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ocrampal
2026-05-25 14:36:27 +02:00
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elements/neuron/presynapse.md
+117 -101
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@@ -9,22 +9,22 @@ Qui comprendiamo:
- PRESYNAPSE: Presynapse
- VGCC-PRE: Voltage-Controlled Gated Channels
## PRESYNAPSE
## {PRESYNAPSE}
```Gen
PRESYNAPSE
{PRESYNAPSE}
type: comprehension
expand_comprehension:
_VgccPre: VGCC-PRE [ full: 10x, active: 5x, empty: 2x ]
_VgccPre: {VGCC-PRE} [ full: 10x, active: 5x, empty: 2x ]
instantiate_container:
@: $BehaviorPre []
@: $TunVgccPre [pass: _VgccPre]
BEHAVIOR_PRE: CONTAINER []
TUNE_VGCC_PRE: CONTAINER [pass: _VgccPre]
```
### $BehaviorPre
### BEHAVIOR_PRE
**Tubs:**
@@ -36,10 +36,10 @@ PRESYNAPSE
- **_eCB**: retrograde signal updates from postsynapsis (postsynaptic input)
```Gen
$BehaviorPre
BEHAVIOR_PRE
type: container
activity_scope: !DAY
type: container
tub_local:
_Ca2+: TUB [ full: 60x, active: 30x, empty: 0x ]
@@ -58,16 +58,26 @@ $BehaviorPre
snippets:
# &AP
NTreleaseLow: [RF: active 12x, type: accumulator]
NTreleaseMedium [RF active 9x, type: accumulator]
NTreleaseHigh: [RF active 9x, type: accumulator]
NTreleaseLow: ACCUMULATOR [RF: active 12x]
NTreleaseMedium: ACCUMULATOR [RF active 9x]
NTreleaseHigh: ACCUMULATOR [RF active 9x]
Ca2+TracesAccLow: [RF active 3x, type: accumulator]
Ca2+TracesAccMedium: [RF active 6x, type: accumulator]
Ca2+TracesAccHigh: [RF active 10x, type: accumulator]
Ca2+TracesAccLow: ACCUMULATOR [RF active 3x]
Ca2+TracesAccMedium: ACCUMULATOR [RF active 6x]
Ca2+TracesAccHigh: ACCUMULATOR [RF active 10x]
# NOT &AP
eCBClearence: RF [active: 24x]
eCBClearenceMedium: ACCUMULATOR [RF: active: 24x]
eCBClearenceLow: ACCUMULATOR [RF: active: 248x]
RPShuttleLow: ACCUMULATOR [RF: active: 24x]
RPShuttleMedium: ACCUMULATOR [RF: active: 48x]
RefillGlutamine: ACCUMULATOR [RF: active: 24x]
Ca2+TracesClearance: ACCUMULATOR [RF: active: 30x]
```
#### &AP
@@ -94,6 +104,7 @@ In tutti i casi di NT
NTreleaseLow
in_context: &AP
hypothesis: ( _Ca2+ mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty )
action: [_Rrp decrease, _Nt increase, _ATP decrease]
trace: None
@@ -104,7 +115,8 @@ NTreleaseLow
```Gen
NTreleaseMedium
in_context: AP_ctx
in_context: &AP
hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR
( Ca2+ mediumness ) AND ( Rrp fullness )) AND
NOT( ATP empty )
@@ -117,7 +129,8 @@ NTreleaseMedium
```Gen
NTreleaseHigh
in_context: AP_ctx
in_context: &AP
hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND
NOT( ATP empty )
action: [Rrp decrease, NT increase, ATP decrease]
@@ -130,16 +143,17 @@ Serve a:
- fare il tuning dei VGCC
- dare la velocita' al trasporto di vesicles da RP a RRP, anche se non avendo ancora compreso ATP, la velocita' non cambia molto la sostanza.
- le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, TunPossible_ctx
- le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, &TunePossible
- Abbiamo 3 tracce, high, medium and low. Andiamo a verificare una combinazione di queste per fare la modulazione
- RF e' a 10, questo dovrebbe essere un RF di campionamento durante AP_ctx context che dovremmo assicurarci sia tipo 100. Il che implicherebbe 10 campionamenti.
- RF e' a 10, questo dovrebbe essere un RF di campionamento durante &AP context che dovremmo assicurarci sia tipo 100. Il che implicherebbe 10 campionamenti.
- The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly.
- So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds.
```Gen
Ca2+TracesAccuLow
in_context: AP_ctx
in_context: &AP
hypothesis: (Ca2+ emptiness)
action: [CaTraceLow increase]
trace: None
@@ -150,7 +164,8 @@ Ca2+TracesAccuLow
```Gen
Ca2+TracesAccMedium
in_context: AP_ctx
in_context: &AP
hypothesis: (Ca2+ mediumness)
action: [CaTraceMed increase]
trace: None
@@ -161,7 +176,8 @@ Ca2+TracesAccMedium
```Gen
Ca2+TracesAccumulationHigh
in_context: AP_ctx
in_context: &AP
hypothesis: (Ca2+ fullness)
action: [CaTraceHigh increase]
trace: None
@@ -169,26 +185,23 @@ Ca2+TracesAccumulationHigh
#### NOT &AP
##### eCB clearance: accumulator
##### eCBClearance
eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.
Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.
##### eCBClearance: ( active: 24x ) accumulator
```Gen
eCBClearance: ( active: 24x ) # Slow
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: NOT AP_ctx
in_context: NOT &AP
hypothesis: NOT (eCB empty)
action: [eCB decrease]
trace: None
```
##### RPShuttleLow: ( active: 48x ) accumulator
##### RPShuttleLow
This happens in the seconds loop, once per second.
@@ -197,11 +210,10 @@ The "Hard Bottleneck" State. Recruitment is throttled by a lack of signal, a lac
Rate: 0.00 – 0.25
```Gen
RPShuttleLow: ( active: 48x ) # Low
type: accumulator
contained_by: PRESYNAPSE-BEH
RPShuttleLow
in_context: NOT &AP
in_context: NOT AP_ctx
hypothesis: (CaTraceLow fullness) OR
(RP emptiness) OR
(RRP fullness)
@@ -209,18 +221,17 @@ RPShuttleLow: ( active: 48x ) # Low
trace: None
```
##### RPShuttleMedium: ( active: 24x ) accumulator
##### RPShuttleMedium
The "Sub-Optimal" State. The machinery is working, but it's held back by partial limitations. This covers cases where the signal is steady but the "piston" isn't firing at full speed, or where a high vacancy in the RRP (emptiness) forces a low signal to work a bit harder.
Rate: 0.50 – 0.97
```Gen
RPShuttleMedium: ( active: 24x ) # Medium
type: accumulator
contained_by: PRESYNAPSE-BEH
RPShuttleMedium
in_context: &AP
in_context: AP_ctx
hypothesis: (CaTraceMedium fullness) AND (RP mediumness) AND (RRP mediumness) OR
(CaTraceHigh fullness) AND (RP mediumness) AND (RRP mediumness) OR # signal boost
(CaTraceMedium fullness) AND (RP fullness) AND (RRP mediumness) OR # supply boost
@@ -229,18 +240,17 @@ RPShuttleMedium: ( active: 24x ) # Medium
trace: None
```
##### RPShuttleHigh: ( active: 12x ) accumulator
##### RPShuttleHigh
The "High Performance" State. Multiple systems are optimized, but one is still at a "mediumness" level. This represents an active synapse that hasn't reached its absolute peak because either the supply is only 50% or the RRP isn't empty enough to create that "maximal vacuum" pull.
Rate: 1.25 – 1.94
```Gen
RPShuttleHigh: ( active: 12x ) # Fast
type: accumulator
contained_by: PRESYNAPSE-BEH
RPShuttleHigh
in_context: &AP
in_context: AP_ctx
hypothesis: (CaTraceHigh fullness) AND (RP fullness) AND (RRP mediumness) OR # signal + supply
(CaTraceHigh fullness) AND (RP mediumness) AND (RRP emptiness) OR # signal + vacancy
(CaTraceMedium fullness) AND (RP fullness) AND (RRP emptiness) # supply + vacancy
@@ -248,7 +258,7 @@ RPShuttleHigh: ( active: 12x ) # Fast
trace: None
```
##### RefillRPGlutamine: accumulator
##### RefillRPGlutamine
This happens in the minutes loop, once per minute, via the glutamine shuttle from the astrocyte. It is a two-step process across two cells.
@@ -278,16 +288,15 @@ Gln — depletes over bursts, refilled by glucose (slowest, astrocyte-depend
Each tier buys time for the one below it to respond. When all three are depleted simultaneously — which only happens under prolonged high-frequency firing with insufficient glucose — the synapse has no remaining buffer and goes silent until the minutes loop restores the Glutamine_pool.
##### Ca2+TracesClearance: ( active: 30x ) accumulator
##### Ca2+TracesClearance
Qui facciamo un flush di CaTraceX. Deve essere fatto a valle del tuning.
```Gen
Ca2+TracesClearance: ( active: 30x ) # Slow
type: accumulator
contained_by: PRESYNAPSE-BHE
Ca2+TracesClearance
in_context: NOT &TunePossible
in_context: NOT TunPossible_ctx
hypothesis: NOT (CaTraceHigh empty)
action: [CaTRaceHigh decrease]
trace: None
@@ -301,41 +310,45 @@ Ca2+TracesClearance: ( active: 30x ) # Slow
trace: None
```
### VGCC-PRE-TUN: Container
### TUNE_VGCC_PRE
```Gen
VGCC-PRE-TUN
TUNE_VGCC_PRE
# qui stiamo aggiungendo o eliminando VGCC-PRE. Fra un massimo full e minimo empty (empty puo' non essere 0)
# contained_by: PRESYNAPSE non e' contenuto, si attacca.
type: container
activity_scope: !DAY
type: container
context_intricated:
- TunPossible_ctx ( contained_by: DAY-N )
- &TunePossible ( contained_by: DAY-N )
tub_passed:
VGCC-PRE_ALL: pass.VGCC-PRE_ALL
_VgccPre: pass._VgccPre
tub_local:
tub_intricated:
snippets:
CheckVgccPreTun: CONTEXTOR [RF: active 60x]
PossibleUpPreVgccTun: ACCUMULATOR [RF:active 10x]
PossibleDownPreVgccTun: ACCUMULATOR [RF:active 10x]
```
#### TunPossible_ctx
#### &TunePossible
##### CheckVgccPreTun: ( active: 60x ) contexting
##### CheckVgccPreTun
Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantita' di VGCC
```Gen
CheckVgccPreTun: ( active: 60x )
type: contexting
contained_by: VGCC-PRE-TUN
CheckVgccPreTun
in_context: &TunePossible
in_context: TunPossible_ctx
condition: ( CaTraceHigh fullness )
out_context: TryTunUpPreVcgg_ctx
@@ -343,14 +356,13 @@ CheckVgccPreTun: ( active: 60x )
out_context: TryTunDownPreVcgg_ctx
```
##### PossibleUpPreVgccTun: ( active: 10x ) accumulator
##### PossibleUpPreVgccTun
```Gen
PossibleUpPreVgccTun: ( active: 10x )
type: accumulator
contained_by: VGCC-PRE-TUN
PossibleUpPreVgccTun
in_context: TryTunUpPreVcgg_ctx
hypothesis:
action:
trace:
@@ -359,37 +371,36 @@ PossibleUpPreVgccTun: ( active: 10x )
##### PossibleDownPreVgccTun: ( active: 10x ) accumulator
```Gen
PossibleDownPreVgccTun: ( active: 10x )
type: accumulator
contained_by: VGCC-PRE-TUN
PossibleDownPreVgccTun
in_context: TryTunDownPreVcgg_ctx
hypothesis:
action:
trace:
```
## VGCC-PRE: Comprehension
## {VGCC-PRE}
Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare.
```Gen
VGCC-PRE
{VGCC-PRE}
type: comprehension
instantiate_container:
VGCC-PRE-BEH []
BEHAVIOR_VGCC_PRE: CONTAINER []
```
### VGCC-PRE-BEH: Container
### BEHAVIOR_VGCC_PRE
Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare.
```Gen
VGCC-PRE-PRE
BEHAVIOR_VGCC_PRE
type: container
activity_scope: !DAY
type: container
tub_intricated:
- Ca2+ ( contained_by: PRESYNAPSE-BHE )
@@ -397,9 +408,19 @@ VGCC-PRE-PRE
context_intricated:
- AP ( contained_by: SOMA )
snippets:
Ca2+enterLow: ACCUMULATOR [RF: active 12x]
Ca2+enterMedium: ACCUMULATOR [RF: active 6x]
Ca2+enterHigh: ACCUMULATOR [RF: active 3x]
Ca2+ClearanceLow: ACCUMULATOR [RF: active 24x]
Ca2+ClearanceHigh: ACCUMULATOR [RF: active 4x]
```
#### AP_ctx
#### &AP
Da rivedere le condizioni per aggiungere mGluR che ha come proxy NT concentration!!!!!
@@ -421,27 +442,25 @@ Qui semplifichiamo:
Devo controllare che le condizioni sotto siano esaustive. Qui ho confuso high con low, e inoltre ho messo NT per mGluR che devo controllare che abbia senso.
##### Ca2+enterLow: ( active: 12x ) accumulator
##### Ca2+enterLow
```Gen
Ca2+enterLow: ( active: 12x ) # Low
type: accumulator
contained_by: VGCC-PRE-BEH
Ca2+enterLow
in_context: &AP
in_context: AP_ctx
hypothesis: (Ca2+ empty) AND (eCB empty)
action: [Ca2+ increase, ATP decrease]
trace: None
```
##### Ca2+enterMedium: ( active: 6x ) accumulator
##### Ca2+enterMedium
```Gen
Ca2+enterMedium: ( active: 6x ) # Medium
type: accumulator
contained_by: VGCC-PRE-BEH
Ca2+enterMedium
in_context: &AP
in_context: AP_ctx
hypothesis: (Ca2+ mediumness) OR
((eCB mediumness) AND (Ca2+ empty)) OR
((eCB full) AND (Ca2+ empty) AND (NT empty))
@@ -449,23 +468,22 @@ Ca2+enterMedium: ( active: 6x ) # Medium
trace: None
```
##### Ca2+enterHigh: ( active: 3x ) accumulator
##### Ca2+enterHigh
```Gen
Ca2+enterHigh: ( active: 3x ) # High
type: accumulator
contained_by: VGCC-PRE-BEH
Ca2+enterHigh
in_context: &AP
in_context: AP_ctx
hypothesis: (Ca2+ mediumness) AND (eCB full) OR
(eCB mediumness)
action: [Ca2+ increase, ATP decrease]
trace: None
```
#### NOT AP_ctx
#### NOT &AP
Qui eliminiamo Ca2+. Il tempo che ci mette ad eliminare il Ca2+ dovrebbe essere minoe dell'inervallo fra un AP_ctx e un'altra. Siccome non comprendiamo per ora ATP, non c'e' accumulo di Ca2+ per mancanza di ATP (stanchezza).
Qui eliminiamo Ca2+. Il tempo che ci mette ad eliminare il Ca2+ dovrebbe essere minoe dell'inervallo fra un &AP e un'altra. Siccome non comprendiamo per ora ATP, non c'e' accumulo di Ca2+ per mancanza di ATP (stanchezza).
Non non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entranti e uscenti, per ora tutto dipende da AP del SOMA. Non comprendiamo per ora:
@@ -479,27 +497,25 @@ Qui disinguiamo:
- NOT ca2+ fullness che svuota piu' lentamente
- da capire se serve veramente questa distinzione per il tempo di svuotamento.
##### Ca2+ClearanceLow: ( active: 24x ) accumulator
##### Ca2+ClearanceLow
```Gen
Ca2+ClearanceLow: ( active: 24x ) # Low
type: accumulator
contained_by: VGCC-PRE-BEH
Ca2+ClearanceLow
in_context: NOT &AP
in_context: NOT AP_ctx
hypothesis: (NOT Ca2+ fullness) AND (NOT Ca2+ empty)
action: [Ca2+ decrease]
trace: None
```
##### Ca2+ClearanceHigh: ( active: 4x ) accumulator
##### Ca2+ClearanceHigh
```Gen
Ca2+ClearanceHigh: ( active: 4x ) # High
type: accumulator
contained_by: VGCC-PRE-BEH
Ca2+ClearanceHigh
in_context: NOT &AP
in_context: NOT AP_ctx
hypothesis: NOT (Ca2+ empty)
action: [Ca2+ decrease]
trace: None