;;; SUMMARY ;; Cell regneration vs acoustic damage in the vocal folds ;;;; COPYRIGHT ;; Copyright (C) 2005 James P. Steiner ;; All rights reserved ;; Thanks to Nicole Li, lately of the Univerity of Pittsburgh, for describing the intracies of the "inflamation cycle" to me. globals [ ticks ;; hour ;; hour of day date ;; number of the day day ;; day of the week weekday? ;; day 0 -- 4 (no dosage on weekend day 5,6) div-rate ;; hours between mitosis life-span ;; hours cells live, in absense of any stress one-day epi-color bmz-color sllp-color vessel-exterior-color vessel-interior-color ] breeds [ clocks ] patches-own [ status ;; "" = empty, s = sllp, b = epi on bmz, e = epi, ;; c = loosely formed collegen, v = blood vessel, i, vessel interior age div-frame bits ] to startup setup end to setup ca set epi-color pink set bmz-color magenta set sllp-color orange set vessel-exterior-color red set vessel-interior-color violet cct-clocks 1 [ set shape "clock" setxy screen-edge-x - 5 screen-edge-y - 5 set label-color black set size 10 ] set one-day 24 set div-rate one-day set life-span 6 * one-day set ticks -1 let epi-top (- screen-edge-y) + 30 ask patches [ set status "" set div-frame random one-day ] ask patches with [ pycor < epi-top ] [ set pcolor epi-color set status "e" set age (pycor - epi-top) * one-day + random one-day ] ask patches with [ pycor = epi-top - 6 ] [ set pcolor bmz-color set status "b" set age 0 ] ask patches with [ pycor < epi-top - 6 ] [ set pcolor sllp-color set status "s" set age 0 ] let bvw 4 ask patches with [ pxcor mod (bvw * 2 + 1) = int (bvw * 2) and pycor = 0 ] [ ask random-one-of (patches with [ pxcor = pxcor-of myself and status = "s" and pycor < epi-top - 8 - bvw and pycor > (- screen-edge-y - bvw) ]) [ let center self ask patches in-radius-nowrap (bvw) [ set pcolor red set status "w" ] ;; vessel wall ask patches in-radius-nowrap (bvw - 1) [ set pcolor pink set status "i" ] ;; vessel interior ] ] end to go ;; update clock ;; ask patch screen-edge-x screen-edge-y [ set plabel ticks ] set ticks ticks + 1 set hour ticks mod 24 if hour = 0 [ set date date + 1 set day date mod 7 set weekday? day < 5] ask clocks [ rt 15 set label (word date ":" reverse substring reverse ( hour + "0" ) 0 2 " " )] ;; 1 hour per tick ;; once-per-day, apply damage dosage as a near continuous stream at the beginning of the day if working? and weekday? and ticks mod 2 = 0 and hour <= int (dosage / 10) [ ask patches with [ pycor = 0 and random-float 100 * (abs pxcor / screen-edge-x) < (db - 50) ] [ let top-cell patches with [ pxcor = pxcor-of myself and status != "" ] if any? top-cell [ ask max-one-of top-cell [ pycor ] [ dis-cell ] ] ] ] ;; normal wear "ages" exposed cells more quickly... the slough off in 24 hours let wear-and-tear patches with [ (status = "e" or status = "b") and any? neighbors4 with [ status = "" ] ] ask wear-and-tear [ set age age + 1 ] ask patches with [ status = "e" or status = "b" ] [ ifelse age >= life-span [ ;; cell dies dis-cell ] [ set age age + 1 let c 0 ifelse status = "b" [ set c yellow ][ set c violet ] set pcolor scale-color c age (- life-span) (life-span) ] ] ask patches with [ status = "b" and hour = div-frame ] [ ifelse any? neighbors with [ status = "b" or status = "s" ] [ mitosis 0 0 0 "e" timer + 1 ] [ ;; orphan bmz revert to epi set age 0 set status "e" ] ] ;; epis touching bmz and air transform into bmz transform ;; kill orphan cells, not connected to the fold ask patches with [ status != "" and pycor > (- screen-edge-y) ] [ if status-of patch-at 0 -1 = "" and status-of patch-at -1 -1 = "" and status-of patch-at 1 -1 = "" [ dis-cell ] ] ;; dead cells float away ask patches with [ pcolor != black and status = "" ] [ let c random-one-of patches at-points [[ -1 0][ -1 1][0 1][1 1][1 0]] with [ status = "" ] if c != nobody [ set pcolor-of c pcolor * .95] set pcolor black ] diffuse bits .5 ask patches with [ status != "" ] [ set bits 0 ] end to mitosis [ ddx ddy new-age new-status timeout ] if timer > timeout [ stop stop stop] let cell patch-at ddx ddy ifelse cell = self [ set age 0 ;; begin mitosis and migration ;; pick a n4 patch that is not sllp let n4 neighbors4 let t nobody ;; any empty positions? set t n4 with [ status = "" ] set cell nobody ifelse any? t [ set cell random-one-of t ] [ ;; no, any epi positions? set t n4 with [ status = "e" ] if any? t [ set cell random-one-of t ] ] ;; a target direction has been selected, ;; now begin mitosis. ;; mitosis makes the new location cell contain an epi of age 0. ;; if the patch was already occupied, then apply to age, etc ;; of the current patch to the nect patch in that direction, ;; until an empty patch is reached, in effect, bumping all the other ;; cells out of the way ifelse cell = nobody [ stop ] [ set ddx (pxcor-of cell - pxcor) set ddy (pycor-of cell - pycor) mitosis ddx ddy 0 "e" timeout ] ] [ ask cell [ if member? status [ "s" ] or abs (pxcor + ddx) > screen-edge-x or abs (pycor + ddy) > screen-edge-y [ stop ] if status != "" [ mitosis ddx ddy age status timeout ] set age new-age set status new-status ;; promote to BMZ, if appropriate if status = "e" and any? neighbors with [ status = "s" or status = "c" ] [ set status "b" ] ] ] end to transform ask patches with [ status = "e" ] [ let c-b count neighbors4 with [ status = "b" or status = "s" ] if c-b = 1 and c-b = 2 and any? neighbors4 with [ pcolor = black ] [ set status "b" ] ] end to die-cell set age 0 set status "" set pcolor black end to dis-cell set age 0 set status "" set pcolor white set bits 100 end @#$#@#$#@ GRAPHICS-WINDOW 211 10 726 546 50 50 5.0 1 10 1 1 1 0 1 1 1 CC-WINDOW 5 560 735 655 Command Center 0 SLIDER 9 10 181 43 db db 0 100 54 1 1 NIL BUTTON 126 82 181 115 reset setup NIL 1 T OBSERVER T NIL BUTTON 68 118 123 151 go no-display go display T 1 T OBSERVER NIL NIL SLIDER 9 46 181 79 dosage dosage 0 100 31 1 1 % SWITCH 9 82 117 115 working? working? 1 1 -1000 TEXTBOX 19 170 195 440 Adjust damage inputs and toggle working on and off to simulate the use of the voice, and damage to the vocal fold.\n\nStop when damage reaches the basement membrane zone (yellow cells), then see how healing progresses.\n\nThe upward falling "snow" is dead cells sloughing from the fold surface. Under normal use, the surface regenerates perfectly. Under heavy use, regeneration is not enough, and damage occurs to the underlying layers, begin a healing process. @#$#@#$#@ = WHAT IS IT? = A prototype of a model of healing of acoustic damage in the epithelial layers of the vocal fold. This model does not take into account any part of the inflamation cycle, merely the action of cellular division. = HOW TO USE IT = Adjust damage inputs and toggle working on and off to simulate the use of the voice, and damage to the vocal fold. Stop when damage reaches the basement membrane zone (yellow cells), then see how healing progresses. = WHAT IS GOING ON? = The upward falling "snow" is dead cells sloughing from the fold surface. Under normal use, the surface regenerates perfectly. Under heavy use, regeneration is not enough, and damage occurs to the underlying layers, begin a healing process. @#$#@#$#@ default true 0 Polygon -7500403 true true 150 5 40 250 150 205 260 250 airplane true 0 Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15 arrow true 0 Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150 box false 0 Polygon -7500403 true true 150 285 285 225 285 75 150 135 Polygon -7500403 true true 150 135 15 75 150 15 285 75 Polygon -7500403 true true 15 75 15 225 150 285 150 135 Line -16777216 false 150 285 150 135 Line -16777216 false 150 135 15 75 Line -16777216 false 150 135 285 75 bug true 0 Circle -7500403 true true 96 182 108 Circle -7500403 true true 110 127 80 Circle -7500403 true true 110 75 80 Line -7500403 true 150 100 80 30 Line -7500403 true 150 100 220 30 butterfly true 0 Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240 Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240 Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163 Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165 Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225 Circle -16777216 true false 135 90 30 Line -16777216 false 150 105 195 60 Line -16777216 false 150 105 105 60 car false 0 Polygon -7500403 true true 300 180 279 164 261 144 240 135 226 132 213 106 203 84 185 63 159 50 135 50 75 60 0 150 0 165 0 225 300 225 300 180 Circle -16777216 true false 180 180 90 Circle -16777216 true false 30 180 90 Polygon -16777216 true false 162 80 132 78 134 135 209 135 194 105 189 96 180 89 Circle -7500403 true true 47 195 58 Circle -7500403 true true 195 195 58 circle false 0 Circle -7500403 true true 0 0 300 circle 2 false 0 Circle -7500403 true true 0 0 300 Circle -16777216 true false 30 30 240 clock true 0 Circle -16777216 true false 0 0 300 Circle -1 true false 15 15 270 Rectangle -2674135 true false 135 15 165 150 cow false 0 Polygon -7500403 true true 200 193 197 249 179 249 177 196 166 187 140 189 93 191 78 179 72 211 49 209 48 181 37 149 25 120 25 89 45 72 103 84 179 75 198 76 252 64 272 81 293 103 285 121 255 121 242 118 224 167 Polygon -7500403 true true 73 210 86 251 62 249 48 208 Polygon -7500403 true true 25 114 16 195 9 204 23 213 25 200 39 123 cylinder false 0 Circle -7500403 true true 0 0 300 dot false 0 Circle -7500403 true true 90 90 120 face happy false 0 Circle -7500403 true true 8 8 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Polygon -16777216 true false 150 255 90 239 62 213 47 191 67 179 90 203 109 218 150 225 192 218 210 203 227 181 251 194 236 217 212 240 face neutral false 0 Circle -7500403 true true 8 7 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Rectangle -16777216 true false 60 195 240 225 face sad false 0 Circle -7500403 true true 8 8 285 Circle -16777216 true false 60 75 60 Circle -16777216 true false 180 75 60 Polygon -16777216 true false 150 168 90 184 62 210 47 232 67 244 90 220 109 205 150 198 192 205 210 220 227 242 251 229 236 206 212 183 fish false 0 Polygon -1 true false 44 131 21 87 15 86 0 120 15 150 0 180 13 214 20 212 45 166 Polygon -1 true false 135 195 119 235 95 218 76 210 46 204 60 165 Polygon -1 true false 75 45 83 77 71 103 86 114 166 78 135 60 Polygon -7500403 true true 30 136 151 77 226 81 280 119 292 146 292 160 287 170 270 195 195 210 151 212 30 166 Circle -16777216 true false 215 106 30 flag false 0 Rectangle -7500403 true true 60 15 75 300 Polygon -7500403 true true 90 150 270 90 90 30 Line -7500403 true 75 135 90 135 Line -7500403 true 75 45 90 45 flower false 0 Polygon -10899396 true false 135 120 165 165 180 210 180 240 150 300 165 300 195 240 195 195 165 135 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210 165 195 Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195 line true 0 Line -7500403 true 150 0 150 300 line-half true 0 Line -7500403 true 150 0 150 150 pentagon false 0 Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120 person false 0 Circle -7500403 true true 110 5 80 Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90 Rectangle -7500403 true true 127 79 172 94 Polygon -7500403 true true 195 90 240 150 225 180 165 105 Polygon -7500403 true true 105 90 60 150 75 180 135 105 plant false 0 Rectangle -7500403 true true 135 90 165 300 Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285 Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285 Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210 Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135 Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135 Polygon -7500403 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223 75 224 truck false 0 Rectangle -7500403 true true 4 45 195 187 Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194 Rectangle -1 true false 195 60 195 105 Polygon -16777216 true false 238 112 252 141 219 141 218 112 Circle -16777216 true false 234 174 42 Rectangle -7500403 true true 181 185 214 194 Circle -16777216 true false 144 174 42 Circle -16777216 true false 24 174 42 Circle -7500403 false true 24 174 42 Circle -7500403 false true 144 174 42 Circle -7500403 false true 234 174 42 turtle true 0 Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99 wheel false 0 Circle -7500403 true true 3 3 294 Circle -16777216 true false 30 30 240 Line -7500403 true 150 285 150 15 Line -7500403 true 15 150 285 150 Circle -7500403 true true 120 120 60 Line -7500403 true 216 40 79 269 Line -7500403 true 40 84 269 221 Line -7500403 true 40 216 269 79 Line -7500403 true 84 40 221 269 x false 0 Polygon -7500403 true true 270 75 225 30 30 225 75 270 Polygon -7500403 true true 30 75 75 30 270 225 225 270 @#$#@#$#@ NetLogo 3.0.2 @#$#@#$#@ @#$#@#$#@ @#$#@#$#@ @#$#@#$#@