Sergio changes
This commit is contained in:
Sergio Marchetti
+60
-87
@@ -86,7 +86,7 @@ VGCC-PRE
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-- Ca Influx
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Ca2+enterLow: interacting
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Ca2+enterMedium: interacting
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Ca2+enterSuppressed: interacting
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Ca2+enterHigh: interacting
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```
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@@ -109,13 +109,10 @@ container: PRESYNAPSE
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tub_local:
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- Ca2+ ( full: 60x, active: 30x, empty: 0x )
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# developed_by: DEV-PRE-CA2+FULL from DEV.N
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- Rrp ( full: 30x, active: 15x, empty: 0x )
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# developed_by: DEV-PRE-RRP-FULL from DEV.N
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- Rp ( full: 30x, active: 15x, empty: 0x )
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# developed_by: DEV-PRE-RRP-FULL from DEV.N
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- CaTraces ( full: 50x, active: 0x, empty: 0x )
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tub_intricated:
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@@ -129,8 +126,7 @@ container: PRESYNAPSE
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### ms: behaviors
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#### PRE_Status_ms: check_tpc
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#### PRE_Status_ms: check_tpc !!! DA ELINMINARE !!!
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Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
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RF di interacting deve essere MOLTO piu' basso di un RF di AP. In maniera da essere attivo varie volte nel contesto di un episodio di AP. Il che ha senso perche' un AP e' SOMA ad un tempo piu' alto che i comportamenti di PRE. Questo poi per permettere la diversa contestualizzazione degli episodi di NTrelease, a piu' o meno alta velocita'.
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@@ -163,35 +159,20 @@ Non consideriamo le vesicles come liberate, ma direttamente gli NT. Questo perme
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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.
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##### NTreleaseMaximum: interacting
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NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN.
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```Gen
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interacting: NTreleaseMaximum
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contained_by: PRESYNAPSE
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in_context: NTreleaseMax_ctx
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rf: ( active: 3x ) # Maximum
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hypothesis: NOT (NT empty)
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action: [Rrp decrease, Nt increase, ATP decrease]
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trace: None
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```
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##### NTreleaseHigh: interacting
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Solo in questo caso NT modera! NT NOT empty, perche' Ca2+ fullness non full.
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NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN.
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```Gen
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interacting: NTreleaseHigh
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contained_by: PRESYNAPSE
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in_context: NTreleaseHigh_ctx
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rf: ( active: 6x ) # High
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in_context: AP_ctx
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rf: ( active: 3x ) # High
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hypothesis: NOT (NT empty)
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action: [Rrp decrease, Nt increase, ATP decrease]
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hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND
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NOT( ATP empty )
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action: [Rrp decrease, NT increase, ATP decrease]
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trace: None
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```
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@@ -203,10 +184,12 @@ In tutti i casi di NT
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interacting: NTreleaseMedium
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contained_by: PRESYNAPSE
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in_context: NTreleaseMed_ctx
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rf: ( active: 9x ) # Mediumness
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in_context: AP_ctx
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rf: ( active: 9x ) # Medium
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hypothesis: (NT empty) OR NOT (NT empty)
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hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR
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( Ca2+ mediumness ) AND ( Rrp fullness )) AND
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NOT( ATP empty )
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action: [Rrp decrease, Nt increase, ATP decrease]
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trace: None
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```
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@@ -219,9 +202,12 @@ In tutti i casi di NT
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interacting: NTreleaseLow
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contained_by: PRESYNAPSE
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in_context: NTreleaseLow_ctx
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in_context: AP_ctx
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rf: ( active: 12x ) # Low
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hypothesis: (NT empty) OR NOT (NT empty)
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hypothesis: ( Ca2+ mediumness ) AND
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( Rrp mediumness ) AND
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NOT( ATP empty )
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action: [Rrp decrease, Nt increase, ATP decrease]
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trace: None
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```
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@@ -244,7 +230,7 @@ Abbiamo il caso di clearance nel contesto di un AP e non nel contesto di AP, per
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interacting: AP-CaClearanceHigh
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contained_by: PRESYNAPSE
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in_context: AP
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in_context: AP_ctx
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rf: ( active: 3x ) # High
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hypothesis: (Ca2+ fullness)
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@@ -258,7 +244,7 @@ interacting: AP-CaClearanceHigh
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interacting: AP-CaClearanceMediumness
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contained_by: PRESYNAPSE
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in_context: AP
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in_context: AP_ctx
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rf: ( active: 6x ) # mediumness
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hypothesis: (Ca2+ mediumness)
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@@ -320,7 +306,7 @@ interacting: CaTracesAccumulationSlow
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### sec: behaviors
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#### PRE_Status_sec: check_tpc
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#### PRE_Status_sec: check_tpc !!! DA ELINMINARE !!!
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Contestualizziamo in maniera Fixed ogni mezzo secondo?
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@@ -331,13 +317,13 @@ check_tpc: PRE_Status_sec
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in_context: NOT AP_ctx
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rf: ( active: 600x )
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condition: NOT (RP empty) AND NOT (RRP full)
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condition: NOT(RP empty) AND NOT(RRP full)
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out_context: RPShuttle_ctx
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condition: NOT (CaTrace empty)
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condition: NOT(CaTrace empty)
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out_context: CaTracesNotEmpty_ctx
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condition: NOT (eCB empy)
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condition: NOT(eCB empy)
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out_context: eCBNotEmpty_ctx
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```
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@@ -351,7 +337,7 @@ Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un R
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interacting: eCBClearance
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contained_by: PRESYNAPSE
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in_context: eCBNotEmpty_ctx
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in_context: NOT AP_ctx
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rf: ( active: 24x ) # Slow
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hypothesis: NOT (eCB empty)
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@@ -367,7 +353,7 @@ Qui non facciamo un flush di Catrace, riduciamo ogni mezzo secondo (context) di
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interacting: CaTracesClearance
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contained_by: PRESYNAPSE
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in_context: CaTracesNotEmpty_ctx
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in_context: NOT AP_ctx
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rf: ( active: 24x ) # Slow
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hypothesis: NOT (CaTrace empty)
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@@ -386,72 +372,56 @@ The "Hard Bottleneck" State. Recruitment is throttled by a lack of signal, a lac
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Rate: 0.00 – 0.25
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```Gen
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interacting: RPShuttleSlow
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interacting: RPShuttleLow
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contained_by: PRESYNAPSE
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in_context: RPShuttle_ctx
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rf: ( active: 48x ) # Slow
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in_context: NOT AP_ctx
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rf: ( active: 48x ) # Low
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hypothesis: (CaTrace emptiness) OR (RP emptiness) OR (RRP fullness)
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hypothesis: (CaTrace emptiness) OR
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(RP emptiness) OR
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(RRP fullness)
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action: [RP decrease, RRP increase]
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trace: None
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```
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##### RPShuttleModerate: interacting
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##### RPShuttleMedium: interacting
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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.
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Rate: 0.50 – 0.97
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```Gen
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interacting: RPShuttleModerate
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interacting: RPShuttleMedium
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contained_by: PRESYNAPSE
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in_context: RPShuttle_ctx
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rf: ( active: 24x ) # Slow
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in_context: AP_ctx
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rf: ( active: 24x ) # Medium
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hypothesis: ((CaTrace mediumness) AND (RP mediumness) AND (RRP mediumness)) OR
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((CaTrace fullness) AND (RP mediumness) AND (RRP mediumness)) OR # signal boost
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((CaTrace mediumness) AND (RP fullness) AND (RRP mediumness)) OR # supply boost
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((CaTrace mediumness) AND (RP mediumness) AND (RRP emptiness)) # vacancy boost
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hypothesis: (CaTrace mediumness) AND (RP mediumness) AND (RRP mediumness) OR
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(CaTrace fullness) AND (RP mediumness) AND (RRP mediumness) OR # signal boost
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(CaTrace mediumness) AND (RP fullness) AND (RRP mediumness) OR # supply boost
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(CaTrace mediumness) AND (RP mediumness) AND (RRP emptiness) # vacancy boost
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action: [RP decrease, RRP increase]
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trace: None
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```
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##### RPShuttleFast: interacting
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##### RPShuttleHigh: interacting
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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.
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Rate: 1.25 – 1.94
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```Gen
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interacting: RPShuttleFast
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interacting: RPShuttleHigh
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contained_by: PRESYNAPSE
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in_context: RPShuttle_ctx
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in_context: AP_ctx
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rf: ( active: 12x ) # Fast
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hypothesis: ((CaTrace fullness) AND (RP fullness) AND (RRP mediumness)) OR # signal + supply
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((CaTrace fullness) AND (RP mediumness) AND (RRP emptiness)) OR # signal + vacancy
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((CaTrace mediumness) AND (RP fullness) AND (RRP emptiness)) # supply + vacancy
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action: [RP decrease, RRP increase]
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trace: None
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```
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##### RPShuttleMaximal: interacting
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The "Total Recovery" State. All systems are at their theoretical peak for speed.
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Rate: 2.50 – 5.00
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```Gen
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interacting: RPShuttleMaximal
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contained_by: PRESYNAPSE
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in_context: RPShuttle_ctx
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rf: ( active: 6x ) # Maximal
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hypothesis: (CaTrace fullness) AND (RP fullness) AND RRP (emptiness)
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hypothesis: (CaTrace fullness) AND (RP fullness) AND (RRP mediumness) OR # signal + supply
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(CaTrace fullness) AND (RP mediumness) AND (RRP emptiness) OR # signal + vacancy
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(CaTrace mediumness) AND (RP fullness) AND (RRP emptiness) # supply + vacancy
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action: [RP decrease, RRP increase]
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trace: None
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```
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@@ -580,41 +550,44 @@ Devo controllare che le condizioni sotto siano esaustive.
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##### Ca2+enterOpen: interacting
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```Gen
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interacting: Ca2+enterOpen
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interacting: Ca2+enterLow
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contained_by: VGCC-PRE
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in_context: AP_ctx
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rf: ( active: 6x )
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rf: ( active: 12x ) # Low
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hypothesis: (Ca2+ empty) and (eCB empty)
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hypothesis: (Ca2+ empty) AND (eCB empty)
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action: [Ca2+ increase, ATP decrease]
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trace: None
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```
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##### Ca2+enterReduced-partial: interacting
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##### Ca2+enterMedium: interacting
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```Gen
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interacting: Ca2+enterReduced-partial
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interacting: Ca2+enterMedium
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contained_by: VGCC-PRE
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in_context: AP_ctx
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rf: ( active: 6x )
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rf: ( active: 6x ) # Medium
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hypothesis: (Ca2+ mediumness) OR ((eCB mediumness) AND (Ca2+ empty)) OR ((eCB full) AND (Ca2+ empty) AND (NT empty))
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hypothesis: (Ca2+ mediumness) OR
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(eCB mediumness) AND (Ca2+ empty) OR
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(eCB full) AND (Ca2+ empty) AND (NT empty)
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action: [Ca2+ increase, ATP decrease]
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trace: None
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```
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##### Ca2+enterSuppressed: interacting
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##### Ca2+enterHigh: interacting
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```Gen
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interacting: Ca2+enterSupressed
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interacting: Ca2+enterHigh
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contained_by: VGCC-PRE
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in_context: AP_ctx
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rf: ( active: 6x )
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rf: ( active: 3x ) # High
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hypothesis: ((Ca2+ mediumness) AND (eCB full) OR (eCB mediumness))
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hypothesis: (Ca2+ mediumness) AND (eCB full) OR
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(eCB mediumness))
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action: [Ca2+ increase, ATP decrease]
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trace: None
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```
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