Medical Glossary

82 terms explained in plain language. Use this index to understand the clinical terminology used throughout the Field Guide.

acetylcholine

The primary neurotransmitter for memory, learning, and attention. Anticholinergic medications (Benadryl, some antidepressants) block it — a common hidden cause of brain fog.

adenosine

A chemical that builds up during waking hours, creating sleep pressure. Caffeine works by blocking adenosine receptors — which is why it masks fatigue rather than fixing it.

amyloid

A protein that can accumulate in the brain when the glymphatic system isn't clearing waste effectively. Associated with Alzheimer's disease. Deep sleep is essential for amyloid clearance.

anticholinergic

Medications that block acetylcholine — the neurotransmitter for memory and learning. Common culprits: Benadryl, older antidepressants, bladder medications. A leading hidden cause of drug-induced brain fog.

apnea

Sleep apnea — repeated pauses in breathing during sleep that drop oxygen levels and fragment sleep architecture. Causes morning brain fog, daytime fatigue, and long-term cognitive decline if untreated.

autophagy

The cell's self-cleaning process — damaged components are broken down and recycled. Triggered by fasting, exercise, and sleep. Impaired autophagy leads to cellular debris accumulation and cognitive decline.

BBB

Blood-brain barrier — the selective membrane protecting the brain from harmful substances in the bloodstream. Damage to the BBB is a key driver of brain fog.

BDNF

Brain-derived neurotrophic factor — a protein that promotes neuron growth, survival, and new connections. Exercise is the most reliable way to boost it. Low BDNF is linked to depression, cognitive decline, and slow recovery from brain fog.

benzodiazepine

A class of sedative medications (Valium, Xanax, Ativan) that enhance GABA activity. Effective short-term for anxiety but cause cognitive impairment, memory problems, and dependence with regular use.

biomarker

A measurable substance in the body that indicates a biological state or condition. Blood biomarkers like ferritin, hs-CRP, and TSH help identify the root cause of brain fog objectively.

blood-brain barrier

A selective membrane that controls what enters the brain from the bloodstream. When damaged by inflammation, toxins, or gut permeability, harmful substances leak in and trigger neuroinflammation.

butyrate

A short-chain fatty acid produced when gut bacteria ferment dietary fibre. Strengthens the gut lining, reduces inflammation, and crosses the blood-brain barrier to directly support neurons.

CBC

Complete blood count — a basic blood panel that measures red cells, white cells, and platelets. Can reveal anaemia, infection, or immune activation contributing to brain fog.

circadian

Relating to the body's ~24-hour internal clock. Circadian disruption (irregular sleep times, night-shift work, blue light at night) impairs melatonin production, cortisol rhythm, and cognitive performance.

cortisol

The primary stress hormone. Short bursts are useful (focus, alertness). Chronic elevation from ongoing stress damages the hippocampus, impairs sleep, and drives brain fog. Measured via morning saliva or blood test.

cytokine

Chemical messengers released by immune cells. Pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) drive brain fog by disrupting neuron communication. Anti-inflammatory cytokines help resolve it.

DAO

Diamine oxidase — the enzyme that breaks down histamine in the gut. Low DAO activity leads to histamine intolerance: brain fog, headaches, and flushing after aged cheese, wine, or fermented foods.

dendritic

Relating to dendrites — the branch-like extensions of neurons that receive signals from other neurons. Dendritic sprouting (growth of new branches) is a sign of healthy neuroplasticity.

dopamine

A neurotransmitter governing motivation, reward, and focus. Low dopamine = difficulty starting tasks, poor concentration, and lack of drive. Iron (ferritin) is essential for dopamine synthesis.

dysbiosis

An imbalance in gut bacteria — too many inflammatory species, too few protective ones. Drives systemic inflammation, impairs nutrient absorption, and disrupts neurotransmitter production.

elimination diet

A structured approach to identifying food triggers: remove suspected foods for 2–4 weeks, then reintroduce one at a time while monitoring symptoms. The gold standard for finding diet-driven brain fog.

ferritin

The protein that stores iron in your body. Optimal for brain function: 50–100 ng/mL. Below 30 impairs dopamine synthesis even when technically 'in range.' Many labs set the lower limit at 12 — far too low for cognitive health.

folate

Vitamin B9 — essential for methylation, DNA repair, and neurotransmitter production. Low folate impairs memory and mood. Found in leafy greens, legumes, and fortified foods. The methylated form (5-MTHF) is better absorbed.

Free T3

The active form of thyroid hormone that directly affects brain metabolism. Low Free T3 with normal TSH is a common missed cause of brain fog — your brain is running on a low-power setting.

Free T4

The storage form of thyroid hormone. Your body converts T4 → T3. Poor conversion (common with selenium or iron deficiency) means normal T4 but low active T3 — and brain fog.

GABA

Gamma-aminobutyric acid — the brain's main calming neurotransmitter. Balances excitatory signals. Benzodiazepines and alcohol artificially boost GABA, which is why withdrawal causes rebound anxiety and fog.

glutamate

The brain's primary excitatory neurotransmitter. Essential for learning, but excess glutamate is neurotoxic. MSG sensitivity and neuroinflammation can cause glutamate overload.

glymphatic

The brain's waste-clearance system, most active during deep sleep. It flushes out metabolic debris (including amyloid proteins linked to Alzheimer's). Poor sleep = poor glymphatic drainage = brain fog.

Hashimoto

Hashimoto's thyroiditis — an autoimmune condition where the immune system attacks the thyroid gland. The most common cause of hypothyroidism. Detected by elevated TPO antibodies, often years before TSH goes abnormal.

HbA1c

Glycated haemoglobin — measures average blood sugar over 2–3 months. Above 5.7% suggests prediabetes. Blood sugar instability is a major driver of brain fog, even at 'normal' levels.

HBOT

Hyperbaric oxygen therapy — breathing pure oxygen in a pressurised chamber. Promotes neuroplasticity and reduces neuroinflammation. The strongest evidence is for post-COVID brain fog (60-session protocols at 2.0 ATA).

histamine

A compound involved in immune response, digestion, and brain function. Excess histamine (from high-histamine foods or low DAO enzyme) causes brain fog, headaches, skin flushing, and nasal congestion.

HPA axis

Hypothalamic-pituitary-adrenal axis — the brain-to-adrenal gland communication system that controls your stress response. Chronic activation leads to cortisol dysregulation, fatigue, and cognitive impairment.

hs-CRP

High-sensitivity C-reactive protein — a blood marker for systemic inflammation. Optimal: below 1.0 mg/L. Elevated levels indicate your immune system is active, which can drive brain fog. Cheap, widely available test.

hypothyroid

Underactive thyroid — insufficient thyroid hormone production. Causes fatigue, brain fog, weight gain, and cold intolerance. Subclinical hypothyroidism (normal TSH, low Free T3) is frequently missed.

IL-1

Interleukin-1β — a pro-inflammatory cytokine that reduces neurogenesis and disrupts sleep architecture. One of the key drivers of sickness behaviour and brain fog.

IL-6

Interleukin-6 — a pro-inflammatory cytokine. Elevated in Long COVID, chronic stress, and autoimmune conditions. Directly impairs hippocampal function (memory) and prefrontal cortex (focus).

intestinal permeability

Often called 'leaky gut' — when the gut lining develops gaps, allowing bacteria, toxins, and undigested food particles to enter the bloodstream and trigger immune activation.

ketogenic

A very-low-carbohydrate, high-fat diet that shifts the brain's fuel source from glucose to ketones. Some evidence for reducing neuroinflammation and improving mitochondrial function.

LDN

Low-dose naltrexone — naltrexone at 1–4.5 mg (vs. standard 50 mg) modulates the immune system and reduces neuroinflammation. Used off-label for Long COVID, fibromyalgia, and autoimmune brain fog. Requires prescription.

leaky gut

The colloquial term for increased intestinal permeability — gaps in the gut lining that allow inflammatory molecules into the bloodstream, triggering immune activation and brain fog.

lipopolysaccharide

Bacterial fragments (endotoxins) from gram-negative gut bacteria. When they leak through a damaged gut barrier into the bloodstream, they trigger a powerful inflammatory response that reaches the brain.

LPS

Lipopolysaccharides — bacterial endotoxins that trigger inflammation when they leak from the gut into the bloodstream through a damaged intestinal barrier.

mast cell

Immune cells that release histamine and other chemicals during allergic and inflammatory reactions. Overactive mast cells (MCAS) can cause widespread symptoms including brain fog.

MCAS

Mast cell activation syndrome — mast cells release excessive histamine and other mediators, causing brain fog, flushing, hives, GI symptoms, and reactions to foods/chemicals. Often overlaps with POTS and EDS.

melatonin

The hormone that signals your body to sleep. Produced ~16 hours after morning light exposure. Blue light at night suppresses it. Supplementing is less effective than fixing the light cycle.

methylmalonic

Methylmalonic acid (MMA) — a more sensitive marker for B12 deficiency than serum B12 alone. Elevated MMA indicates functional B12 deficiency even when serum B12 is borderline normal.

microbiome

The community of trillions of bacteria, fungi, and viruses in your gut. An imbalanced microbiome (dysbiosis) drives inflammation via the gut-brain axis, directly affecting mood and cognition.

microglia

The brain's resident immune cells. When activated by infection, stress, or injury, they release inflammatory chemicals that can impair cognition. Think of them as the brain's security guards — helpful in short bursts, destructive when they won't stand down.

mitochondri

Mitochondria — the energy-producing structures inside every cell. When they malfunction (from inflammation, nutrient deficiency, or viral damage), cells can't produce enough ATP (energy). Result: fatigue and brain fog.

NAC

N-acetyl cysteine — an amino acid supplement that replenishes glutathione (the body's master antioxidant), reduces neuroinflammation, and helps break down mucus. Dose: 600–1,200 mg/day.

NAD

Nicotinamide adenine dinucleotide — a coenzyme essential for cellular energy production. Declines with age. NAD+ precursors (NR, NMN) are being studied for cognitive recovery, especially in Long COVID.

neurogenesis

The creation of new neurons, primarily in the hippocampus (memory centre). Exercise, sleep, and omega-3s promote it. Chronic inflammation suppresses it.

neuroinflammation

Inflammation specifically in the brain and nervous system. Unlike a swollen ankle, you can't see or feel it directly — but it disrupts processing speed, memory, and executive function. Measured indirectly via hs-CRP and other blood markers.

neuroplasticity

The brain's ability to rewire itself by forming new neural connections. Brain fog doesn't cause permanent damage — neuroplasticity means recovery is possible once the underlying cause is addressed.

NF-kB

Nuclear factor kappa-B — a protein complex that controls inflammation gene expression. When chronically activated, it drives sustained neuroinflammation. Curcumin, omega-3s, and NAC help modulate it.

NMN

Nicotinamide mononucleotide — a precursor to NAD+, the coenzyme essential for mitochondrial energy production. Emerging evidence for cognitive benefits, particularly in age-related and post-viral brain fog.

norepinephrine

A neurotransmitter and stress hormone that governs alertness and attention. Too little = foggy and fatigued. Too much = anxious and scattered. Cold exposure triggers a reliable spike.

Nrf2

A protein that activates your body's antioxidant defence genes. Sulforaphane (from broccoli sprouts), curcumin, and exercise activate Nrf2. It's one of the most powerful natural anti-inflammatory pathways.

parasympathetic

The 'rest-and-digest' branch of the autonomic nervous system, controlled primarily by the vagus nerve. Activating it reduces heart rate, lowers inflammation, and supports cognitive recovery.

PEA

Palmitoylethanolamide — a naturally occurring fatty acid with anti-inflammatory and neuroprotective properties. Works by calming overactive microglia. Dose: 600–1,200 mg/day. Well-tolerated with few interactions.

photobiomodulation

Using specific wavelengths of red or near-infrared light to stimulate mitochondrial function in brain cells. Transcranial devices (worn on the head) have shown cognitive improvements in Long COVID trials.

polysomno

Polysomnography — an overnight sleep study that monitors brain waves, breathing, oxygen levels, and muscle activity. The gold standard for diagnosing sleep apnea, UARS, and other sleep disorders.

POTS

Postural orthostatic tachycardia syndrome — heart rate rises excessively (≥30 bpm) when standing. Causes dizziness, fatigue, and brain fog on standing. Screen: lie down 5 min, take pulse, stand, retake at 2/5/10 min.

prefrontal cortex

The front region of your brain responsible for planning, decision-making, working memory, and focus. It's the first area to go offline under inflammation or stress — which is why brain fog hits complex tasks before simple ones.

RERAs

Respiratory effort-related arousals — brief awakenings caused by increased breathing effort that don't meet the criteria for apnea. Cause fragmented sleep and daytime fog. Many sleep labs don't score them unless asked.

SCFA

Short-chain fatty acids — metabolites produced by gut bacteria from dietary fibre (butyrate, propionate, acetate). They strengthen the gut barrier, reduce inflammation, and support brain function.

serotonin

A neurotransmitter regulating mood, sleep, and gut function. ~95% is produced in the gut, which is why gut health directly affects mood and cognition. Precursor: tryptophan (from protein).

short-chain fatty acid

Metabolites (butyrate, propionate, acetate) produced when gut bacteria ferment fibre. They strengthen the gut lining, reduce systemic inflammation, and directly support neuron health.

SIBO

Small intestinal bacterial overgrowth — bacteria that should live in the large intestine colonise the small intestine, causing bloating, malabsorption, and brain fog via the gut-brain axis. Diagnosed by breath test.

statin

Cholesterol-lowering medications. Some people report cognitive side effects (memory problems, confusion). Lipophilic statins (atorvastatin, simvastatin) cross the blood-brain barrier more readily than hydrophilic ones.

sympathetic

The 'fight-or-flight' branch of the autonomic nervous system. Chronic sympathetic dominance (from ongoing stress) drives cortisol elevation, inflammation, and brain fog.

TIBC

Total iron-binding capacity — measures how much iron your blood can carry. High TIBC with low ferritin confirms iron deficiency, even when haemoglobin looks normal.

TNF

Tumour necrosis factor-alpha — a pro-inflammatory cytokine. Elevated in chronic inflammation, obesity, and autoimmune disease. Impairs synaptic plasticity (the brain's ability to form new connections).

TPO

Thyroid peroxidase antibodies — elevated levels indicate Hashimoto's thyroiditis (autoimmune thyroid disease), one of the most commonly missed causes of brain fog. Can be elevated years before TSH becomes abnormal.

transcranial

Delivered through the skull to the brain — refers to non-invasive therapies like transcranial photobiomodulation (light) or transcranial direct current stimulation (electrical) that target brain tissue from outside.

TSH

Thyroid-stimulating hormone — the standard thyroid screening test. But TSH alone misses subclinical thyroid dysfunction. Always request Free T3, Free T4, and TPO antibodies alongside it.

UARS

Upper airway resistance syndrome — a sleep breathing disorder that causes brain fog and fatigue despite a 'normal' sleep study (normal AHI). Only detected when RERAs are scored. Ask your sleep lab specifically.

vagal

Relating to the vagus nerve — the main nerve of the parasympathetic nervous system. Vagal tone refers to the activity level of this nerve. Higher vagal tone = better stress resilience and lower inflammation.

vagus nerve

The longest cranial nerve, connecting the brain to the gut, heart, and lungs. It controls the parasympathetic (rest-and-digest) nervous system. Stimulating it (cold exposure, deep breathing, gargling) reduces inflammation.

vestibular

Relating to the inner ear balance system. Vestibular dysfunction (from concussion, inner ear problems, or autonomic disorders) causes dizziness, spatial disorientation, and cognitive fog.

zonulin

A protein that regulates the tight junctions between gut lining cells. Gluten and certain bacteria trigger zonulin release, opening gaps in the gut wall (intestinal permeability) and allowing inflammatory molecules into the bloodstream.