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lamthuy
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SelfiesGen

Safetensors
gpt2
Model card Files
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tlhoang commited on
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  1. .gitattributes +35 -0
  2. Examples.ipynb +366 -0
  3. added_tokens.json +472 -0
  4. config.json +39 -0
  5. latest +1 -0
  6. merges.txt +0 -0
  7. model.safetensors +3 -0
  8. rng_state_1.pth +3 -0
  9. special_tokens_map.json +20 -0
  10. tokenizer.json +0 -0
  11. tokenizer_config.json +3783 -0
  12. trainer_state.json +0 -0
  13. training_args.bin +3 -0
  14. vocab.json +0 -0
.gitattributes ADDED
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Examples.ipynb ADDED
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+ "execution_count": 2,
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+ "id": "a1af2321-8860-4a3e-8406-a9ae587b97bf",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
10
+ "from transformers import AutoModelForCausalLM, AutoTokenizer\n",
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+ "import selfies as sf\n",
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+ "from rdkit import Chem\n",
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+ "from typing import Optional\n",
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+ "import numpy as np\n",
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+ "import py3Dmol\n",
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+ "from rdkit import Chem, DataStructs\n",
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+ "from rdkit.Chem import AllChem\n",
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+ "import torch\n",
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+ "\n",
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+ "def smiles_to_3d(smiles_list, width=400, height=300):\n",
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+ " # Visualize the 3D structure using py3Dmol\n",
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+ " view = py3Dmol.view(width=width, height=height)\n",
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+ " for smiles in smiles_list:\n",
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+ " # Generate the RDKit molecule object\n",
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+ " mol = Chem.MolFromSmiles(smiles)\n",
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+ " if mol is None:\n",
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+ " raise ValueError(\"Invalid SMILES string\")\n",
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+ "\n",
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+ " # Add hydrogens to the molecule\n",
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+ " mol = Chem.AddHs(mol)\n",
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+ "\n",
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+ " # Generate 3D coordinates\n",
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+ " AllChem.EmbedMolecule(mol, randomSeed=42)\n",
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+ " AllChem.UFFOptimizeMolecule(mol)\n",
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+ "\n",
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+ " # Generate the 3D structure in the form of a pdb string\n",
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+ " pdb = Chem.MolToPDBBlock(mol)\n",
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+ " view.addModel(pdb, 'pdb')\n",
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+ " view.setStyle({'stick': {}})\n",
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+ " view.zoomTo()\n",
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+ " return view\n",
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+ "\n",
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+ " \n",
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+ "# Load the checkpoint and the tokenizer\n",
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+ "checkpoint_path = \"lamthuy/SelfiesGen\"\n",
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+ "model = AutoModelForCausalLM.from_pretrained(checkpoint_path)\n",
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+ "tokenizer = AutoTokenizer.from_pretrained(checkpoint_path)"
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+ ]
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+ },
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+ ]
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+ "metadata": {},
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+ "output_type": "display_data"
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+ },
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+ {
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+ "data": {
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+ "text/plain": [
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+ "<py3Dmol.view at 0x2afd09c40>"
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+ ]
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+ },
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+ "execution_count": 9,
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+ "metadata": {},
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+ "output_type": "execute_result"
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+ }
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+ ],
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+ "source": [
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+ "# Given a SMILES, get its fingerpint\n",
124
+ "smiles = \"CC(=O)OC1=CC=CC=C1C(=O)O\"\n",
125
+ "smiles_to_3d([smiles])"
126
+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 12,
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+ "id": "05f9bf21-c998-4d63-870e-c1033ff91b31",
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stderr",
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+ "output_type": "stream",
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+ "text": [
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+ "The attention mask and the pad token id were not set. As a consequence, you may observe unexpected behavior. Please pass your input's `attention_mask` to obtain reliable results.\n",
139
+ "Setting `pad_token_id` to `eos_token_id`:50256 for open-end generation.\n"
140
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
146
+ "[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=S][O][SEP]\n",
147
+ "[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=NH2+1][O]\n",
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+ "CC(=O)OC1=CC=CC=C1C(=[NH2+1])O\n"
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+ ]
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+ },
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+ {
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+ "if(warn) {\n",
190
+ " warn.parentNode.removeChild(warn);\n",
191
+ "}\n",
192
+ "$3Dmolpromise.then(function() {\n",
193
+ "viewer_1753264053659028 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1753264053659028\"),{backgroundColor:\"white\"});\n",
194
+ "viewer_1753264053659028.zoomTo();\n",
195
+ "\tviewer_1753264053659028.addModel(\"HETATM 1 C1 UNL 1 2.411 -2.582 -1.327 1.00 0.00 C \\nHETATM 2 C2 UNL 1 1.777 -1.233 -1.311 1.00 0.00 C \\nHETATM 3 O1 UNL 1 1.971 -0.444 -2.275 1.00 0.00 O \\nHETATM 4 O2 UNL 1 0.887 -0.908 -0.278 1.00 0.00 O \\nHETATM 5 C3 UNL 1 0.406 0.380 0.005 1.00 0.00 C \\nHETATM 6 C4 UNL 1 1.187 1.525 -0.250 1.00 0.00 C \\nHETATM 7 C5 UNL 1 0.691 2.798 0.033 1.00 0.00 C \\nHETATM 8 C6 UNL 1 -0.580 2.947 0.586 1.00 0.00 C \\nHETATM 9 C7 UNL 1 -1.357 1.822 0.866 1.00 0.00 C \\nHETATM 10 C8 UNL 1 -0.876 0.529 0.582 1.00 0.00 C \\nHETATM 11 C9 UNL 1 -1.702 -0.662 0.905 1.00 0.00 C \\nHETATM 12 N1 UNL 1 -2.996 -0.640 0.776 1.00 0.00 N1+\\nHETATM 13 O3 UNL 1 -1.073 -1.826 1.349 1.00 0.00 O \\nHETATM 14 H1 UNL 1 1.780 -3.281 -1.914 1.00 0.00 H \\nHETATM 15 H2 UNL 1 2.512 -2.964 -0.290 1.00 0.00 H \\nHETATM 16 H3 UNL 1 3.421 -2.524 -1.787 1.00 0.00 H \\nHETATM 17 H4 UNL 1 2.190 1.435 -0.643 1.00 0.00 H \\nHETATM 18 H5 UNL 1 1.299 3.672 -0.166 1.00 0.00 H \\nHETATM 19 H6 UNL 1 -0.957 3.936 0.813 1.00 0.00 H \\nHETATM 20 H7 UNL 1 -2.325 1.965 1.329 1.00 0.00 H \\nHETATM 21 H8 UNL 1 -3.567 -1.482 1.010 1.00 0.00 H \\nHETATM 22 H9 UNL 1 -3.499 0.198 0.408 1.00 0.00 H \\nHETATM 23 H10 UNL 1 -1.599 -2.662 1.576 1.00 0.00 H \\nCONECT 1 2 14 15 16\\nCONECT 2 3 3 4\\nCONECT 4 5\\nCONECT 5 6 6 10\\nCONECT 6 7 17\\nCONECT 7 8 8 18\\nCONECT 8 9 19\\nCONECT 9 10 10 20\\nCONECT 10 11\\nCONECT 11 12 12 13\\nCONECT 12 21 22\\nCONECT 13 23\\nEND\\n\",\"pdb\");\n",
196
+ "\tviewer_1753264053659028.setStyle({\"stick\": {}});\n",
197
+ "\tviewer_1753264053659028.zoomTo();\n",
198
+ "viewer_1753264053659028.render();\n",
199
+ "});\n",
200
+ "</script>"
201
+ ]
202
+ },
203
+ "metadata": {},
204
+ "output_type": "display_data"
205
+ },
206
+ {
207
+ "data": {
208
+ "text/plain": [
209
+ "<py3Dmol.view at 0x2afbaf020>"
210
+ ]
211
+ },
212
+ "execution_count": 12,
213
+ "metadata": {},
214
+ "output_type": "execute_result"
215
+ }
216
+ ],
217
+ "source": [
218
+ "s = sf.encoder(smiles)\n",
219
+ "s = s + \"[SEP]\"\n",
220
+ "print(s)\n",
221
+ "input_ids = tokenizer.encode(s, return_tensors=\"pt\")\n",
222
+ "n = input_ids.size(1)\n",
223
+ "# Generate output sequence\n",
224
+ "output_ids = model.generate(input_ids, max_length=128, num_beams=5, num_return_sequences=5,\n",
225
+ " early_stopping=True)\n",
226
+ "output = tokenizer.decode(output_ids[1][n:], skip_special_tokens=True)\n",
227
+ "print(output)\n",
228
+ "smiles = sf.decoder(output)\n",
229
+ "print(smiles)\n",
230
+ "smiles_to_3d([smiles])"
231
+ ]
232
+ },
233
+ {
234
+ "cell_type": "code",
235
+ "execution_count": 13,
236
+ "id": "dbe6cebd-c7d5-4da9-aac0-114f232cf147",
237
+ "metadata": {},
238
+ "outputs": [
239
+ {
240
+ "name": "stderr",
241
+ "output_type": "stream",
242
+ "text": [
243
+ "The attention mask and the pad token id were not set. As a consequence, you may observe unexpected behavior. Please pass your input's `attention_mask` to obtain reliable results.\n",
244
+ "Setting `pad_token_id` to `eos_token_id`:50256 for open-end generation.\n"
245
+ ]
246
+ },
247
+ {
248
+ "name": "stdout",
249
+ "output_type": "stream",
250
+ "text": [
251
+ "[C][C][=Branch1][C][=O][N][C][=C][C][=N][C][=C][Ring1][=Branch1][C][=Branch1][C][=S][O-1]\n",
252
+ "CC(=O)NC1=CC=NC=C1C(=S)[O-1]\n"
253
+ ]
254
+ },
255
+ {
256
+ "data": {
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261
+ " </div>\n",
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+ "<script>\n",
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+ "\n",
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+ "var loadScriptAsync = function(uri){\n",
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+ " var tag = document.createElement('script');\n",
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+ " tag.src = uri;\n",
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+ " warn.parentNode.removeChild(warn);\n",
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+ "$3Dmolpromise.then(function() {\n",
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+ "viewer_17532640697518232.zoomTo();\n",
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+ "viewer_17532640697518232.render();\n",
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+ "});\n",
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+ "</script>"
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+ ]
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+ },
307
+ "metadata": {},
308
+ "output_type": "display_data"
309
+ },
310
+ {
311
+ "data": {
312
+ "text/plain": [
313
+ "<py3Dmol.view at 0x11fd5a780>"
314
+ ]
315
+ },
316
+ "execution_count": 13,
317
+ "metadata": {},
318
+ "output_type": "execute_result"
319
+ }
320
+ ],
321
+ "source": [
322
+ "input_ids[0][5] = tokenizer.mask_token_id\n",
323
+ "input_ids[0][9] = tokenizer.mask_token_id\n",
324
+ "input_ids[0][18] = tokenizer.mask_token_id\n",
325
+ "input_ids[0][11] = tokenizer.mask_token_id\n",
326
+ "# Generate output sequence\n",
327
+ "output_ids = model.generate(input_ids, max_length=128, num_beams=5, num_return_sequences=5,\n",
328
+ " early_stopping=True)\n",
329
+ "output = tokenizer.decode(output_ids[1][n:], skip_special_tokens=True)\n",
330
+ "print(output)\n",
331
+ "smiles = sf.decoder(output)\n",
332
+ "print(smiles)\n",
333
+ "smiles_to_3d([smiles])"
334
+ ]
335
+ },
336
+ {
337
+ "cell_type": "code",
338
+ "execution_count": null,
339
+ "id": "f696bb9c-2870-4b0b-9b62-1623411e5df6",
340
+ "metadata": {},
341
+ "outputs": [],
342
+ "source": []
343
+ }
344
+ ],
345
+ "metadata": {
346
+ "kernelspec": {
347
+ "display_name": "Python 3 (ipykernel)",
348
+ "language": "python",
349
+ "name": "python3"
350
+ },
351
+ "language_info": {
352
+ "codemirror_mode": {
353
+ "name": "ipython",
354
+ "version": 3
355
+ },
356
+ "file_extension": ".py",
357
+ "mimetype": "text/x-python",
358
+ "name": "python",
359
+ "nbconvert_exporter": "python",
360
+ "pygments_lexer": "ipython3",
361
+ "version": "3.12.10"
362
+ }
363
+ },
364
+ "nbformat": 4,
365
+ "nbformat_minor": 5
366
+ }
added_tokens.json ADDED
@@ -0,0 +1,472 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "[#11C-1]": 50724,
3
+ "[#14C]": 50531,
4
+ "[#Al]": 50558,
5
+ "[#B]": 50433,
6
+ "[#Branch1]": 50363,
7
+ "[#Branch2]": 50310,
8
+ "[#Branch3]": 50524,
9
+ "[#C-1]": 50471,
10
+ "[#C]": 50385,
11
+ "[#N+1]": 50527,
12
+ "[#N]": 50379,
13
+ "[#O+1]": 50351,
14
+ "[#Ring1]": 50659,
15
+ "[#Ring2]": 50590,
16
+ "[#S]": 50375,
17
+ "[-/Ring1]": 50311,
18
+ "[-/Ring2]": 50367,
19
+ "[-\\Ring1]": 50421,
20
+ "[-\\Ring2]": 50638,
21
+ "[/-Ring1]": 50274,
22
+ "[/-Ring2]": 50459,
23
+ "[/11CH3]": 50687,
24
+ "[/123I]": 50580,
25
+ "[/125I]": 50671,
26
+ "[/131I]": 50561,
27
+ "[/13CH1]": 50625,
28
+ "[/13C]": 50632,
29
+ "[/14CH1]": 50635,
30
+ "[/14C]": 50706,
31
+ "[/As]": 50409,
32
+ "[/B]": 50655,
33
+ "[/Br]": 50272,
34
+ "[/C-1]": 50700,
35
+ "[/C@@H1]": 50323,
36
+ "[/C@@]": 50497,
37
+ "[/C@H1]": 50516,
38
+ "[/C@]": 50358,
39
+ "[/CH1-1]": 50716,
40
+ "[/C]": 50449,
41
+ "[/Cl]": 50492,
42
+ "[/F]": 50693,
43
+ "[/I]": 50404,
44
+ "[/N+1]": 50283,
45
+ "[/N-1]": 50615,
46
+ "[/NH1+1]": 50415,
47
+ "[/NH1]": 50521,
48
+ "[/N]": 50350,
49
+ "[/O-1]": 50650,
50
+ "[/O]": 50457,
51
+ "[/P@]": 50653,
52
+ "[/P]": 50667,
53
+ "[/S+1]": 50682,
54
+ "[/S-1]": 50621,
55
+ "[/S]": 50406,
56
+ "[/Se]": 50704,
57
+ "[/Si]": 50664,
58
+ "[/Te]": 50628,
59
+ "[10B]": 50540,
60
+ "[11C@H1]": 50622,
61
+ "[11CH1]": 50606,
62
+ "[11CH2]": 50648,
63
+ "[11CH3]": 50608,
64
+ "[11C]": 50617,
65
+ "[123I-1]": 50641,
66
+ "[123IH1]": 50566,
67
+ "[123I]": 50697,
68
+ "[123Te]": 50550,
69
+ "[124I-1]": 50677,
70
+ "[124I]": 50663,
71
+ "[125I-1]": 50544,
72
+ "[125IH1]": 50703,
73
+ "[125I]": 50681,
74
+ "[127I]": 50552,
75
+ "[127Xe]": 50535,
76
+ "[129Xe]": 50548,
77
+ "[131Cs]": 50688,
78
+ "[131I-1]": 50684,
79
+ "[131I]": 50689,
80
+ "[133Xe]": 50589,
81
+ "[135I]": 50626,
82
+ "[13CH1]": 50579,
83
+ "[13CH2]": 50698,
84
+ "[13CH3]": 50619,
85
+ "[13C]": 50633,
86
+ "[13NH3]": 50631,
87
+ "[14C@@H1]": 50627,
88
+ "[14C@H1]": 50594,
89
+ "[14C@]": 50721,
90
+ "[14CH1]": 50598,
91
+ "[14CH2]": 50585,
92
+ "[14CH3]": 50675,
93
+ "[14C]": 50712,
94
+ "[15NH1]": 50553,
95
+ "[15N]": 50595,
96
+ "[15OH2]": 50578,
97
+ "[17F]": 50611,
98
+ "[18F-1]": 50690,
99
+ "[18FH1]": 50582,
100
+ "[18F]": 50549,
101
+ "[18OH1]": 50604,
102
+ "[19F]": 50529,
103
+ "[223Ra+2]": 50715,
104
+ "[223Ra]": 50577,
105
+ "[22Na+1]": 50647,
106
+ "[2H]": 50282,
107
+ "[32PH1]": 50643,
108
+ "[32P]": 50670,
109
+ "[35S]": 50656,
110
+ "[3H]": 50612,
111
+ "[42K+1]": 50616,
112
+ "[45Ca+2]": 50645,
113
+ "[47Ca+2]": 50592,
114
+ "[4H]": 50673,
115
+ "[73Se]": 50574,
116
+ "[75Se]": 50705,
117
+ "[76BrH1]": 50649,
118
+ "[76Br]": 50713,
119
+ "[81Kr]": 50559,
120
+ "[82Rb+1]": 50547,
121
+ "[82Rb]": 50538,
122
+ "[85Sr+2]": 50672,
123
+ "[85SrH2]": 50668,
124
+ "[89Sr+2]": 50723,
125
+ "[=11C]": 50542,
126
+ "[=13CH1]": 50568,
127
+ "[=13C]": 50654,
128
+ "[=14CH1]": 50714,
129
+ "[=14C]": 50701,
130
+ "[=18O]": 50678,
131
+ "[=Al]": 50545,
132
+ "[=As]": 50448,
133
+ "[=B-1]": 50607,
134
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387
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388
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389
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390
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391
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392
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393
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394
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395
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396
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397
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399
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400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
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441
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442
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444
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445
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447
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453
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455
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456
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457
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458
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459
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460
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461
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462
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463
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464
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465
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466
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467
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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485
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486
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487
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488
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489
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490
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491
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492
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493
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495
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496
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497
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498
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499
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500
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501
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502
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503
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504
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505
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506
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508
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509
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510
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511
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512
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513
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514
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515
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516
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517
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519
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520
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521
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522
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523
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524
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525
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526
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527
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528
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529
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530
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532
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533
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535
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536
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537
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538
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541
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544
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545
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546
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547
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548
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549
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550
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551
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552
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553
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554
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555
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556
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557
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558
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559
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560
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561
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562
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563
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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578
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579
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580
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581
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582
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583
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584
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585
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586
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587
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588
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589
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590
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591
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592
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593
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594
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595
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597
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599
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600
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601
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602
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605
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606
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607
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608
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609
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610
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611
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613
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615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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629
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631
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632
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633
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634
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637
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639
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640
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641
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642
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643
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645
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647
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648
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649
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650
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651
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652
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653
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655
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657
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658
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659
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661
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663
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665
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666
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669
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672
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673
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674
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675
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677
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679
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680
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681
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682
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683
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685
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687
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688
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689
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690
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691
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693
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695
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696
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697
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698
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699
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701
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703
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704
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705
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706
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707
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709
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711
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712
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713
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714
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715
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717
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719
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720
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721
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722
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725
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729
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730
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731
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733
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734
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735
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736
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737
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738
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741
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743
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744
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745
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749
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753
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754
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761
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762
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765
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769
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770
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773
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775
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776
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777
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778
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779
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780
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781
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783
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785
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789
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791
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792
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793
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794
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797
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799
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800
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801
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802
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804
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805
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806
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807
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808
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809
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810
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811
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812
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813
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815
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816
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817
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818
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821
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825
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826
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827
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829
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831
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832
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833
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834
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837
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840
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841
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842
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847
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849
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850
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853
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855
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857
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861
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866
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867
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869
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871
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872
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873
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874
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875
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877
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880
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881
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882
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885
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893
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895
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896
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897
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898
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901
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903
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905
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906
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909
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912
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915
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917
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920
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921
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925
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930
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933
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937
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969
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970
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1009
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1010
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1013
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1016
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1017
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1025
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1029
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1037
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1050
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1053
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1077
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1092
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1093
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1094
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1095
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1096
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1097
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1098
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1099
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1100
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1101
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1102
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1103
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1104
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1105
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1106
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1107
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1108
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1109
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1110
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1111
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1112
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1113
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1114
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1115
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1116
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1117
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1118
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1119
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1120
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1121
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1122
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1123
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1124
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1125
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1126
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1127
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1128
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1129
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1130
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1131
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1132
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1133
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1134
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1135
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1136
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1137
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1138
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1139
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1140
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1141
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1142
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1143
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1144
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1145
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1146
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1147
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1148
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1149
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1150
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1151
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1152
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1153
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1154
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1155
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1156
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1157
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1168
+ "rstrip": false,
1169
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1170
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1171
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1172
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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1184
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1185
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1186
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1187
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1188
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1189
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1190
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1191
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1192
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1193
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1194
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1195
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1196
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1197
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1198
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1199
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1200
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1201
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1202
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1203
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1204
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1205
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1206
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1207
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1208
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1216
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1217
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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1230
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1231
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1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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1245
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1246
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1247
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1248
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1249
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1250
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1251
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1252
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1253
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1254
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1255
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1256
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1257
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1258
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1259
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1260
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1268
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1281
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1282
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1283
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1284
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1285
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1286
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1287
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1288
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1289
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1290
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1291
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1292
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1293
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1294
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1295
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1296
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1297
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1298
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1299
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1300
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1301
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1302
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1303
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1304
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1305
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1306
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1307
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1308
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1309
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1310
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1311
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1312
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1313
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1314
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1315
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1316
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1317
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1318
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1319
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1320
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1321
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1322
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1323
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1324
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1325
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1326
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1327
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1328
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1329
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1330
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1331
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1332
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1333
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1334
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1335
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1336
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1337
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1338
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1339
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1340
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1341
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1342
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1343
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1344
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1345
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1346
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1347
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1348
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1349
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1350
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1351
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1352
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1353
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1354
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1355
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1356
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1357
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1358
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1359
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1360
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1361
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1362
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1363
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1364
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1365
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1366
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1367
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1368
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1369
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1370
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1371
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1372
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1373
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1374
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1375
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1376
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1377
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1378
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1379
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1380
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1381
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1382
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1383
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1384
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1385
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1386
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1387
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1388
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1389
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1390
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1391
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1392
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1393
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1394
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1395
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1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1404
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1405
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1406
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1407
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1408
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1409
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1410
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1411
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1412
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1413
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1414
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1415
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1416
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1417
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1418
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1419
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1420
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1421
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1422
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1423
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1424
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1425
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1426
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1427
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1428
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1429
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1437
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1438
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1439
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1440
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1441
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1442
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1443
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1444
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1445
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1446
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1447
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1448
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1449
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1450
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1451
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1452
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1453
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1454
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1462
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1463
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1464
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1465
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1466
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1467
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1468
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1469
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1470
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1471
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1472
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1473
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1474
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1475
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1476
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1477
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1478
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1479
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1480
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1481
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1482
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1483
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1484
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1485
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1486
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1487
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1488
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1489
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1490
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1491
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1492
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1493
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1494
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1495
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1496
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1497
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1498
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1499
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1500
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1501
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1502
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1503
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1504
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1505
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1506
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1507
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1508
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1509
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1510
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1511
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1512
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1513
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1514
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1515
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1516
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1517
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1518
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1519
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1520
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1521
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1522
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1523
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1524
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1525
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1526
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1527
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1528
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1529
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1530
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1531
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1532
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1533
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1534
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1535
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1536
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1537
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1538
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1539
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1540
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1541
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1542
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1543
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1544
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1545
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1546
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1547
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1549
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1551
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1552
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1553
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1554
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1555
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1556
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1557
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1558
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1559
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1560
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1561
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1562
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1563
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1564
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1565
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1566
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1567
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1568
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1569
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1570
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
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1582
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1583
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1584
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1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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1594
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1595
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1596
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1597
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1598
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1599
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1600
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1601
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1602
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1603
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1604
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1605
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1606
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1607
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1608
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1609
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1610
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1611
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1612
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1613
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1614
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1615
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1616
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1617
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1618
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1619
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1620
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1621
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1622
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1623
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1624
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1625
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1626
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1627
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1628
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1629
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1630
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1631
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1632
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1633
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1634
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1635
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1636
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1637
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1638
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1639
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1640
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1641
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1642
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1643
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1644
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1645
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1646
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1647
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1648
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1649
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1650
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1651
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1652
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1653
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1654
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1655
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1656
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1657
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1658
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1659
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1660
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1661
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1663
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1664
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1665
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1666
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1667
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1668
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1669
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1670
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1671
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1672
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1673
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1674
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1675
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1676
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1677
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1678
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1679
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1680
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1681
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1682
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1683
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1684
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1685
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1686
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1687
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1688
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1689
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1690
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1691
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1692
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1693
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1694
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1695
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1696
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1697
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1698
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1699
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1700
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1701
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1702
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1703
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1704
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1705
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1706
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1707
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1709
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1710
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1711
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1712
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1713
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1714
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1715
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1716
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1717
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1718
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1719
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1720
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1721
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1722
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1723
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1724
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1725
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1726
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1727
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1728
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1729
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1730
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1731
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1732
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1733
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1734
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1735
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1736
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1737
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1738
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1739
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1741
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1743
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1744
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1745
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1746
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1747
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1749
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1750
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1751
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1752
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1753
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1754
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
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1766
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1767
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1768
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1769
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1770
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1771
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1772
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1773
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1774
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1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
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1784
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1785
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1786
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1787
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1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
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1799
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1800
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1801
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1802
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1803
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1804
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1805
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1806
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1807
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1808
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1809
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1810
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1811
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1812
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1813
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1814
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1815
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1816
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1817
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1818
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1819
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
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1829
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1830
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1831
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1832
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1833
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1834
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1835
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1836
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1837
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1838
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1839
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1840
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1841
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1842
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1843
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1844
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1845
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1846
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1847
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1848
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1849
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1850
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1851
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1852
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1853
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1854
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1855
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1856
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1857
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1858
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1859
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1860
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1861
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1862
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1863
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1864
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1865
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1866
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1867
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1868
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1869
+ "content": "[\\-Ring1]",
1870
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1871
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1872
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1873
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1874
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1875
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1876
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1877
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1878
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1879
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1880
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1881
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1882
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1883
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1884
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1885
+ "content": "[C@@]",
1886
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1887
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1888
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1889
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1890
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1891
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1892
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1893
+ "content": "[/Cl]",
1894
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1895
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1896
+ "rstrip": false,
1897
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1898
+ "special": false
1899
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1900
+ "50493": {
1901
+ "content": "[Cu+2]",
1902
+ "lstrip": false,
1903
+ "normalized": true,
1904
+ "rstrip": false,
1905
+ "single_word": false,
1906
+ "special": false
1907
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1908
+ "50494": {
1909
+ "content": "[Cd]",
1910
+ "lstrip": false,
1911
+ "normalized": true,
1912
+ "rstrip": false,
1913
+ "single_word": false,
1914
+ "special": false
1915
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1916
+ "50495": {
1917
+ "content": "[CaH2]",
1918
+ "lstrip": false,
1919
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1920
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1921
+ "single_word": false,
1922
+ "special": false
1923
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1924
+ "50496": {
1925
+ "content": "[=Co]",
1926
+ "lstrip": false,
1927
+ "normalized": true,
1928
+ "rstrip": false,
1929
+ "single_word": false,
1930
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1931
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1932
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1933
+ "content": "[/C@@]",
1934
+ "lstrip": false,
1935
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1936
+ "rstrip": false,
1937
+ "single_word": false,
1938
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1939
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1940
+ "50498": {
1941
+ "content": "[Li]",
1942
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1943
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1944
+ "rstrip": false,
1945
+ "single_word": false,
1946
+ "special": false
1947
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1948
+ "50499": {
1949
+ "content": "[Ti]",
1950
+ "lstrip": false,
1951
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1952
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1953
+ "single_word": false,
1954
+ "special": false
1955
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1956
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1957
+ "content": "[=C]",
1958
+ "lstrip": false,
1959
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1960
+ "rstrip": false,
1961
+ "single_word": false,
1962
+ "special": false
1963
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1964
+ "50501": {
1965
+ "content": "[P+1]",
1966
+ "lstrip": false,
1967
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1968
+ "rstrip": false,
1969
+ "single_word": false,
1970
+ "special": false
1971
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1972
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1973
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1974
+ "lstrip": false,
1975
+ "normalized": true,
1976
+ "rstrip": false,
1977
+ "single_word": false,
1978
+ "special": false
1979
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1980
+ "50503": {
1981
+ "content": "[=Y]",
1982
+ "lstrip": false,
1983
+ "normalized": true,
1984
+ "rstrip": false,
1985
+ "single_word": false,
1986
+ "special": false
1987
+ },
1988
+ "50504": {
1989
+ "content": "[V+2]",
1990
+ "lstrip": false,
1991
+ "normalized": true,
1992
+ "rstrip": false,
1993
+ "single_word": false,
1994
+ "special": false
1995
+ },
1996
+ "50505": {
1997
+ "content": "[SiH1]",
1998
+ "lstrip": false,
1999
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2000
+ "rstrip": false,
2001
+ "single_word": false,
2002
+ "special": false
2003
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2004
+ "50506": {
2005
+ "content": "[V]",
2006
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2007
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2008
+ "rstrip": false,
2009
+ "single_word": false,
2010
+ "special": false
2011
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2012
+ "50507": {
2013
+ "content": "[La+3]",
2014
+ "lstrip": false,
2015
+ "normalized": true,
2016
+ "rstrip": false,
2017
+ "single_word": false,
2018
+ "special": false
2019
+ },
2020
+ "50508": {
2021
+ "content": "[Ru+3]",
2022
+ "lstrip": false,
2023
+ "normalized": true,
2024
+ "rstrip": false,
2025
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2026
+ "special": false
2027
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2028
+ "50509": {
2029
+ "content": "[=Cu]",
2030
+ "lstrip": false,
2031
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2032
+ "rstrip": false,
2033
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2034
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2035
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2036
+ "50510": {
2037
+ "content": "[C@]",
2038
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2039
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2040
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2041
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2042
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2043
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2044
+ "50511": {
2045
+ "content": "[Fe+3]",
2046
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2047
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2048
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2049
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2050
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2051
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2052
+ "50512": {
2053
+ "content": "[Te]",
2054
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2055
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2056
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2057
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2058
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2059
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2060
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2061
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2062
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2063
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2064
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2065
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2066
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2067
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2068
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2069
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2070
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2071
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2072
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2073
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2074
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2075
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2076
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2077
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2078
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2079
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2080
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2081
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2082
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2083
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2084
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2085
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2086
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2087
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2088
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2089
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2090
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2091
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2092
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2093
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2094
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2095
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2096
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2097
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2098
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2099
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2100
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2101
+ "content": "[SH0]",
2102
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2103
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2104
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2105
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2106
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2107
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2108
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2109
+ "content": "[Pt+4]",
2110
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2111
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2112
+ "rstrip": false,
2113
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2114
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2115
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2116
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2117
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2118
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2119
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2120
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2121
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2122
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2123
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2124
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2125
+ "content": "[/NH1]",
2126
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2127
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2128
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2129
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2130
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2131
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2132
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2133
+ "content": "[Nop]",
2134
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2135
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2136
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2137
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2138
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2139
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2140
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2141
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2142
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2143
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2144
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2145
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2146
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2147
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2148
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2149
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2150
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2151
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2152
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2153
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2154
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2155
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2156
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2157
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2158
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2159
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2160
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2161
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2162
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2163
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2164
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2165
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2166
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2167
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2168
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2169
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2170
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2171
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2172
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2173
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2174
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2175
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2176
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2177
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2178
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2179
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2180
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2181
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2182
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2183
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2184
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2185
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2186
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2187
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2188
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2189
+ "content": "[19F]",
2190
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2191
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2192
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2193
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2194
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2195
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2196
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2197
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2198
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2199
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2200
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2201
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2202
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2203
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2204
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2205
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2206
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2207
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2208
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2209
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2210
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2211
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2212
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2213
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2214
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2215
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2216
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2217
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2218
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2219
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2220
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2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
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2238
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2239
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2240
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2241
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2242
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2243
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2244
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2245
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2246
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2247
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2248
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2249
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2250
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2251
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2252
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2253
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2254
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2255
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2256
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2257
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2258
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2259
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2260
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2261
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2262
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2263
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2264
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2265
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2266
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2267
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2268
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2269
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2270
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2271
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2272
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2273
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2274
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2275
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2276
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2277
+ "content": "[10B]",
2278
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2279
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2280
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2281
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2282
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2283
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2284
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2285
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2286
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2287
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2288
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2289
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2290
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2291
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2292
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2293
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2294
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2295
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2296
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2297
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2298
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2299
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2300
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2301
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2302
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2303
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2304
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2305
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2306
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2307
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2308
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2309
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2310
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2311
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2312
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2313
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2314
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
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2324
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2325
+ "content": "[=Se+1]",
2326
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2327
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2328
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2329
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2330
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2331
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2332
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2333
+ "content": "[82Rb+1]",
2334
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2335
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2336
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2337
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2338
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2339
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2340
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2341
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
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2353
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2354
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2355
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2356
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2357
+ "content": "[123Te]",
2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
+ "content": "[OH1+1]",
2366
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2367
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2368
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2369
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2370
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2371
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2372
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2373
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2374
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2375
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2376
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2377
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2378
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2379
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2380
+ "50553": {
2381
+ "content": "[15NH1]",
2382
+ "lstrip": false,
2383
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2384
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2385
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2386
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2387
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2388
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2389
+ "content": "[Zn-2]",
2390
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2391
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2392
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2393
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2394
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2395
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2396
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2397
+ "content": "[\\Si]",
2398
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2399
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2400
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2401
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2402
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2403
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2404
+ "50556": {
2405
+ "content": "[NH1-1]",
2406
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2407
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2408
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2409
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2410
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2411
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2412
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2413
+ "content": "[\\131I]",
2414
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2415
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2416
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2417
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2418
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2419
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2420
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2421
+ "content": "[#Al]",
2422
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2423
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2424
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2425
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2426
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2427
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2428
+ "50559": {
2429
+ "content": "[81Kr]",
2430
+ "lstrip": false,
2431
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2432
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2433
+ "single_word": false,
2434
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2435
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2436
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2437
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2438
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2439
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2440
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2441
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2442
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2443
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2444
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2445
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2446
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2447
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2448
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2449
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2450
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2451
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2452
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2453
+ "content": "[Mg+1]",
2454
+ "lstrip": false,
2455
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2456
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2457
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2458
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2459
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2460
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2461
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2462
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2463
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2464
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2465
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2466
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2467
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2468
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2469
+ "content": "[PH2]",
2470
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2471
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2472
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2473
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2474
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2475
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2476
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2477
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2478
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2479
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2480
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2481
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2482
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2483
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2484
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2485
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2486
+ "lstrip": false,
2487
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2488
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2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
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2499
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2500
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2501
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2502
+ "lstrip": false,
2503
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2504
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2505
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2506
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2507
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2508
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2509
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2510
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2511
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2512
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2513
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2514
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2515
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2516
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2517
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2518
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2519
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2520
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2521
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2522
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2523
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2524
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2525
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2526
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2527
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2528
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2529
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2530
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2531
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2532
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2533
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2534
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2535
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2536
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2537
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2538
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2539
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2540
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2541
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2542
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2543
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2544
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2545
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2546
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2547
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2548
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2549
+ "content": "[73Se]",
2550
+ "lstrip": false,
2551
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2552
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2553
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2554
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2555
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2556
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2557
+ "content": "[OH1]",
2558
+ "lstrip": false,
2559
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2560
+ "rstrip": false,
2561
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2562
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2563
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2564
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2565
+ "content": "[SrH2]",
2566
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2567
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2568
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2569
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2570
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2571
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2572
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2573
+ "content": "[223Ra]",
2574
+ "lstrip": false,
2575
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2576
+ "rstrip": false,
2577
+ "single_word": false,
2578
+ "special": false
2579
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2580
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2581
+ "content": "[15OH2]",
2582
+ "lstrip": false,
2583
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2584
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2585
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2586
+ "special": false
2587
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2588
+ "50579": {
2589
+ "content": "[13CH1]",
2590
+ "lstrip": false,
2591
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2592
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2593
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2594
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2595
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2596
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2597
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2598
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2599
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2600
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2601
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2602
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2603
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2604
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2605
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2606
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2607
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2608
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2609
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2610
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2611
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2612
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2613
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2614
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2615
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2616
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2617
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2618
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2619
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2620
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2621
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2622
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2623
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2624
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2625
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2626
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2627
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2628
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2629
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2630
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2631
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2632
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2633
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2634
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2635
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2636
+ "50585": {
2637
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2638
+ "lstrip": false,
2639
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2640
+ "rstrip": false,
2641
+ "single_word": false,
2642
+ "special": false
2643
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2644
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2645
+ "content": "[Se-2]",
2646
+ "lstrip": false,
2647
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2648
+ "rstrip": false,
2649
+ "single_word": false,
2650
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2651
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2652
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2653
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2654
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2655
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2656
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2657
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2658
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2659
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2660
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2661
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2662
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2663
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2664
+ "rstrip": false,
2665
+ "single_word": false,
2666
+ "special": false
2667
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2668
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2669
+ "content": "[133Xe]",
2670
+ "lstrip": false,
2671
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2672
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2673
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2674
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2675
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2676
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2677
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2678
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2679
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2680
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2681
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2682
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2683
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2684
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2685
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2686
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2687
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2688
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2689
+ "single_word": false,
2690
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2691
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2692
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2693
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2694
+ "lstrip": false,
2695
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2696
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2697
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2698
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2699
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2700
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2701
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2702
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2703
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2704
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2705
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2706
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2707
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2708
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2709
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2710
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2711
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2712
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2713
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2714
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2715
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2716
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2717
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2718
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2719
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2720
+ "rstrip": false,
2721
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2722
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2723
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2724
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2725
+ "content": "[Te+1]",
2726
+ "lstrip": false,
2727
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2728
+ "rstrip": false,
2729
+ "single_word": false,
2730
+ "special": false
2731
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2732
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2733
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2734
+ "lstrip": false,
2735
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2736
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2737
+ "single_word": false,
2738
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2739
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2740
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2741
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2742
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2743
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2744
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2745
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2746
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2747
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2748
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2749
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2750
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2751
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2752
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2753
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2754
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2755
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2756
+ "50600": {
2757
+ "content": "[Te-1]",
2758
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2759
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2760
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2761
+ "single_word": false,
2762
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2763
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2764
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2765
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2766
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2767
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2768
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2769
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2770
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2771
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2772
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2773
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2774
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2775
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2776
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2777
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2778
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2779
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2780
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2781
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2782
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2783
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2784
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2785
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2786
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2787
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2788
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2789
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2790
+ "lstrip": false,
2791
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2792
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2793
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2794
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2795
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2796
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2797
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2798
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2799
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2800
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2801
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2802
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2803
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2804
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2805
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2806
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2807
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2808
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2809
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2810
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2811
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2812
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2813
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2814
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2815
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2816
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2817
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2818
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2819
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2820
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2821
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2822
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2823
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2824
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2825
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2826
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2827
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2828
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2829
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2830
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2831
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2832
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2833
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2834
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2835
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2836
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2837
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2838
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2839
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2840
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2841
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2842
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2843
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2844
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2845
+ "content": "[17F]",
2846
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2847
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2848
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2849
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2850
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2851
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2852
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2853
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2854
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2855
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2856
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2857
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2858
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2859
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2860
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2861
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2862
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2863
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2864
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2865
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2866
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2867
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2868
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2869
+ "content": "[He]",
2870
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2871
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2872
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2873
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2874
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2875
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2876
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2877
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2878
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2879
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2880
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2881
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2882
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2883
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2884
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2885
+ "content": "[42K+1]",
2886
+ "lstrip": false,
2887
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2888
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2889
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2890
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2891
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2892
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2893
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2894
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2895
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2896
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2897
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2898
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2899
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2900
+ "50618": {
2901
+ "content": "[\\NH1-1]",
2902
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2903
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2904
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2905
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2906
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2907
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2908
+ "50619": {
2909
+ "content": "[13CH3]",
2910
+ "lstrip": false,
2911
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2912
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2913
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2914
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2915
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2916
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2917
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2918
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2919
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2920
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2921
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2922
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2923
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2924
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2925
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2926
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2927
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2928
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2929
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2930
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2931
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2932
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2933
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2934
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2935
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2936
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2937
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2938
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2939
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2940
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2941
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2942
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2943
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2944
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2945
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2946
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2947
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2948
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2949
+ "content": "[Be+2]",
2950
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2951
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2952
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2953
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2954
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2955
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2956
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2957
+ "content": "[/13CH1]",
2958
+ "lstrip": false,
2959
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2960
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2961
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2962
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2963
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2964
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2965
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2966
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2967
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2968
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2969
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2970
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2971
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2972
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2973
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2974
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2975
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2976
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2977
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2978
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2979
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2980
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2981
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2982
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2983
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2984
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2985
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2986
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2987
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2988
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2989
+ "content": "[BH1-1]",
2990
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2991
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2992
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2993
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2994
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2995
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2996
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2997
+ "content": "[Kr]",
2998
+ "lstrip": false,
2999
+ "normalized": true,
3000
+ "rstrip": false,
3001
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3002
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3003
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3004
+ "50631": {
3005
+ "content": "[13NH3]",
3006
+ "lstrip": false,
3007
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3008
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3009
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3010
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3011
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3012
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3013
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3014
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3015
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3016
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3017
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3018
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3019
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3020
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3021
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3022
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3023
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3024
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3025
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3026
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3027
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3028
+ "50634": {
3029
+ "content": "[=Mg]",
3030
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3031
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3032
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3033
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3034
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3035
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3036
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3037
+ "content": "[/14CH1]",
3038
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3039
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3040
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3041
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3042
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3043
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3044
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3045
+ "content": "[N@@+1]",
3046
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3047
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3048
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3049
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3050
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3051
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3052
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3053
+ "content": "[SeH1]",
3054
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3055
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3056
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3057
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3058
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3059
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3060
+ "50638": {
3061
+ "content": "[-\\Ring2]",
3062
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3063
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3064
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3065
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3066
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3067
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3068
+ "50639": {
3069
+ "content": "[SiH3-1]",
3070
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3071
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3072
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3073
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3074
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3075
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3076
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3077
+ "content": "[N@@]",
3078
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3079
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3080
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3081
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3082
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3083
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3084
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3085
+ "content": "[123I-1]",
3086
+ "lstrip": false,
3087
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3088
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3089
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3090
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3091
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3092
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3093
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3094
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3095
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3096
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3097
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3098
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3099
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3100
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3101
+ "content": "[32PH1]",
3102
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3103
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3104
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3105
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3106
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3107
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3108
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3109
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3110
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3111
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3112
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3113
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3114
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3115
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3116
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3117
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3118
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3119
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3120
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3121
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3122
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3123
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3125
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3126
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3129
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3130
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3131
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3132
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3133
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3134
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3135
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3136
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3137
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3138
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3139
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3140
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3141
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3142
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3143
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3144
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3145
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3146
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3147
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3148
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3149
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3150
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3151
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3152
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3153
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3154
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3157
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3158
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3165
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3169
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3170
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3171
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3172
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3173
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3174
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3175
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3176
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3177
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3178
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3179
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3181
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3182
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3185
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3186
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3189
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3193
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3197
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3199
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3200
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3201
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3202
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3204
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3209
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3210
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3211
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3212
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3213
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3214
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3215
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3216
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3217
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3218
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3219
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3220
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3221
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3222
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3223
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3224
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3225
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3226
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3227
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3228
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3229
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3230
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3231
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3232
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3233
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3234
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3235
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3236
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3237
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3238
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3239
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3240
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3241
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3242
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3245
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3249
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3250
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3254
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3257
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3258
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3260
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3261
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3262
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3263
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3264
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3265
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3266
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3268
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3269
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3270
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3273
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3277
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3279
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3280
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3281
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3282
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3284
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3285
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3290
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3297
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3298
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3300
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3301
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3302
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3304
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3305
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3306
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3307
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3308
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3309
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3310
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3311
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3312
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3313
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3314
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3316
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3317
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3319
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3320
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3321
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3322
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3325
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3329
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3330
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3332
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3333
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3337
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3338
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3340
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3341
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3349
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3353
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3354
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3355
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3356
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3357
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3359
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3360
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3361
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3362
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3364
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3365
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3367
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3368
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3369
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3370
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3372
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3373
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3377
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3378
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3381
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3385
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3386
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3388
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3389
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3391
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3392
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3393
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3394
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3397
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3399
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3400
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3401
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3402
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3404
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3405
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3407
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3408
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3413
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3420
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3421
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3425
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3426
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3428
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3429
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3432
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3433
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3434
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3437
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3445
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3453
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3457
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3458
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3460
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3461
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3465
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3469
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3477
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3493
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3509
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3512
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3513
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3514
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3517
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3520
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3521
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3522
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3525
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3529
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3530
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3533
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3537
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3538
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3540
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3541
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3543
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3544
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3545
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3546
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3549
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3553
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3554
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3557
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3560
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3561
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3562
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3565
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3569
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3570
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3573
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3576
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3577
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3578
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3579
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3581
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3584
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3585
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3586
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3589
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3592
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3593
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3594
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3596
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3597
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3599
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3600
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3601
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3602
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3605
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3607
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3610
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3613
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3617
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3621
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3625
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3626
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3627
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3628
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3629
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3631
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3632
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3633
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3634
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3635
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3636
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3637
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3639
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3640
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3641
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3642
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3645
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3647
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3648
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3649
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3650
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3652
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3653
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3655
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3656
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3657
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3658
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3659
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3660
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3661
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3663
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3664
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3665
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3666
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3667
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3668
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3669
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3671
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3672
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3673
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3674
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3675
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3676
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3677
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3678
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3679
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3680
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3681
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3682
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3685
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3688
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3689
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3690
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3691
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3692
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3693
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3695
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3697
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3705
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3706
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3707
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3708
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3709
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3710
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3711
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3712
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3713
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3721
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3722
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3724
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3725
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3726
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3727
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3728
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3729
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3730
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3733
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3737
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3738
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3739
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3740
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3741
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3743
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3744
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3745
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