--- a
+++ b/processing/MACCROBAT/28216610.ann
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+T1	Age 2 13	34-year-old
+T2	Personal_background 14 22	Hispanic
+T3	Sex 23 27	male
+T4	History 28 68	without significant past medical history
+T5	Clinical_event 69 78	presented
+E1	Clinical_event:T5 
+T6	Nonbiological_location 86 94	hospital
+R1	MODIFY Arg1:T6 Arg2:E1	
+T7	Duration 102 111	one month
+E2	Duration:T7 
+T8	Sign_symptom 123 128	cough
+E3	Sign_symptom:T8 
+T9	Sign_symptom 152 158	sputum
+E4	Sign_symptom:T9 
+T10	Color 144 151	whitish
+R2	MODIFY Arg1:T10 Arg2:E4	
+T11	Sign_symptom 187 192	fever
+E5	Sign_symptom:T11 
+A1	POLARITY E5 NEG
+T12	Sign_symptom 194 200	chills
+E6	Sign_symptom:T12 
+A2	POLARITY E6 NEG
+T13	Sign_symptom 202 214	night sweats
+E7	Sign_symptom:T13 
+A3	POLARITY E7 NEG
+T14	Sign_symptom 222 226	pain
+E8	Sign_symptom:T14 
+A4	POLARITY E8 NEG
+T15	Biological_structure 216 221	chest
+R3	MODIFY Arg1:T15 Arg2:E8	
+T16	Sign_symptom 228 238	hemoptysis
+E9	Sign_symptom:T16 
+A5	POLARITY E9 NEG
+T17	Sign_symptom 245 249	pain
+E10	Sign_symptom:T17 
+A6	POLARITY E10 NEG
+T18	Biological_structure 240 244	back
+R4	MODIFY Arg1:T18 Arg2:E10	
+T19	Clinical_event 258 264	travel
+E11	Clinical_event:T19 
+A7	POLARITY E11 NEG
+T20	Clinical_event 273 281	contacts
+E12	Clinical_event:T20 
+A8	POLARITY E12 NEG
+T21	Detailed_description 251 257	recent
+T22	Detailed_description 268 272	sick
+R5	MODIFY Arg1:T22 Arg2:E12	
+R6	MODIFY Arg1:T21 Arg2:E11	
+T23	Sign_symptom 335 346	weight loss
+E13	Sign_symptom:T23 
+R7	MODIFY Arg1:E4 Arg2:E3	
+T24	Lab_value 323 334	15–20 pound
+R8	MODIFY Arg1:T24 Arg2:E13	
+T25	Duration 358 373	last six months
+E14	Duration:T25 
+T27	History 378 392	denied smoking
+T28	History 403 416	drank alcohol
+T29	History 422 479	had unprotected sexual intercourse with multiple partners
+T26	Diagnostic_procedure 511 522	temperature
+E15	Diagnostic_procedure:T26 
+T30	Lab_value 527 533	97.9°F
+R9	MODIFY Arg1:T30 Arg2:E15	
+T31	Diagnostic_procedure 535 545	heart rate
+E16	Diagnostic_procedure:T31 
+T32	Lab_value 550 569	85 beats per minute
+R10	MODIFY Arg1:T32 Arg2:E16	
+T33	Diagnostic_procedure 571 587	respiratory rate
+E17	Diagnostic_procedure:T33 
+T34	Lab_value 592 613	16 breaths per minute
+R11	MODIFY Arg1:T34 Arg2:E17	
+T35	Diagnostic_procedure 615 629	blood pressure
+E18	Diagnostic_procedure:T35 
+T36	Lab_value 634 646	107/66 mm Hg
+R12	MODIFY Arg1:T36 Arg2:E18	
+T37	Diagnostic_procedure 652 669	oxygen saturation
+E19	Diagnostic_procedure:T37 
+T38	Lab_value 674 678	100%
+T39	Detailed_description 682 690	room air
+R13	MODIFY Arg1:T39 Arg2:E19	
+R14	MODIFY Arg1:T38 Arg2:E19	
+T40	Diagnostic_procedure 692 703	Examination
+E20	Diagnostic_procedure:T40 
+T41	Sign_symptom 716 722	thrush
+E21	Sign_symptom:T41 
+T42	Biological_structure 711 715	oral
+R15	MODIFY Arg1:T42 Arg2:E21	
+T43	Diagnostic_procedure 734 747	breath sounds
+E22	Diagnostic_procedure:T43 
+T44	Lab_value 724 733	decreased
+R16	MODIFY Arg1:T44 Arg2:E22	
+T45	Sign_symptom 752 760	crackles
+E23	Sign_symptom:T45 
+T46	Biological_structure 768 789	right lower lung base
+R17	MODIFY Arg1:T46 Arg2:E23	
+T47	Sign_symptom 804 811	lesions
+E24	Sign_symptom:T47 
+A9	POLARITY E24 NEG
+T48	Biological_structure 794 803	cutaneous
+R18	MODIFY Arg1:T48 Arg2:E24	
+T49	Diagnostic_procedure 842 862	clinical examination
+E25	Diagnostic_procedure:T49 
+T50	Lab_value 867 879	unremarkable
+R19	MODIFY Arg1:T50 Arg2:E25	
+T51	Diagnostic_procedure 885 905	complete blood count
+E26	Diagnostic_procedure:T51 
+T52	Diagnostic_procedure 907 910	CBC
+E27	Diagnostic_procedure:T52 
+R20	IDENTICAL Arg1:E27 Arg2:E26	
+T53	Diagnostic_procedure 919 929	hemoglobin
+E28	Diagnostic_procedure:T53 
+T54	Lab_value 933 941	9.7 g/dL
+R21	MODIFY Arg1:T54 Arg2:E28	
+T55	Diagnostic_procedure 943 947	WBCs
+E29	Diagnostic_procedure:T55 
+T56	Lab_value 948 957	2.3×109/L
+R22	MODIFY Arg1:T56 Arg2:E29	
+T57	Diagnostic_procedure 963 972	platelets
+E30	Diagnostic_procedure:T57 
+T58	Lab_value 976 985	164×109/L
+R23	MODIFY Arg1:T58 Arg2:E30	
+R24	SUB_PROCEDURE Arg1:E28 Arg2:E26	
+R25	SUB_PROCEDURE Arg1:E29 Arg2:E26	
+R26	SUB_PROCEDURE Arg1:E30 Arg2:E26	
+T59	Diagnostic_procedure 991 1001	creatinine
+E31	Diagnostic_procedure:T59 
+T60	Lab_value 1006 1016	0.62 mg/dL
+R27	MODIFY Arg1:T60 Arg2:E31	
+T61	Diagnostic_procedure 1022 1041	blood urea nitrogen
+E32	Diagnostic_procedure:T61 
+T62	Lab_value 1046 1054	10 mg/dL
+R28	MODIFY Arg1:T62 Arg2:E32	
+T63	Diagnostic_procedure 1056 1066	Radiograph
+E33	Diagnostic_procedure:T63 
+T64	Biological_structure 1074 1079	chest
+R29	MODIFY Arg1:T64 Arg2:E33	
+T65	Sign_symptom 1122 1129	opacity
+E34	Sign_symptom:T65 
+T66	Biological_structure 1112 1121	perihilar
+R30	MODIFY Arg1:T66 Arg2:E34	
+T67	Severity 1087 1096	extensive
+R31	MODIFY Arg1:T67 Arg2:E34	
+T68	Biological_structure 1097 1102	right
+T69	Biological_structure 1107 1111	left
+R32	MODIFY Arg1:T69 Arg2:E34	
+R33	MODIFY Arg1:T68 Arg2:E34	
+T70	Biological_structure 1130 1152	more on the right side
+R34	MODIFY Arg1:T70 Arg2:E34	
+T71	Diagnostic_procedure 1158 1177	computed tomography
+E35	Diagnostic_procedure:T71 
+T72	Diagnostic_procedure 1179 1181	CT
+E36	Diagnostic_procedure:T72 
+R35	IDENTICAL Arg1:E36 Arg2:E35	
+T73	Biological_structure 1195 1200	chest
+R36	MODIFY Arg1:T73 Arg2:E35	
+T74	Sign_symptom 1238 1242	mass
+E37	Sign_symptom:T74 
+T75	Biological_structure 1228 1237	perihilar
+R37	MODIFY Arg1:T75 Arg2:E37	
+T76	Sign_symptom 1328 1335	lesions
+E38	Sign_symptom:T76 
+T77	Detailed_description 1259 1267	multiple
+T78	Biological_structure 1288 1297	vertebrae
+T79	Biological_structure 1281 1287	lumbar
+T80	Biological_structure 1268 1276	thoracic
+R38	MODIFY Arg1:T79 Arg2:T78	
+R39	MODIFY Arg1:T80 Arg2:T78	
+T81	Biological_structure 1299 1303	ribs
+T82	Biological_structure 1309 1316	sternal
+T83	Severity 1317 1321	tiny
+T84	Detailed_description 1322 1327	lytic
+R40	MODIFY Arg1:T84 Arg2:E38	
+R41	MODIFY Arg1:T83 Arg2:E38	
+R42	MODIFY Arg1:T82 Arg2:E38	
+R43	MODIFY Arg1:T81 Arg2:E38	
+T85	Severity 1222 1227	large
+R44	MODIFY Arg1:T85 Arg2:E37	
+T86	Biological_structure 1210 1221	right sided
+R45	MODIFY Arg1:T86 Arg2:E37	
+R46	MODIFY Arg1:T77 Arg2:E38	
+R47	MODIFY Arg1:T78 Arg2:E38	
+T87	Disease_disorder 1357 1367	metastasis
+E39	Disease_disorder:T87 
+T88	Biological_structure 1352 1356	bony
+R48	MODIFY Arg1:T88 Arg2:E39	
+T89	Diagnostic_procedure 1397 1405	cultures
+E40	Diagnostic_procedure:T89 
+T90	Biological_structure 1390 1396	sputum
+T91	Biological_structure 1380 1385	Blood
+R49	MODIFY Arg1:T90 Arg2:E40	
+R50	MODIFY Arg1:T91 Arg2:E40	
+T92	Lab_value 1411 1419	negative
+R51	MODIFY Arg1:T92 Arg2:E40	
+T93	Disease_disorder 1421 1433	Tuberculosis
+E41	Disease_disorder:T93 
+A10	POLARITY E41 NEG
+T94	Diagnostic_procedure 1478 1491	sputum smears
+E42	Diagnostic_procedure:T94 
+T95	Detailed_description 1496 1513	acid fast bacilli
+R52	MODIFY Arg1:T95 Arg2:E42	
+T96	Detailed_description 1451 1468	three consecutive
+T97	Lab_value 1469 1477	negative
+R53	MODIFY Arg1:T96 Arg2:T97	
+R54	MODIFY Arg1:T97 Arg2:E42	
+T98	Diagnostic_procedure 1529 1550	QUANTIferon gold test
+E43	Diagnostic_procedure:T98 
+T99	Lab_value 1520 1528	negative
+R55	MODIFY Arg1:T99 Arg2:E43	
+T100	Lab_value 1562 1570	positive
+T101	Diagnostic_procedure 1575 1603	human immunodeficiency virus
+E44	Diagnostic_procedure:T101 
+T102	Diagnostic_procedure 1605 1608	HIV
+E45	Diagnostic_procedure:T102 
+R56	IDENTICAL Arg1:E45 Arg2:E44	
+R57	MODIFY Arg1:T100 Arg2:E44	
+#1	AnnotatorNotes E44	This is a test with a positive result, so it's also diagnosis of the infection
+T103	Disease_disorder 1575 1603	human immunodeficiency virus
+E46	Disease_disorder:T103 
+T104	Disease_disorder 1605 1608	HIV
+E47	Disease_disorder:T104 
+R58	IDENTICAL Arg1:E47 Arg2:E46	
+T105	Diagnostic_procedure 1618 1628	CD4 counts
+E48	Diagnostic_procedure:T105 
+T106	Lab_value 1642 1652	7 cells/uL
+R59	MODIFY Arg1:T106 Arg2:E48	
+T107	Therapeutic_procedure 1672 1683	prophylaxis
+E49	Therapeutic_procedure:T107 
+T108	Medication 1689 1696	bactrim
+E50	Medication:T108 
+T109	Dosage 1697 1712	80–160 mg daily
+R60	MODIFY Arg1:T109 Arg2:E50	
+T110	Medication 1717 1729	azithromycin
+E51	Medication:T110 
+T111	Dosage 1730 1744	1200 mg weekly
+R61	MODIFY Arg1:T111 Arg2:E51	
+T112	Diagnostic_procedure 1775 1787	Bronchoscopy
+E52	Diagnostic_procedure:T112 
+T113	Diagnostic_procedure 1793 1799	biopsy
+E53	Diagnostic_procedure:T113 
+T114	Lab_value 1822 1833	unrevealing
+R62	MODIFY Arg1:T114 Arg2:E52	
+T115	Diagnostic_procedure 1868 1883	mediastinoscopy
+E54	Diagnostic_procedure:T115 
+T116	Diagnostic_procedure 1889 1897	biopsies
+E55	Diagnostic_procedure:T116 
+T117	Detailed_description 1853 1867	video assisted
+R63	MODIFY Arg1:T117 Arg2:E54	
+T118	Biological_structure 1905 1916	right hilar
+T119	Sign_symptom 1917 1921	mass
+E56	Sign_symptom:T119 
+R64	MODIFY Arg1:T118 Arg2:E56	
+R65	MODIFY Arg1:E56 Arg2:E55	
+T120	Diagnostic_procedure 1923 1932	Pathology
+E57	Diagnostic_procedure:T120 
+T121	Sign_symptom 1940 1953	spindle cells
+E58	Sign_symptom:T121 
+T122	Diagnostic_procedure 1967 1971	CD34
+E59	Diagnostic_procedure:T122 
+T123	Diagnostic_procedure 1973 1977	BCL2
+E60	Diagnostic_procedure:T123 
+T124	Diagnostic_procedure 1979 1987	vimentin
+E61	Diagnostic_procedure:T124 
+T125	Diagnostic_procedure 1993 1998	HHV-8
+E62	Diagnostic_procedure:T125 
+T126	Lab_value 1954 1962	positive
+R66	MODIFY Arg1:T126 Arg2:E59	
+R67	MODIFY Arg1:T126 Arg2:E60	
+R68	MODIFY Arg1:T126 Arg2:E61	
+R69	MODIFY Arg1:T126 Arg2:E62	
+T127	Diagnostic_procedure 2027 2031	CD31
+E63	Diagnostic_procedure:T127 
+T128	Lab_value 2012 2022	positivity
+R70	MODIFY Arg1:T128 Arg2:E63	
+T129	Detailed_description 2004 2011	diffuse
+R71	MODIFY Arg1:T129 Arg2:T128	
+R72	MODIFY Arg1:E58 Arg2:E59	
+R73	MODIFY Arg1:E58 Arg2:E60	
+R74	MODIFY Arg1:E58 Arg2:E61	
+R75	MODIFY Arg1:E58 Arg2:E62	
+R76	MODIFY Arg1:E58 Arg2:E63	
+T130	Disease_disorder 2046 2048	KS
+E64	Disease_disorder:T130 
+#2	AnnotatorNotes E64	Kaposi Sarcoma
+T131	Medication 2076 2081	HAART
+E65	Medication:T131 
+R77	SUB_PROCEDURE Arg1:E50 Arg2:E49	
+R78	SUB_PROCEDURE Arg1:E51 Arg2:E49	
+T132	Medication 2097 2144	emtricitabine and tenofovir disoproxil fumarate
+E66	Medication:T132 
+T133	Lab_value 2145 2155	200/300 mg
+R79	MODIFY Arg1:T133 Arg2:E66	
+T134	Medication 2160 2172	dolutegravir
+E67	Medication:T134 
+T135	Lab_value 2173 2178	50 mg
+R80	MODIFY Arg1:T135 Arg2:E67	
+T136	Medication 2299 2322	additional chemotherapy
+E68	Medication:T136 
+A11	POLARITY E68 NEG
+T137	Sign_symptom 2356 2376	clinical improvement
+E69	Sign_symptom:T137 
+T138	Diagnostic_procedure 2387 2389	CT
+E70	Diagnostic_procedure:T138 
+T139	Biological_structure 2402 2407	chest
+R81	MODIFY Arg1:T139 Arg2:E70	
+T140	Date 2411 2423	three months
+E71	Date:T140 
+T141	Sign_symptom 2440 2450	regression
+E72	Sign_symptom:T141 
+T142	Sign_symptom 2500 2507	lesions
+E73	Sign_symptom:T142 
+A12	POLARITY E73 MAYBE_NEG
+R82	AFTER Arg1:E1 Arg2:E2	
+*	OVERLAP E2 E3 E4
+R83	BEFORE Arg1:E4 Arg2:E5	
+*	OVERLAP E5 E6 E7 E8 E9 E10 E11 E12
+R84	AFTER Arg1:E12 Arg2:E13	
+*	OVERLAP E13 E14 E76 E77 E78
+*	OVERLAP E15 E16 E17 E18 E19 E20 E21 E22 E23 E24 E25 E26 E31 E32 E33 E34 E35 E37 E38 E39 E40 E41 E42 E43 E44 E46 E48
+R86	BEFORE Arg1:E48 Arg2:E49	
+*	OVERLAP E49 E52 E53 E54 E55 E57 E58 E59 E60 E61 E62 E63 E64
+R87	BEFORE Arg1:E64 Arg2:E65	
+R88	SUB_PROCEDURE Arg1:E66 Arg2:E65	
+R89	SUB_PROCEDURE Arg1:E67 Arg2:E65	
+T143	Clinical_event 2217 2226	decisions
+E74	Clinical_event:T143 
+T144	Detailed_description 2237 2255	management options
+R90	MODIFY Arg1:T144 Arg2:E74	
+T145	Detailed_description 2196 2213	actively involved
+R91	MODIFY Arg1:T145 Arg2:E74	
+R92	BEFORE Arg1:E65 Arg2:E74	
+T146	Medication 2268 2273	HAART
+E75	Medication:T146 
+R93	BEFORE Arg1:E74 Arg2:E75	
+*	OVERLAP E75 E68
+R94	BEFORE Arg1:E68 Arg2:E69	
+*	OVERLAP E69 E70 E71 E72 E73
+T147	Activity 385 392	smoking
+E76	Activity:T147 
+A13	POLARITY E76 NEG
+T148	Activity 403 416	drank alcohol
+E77	Activity:T148 
+T149	Activity 438 456	sexual intercourse
+E78	Activity:T149 
+T150	Detailed_description 426 437	unprotected
+T151	Detailed_description 462 479	multiple partners
+R95	MODIFY Arg1:T150 Arg2:E78	
+R96	MODIFY Arg1:T151 Arg2:E78	
+R85	BEFORE Arg1:E78 Arg2:E15