{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "560b51c8-f47b-437a-a102-4299610fa450",
   "metadata": {},
   "source": [
    "# Results\n",
    "\n",
    "## Reduced iron content, IRE binding activity, and transferrin receptor expression in the failing human heart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "fb363562-f846-4caa-8336-0dca21ce3ed8",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Installing dependencies: 100%|████████████████████| 3/3 [00:01<00:00,  1.78it/s]\n"
     ]
    }
   ],
   "source": [
    "from math import ceil\n",
    "import pandas as pd\n",
    "from orkg import ORKG\n",
    "from scipy.stats import ttest_ind\n",
    "\n",
    "orkg = ORKG(host='https://orkg.org/orkg')\n",
    "orkg.templates.materialize_templates(['R12002', 'R12006', 'R12008'])\n",
    "tp = orkg.templates\n",
    "\n",
    "df = pd.read_csv('data.csv') \n",
    "tt = ttest_ind(df['non-failing heart (NF)'], \n",
    "               df['failing heart (F)'], \n",
    "               equal_var=False, nan_policy='omit')\n",
    "pvalue = tt.pvalue\n",
    "pvalue_ceil = ceil(pvalue * 1000) / 1000.0\n",
    "\n",
    "tp.students_ttest(\n",
    "  'Statistically significant hypothesis test with IRE binding dependent variable on failing and non-failing hearts (p<{})'.format(pvalue_ceil),\n",
    "  'http://purl.obolibrary.org/obo/GO_0030350', # the study design dependent variable\n",
    "  tp.pvalue('the p-value of the statistical hypothesis test (p<{})'.format(pvalue_ceil), tp.scalar_value_specification(pvalue)),\n",
    "  'data.csv', # the input dataset\n",
    ").serialize_to_file('article.contribution.1.json', as_jsonld=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "55f79078-9c87-45a1-b578-64a9cda81973",
   "metadata": {},
   "source": [
    "Consistent with previous reports (@bib1; @bib2) iron concentration was significantly lower in LV tissue samples from patients with advanced heart failure than in LV tissue samples from unused donor hearts. As shown by electrophoretic mobility shift assays, IRE binding activity was significantly (p<0.001) reduced in failing hearts (most pronounced in patients with ischemic cardiomyopathy) ([Figure 1](#fig1)). Protein expression levels of the transferrin receptor were significantly lower in failing hearts than in the controls."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2cbe80dc-08da-4e8c-8db1-766dcc9b3573",
   "metadata": {
    "caption": "### IRE binding activity for non-failing (NF) and failing (F) hearts.",
    "id": "fig1",
    "label": "Figure 1",
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AxesSubplot:>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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6ZKqqo/YHmAAeA87o5q8Cfqmbvg346W76N4B3ddO7gP/RTZ8PfHLIti8H3tQ3f3z3uALYCzyjm78bWN1Nf7Ovrr3d9MXAXcBKYDlwD72bxJ7Z9T0eWAbcCFwxpI6/Av4pvVu/v96tvxb4X8Cybr3fBV4zo9Yl3fP95321vrlv27uAySHPfxvwczPXBT4FnNtN7+qWnQPsB27tfjb39dsMvHGxj5Uj7WfGcfWDwNJu+oXAn/b93j/ad5xdMfPYHXa8A28Cfq+bXkfv7+hJx0JXx8Zu+nXAH3TT/5Xv/a2tAv4WeBpwLLC8az8VmOqr9VvAKTP/Rgbs8xjggb75CeCRvuPrd/qWvQp4z2L/e43jx6/Zgy9X1a3d9B5gIslKYFVVfbpr3wb8SV+fa/rXn+V+Lk3yC930s+gduF+fZd8bqmo/QJI76H2exGrg01X1f7v2PwF+fEj/HVX1HeA7SR4ETgDOA/4F8Lkk0PtP58Fu/Qu7VxdLgRPpfbrnbd2yD8+y5hOB6QHtbwP+E/CWGe03VtWgM6gHgdNmuU8NthLYluRUoOj95z4Xg473FwDvBqiqvUluG9BvUP9f7KZfBPx8vvd+0HLgh4GvAlckOQN4nO8/pj9bVV+eRb2rgYdntH2pqs4YsO6DDBlaPNIZ7vCdvunH6YXcbPs8Tvc7TPKHwJnAV6vq/P6Vk5xD74zpJ6vq2+m9kbh8hBrn+u82qH+AbVX16zNqPYXeWdm/rKqHknxgRq3fmuU+H2HAc6yqTyV5G3D2LLezvNuW5u+/ADur6heSTNA7G5+LJx3vC9A/wMur6vs+MDDJ5cDXgOfSGzZ+tG/xSMfeEM0eX0f1mPsw3VnyQ33j6a8GPn2QLlTVa6v3Rs35AxavBB7qgv00Zh9sB/M54KeTHNe9wfTyOfa/AXhFkh8CSHJ8kh+h9xL+W8D+JCfQ+1z+Yb4BPH3Isn3Ajw1Z9jbgzbOs88fpDWNp/lbyvc93uniBtvmXwIUA6X1fw3Pm2P/P6Y3Fp9vGmV37SuD+qvpHen93S4b0H3rsVdVDwJIkswn4Zo8vw3249cA7u5ebZ9Abd5+vjwNLk+yj90bQZ0Ytrqruozdu+Vl6f2h30xu3nm3/O+gNj1zfPcdPACdW1eeBW4C/Bv6o2/YwHwDeN+QN1R30xkkH7ftjDB6yGeT5XW2av98E/luSW1i4V+u/C6zphgnfBtzOHI4/eq8mlgG3Jbm9m39iu+uTfJ7ecNzAs/Wq+jrwl0n2DnlD9Xp6Q0dP5Vx6x2pz/PiBI1iSH6iqb3Zn7h+h9zk+H1nsup6QZDfw0ppxqecc+p8JvKGqXr2ghWlk3ZVVy6rq0fTu4/gk8OzqXWK46JI8D3j9wY6d7pXpH1XVeYeuskPHMfcj2+VJXkhv3PB64M8Wt5wneSO9N8kenmf/1cB/XrBqtJCOBXYmWUZv/Px1h0uwA1TVzUl2JllS37vWfaYfpneMNskzd0lqkGPuktQgw12SGmS4S1KDDHdJapDhLkkN+v+hyZTERUMDbQAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
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     "output_type": "display_data"
    }
   ],
   "source": [
    "df.plot.box()"
   ]
  }
 ],
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  "description": "Iron deficiency (ID) is associated with adverse outcomes in heart failure (HF) but the underlying mechanisms are incompletely understood ...",
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    "content": [
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      "content": [
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       {
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