":394,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"TH","organs":["adrenals","heart"],"evidence":"established","description":"Makes dopamine and then norepinephrine and adrenaline in the adrenal medulla and in sympathetic nerves.","clinvar_variants":1297,"clinvar_pathogenic_or_likely":225,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"DDC","organs":["adrenals","kidneys","gut"],"evidence":"established","description":"Makes dopamine and serotonin, including in the kidney and gut.","clinvar_variants":694,"clinvar_pathogenic_or_likely":111,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"DBH","organs":["adrenals","heart"],"evidence":"established","description":"Turns dopamine into norepinephrine in the adrenal medulla and in sympathetic nerves.","clinvar_variants":636,"clinvar_pathogenic_or_likely":53,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"SLC6A2","organs":["heart","adrenals"],"evidence":"established","description":"The norepinephrine transporter clears norepinephrine at sympathetic nerve endings in the heart and in the adrenal gland.","clinvar_variants":138,"clinvar_pathogenic_or_likely":18,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"DRD2","organs":["gut"],"evidence":"established","description":"Dopamine D2 receptors slow gut movement; drugs that block them (such as metoclopramide) speed it up.","clinvar_variants":196,"clinvar_pathogenic_or_likely":17,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"CHAT","organs":["muscle","gut"],"evidence":"established","description":"Makes acetylcholine for motor nerves reaching muscle and for enteric nerves in the gut.","clinvar_variants":1492,"clinvar_pathogenic_or_likely":179,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"CHRNA7","organs":["spleen","lungs"],"evidence":"supported","description":"The nicotinic receptor on immune cells links the vagus nerve to inflammation control.","clinvar_variants":472,"clinvar_pathogenic_or_likely":203,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"NR3C1","organs":["adrenals","liver","heart","gut","spleen","muscle"],"evidence":"established","description":"The glucocorticoid receptor is present in almost every tissue, so cortisol reaches the whole body.","clinvar_variants":367,"clinvar_pathogenic_or_likely":31,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"FKBP5","organs":["adrenals","liver","spleen"],"evidence":"supported","description":"Tunes how strongly cells respond to cortisol, so it shapes the stress response beyond the brain.","clinvar_variants":84,"clinvar_pathogenic_or_likely":7,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"SCN1A","organs":["heart"],"evidence":"supported","description":"Also active in heart muscle; heart-rhythm effects are being studied as a link to SUDEP in Dravet syndrome.","clinvar_variants":5536,"clinvar_pathogenic_or_likely":2322,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"BDNF","organs":["muscle"],"evidence":"supported","description":"Exercise raises BDNF made by muscle as well as by the brain.","clinvar_variants":251,"clinvar_pathogenic_or_likely":23,"clinvar_snapshot":"2026-10-09","identifiers":null},{"gene":"APOE","organs":["liver","heart"],"evidence":"established","description":"Mostly made by the liver, which carries fats in the blood; the e4 form also raises heart-disease risk.","clinvar_variants":311,"clinvar_pathogenic_or_likely":34,"clinvar_snapshot":"2026-10-09","identifiers":null}],"layout":{"landmarks_cm_below_notch":{"sternalAngle":-5,"xiphisternal":-17,"transpyloric":-29,"umbilicus":-40,"iliacCrest":-42,"pubicSymphysis":-54},"vertebral_body_centres_cm":{"C1":11.5,"C2":10,"C3":8.5,"C4":7,"C5":5.5,"C6":4,"C7":2.5,"T1":1,"T2":-1.5,"T3":-4,"T4":-6.5,"T5":-9,"T6":-11.5,"T7":-14,"T8":-16.5,"T9":-19,"T10":-21.5,"T11":-24,"T12":-26.5,"L1":-29.5,"L2":-32.9,"L3":-36.3,"L4":-39.7,"L5":-43.1,"S1":-45,"S5":-54,"Coccyx":-57},"organ_placements":{"heart":{"centre_cm":[-2.2,1.6,-10.5],"size_cm":[8.5,6.5,12],"note":"T5-T8, behind the sternum, two thirds to the left, apex at the 5th intercostal space 8-9 cm left of the midline"},"rightLung":{"centre_cm":[9,-1.5,-10],"size_cm":[11,16,26],"note":"apex above the first rib, base on the diaphragm at the 6th rib (front) to the 10th rib (back); three lobes"},"leftLung":{"centre_cm":[-9,-1.5,-10],"size_cm":[11,16,26],"note":"two lobes; cardiac notch and lingula where it wraps the heart"},"liver":{"centre_cm":[4,1.5,-22],"size_cm":[22,15,14],"note":"right upper abdomen under the diaphragm, from the 5th rib down to the costal margin, left lobe crosses the midline"},"gallbladder":{"centre_cm":[8,4,-29],"size_cm":[3.2,3.2,8],"note":"under the liver where the 9th costal cartilage meets the right edge of the rectus, on the transpyloric plane"},"stomach":{"centre_cm":[-4,3,-26],"size_cm":[12,8,20],"note":"cardia T10-T11, fundus under the left dome, pylorus 2.5 cm right of the midline at L1"},"spleen":{"centre_cm":[-12,-4.5,-24.5],"size_cm":[4,7,12],"note":"behind the 9th-11th ribs on the left, lower border near L1"},"pancreas":{"centre_cm":[-1,-2,-31],"size_cm":[15,3,5],"note":"L1-L2 behind the stomach, head in the duodenal loop, tail at the spleen"},"rightKidney":{"centre_cm":[7.5,-5.5,-33],"size_cm":[5.5,3.2,11],"note":"T12-L3, about 1 cm lower than the left, hilum 5 cm from the midline at L1-L2"},"leftKidney":{"centre_cm":[-7.5,-5.5,-32],"size_cm":[5.5,3.2,11],"note":"T12-L3"},"rightAdrenal":{"centre_cm":[5.5,-6,-26.5],"size_cm":[3,1,4],"note":"cap on the upper pole of the right kidney"},"leftAdrenal":{"centre_cm":[-5.5,-6,-26.5],"size_cm":[3,1,4],"note":"crescent on the upper pole of the left kidney"},"bladder":{"centre_cm":[0,3.5,-53],"size_cm":[8,7,7],"note":"pelvis, behind the pubic symphysis"},"diaphragmRightDome":{"centre_cm":[6,-1,-16.5],"size_cm":[16,20,6],"note":"right dome reaches the 5th rib (nipple line), higher because of the liver"},"diaphragmLeftDome":{"centre_cm":[-6.5,-1,-18],"size_cm":[15,20,6],"note":"left dome about one rib space lower"}},"spinal_cord":{"length_cm":45,"ends_at_cm":-31.2,"ends_at_vertebra":"L1-L2","segments":{"C":8,"T":12,"L":5,"S":5},"nerve_pairs":31}},"physiology":{"healthy":{"phase":"baseline","heart":{"bpm":72,"irregular":0,"contractility":1},"lungs":{"rpm":14,"depth":1,"apnea":0,"consolidation":0,"spo2":98},"diaphragm":1,"esophagus":1,"stomach":1,"gut":1,"adrenals":1,"kidneys":1,"bladder":{"urgency":0.2,"control":1},"muscle":{"strengthL":1,"strengthR":1,"tone":1,"tremor":0,"spasm":0},"cord":{"motorFromLeftBrain":1,"motorFromRightBrain":1,"sensoryL":1,"sensoryR":1,"autonomic":1,"vagal":1,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":1}},"stroke":{"phase":"baseline","heart":{"bpm":88,"irregular":0.35,"contractility":1},"lungs":{"rpm":18,"depth":0.9,"apnea":0,"consolidation":0.6,"spo2":94},"diaphragm":1,"esophagus":0.5,"stomach":0.8,"gut":0.8,"adrenals":1.3,"kidneys":1,"bladder":{"urgency":0.6,"control":0.5},"muscle":{"strengthL":1,"strengthR":0.55,"tone":1.2,"tremor":0,"spasm":0},"cord":{"motorFromLeftBrain":0.45,"motorFromRightBrain":1,"sensoryL":1,"sensoryR":0.7,"autonomic":1.1,"vagal":0.85,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":1}},"tbi":{"phase":"baseline","heart":{"bpm":128,"irregular":0.2,"contractility":1.35},"lungs":{"rpm":26,"depth":0.8,"apnea":0,"consolidation":0,"spo2":95},"diaphragm":1,"esophagus":0.6,"stomach":0.4,"gut":0.45,"adrenals":2,"kidneys":0.7,"bladder":{"urgency":0.7,"control":0.5},"muscle":{"strengthL":0.7,"strengthR":0.7,"tone":1.7,"tremor":0.35,"spasm":0.3},"cord":{"motorFromLeftBrain":0.7,"motorFromRightBrain":0.7,"sensoryL":0.8,"sensoryR":0.8,"autonomic":1.7,"vagal":0.7,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":1}},"occipital":{"phase":"baseline","heart":{"bpm":72,"irregular":0,"contractility":1},"lungs":{"rpm":14,"depth":1,"apnea":0,"consolidation":0,"spo2":98},"diaphragm":1,"esophagus":1,"stomach":1,"gut":1,"adrenals":1,"kidneys":1,"bladder":{"urgency":0.2,"control":1},"muscle":{"strengthL":1,"strengthR":1,"tone":1,"tremor":0,"spasm":0},"cord":{"motorFromLeftBrain":1,"motorFromRightBrain":1,"sensoryL":1,"sensoryR":1,"autonomic":1,"vagal":1,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":0.05}},"alz":{"phase":"baseline","heart":{"bpm":74,"irregular":0.12,"contractility":1},"lungs":{"rpm":15,"depth":0.95,"apnea":0,"consolidation":0,"spo2":96},"diaphragm":1,"esophagus":0.8,"stomach":0.8,"gut":0.7,"adrenals":1.3,"kidneys":1,"bladder":{"urgency":0.5,"control":0.6},"muscle":{"strengthL":0.85,"strengthR":0.85,"tone":1.1,"tremor":0.1,"spasm":0},"cord":{"motorFromLeftBrain":0.9,"motorFromRightBrain":0.9,"sensoryL":1,"sensoryR":1,"autonomic":0.9,"vagal":0.85,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":1}},"epilepsy":{"cycle_seconds":18,"between_seizures":{"phase":"baseline","heart":{"bpm":74,"irregular":0,"contractility":1},"lungs":{"rpm":14,"depth":1,"apnea":0,"consolidation":0,"spo2":98},"diaphragm":1,"esophagus":1,"stomach":1,"gut":1,"adrenals":1,"kidneys":1,"bladder":{"urgency":0.2,"control":1},"muscle":{"strengthL":1,"strengthR":1,"tone":1,"tremor":0,"spasm":0},"cord":{"motorFromLeftBrain":1,"motorFromRightBrain":1,"sensoryL":1,"sensoryR":1,"autonomic":1,"vagal":1,"phrenic":1},"visual":{"leftBrain":1,"rightBrain":1}},"seizure":{"phase":"seizure","heart":{"bpm":150,"irregular":0.25,"contractility":1.3},"lungs":{"rpm":5,"depth":0.19999999999999996,"apnea":0.85,"consolidation":0,"spo2":82},"diaphragm":0.25,"esophagus":0.19999999999999996,"stomach":0.30000000000000004,"gut":0.25,"adrenals":2.6,"kidneys":0.8,"bladder":{"urgency":1,"control":0},"muscle":{"strengthL":1,"strengthR":1,"tone":2.2,"tremor":0.6,"spasm":1},"cord":{"motorFromLeftBrain":1.5,"motorFromRightBrain":1.5,"sensoryL":0.6,"sensoryR":0.6,"autonomic":2,"vagal":0.5,"phrenic":0.30000000000000004},"visual":{"leftBrain":1,"rightBrain":1}},"after_the_seizure":{"phase":"after the seizure","heart":{"bpm":98,"irregular":0.1,"contractility":1},"lungs":{"rpm":9,"depth":1.4,"apnea":0.1,"consolidation":0,"spo2":92},"diaphragm":1,"esophagus":0.6,"stomach":0.6,"gut":0.5,"adrenals":1.8,"kidneys":0.9,"bladder":{"urgency":0.4,"control":0.4},"muscle":{"strengthL":0.55,"strengthR":0.55,"tone":0.5,"tremor":0.15,"spasm":0},"cord":{"motorFromLeftBrain":0.6,"motorFromRightBrain":0.6,"sensoryL":0.8,"sensoryR":0.8,"autonomic":1.4,"vagal":1.1,"phrenic":0.9},"visual":{"leftBrain":1,"rightBrain":1}}}},"pathways":[{"id":"corticospinal.-1","label":"Left brain to right body (motor, corticospinal)"},{"id":"corticospinal.1","label":"Right brain to left body (motor, corticospinal)"},{"id":"sensory.-1","label":"Left body to brain (touch and position, dorsal column)"},{"id":"sensory.1","label":"Right body to brain (touch and position, dorsal column)"},{"id":"autonomic.1","label":"Sympathetic outflow (hypothalamus to T1-L2)"},{"id":"vagus.1","label":"Vagus nerves (rest and digest)"},{"id":"phrenic.1","label":"Phrenic nerves to the diaphragm (C3-C5)"},{"id":"visual.-1","label":"Visual pathway to the left occipital lobe (right visual field)"},{"id":"visual.1","label":"Visual pathway to the right occipital lobe (left visual field)"}]}