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T1 Age 2 13 42 year-old T3 Disease_disorder 31 51 lymphocytic leukemia E1 Disease_disorder:T3 T4 Detailed_description 23 30 chronic R1 MODIFY Arg1:T4 Arg2:E1 T5 Therapeutic_procedure 73 95 bone marrow transplant E2 Therapeutic_procedure:T5 T6 Detailed_description 62 72 allogeneic R2 MODIFY Arg1:T6 Arg2:E2 T7 Date 99 113 September 2013 E3 Date:T7 T8 Coreference 119 124 graft E4 Coreference:T8 R3 IDENTICAL Arg1:E4 Arg2:E2 T9 Activity 2994 2998 died E5 Activity:T9 T10 Date 3006 3016 end of May E6 Date:T10 T2 Sex 14 17 man T11 Detailed_description 129 182 mismatched at a single human leukocyte antigen allele T12 Medication 229 240 alemtuzumab E7 Medication:T12 T13 Detailed_description 199 214 T-cell depleted #1 AnnotatorNotes T13 technically not a procedure done to the patient, but the transplanted cells R4 MODIFY Arg1:T11 Arg2:E4 R5 MODIFY Arg1:T13 Arg2:E4 R6 MODIFY Arg1:E7 Arg2:T13 T14 Therapeutic_procedure 245 254 engrafted E8 Therapeutic_procedure:T14 T15 Date 258 264 day 12 E9 Date:T15 T16 Therapeutic_procedure 271 281 transplant E10 Therapeutic_procedure:T16 T17 Sign_symptom 305 316 lymphopenia E11 Sign_symptom:T17 T18 Detailed_description 294 304 persistent R7 MODIFY Arg1:T18 Arg2:E11 T19 Sign_symptom 321 329 diarrhea E12 Sign_symptom:T19 T20 Disease_disorder 335 344 norovirus E13 Disease_disorder:T20 R8 CAUSE Arg1:E13 Arg2:E12 R9 CAUSE Arg1:E13 Arg2:E11 T21 Diagnostic_procedure 360 381 posttransplant course E14 Diagnostic_procedure:T21 T22 Lab_value 386 398 unremarkable E15 Lab_value:T22 R10 MODIFY Arg1:E15 Arg2:E14 T23 Date 405 416 mid-October E16 Date:T23 T24 Sign_symptom 435 443 tinnitus E17 Sign_symptom:T24 T25 Disease_disorder 468 490 sensorineural deafness E18 Disease_disorder:T25 A1 TREND E18 INC T26 Detailed_description 448 467 rapidly progressive R11 MODIFY Arg1:T26 Arg2:E18 T27 Sign_symptom 514 526 hearing loss E19 Sign_symptom:T27 T29 Lab_value 540 546 >95 dB E21 Lab_value:T29 T30 Detailed_description 505 513 subtotal T28 Detailed_description 527 538 bilaterally R12 MODIFY Arg1:T28 Arg2:E19 R13 MODIFY Arg1:T30 Arg2:E19 R14 MODIFY Arg1:E21 Arg2:E19 T31 Duration 548 562 over 2–3 weeks E20 Duration:T31 T32 Diagnostic_procedure 570 596 magnetic resonance imaging E22 Diagnostic_procedure:T32 T33 Biological_structure 564 569 Brain R15 MODIFY Arg1:T33 Arg2:E22 T34 Diagnostic_procedure 598 601 MRI E23 Diagnostic_procedure:T34 R16 IDENTICAL Arg1:E23 Arg2:E22 T35 Diagnostic_procedure 628 647 cerebrospinal fluid E24 Diagnostic_procedure:T35 T36 Diagnostic_procedure 649 652 CSF E25 Diagnostic_procedure:T36 R17 IDENTICAL Arg1:E25 Arg2:E24 T37 Diagnostic_procedure 689 700 neutrophils E26 Diagnostic_procedure:T37 T38 Diagnostic_procedure 709 720 lymphocytes E27 Diagnostic_procedure:T38 T39 Lab_value 664 679 4 leukocytes/µL E28 Lab_value:T39 R18 MODIFY Arg1:E28 Arg2:E24 T40 Lab_value 685 688 50% E29 Lab_value:T40 T41 Lab_value 705 708 50% E30 Lab_value:T41 R19 MODIFY Arg1:E29 Arg2:E26 R20 MODIFY Arg1:E30 Arg2:E27 R21 SUB_PROCEDURE Arg1:E26 Arg2:E24 R22 SUB_PROCEDURE Arg1:E27 Arg2:E24 T42 Lab_value 722 742 6 red blood cells/µL E31 Lab_value:T42 R23 MODIFY Arg1:E31 Arg2:E24 T43 Diagnostic_procedure 744 751 glucose E32 Diagnostic_procedure:T43 T44 Diagnostic_procedure 851 868 oligoclonal bands E33 Diagnostic_procedure:T44 T45 Lab_value 840 847 absence E34 Lab_value:T45 R24 MODIFY Arg1:E34 Arg2:E33 T46 Diagnostic_procedure 795 802 protein E35 Diagnostic_procedure:T46 T47 Lab_value 752 762 2.4 mmol/L E36 Lab_value:T47 T48 Lab_value 803 811 61 mg/dL E37 Lab_value:T48 R25 MODIFY Arg1:E37 Arg2:E35 R26 MODIFY Arg1:E36 Arg2:E32 R27 SUB_PROCEDURE Arg1:E32 Arg2:E24 R28 SUB_PROCEDURE Arg1:E35 Arg2:E24 R29 SUB_PROCEDURE Arg1:E33 Arg2:E24 T49 Diagnostic_procedure 877 902 polymerase chain reaction E38 Diagnostic_procedure:T49 T50 Detailed_description 920 923 CSF R30 MODIFY Arg1:T50 Arg2:E38 T51 Detailed_description 871 876 Viral R31 MODIFY Arg1:T51 Arg2:E38 #2 AnnotatorNotes T51 testing for viral DNA; the test itself is not viral T52 Medication 1031 1043 valacyclovir E39 Medication:T52 T53 Medication 1060 1071 antibiotics E40 Medication:T53 T54 Medication 1096 1110 immunoglobulin E41 Medication:T54 T55 Sign_symptom 1185 1192 dyspnea E42 Sign_symptom:T55 T56 Sign_symptom 1203 1214 hypotension E43 Sign_symptom:T56 T57 Sign_symptom 1216 1222 nausea E44 Sign_symptom:T57 T58 Diagnostic_procedure 1248 1255 balance E45 Diagnostic_procedure:T58 T59 Lab_value 1228 1247 gradually worsening E46 Lab_value:T59 R32 MODIFY Arg1:E46 Arg2:E45 T60 Disease_disorder 941 952 enterovirus E47 Disease_disorder:T60 A2 POLARITY E47 NEG T61 Disease_disorder 957 968 herpesvirus E48 Disease_disorder:T61 A3 POLARITY E48 NEG T62 Dosage 1077 1083 2 g/kg R33 MODIFY Arg1:T62 Arg2:E41 T63 Administration 1084 1095 intravenous R34 MODIFY Arg1:T63 Arg2:E41 T64 Medication 1112 1116 IVIG E49 Medication:T64 R35 IDENTICAL Arg1:E49 Arg2:E41 T65 Diagnostic_procedure 1264 1287 neurological assessment E50 Diagnostic_procedure:T65 T66 Disease_disorder 1309 1338 vestibulocochlear dysfunction E51 Disease_disorder:T66 T67 Detailed_description 1298 1308 persistent R36 MODIFY Arg1:T67 Arg2:E51 T68 Date 1339 1352 6 weeks after E52 Date:T68 T69 Date 1371 1383 mid-December E53 Date:T69 T70 Sign_symptom 1421 1430 withdrawn E54 Sign_symptom:T70 T71 Sign_symptom 1432 1441 irritable E55 Sign_symptom:T71 T72 Sign_symptom 1462 1470 agitated E56 Sign_symptom:T72 T73 Detailed_description 1447 1461 intermittently R37 MODIFY Arg1:T73 Arg2:E56 A4 TREND E54 INC A5 TREND E55 INC A6 TREND E56 INC T74 Sign_symptom 1484 1495 lymphopenic E57 Sign_symptom:T74 T75 Diagnostic_procedure 1497 1508 lymphocytes E58 Diagnostic_procedure:T75 T76 Lab_value 1509 1522 0.54 × 106/μL E59 Lab_value:T76 R38 MODIFY Arg1:E59 Arg2:E58 T77 Diagnostic_procedure 1558 1561 MRI E60 Diagnostic_procedure:T77 T78 Biological_structure 1575 1580 brain T79 Lab_value 1586 1598 unremarkable E61 Lab_value:T79 R39 MODIFY Arg1:T78 Arg2:E60 R40 MODIFY Arg1:E61 Arg2:E60 T80 Diagnostic_procedure 1625 1648 antineuronal antibodies E62 Diagnostic_procedure:T80 T81 Detailed_description 1607 1620 serum testing R41 MODIFY Arg1:T81 Arg2:E62 R42 MODIFY Arg1:E61 Arg2:E62 T82 Diagnostic_procedure 1653 1673 electroencephalogram E63 Diagnostic_procedure:T82 T83 Disease_disorder 1696 1710 encephalopathy E64 Disease_disorder:T83 T84 Disease_disorder 1744 1749 viral E65 Disease_disorder:T84 A7 POLARITY E65 UNCERTAIN T85 Medication 1799 1814 glucocorticoids E66 Medication:T85 T86 Dosage 1789 1798 high-dose R43 MODIFY Arg1:T86 Arg2:E66 T87 Medication 1830 1834 IVIG E67 Medication:T87 T88 Activity 1854 1860 fluids E68 Activity:T88 A8 POLARITY E68 NEG T89 Activity 1862 1866 food E69 Activity:T89 A9 POLARITY E69 NEG T90 Medication 1872 1882 medication E70 Medication:T90 A10 POLARITY E70 NEG T91 Clinical_event 1892 1900 detained E71 Clinical_event:T91 T92 Detailed_description 1911 1931 UK Mental Health Act R44 MODIFY Arg1:T92 Arg2:E71 T93 Diagnostic_procedure 1940 1943 MRI E72 Diagnostic_procedure:T93 T94 Sign_symptom 2002 2022 signal abnormalities E73 Sign_symptom:T94 T95 Detailed_description 1989 2001 nonenhancing T96 Detailed_description 1984 1987 new R45 MODIFY Arg1:T95 Arg2:E73 R46 MODIFY Arg1:T96 Arg2:E73 T97 Detailed_description 184 188 DQB1 R47 MODIFY Arg1:T97 Arg2:T11 T98 Detailed_description 221 228 in vivo R48 MODIFY Arg1:T98 Arg2:E7 T99 Biological_structure 2026 2038 both thalami T100 Biological_structure 2043 2051 midbrain R49 MODIFY Arg1:T99 Arg2:E73 R50 MODIFY Arg1:T100 Arg2:E73 T101 Biological_structure 2057 2070 cranial nerve R51 MODIFY Arg1:T101 Arg2:E73 T102 Sign_symptom 2100 2111 enhancement E74 Sign_symptom:T102 A11 POLARITY E74 NEG T103 Biological_structure 2090 2099 meningeal R52 MODIFY Arg1:T103 Arg2:E74 T104 Date 2126 2150 Near the end of December E75 Date:T104 T105 Diagnostic_procedure 2167 2173 biopsy E76 Diagnostic_procedure:T105 T106 Biological_structure 2154 2166 frontal lobe R53 MODIFY Arg1:T106 Arg2:E76 T107 Diagnostic_procedure 2189 2198 Histology E77 Diagnostic_procedure:T107 T108 Sign_symptom 2217 2224 gliosis E78 Sign_symptom:T108 T109 Detailed_description 2208 2216 reactive R54 MODIFY Arg1:T109 Arg2:E78 T110 Sign_symptom 2237 2249 infiltration E79 Sign_symptom:T110 T111 Detailed_description 2229 2236 diffuse R55 MODIFY Arg1:T111 Arg2:E79 T112 Detailed_description 2255 2274 CD3+/8+ lymphocytes R56 MODIFY Arg1:T112 Arg2:E79 T113 Diagnostic_procedure 2298 2321 microbiological testing E80 Diagnostic_procedure:T113 T114 Detailed_description 2329 2342 biopsy tissue R57 MODIFY Arg1:T114 Arg2:E80 T115 Lab_value 2374 2382 negative E81 Lab_value:T115 T116 Detailed_description 2350 2369 infectious etiology R58 MODIFY Arg1:T116 Arg2:E80 R59 MODIFY Arg1:E81 Arg2:E80 T117 Disease_disorder 2471 2497 neurological deterioration E82 Disease_disorder:T117 A12 TREND E82 INC T118 Diagnostic_procedure 2572 2598 next-generation sequencing E83 Diagnostic_procedure:T118 T119 Diagnostic_procedure 2600 2603 NGS E84 Diagnostic_procedure:T119 R60 IDENTICAL Arg1:E84 Arg2:E83 T120 Detailed_description 2560 2571 metagenomic R61 MODIFY Arg1:T120 Arg2:E83 T121 Date 2544 2556 January 2014 E85 Date:T121 T122 Detailed_description 2499 2526 CSF and brain biopsy tissue R62 MODIFY Arg1:T122 Arg2:E83 T123 Diagnostic_procedure 2610 2613 NGS E86 Diagnostic_procedure:T123 T124 Detailed_description 2630 2642 brain biopsy R63 MODIFY Arg1:T124 Arg2:E86 T125 Diagnostic_procedure 2644 2659 genome assembly E87 Diagnostic_procedure:T125 R64 SUB_PROCEDURE Arg1:E87 Arg2:E86 T126 Diagnostic_procedure 2665 2686 in situ hybridization E88 Diagnostic_procedure:T126 T127 Disease_disorder 2722 2732 astrovirus E89 Disease_disorder:T127 T128 Disease_disorder 2734 2738 AstV E90 Disease_disorder:T128 R65 IDENTICAL Arg1:E90 Arg2:E89 T129 Detailed_description 2708 2721 neuroinvasive R66 MODIFY Arg1:T129 Arg2:E89 T130 Medication 2816 2825 ribavirin E91 Medication:T130 T131 Medication 2830 2834 IVIG E92 Medication:T131 T132 Sign_symptom 2906 2931 minimally conscious state E93 Sign_symptom:T132 T133 Medication 2956 2964 sedation E94 Medication:T133 A13 POLARITY E94 NEG T134 Date 2968 2978 March 2014 E95 Date:T134 T135 Date 3018 3032 4 months after E96 Date:T135 T136 Diagnostic_procedure 3037 3040 NGS E97 Diagnostic_procedure:T136 T137 Date 3069 3085 7.5 months after E98 Date:T137 T138 Sign_symptom 3095 3103 symptoms E99 Sign_symptom:T138 R67 BEFORE Arg1:E1 Arg2:E2 * OVERLAP E2 E3 E4 E7 R68 BEFORE Arg1:E7 Arg2:E8 * OVERLAP E8 E9 R69 AFTER Arg1:E9 Arg2:E10 R70 BEFORE Arg1:E10 Arg2:E11 * OVERLAP E11 E12 E13 E14 R71 BEFORE Arg1:E14 Arg2:E16 * OVERLAP E16 E17 E18 E19 E20 E22 E24 E38 E47 E48 R72 BEFORE Arg1:E48 Arg2:E39 * OVERLAP E39 E40 E41 R73 BEFORE Arg1:E41 Arg2:E42 * OVERLAP E42 E43 E44 E45 T139 Detailed_description 1194 1202 postural R74 MODIFY Arg1:T139 Arg2:E43 R75 BEFORE Arg1:E45 Arg2:E50 * OVERLAP E50 E51 E52 T140 Sign_symptom 1353 1360 symptom E100 Sign_symptom:T140 R76 AFTER Arg1:E52 Arg2:E100 R77 BEFORE Arg1:E100 Arg2:E53 * OVERLAP E53 E54 E55 E56 E57 E58 E60 E62 E63 E64 E65 E66 E67 R78 BEFORE Arg1:E67 Arg2:E68 * OVERLAP E68 E69 E70 R79 BEFORE Arg1:E70 Arg2:E71 * OVERLAP E71 E72 E73 E74 R80 BEFORE Arg1:E74 Arg2:E75 * OVERLAP E75 E76 E77 E78 E79 E80 E82 R81 BEFORE Arg1:E82 Arg2:E85 * OVERLAP E85 E83 E86 E88 E89 R82 BEFORE Arg1:E89 Arg2:E91 * OVERLAP E91 E92 R83 BEFORE Arg1:E92 Arg2:E93 * OVERLAP E93 E94 E95 R84 BEFORE Arg1:E95 Arg2:E5 * OVERLAP E5 E6 E96 R85 AFTER Arg1:E96 Arg2:E97 R86 BEFORE Arg1:E97 Arg2:E98 R87 AFTER Arg1:E98 Arg2:E99