skibidy/modules/mmp/SOURCES.yaml at master · stanbot8/skibidy · GitHub

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# Literature sources for mmp module
mmp_ecm_remodeling:
  description: MMP/TIMP dynamics and ECM degradation in wound healing
  sources:
  - id: lobmann2002
    authors: Lobmann R, Ambrosch A, Schultz G, Waldmann K, Schiweck S, Lehnert H
    year: 2002
    title: Expression of matrix-metalloproteinases and their inhibitors in the wounds of diabetic and non-diabetic patients
    journal: Diabetologia 45:1011-1016
    doi: 10.1007/s00125-002-0868-8
    notes: 'MMP-1 elevated 65-fold and MMP-9 14-fold in diabetic vs acute wounds. TIMP-2 reduced 2-fold. Supports diabetic_mmp_factor=3.0
      and diabetic_timp_factor=0.5 parameters.

      '
  - id: nagase1999
    authors: Nagase H, Woessner JF
    year: 1999
    title: Matrix metalloproteinases
    journal: J Biol Chem 274(31):21491-21494
    doi: 10.1074/jbc.274.31.21491
    notes: 'Review of MMP family biochemistry. MMP-1 (fibroblast collagenase), MMP-9 (gelatinase B from macrophages/neutrophils).
      Supports mmp_diffusion and fibroblast MMP production parameters.

      '
  - id: ladwig2002
    authors: Ladwig GP, Robson MC, Liu R, Kuhn MA, Muir DF, Schultz GS
    year: 2002
    title: Ratios of activated matrix metalloproteinase-9 to tissue inhibitor of matrix metalloproteinase-1 in wound fluids
      are inversely correlated with healing of pressure ulcers
    journal: Wound Repair Regen 10(1):26-37
    doi: 10.1046/j.1524-475x.2002.10903.x
    notes: 'High MMP-9:TIMP-1 ratio inversely correlates with healing. Supports MMP-collagen degradation rate calibration.

      '
  - id: pilcher1997
    authors: Pilcher BK, Dumin JA, Sudbeck BD, Krane SM, Welgus HG, Parks WC
    year: 1997
    title: The activity of collagenase-1 is required for keratinocyte migration on a type I collagen matrix
    journal: J Cell Biol 137(6):1445-1457
    doi: 10.1083/jcb.137.6.1445
    notes: 'Keratinocytes at the wound migration front produce MMP-1 (collagenase-1) to cleave collagen I and enable re-epithelialization.
      Supports mmp_keratinocyte_rate parameter.

      '
mmp_kinetics:
  description: Aggregate MMP activity (MMP-1, -2, -8, -9), peak-normalized
  consensus: data/mmp_kinetics.csv
  columns:
  - day
  - mmp_normalized
  units:
    day: days
    mmp_normalized: fraction of peak
  normalization: peak-normalized (1.0 = maximum at day 3 to 5)
  notes: 'Aggregate MMP activity weighted toward MMP-8 (neutrophil collagenase, 100x to 200x more abundant than MMP-1). MMP-9
    peaks at 24h, MMP-8 at day 4, MMP-1 at day 7. Activity normalizes by day 14 to 21 as TIMP-1 rises.

    '
  sources:
  - id: nwomeh1998
    authors: Nwomeh BC, Liang HX, Diegelmann RF, Cohen IK, Yager DR
    year: 1998
    title: Dynamics of the matrix metalloproteinases MMP-1 and MMP-8 in acute open human dermal wounds
    journal: Wound Repair Regen 6(2):127-134
    doi: 10.1046/j.1524-475X.1998.60206.x
  - id: gill2008
    authors: Gill SE, Parks WC
    year: 2008
    title: 'Metalloproteinases and their inhibitors: regulators of wound healing'
    journal: Int J Biochem Cell Biol 40(6-7):1334-1347
    doi: 10.1016/j.biocel.2007.10.024
  - id: caley2015
    authors: Caley MP, Martins VLC, O'Toole EA
    year: 2015
    title: Metalloproteinases and wound healing
    journal: Adv Wound Care 4(4):225-234
    doi: 10.1089/wound.2014.0581