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neuron/presynapse.md

@@ -42,36 +42,37 @@ Qui comprendiamo:
 **G expression**:
 
 ```Gen
-PRESYNAPSE
+# indexG
-  - AP_ctx
-    -- NT Release
-    NTreleaseHigh: interacting 
-    NTreleaseMedium: interacting
-    NTreleaseLow: interacting
-    -- Ca Clearence
-    AP-CaClearanceHigh: interacting
-    AP-CaClearanceMedium: interacting
 
-  - NOT AP_ctx:
+PRESYNAPSE
-    -- Ca Clearence
+  AP_ctx
-    NotAP-CaClearance: interacting
+    ms
-    -- Ca Traces
+      NTreleaseHigh: interacting 
-    CaTracesAccumulationFast: interacting
+      NTreleaseMedium: interacting
-    CaTracesAccumulationSlow: interacting
+      NTreleaseLow: interacting
-    CaTracesClearance: interacting
+      AP-CaClearanceHigh: interacting
-    -- eCB Clearence
+      AP-CaClearanceMedium: interacting
-    eCBClearance: interacting
+
-    -- RP Shuttle
+  NOT AP_ctx:
-    RPShuttleLow: interacting
+    ms
-    RPShuttleMedium: interacting
+      NotAP-CaClearance: interacting
-    RPShuttleHigh: interacting
+      CaTracesAccumulationFast: interacting
+      CaTracesAccumulationSlow: interacting
+      CaTracesClearance: interacting
+    sec
+      eCBClearance: interacting
+      RPShuttleLow: interacting
+      RPShuttleMedium: interacting
+      RPShuttleHigh: interacting
+    min
+      Refill RP from Glutamine
 
 VGCC-PRE
-  - AP_ctx
+  AP_ctx
-    -- Ca Influx
+    ms
-    Ca2+enterLow: interacting
+      Ca2+enterLow: interacting
-    Ca2+enterMedium: interacting
+      Ca2+enterMedium: interacting
-    Ca2+enterHigh: interacting
+      Ca2+enterHigh: interacting
 ```
 
 **Tubs:**
@@ -108,9 +109,11 @@ container: PRESYNAPSE
   - AP ( contained_by: SOMA ) 
 ```
 
-### ms: behaviors
+### AP_ctx: PRESYNAPSE
 
-#### NTrelease
+#### ms: AP_ctx: PRESYNAPSE
+
+##### NTreleaseHigh: interacting
 
 Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
 
@@ -122,7 +125,7 @@ Non consideriamo le vesicles come liberate, ma direttamente gli NT. Questo perme
 
 Ci sono 4 casi che dipendono da RRP, Ca2+ e indirettamente da concentrazione di NT nella SYN che diventa mGLur che limita in VGCC l'entrata di Ca2+. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e Ca2+ e di meno (indirettamente) al crescere della concentrazione di NT gia' liberati nella SYN. Gli NT nella sinapsi fanno da moderazione alla ulteriore liberazione di NT, ma non bloccano mai totalmente. NT suppression only matters when everything else is already at maximum, which is exactly the biological purpose: it prevents runaway release during peak activity, not during moderate activity.
 
-##### NTreleaseHigh: interacting
+---
 
 NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN.
 
@@ -175,7 +178,7 @@ interacting: NTreleaseLow
     trace: None
 ```
 
-#### CaClearance
+##### AP-CaClearanceHigh: interacting
 
 Qui eliminiamo Ca2+. Non comprendiamo per ora:
 
@@ -187,7 +190,7 @@ Quindi non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entr
 
 Abbiamo il caso di clearance nel contesto di un AP e non nel contesto di AP, per eliminare il Ca2+ fra le spike.
 
-##### AP-CaClearanceHigh: interacting
+---
 
 ```Gen
 interacting: AP-CaClearanceHigh
@@ -215,6 +218,10 @@ interacting: AP-CaClearanceMediumness
     trace: None
 ```
 
+### NOT AP_ctx: PRESYNAPSE
+
+#### ms: NOT AP_ctx: PRESYNAPSE
+
 ##### NotAP-CaClearance: interacting
 
 ```Gen
@@ -229,7 +236,7 @@ interacting: NotAP-CaClearance
     trace: None
 ```
 
-#### CaTraces accumulation
+##### CaTracesAccumulationFast: interacting
 
 Serve a dare la velocita' al trasporto di vesicles da RP a RRP. 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.
 
@@ -237,7 +244,7 @@ So after one second of silence CaTrace has fallen to ~37% of its peak value, aft
 
 The result is that Tr_Ca 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.
 
-##### CaTracesAccumulationFast: interacting
+---
 
 Qui le tracce CaTrace si accumulano di piu' perche' RF e' minore, se c'e' la condizione, perche' va a fare il controllo piu' spesso.
 
@@ -267,9 +274,9 @@ interacting: CaTracesAccumulationSlow
     trace: None
 ```
 
-### sec: behaviors
+#### sec: NOT AP_ctx: PRESYNAPSE
 
-#### eCB clearance: interacting
+##### eCB clearance: interacting
 
 eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.
 
@@ -287,7 +294,7 @@ interacting: eCBClearance
     trace: None
 ```
 
-#### CaTracesClearance: interacting
+##### CaTracesClearance: interacting
 
 Qui non facciamo un flush di Catrace, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.
 
@@ -303,12 +310,10 @@ interacting: CaTracesClearance
     trace: None
 ```
 
-#### RPShuttling
+##### RPShuttleSlow: interacting
 
 This happens in the seconds loop, once per second.
 
-##### RPShuttleSlow: interacting
-
 The "Hard Bottleneck" State. Recruitment is throttled by a lack of signal, a lack of supply, or a lack of space. If even one of these "Near-Stop" conditions is met, the rate cannot exceed "Slow," regardless of the other two conditions.
 
 Rate: 0.00 – 0.25
@@ -368,9 +373,9 @@ interacting: RPShuttleHigh
     trace: None
 ```
 
-### min: behaviors
+#### min: NOT AP_ctx: PRESYNAPSE
 
-#### Refill RP from Glutamine
+##### Refill RP from Glutamine
 
 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.
 
@@ -425,10 +430,10 @@ tuner: VGCC-PRE-TUN
  tub_intricated:
 ```
 
-##### check_tpc
+##### contexting
 
 ```Gen
-context: Check
+contexting: Check
   contained_by: VGCC-PRE-TUN
 
   in_context: TunPossible
@@ -467,9 +472,9 @@ container: VGCC-PRE
     - AP ( contained_by: SOMA )
 ```
 
-### ms: behavior
+### AP_ctx: VGCC-PRE
 
-#### Ca2+enter
+#### ms: AP_ctx: VGCC-PRE
 
 Here we comprehend the breaking activity on VGCC by: CDI, eCB and mGluR: