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e3c_v3.0_en_val.json

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+[
+    {
+        "text": "We report a case of a 63 - year-old woman with a minute ampullary carcinoid tumor that was 7 mm in diameter , but was associated with 2 peripancreatic lymph node metastases .",
+        "entities": [
+            {
+                "entity_text": "carcinoid tumor",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "lymph node metastases",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Mild elevation of liver enzymes was found at her regular medical check-up .",
+        "entities": [
+            {
+                "entity_text": "elevation of liver enzymes",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Computed tomography ( CT ) revealed a markedly dilated common bile duct ( CBD ) and two enlarged peripancreatic lymph nodes .",
+        "entities": [
+            {
+                "entity_text": "dilated common bile duct",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "CBD",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "enlarged peripancreatic lymph nodes",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Endoscopy showed that the ampulla was slightly enlarged by a submucosal tumor .",
+        "entities": [
+            {
+                "entity_text": "tumor",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The biopsy specimen revealed tumor cells that showed monotonous proliferation suggestive of a carcinoid tumor .",
+        "entities": [
+            {
+                "entity_text": "carcinoid tumor",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "She underwent a pylorus-preserving whipple resection with lymph node dissection .",
+        "entities": []
+    },
+    {
+        "text": "The resected lesion was a small submucosal tumor ( 7 mm in diameter ) at the ampulla , with metastasis to 2 peripancreatic lymph nodes , and it was diagnosed as a malignant carcinoid tumor .",
+        "entities": [
+            {
+                "entity_text": "tumor",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "metastasis to 2 peripancreatic lymph nodes",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "malignant carcinoid tumor",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The patient was a 35 - year old female who presented with urinary frequency for 2 months .",
+        "entities": []
+    },
+    {
+        "text": "Her past medical history showed a nonsmoking history and no significant family history .",
+        "entities": []
+    },
+    {
+        "text": "The physical examination was unremarkable .",
+        "entities": []
+    },
+    {
+        "text": "She was treated as urinary tract infection , but there was no improvement in her symptoms .",
+        "entities": [
+            {
+                "entity_text": "urinary tract infection",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Urine analysis and culture were performed several times that was negative for infection .",
+        "entities": []
+    },
+    {
+        "text": "Other laboratory data were also insignificant .",
+        "entities": []
+    },
+    {
+        "text": "Through a routine evaluation , urinary system ultrasonography ( US ) revealed a bladder lesion measuring 7 mm .",
+        "entities": [
+            {
+                "entity_text": "bladder lesion",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "In order to confirm the diagnosis , magnetic resonance imaging ( MRI ) of the abdomen and pelvic cavity was done ; it revealed a lesion in the dome of the bladder .",
+        "entities": [
+            {
+                "entity_text": "lesion in the dome of the bladder",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "To confirm the diagnosis and for histopathological examination , the patient underwent Transurethral Resection of Bladder Tumor ( TURBT ) in April 2018 .",
+        "entities": []
+    },
+    {
+        "text": "Before starting the procedure , the urethra was dilated till Fr : 28 ; at first , the tumor location was specified by cystoscopy .",
+        "entities": [
+            {
+                "entity_text": "tumor",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Then , it was resected by monopolar cautery from superficial to deeper parts with removal of the muscle layers .",
+        "entities": []
+    },
+    {
+        "text": "Proper bleeders were taken and three way Foley catheter was applied for a continuous irrigation .",
+        "entities": []
+    },
+    {
+        "text": "The patient was transferred to the recovery room with complete stability .",
+        "entities": []
+    },
+    {
+        "text": "The histopathology slides show a well-defined mass composed of bland looking spindle cells .",
+        "entities": []
+    },
+    {
+        "text": "Subsequent immunohistochemistry ( IHC ) was done which showed diffuse immunoreactivity for S 100 , but other markers including smooth muscle actin ( SMA ) , desmin , cytokeratin , CD 34 and beta catenin were negative .",
+        "entities": []
+    },
+    {
+        "text": "Ki 67 was 2-3 % , so the diagnosis of schwannoma was confirmed .",
+        "entities": []
+    },
+    {
+        "text": "Then , the neck , abdomen , pelvic and chest computed tomography ( CT ) scans were done that were normal .",
+        "entities": []
+    },
+    {
+        "text": "Brain and spine MRI and physical examination showed no evidence of other schwannoma or evidence of neurofibromatosis .",
+        "entities": [
+            {
+                "entity_text": "neurofibromatosis",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "She had no history of neurofibromatosis in her family .",
+        "entities": [
+            {
+                "entity_text": "neurofibromatosis",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Skin examination was normal and had no caf au lait spot .",
+        "entities": []
+    },
+    {
+        "text": "She was not a case of von Recklinghausen disease .",
+        "entities": [
+            {
+                "entity_text": "von Recklinghausen disease",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "We observed a 29 y . o . female proband with the episode of venous thrombosis at the age of 18 and family history of thrombosis .",
+        "entities": [
+            {
+                "entity_text": "venous thrombosis",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The antithrombin level in our patient was low , 44-48 % ( AT deficiency type I ) .",
+        "entities": []
+    },
+    {
+        "text": "A new genetic variant c . 662 G > C ( p . W 221 S ) in the SERPINC 1 gene was detected in proband and affected father but was absent in healthy sister .",
+        "entities": []
+    },
+    {
+        "text": "We used in silico tools to evaluate the possible impact of p . W 221 S variant on protein structure and function .",
+        "entities": []
+    },
+    {
+        "text": "In mutated SERPINC 1 protein a new N-linked glycosylation site is formed , however , it is unclear if the glycosylation at 219-221 site is possible .",
+        "entities": []
+    },
+    {
+        "text": "We report a case of a male near-term neonate with gestational age of 35 weeks .",
+        "entities": []
+    },
+    {
+        "text": "He was the third born child to a 27 - year-old mother with no significant past history .",
+        "entities": []
+    },
+    {
+        "text": "He was derived from a third degree consanguineous marriage .",
+        "entities": []
+    },
+    {
+        "text": "He was born by means of normal vaginal delivery with a normal extra-uterine adaptation .",
+        "entities": []
+    },
+    {
+        "text": "Meconium-stained amniotic fluid was noted .",
+        "entities": []
+    },
+    {
+        "text": "His birth weight was 3030 g ( 75 th Percentile ) .",
+        "entities": []
+    },
+    {
+        "text": "The baby had normal physical examination at birth aside transitory respiratory distress .",
+        "entities": [
+            {
+                "entity_text": "respiratory distress",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "He had been hospitalized for four days in a private clinic , for the suspicion of materno-foetal infection , where he had antibiotics for 48 hours .",
+        "entities": []
+    },
+    {
+        "text": "He had developed no symptoms during his hospitalization .",
+        "entities": []
+    },
+    {
+        "text": "The output ' s weight was 2400 g which signify the loss of 630 g .",
+        "entities": []
+    },
+    {
+        "text": "Back home , he received exclusive maternal breastfeeding .",
+        "entities": []
+    },
+    {
+        "text": "On his fifth day of life , he presented multiple yellowish-watery stools ( ab 12 times ) and refuse feeding with apyrexia context .",
+        "entities": []
+    },
+    {
+        "text": "He had clinical signs of severe dehydration without fever or vomiting .",
+        "entities": [
+            {
+                "entity_text": "dehydration",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "fever",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "vomiting",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "He lost 930 g relative to the birth ' s weight .",
+        "entities": []
+    },
+    {
+        "text": "The abdomen appeared neither tender nor distended , and the rest of his physical examination was normal .",
+        "entities": []
+    },
+    {
+        "text": "The laboratory findings revealed hypernatremia of 152 mEq / L , hyperkalemia of 7 , 8 mEq / L and severe metabolic acidosis : blood PH : 7 , 1 , HCO 3 : 4 mEq / L .",
+        "entities": [
+            {
+                "entity_text": "hypernatremia",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "hyperkalemia",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "severe metabolic acidosis",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The osmotic gap was 45 .",
+        "entities": []
+    },
+    {
+        "text": "There was no leukocytosis , and the serum level of C-reactive protein was normal .",
+        "entities": [
+            {
+                "entity_text": "leukocytosis",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The infant was treated with intravenous fluids and electrolytes as well as antibiotics after obtaining blood and stool cultures , assuming an infectious etiology .",
+        "entities": []
+    },
+    {
+        "text": "After 26 hours of rehydration therapy , the dehydration resolved , however , a functional acute renal failure complicated by acidosis and hyperkalemia appeared .",
+        "entities": [
+            {
+                "entity_text": "dehydration",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "functional acute renal failure",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "acidosis",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "hyperkalemia",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The chest radiograph showed \" bat wings \" pattern and the cardiothoracic index was 0 , 45 .",
+        "entities": []
+    },
+    {
+        "text": "The renal ultrasound showed discretely hyperechoic kidneys cortex and the absence of renal malformations .",
+        "entities": []
+    },
+    {
+        "text": "On the 11 th day of life , he was transferred to the pediatric intensive care unit .",
+        "entities": []
+    },
+    {
+        "text": "He needed mechanical ventilation for three days and exclusive parenteral feeding by central catheter .",
+        "entities": []
+    },
+    {
+        "text": "The evolution was burdened by cholestasis due to the prolonged parenteral feeding and nosocomial infection by staphylococcus epidermidis .",
+        "entities": []
+    },
+    {
+        "text": "Since his admission , he had developed a slimy diarrhea with 3 to 4 stools per day .",
+        "entities": [
+            {
+                "entity_text": "diarrhea",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "He presented a profuse diarrhea during each attempt to introduce enteral feeding by hydrolyzed milk formula .",
+        "entities": [
+            {
+                "entity_text": "diarrhea",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "He was discharged after 32 days with output ' s weight 3250 g .",
+        "entities": []
+    },
+    {
+        "text": "The oesophago-gastro-duodenoscopy and duodenal biopsy showed partial villous atrophy associated to the brush border abnormalities .",
+        "entities": [
+            {
+                "entity_text": "partial villous atrophy",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The periodic acid Schiff ( PAS ) stain revealed abnormalities in the brush border characterized by loss of the linear part of enterocytes with the presence of intra-cytoplasmic PAS + band in the apical pole of enterocytes uneven thickness and sometimes with double contours pattern .",
+        "entities": []
+    },
+    {
+        "text": "In the submucosa , there were numerous Brunner glands .",
+        "entities": []
+    },
+    {
+        "text": "We find the existence of numerous hemorrhagic suffusions .",
+        "entities": []
+    },
+    {
+        "text": "The CD 10 immunostain was positive .",
+        "entities": []
+    },
+    {
+        "text": "Thus , a diagnosis hypothesis of MVID was raised .",
+        "entities": [
+            {
+                "entity_text": "MVID",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The electron microscopic examination confirmed the diagnosis .",
+        "entities": []
+    },
+    {
+        "text": "Mutation analysis of peripheral blood samples of the neonate revealed a mutation at the homozygous status of MYO 5 B gene .",
+        "entities": []
+    },
+    {
+        "text": "The baby died , after 97 days of life , of septic shock and multiple organ failure .",
+        "entities": []
+    },
+    {
+        "text": "A 12 - year-old girl presented an abdominal pain , high persistent fever of ( 40 ° C ) and severe fatigue .",
+        "entities": [
+            {
+                "entity_text": "abdominal pain",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The physical exam revealed pallor , hepatomegaly , and grade III splenomegaly .",
+        "entities": [
+            {
+                "entity_text": "hepatomegaly",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "splenomegaly",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The investigation revealed an elevated white blood cell count ( WBC ) : 545 , 000 / mm .",
+        "entities": []
+    },
+    {
+        "text": "PNN : 49 , 050 / mm , hemoglobin : 11 . 6 g / dl , platelets : 328 , 000 / mm .",
+        "entities": []
+    },
+    {
+        "text": "The patient ' s peripheral blood smear revealed marked leukocytosis with a significant number of immature myeloid precursors and 21 % blasts .",
+        "entities": []
+    },
+    {
+        "text": "The analysis of the BCR-ABL shows 94 % in the peripheral blood .",
+        "entities": []
+    },
+    {
+        "text": "The patient was diagnosed with CML .",
+        "entities": [
+            {
+                "entity_text": "CML",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "She received a chemotherapy protocol made of hyperalkalinisation , allopurinol , hydroxyurea and a treatment based on imatinib at the dose of 400 mg per day .",
+        "entities": []
+    },
+    {
+        "text": "Patient achieved complete hematological remission at three months and complete cytogenetic remission at 12 months .",
+        "entities": []
+    },
+    {
+        "text": "The patient was readmitted into our pediatric department with complains of severe headache , vomiting , pain and bilateral visual loss since three days .",
+        "entities": [
+            {
+                "entity_text": "severe headache",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "vomiting",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "pain",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "bilateral visual loss",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "On examination , patient was afebrile and appeared pale .",
+        "entities": []
+    },
+    {
+        "text": "Blood pressure was 100 / 60 mm / hg and the heart rate 98 beat / minute .",
+        "entities": []
+    },
+    {
+        "text": "There was no lymphadenopathy and the nervous system examination was normal .",
+        "entities": []
+    },
+    {
+        "text": "Intraocular muscle testing was normal ; however , there was an exophthalmia in both eyes .",
+        "entities": [
+            {
+                "entity_text": "exophthalmia",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The pupil was sluggish to react to light .",
+        "entities": []
+    },
+    {
+        "text": "Fundoscopy revealed bilateral stade III disc edema and hemorrhages of the retina .",
+        "entities": [
+            {
+                "entity_text": "bilateral stade III disc edema",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "hemorrhages of the retina",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "She underwent a brain computed tomography ( CT ) scan with the suspicion of leukemic involvement or any other intracranial event ( cerebral edema ) ; however , nothing was found .",
+        "entities": []
+    },
+    {
+        "text": "A subsequent bone marrow exam showed no morphologic or molecular evidence of CML or acute leukemia .",
+        "entities": []
+    },
+    {
+        "text": "Cytological evaluation of cerebrospinal fluid ( CSF ) was also negative .",
+        "entities": []
+    },
+    {
+        "text": "The patient had no other known pathology that could be held responsible for retina edema .",
+        "entities": []
+    },
+    {
+        "text": "We suggested that it was a side effect of imatinib so its administration was temporary interrupted .",
+        "entities": []
+    },
+    {
+        "text": "The patient was put on an anti-edema therapy ( mannitol , dexamethasone ) .",
+        "entities": []
+    },
+    {
+        "text": "However , few months later , the patient presented in the emergency room with a headache and severe vomiting .",
+        "entities": [
+            {
+                "entity_text": "headache",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "vomiting",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "She described a recurrence of the same character of headaches accompanied with weakness of extremities and seizures .",
+        "entities": [
+            {
+                "entity_text": "headaches",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "weakness of extremities",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "seizures",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Nervous system examination revealed neck rigidity , presence of meningeal signs and lower limb paraplegia .",
+        "entities": [
+            {
+                "entity_text": "neck rigidity",
+                "type": "CLINENTITY"
+            },
+            {
+                "entity_text": "lower limb paraplegia",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "CT of the brain revealed subdural chronic hematoma and a serpenginous gyriform enhancement around the contusion in the right parietal and occipital lobes .",
+        "entities": [
+            {
+                "entity_text": "subdural chronic hematoma",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Analysis of the CSF collected showed lymphoblasts in a WBC count of 11000 cells / ml .",
+        "entities": []
+    },
+    {
+        "text": "Flow cytometry of the CSF showed that blast cells were positive for a cluster of differentiation markers ( CD ) ( CD 34 , CD 19 , CD 10 , CD 22 and partially positive for CD 45 ) confirming CNS extramedullary lymphoid blast infiltration .",
+        "entities": []
+    },
+    {
+        "text": "A bone marrow aspiration was done to evaluate the status of her chronic myelogenous leukemia and result was consistent with a chronic phase .",
+        "entities": [
+            {
+                "entity_text": "chronic myelogenous leukemia",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "Fundus examination showed bilateral optic atrophy .",
+        "entities": [
+            {
+                "entity_text": "bilateral optic atrophy",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The diagnosis of extramedullary isolated CNS blast crises ( lymphoid type ) was based on the presence of blasts in CSF ( confirmed by flow cytometry ) .",
+        "entities": [
+            {
+                "entity_text": "extramedullary isolated CNS blast crises",
+                "type": "CLINENTITY"
+            }
+        ]
+    },
+    {
+        "text": "The patient received a high-dose systemic induction chemotherapy and intrathecal therapy ( methotrexate , arabinoside and dexamethasone ) .",
+        "entities": []
+    },
+    {
+        "text": "The imatinib was replaced by dasatinib at the dose of 100 mg per day .",
+        "entities": []
+    },
+    {
+        "text": "She was treated with 24 Gy of whole-brain radiation therapy .",
+        "entities": []
+    },
+    {
+        "text": "Allogenic stem cell transplantation was not feasible .",
+        "entities": []
+    },
+    {
+        "text": "We noticed a rapidly progressive amelioration in her neurological status after finishing systemic chemotherapy and physical therapy ; however , the patient ' s visual loss showed no signs of improvement .",
+        "entities": []
+    }
+]