Merge pull request #40 from monarch-initiative/output_texts_from_text…

…_mining

extend output to get text mining prompts

docs/cases/PMID_16636245.txt

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+[source]
+pmid = PMID:16636245
+title = New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2
+[diagnosis]
+disease_id = OMIM:201300
+disease_label = Neuropathy, hereditary sensory and autonomic, type II
+[text]
+A 39-year-old man first noted that he
+felt no pain in his extremities during his teenage years. He had no
+other developmental abnormalities. His parents and grandparents
+were consanguineous (figure, A). The origins of the oldest family
+members were Japanese. Neither his parents nor siblings were
+affected.
+He had a history of dermatitis factitia (onychotillomania) and
+recurrent skin ulcers at the tip of his fingers and toes since his
+twenties. He was diagnosed with Buerger’s disease at age 26
+years. He had episodes of being febrile due to skin lesion infections,
+resulting in the spontaneous or surgical amputation of affected fingers or toes.
+He was admitted to our hospital at age 39
+years. Neurologic examination revealed the loss of pain and thermal, vibratory,
+or tactile sense in the distal limbs, showing a
+“glove-and-stocking-type” distribution.
+Tendon reflexes were almost absent in both the upper and lower limbs. He did not show
+muscle weakness. Three fingertips of the right hand and two
+fingertips of the left hand were defective; likewise, his toes were
+shortened because of amputations (figure, B). With regard to his
+autonomic functions, there were no complaints of sweating abnormality in the face,
+body, and extremities. The sympathetic skin
+response recorded from the palms was normal. There was no
+evidence of orthostatic hypotension during the head-up tilt test.
+Infrared thermographic analysis revealed that the resting skin
+temperatures of his hands and feet were normal. There was no
+impotence, constipation, or urinary disturbance.
+A nerve conduction study showed the absence of SNAPs in the
+median and sural nerves of both sides, whereas compound muscle
+action potentials and motor conduction velocities in the median
+and tibial nerves were within the normal range. Nerve biopsy was
+performed on the sural nerve  showed typical
+complete loss of myelinated fibers and a decreased number of unmyelinated fibers were
+observed in the sural nerve. There was mild subperineurial edema; however, no inflammatory
+cell infiltration or vasculitis was observed. The complete
+loss of myelinated fibers without onion-bulb formation or
+axonal degeneration is demonstrated. There is mild subperineurial edema; however, there is no inflammatory cell
+infiltration or vasculitis
+

docs/cases/PMID_24969041.txt

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+[source]
+pmid = PMID:24969041
+title = Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report
+[diagnosis]
+disease_id = OMIM:149400
+disease_label = Hyperekplexia 1
+[text]
+A male neonate was born to term at the 40th week of gestation by cesarean section delivery after an uneventful pregnancy.
+His birth weight was 3990g and Apgar score was 9/10. At day 1 post-term, he developed a pneumothorax and was admitted
+to the perinatal intensive care unit for extra oxygen and parenteral fluid therapy. At day 4 post-term, abnormal movements,
+stiffness of the muscles and convulsions were observed, and phenobarbital therapy was initiated. A neurogical investigation
+described dyskinesia. At day 11 post-term, he was hospitalized in a developmental neurology ward. An examination did not
+identify any hypoxia-induced regulatory abnormalities. The observed recurrent muscular hypertonia was attributed to a
+suspected ion channel disorder and carbamazepine therapy was initiated.
+Ultrasonography of his hip indicated the possibility of dysplasia on the left side, and ultrasonography of his abdomen
+revealed bilateral mild pyelectasis. The results of neurosonography, electroencephalography and magnetic resonance
+imaging of the head did not indicate any abnormalities of the central nervous system.

docs/cases/PMID_27057656.txt

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+[source]
+pmid = PMID:27057656
+title = Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I
+[diagnosis]
+disease_id = OMIM:231050
+disease_label = Geleophysic dysplasia 1
+[text]
+The patient was the first child of healthy and nonconsanguineous German parents. Polyhydramnios and
+short extremities were observed on prenatal ultrasound.
+He was born after an uneventful pregnancy in the 34th
+gestational week with normal birth measurements
+(length 43 cm, 10–25th centile; weight 2260 g, 30th centile; occipitofrontal head circumference 34 cm, 75th
+centile). The patient had mild pulmonary stenosis.
+He presented with recurrent respiratory infections, progressive short stature and
+unusual facial features. Skeletal
+survey at the age of 1 year and 3 months (Fig. 1) indicated severe brachydactyly,
+with shortening of metacarpalia and phalanges. Bone age was severely delayed
+and he showed poor diaphyseal modelling of the phalanges. The femur, humerus and ulna were short, which
+had already been observed on prenatal ultrasound. As no
+lateral radiography of the spine had been performed,
+there was no information on vertebral anomalies.
+On examination at the age of 15 months, our patient
+presented with short stature [height 66 cm, 9 cm < 3rd
+centile; weight 6870 g, 2000 g <3rd centile (corrected for
+length: 25th centile)]; occipitofrontal head circumference
+was normal (48.7 cm, 75th centile). Facial dysmorphism
+included thin lip vermilion, long philtrum, a broad nasal
+tip and bilateral ptosis (Fig. 2). The elbows and knees
+were not fully extendable. Psychomotor development
+was delayed; he could neither walk nor talk at that age.

docs/cases/PMID_27435956.txt

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+[source]
+pmid = PMID:27435956
+title = Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation
+[diagnosis]
+disease_id = OMIM:191900
+disease_label = Muckle-Wells syndrome
+[text]
+A 5-year-old girl presented with a 4-year history of
+recurrent urticarial skin eruptions. We first examined
+the child at the age of 11 months, when she had an
+urticarial rash flare consisting of different-sized
+plaques on the trunk, extremities, and face (Fig. 1).
+These skin lesions were evanescent in 24 hours and
+were asymptomatic. Her body temperature was 36°C,
+without any previous episodes of fever. She never had
+conjunctivitis. She was born at 29 weeks weighing
+1,200 g. She exhibited slight growth retardation
+(height 72 cm, weight 7.8 kg). Her Romanian mother
+had a history of chronic urticaria, arthralgias, and
+deafness. Her 11-year-old brother and father were
+healthy.
+Laboratory examination revealed an elevated
+white blood cell count (438,000/lL), a high erythrocyte sedimentation rate (ESR; 48 mm at 1 hour), and
+high C-reactive protein (CRP; 8–10 mg/dL). Laboratory investigations of complete blood cell count,
+electrolytes, rheumatoid factor, antinuclear antibody,
+and complement components (C3, C4, CH50) and
+liver and renal tests yielded normal results. A chest
+radiograph was also normal. Skin biopsy showed
+moderate, nonspecific dermal inflammation and
+perivascular infiltration with predominantly polymorphonuclear cells, compatible with common urticaria
+without signs of vasculitis (Fig. 2A, B). Direct
+immunofluorescence was negative.
+A diagnosis of chronic urticaria was made and
+therapy with systemic antihistamines was initiated,
+with variable response. The intermittent urticarial
+rash persisted for several years. The few laboratory
+tests performed during this time showed anemia,
+leukocytosis, and high CRP and ESR levels.
+When she was 5 years old, the patient presented
+with a severe headache. Magnetic resonance imaging
+examination and lumbar puncture with an analysis of
+the cerebrospinal fluid (CSF) revealed intracranial
+hypertension (opening pressure 40–45 mm H2O).
+Ophthalmologic examination found bilateral papillary edema without any other ocular abnormalities
+(Fig. 3A).

docs/cases/PMID_27587992.txt

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+[source]
+pmid = PMID:27587992
+title = New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report
+[diagnosis]
+disease_id = OMIM:230740
+disease_label = GAPO syndrome
+[text]
+The 2 male siblings diagnosed with GAPO syndrome were 13 and 14 years of age.
+The parents denied consanguinity. Both patients presented with alopecia (fig. 1b),
+a saddle nose, thickened eyelids and thick lips, in addition to dwarfism, hypotrichosis,
+strabismus, shallow orbits, protruding auricles, prominent supraorbital ridges,
+high and bossed forehead, and a small face with dysplasia.
+Oral examination showed thickened upper and lower alveolar ridges in a
+buccolingual direction and lined with normal mucosa; pseudoanodontia was also present.

docs/cases/PMID_28392951.txt

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+[source]
+pmid = PMID:28392951
+title = Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome
+[diagnosis]
+disease_id = OMIM:256300
+disease_label = Nephrotic syndrome, type 1
+[text]
+Patient 1
+A 40-day-old boy was admitted in the Department of Pediatrics,
+Vietnam National Hospital of Pediatrics. He was a full-term
+normal delivery with a birth weight of 2.8 kg.
+The weight of the placenta was unknown. The biochemical indices
+of the blood serum revealed 27.2 g/L serum total protein
+(normal is > 56 g/L), 8.84 g/L albumin (normal is > 25 g/L),
+and 10.9 mM/L cholesterol. The biochemical indices of the urine
+revealed 6,100 mg/L protein (normal is < 200 mg/L) and
+8,918 mg/L protein/creatinine (normal is < 300 mg/L).
+Patient had a whole-body edema, multimembrane effusion,
+severe pneumonia, severe decrease blood protein and plasma albumin,
+and high levels of protein in urine, recurrent many times.
+

docs/cases/PMID_29110636.txt

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+[source]
+pmid = PMID:29110636
+title = Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation
+[diagnosis]
+disease_id = OMIM:107480
+disease_label = Townes-Brocks syndrome 1
+[text]
+The proband, VMFS, who was 5 years old at the time this report was written,
+was born by normal vaginal delivery at 38.5 weeks gestational age with Apgar scores of 9 and 10
+ (first and fifth minutes, respectively). His birth weight (2.735 kg), length (48 cm), and
+ head circumference (34.5 cm) were within normal ranges. The pregnancy occurred with no
+ intercurrences and no concerns were raised in prenatal examinations. The child was born with
+ anal atresia, which was corrected by posterior sagittal anorretoplasty on his second day of life.
+ After the operation, VMFS remained hospitalized for 10 days in the neonatal intensive care unit.
+VMFS is the second child of non-consanguineous healthy young adult parents. He has a brother
+(11 years old) with attention deficit hyperactivity disorder and a cousin who was born with an
+imperforate anus. The patient has exhibited developmental and speech delays. He displays
+hyperactive and sometimes aggressive behavior, which has been managed with antipsychotic drugs
+starting from the age of 4. He has a short stature for his age, a low anterior hairline,
+left microtia with agenesis of the helix, bilateral preauricular tags, low set ears,
+long eyelashes, epicanthus, a deviated nose with a downward pointing tip, and a short neck.
+Skeletal anomalies were prominent and included a bifid thumb on the right hand,
+a long left thumb with a size and shape similar to that of the second left hand finger,
+and overlapping toes on the feet.
+VFMS was also noted to have hypospadias and a hypochromic spot on the right thigh.
+An abdominal ultrasound was normal. Echocardiography showed an atrial septal defect.
+Cystourethrography showed vesicoureteral reflux (grade II) and
+bilateral reduction of the distal urethral caliber.
+However, blood tests results ruled out renal insufficiency,
+and renal scintigraphy and ultrasonography findings were normal.
+Analysis of auditory brainstem evoked potentials indicated bilateral moderate hearing,
+with better responses to low-frequency stimuli. Brain computerized axial tomography and
+ magnetic resonance imaging scans were normal (Fig. 1).
+ An electroencephalogram (International 10–20 System of Electrode Placement), showed normal
+ background activity. X-rays showed preaxial polydactyly with ulnar deviation (Fig. 2),
+ and a rudimentary rib at T12.

docs/cases/PMID_30034812.txt

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+[source]
+pmid = PMID:30034812
+title = Camurati-Engelmann disease: a case report from sub-Saharan Africa
+[diagnosis]
+disease_id = OMIM:131300
+disease_label = Camurati-Engelmann disease
+[text]
+A 35-year-old female patient was referred to us. She had a 15-year history of left shoulder joint pain,
+bone pain, progressive enlargement of bones in the arms and legs and waddling gait,
+associated with general body weakness. Also protrusion of both eyes was reported.
+There were no associated hearing and visual problems. Her cognitive and motor development was normal,
+though from the age of 10 years she could not keep pace with her peers in sports activities.
+No close relative had the same or similar symptoms; she has a 3 years old healthy daughter.
+On physical examination she had prominent forehead, proptosis and blepharoptosis (Fig. 1).
+Prominent palpable bones in upper limbs, humerus, ulna and radius (Fig. 2) and lower limbs (Fig. 3)
+were noted with muscle wasting and pseudo-atrophy of skin above affected bones.
+The left shoulder joint was tender, but not swollen. There were good passive and active joint movements.
+Cranial nerve examination was normal.
+She had elevated alkaline phosphatase of 256 μmol/L (normal range50-150 μmol/L) and
+low calcium of 2.01 mmol/L (normal range 2.15–2.65 mmol/L). Full blood count, creatinine,
+thyroid function test and uric acid were normal. ECG and chest radiography were normal.
+Radiographs of left and right upper limbs (Fig. 4) showed bilateral, dense cortices of diaphyses,
+sparing metaphyses and epiphyses.
+Hyperostosis of diaphyses of long bones of upper limbs (arrows).
+(A) Left humerus with irregular cortical thickening and medullary canal stenosis.
+(B) Right humerus with irregular cortical thickening and medullary canal stenosis.
+(C) Right radius and ulna with cortical thickening, medullary canal obliteration
+and narrowing of space between radius and ulna.
+(D) Left radius and ulna with cortical thickening, medullary canal obliteration and
+narrowing of space between radius and ulna.

docs/cases/PMID_30053862.txt

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+[source]
+pmid = PMID:30053862
+title = A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report
+[diagnosis]
+disease_id = OMIM:617730
+disease_label = Galloway-Mowat syndrome 4
+[text]
+Case II-1
+This female baby was born after a gestational period of 39+3 weeks. The birth weight was 2250 g
+(< 3rd percentile), height was 46 cm (5–10th percentile), head circumference was 29 cm (< 3rd percentile),
+and the Apgar scores at 1 and 5 min were 5 and 7, respectively.
+A diaphragmatic hernia was noted in the delivery room.
+The initial serum albumin level at day one was 3.3 g/dL and the initial serum creatinine level,
+which reflects the mother’s renal function, was 0.58 mg/dL. Imaging revealed a hiatal hernia
+with gastric volvulus (Fig. 1). She also had facial dysmorphism including ocular hypertelorism
+and low-set ears, and a brain magnetic resonance image (MRI) revealed microcephaly with a
+simplified gyral pattern (Fig. 2a). Surgical repair of the hiatal hernia was performed 6 days
+after birth without any serious events. The baby started to feed on a mix of breast milk and formula.
+Two days after surgery, generalized edema developed with a decrease in urine volume.
+Serum albumin levels decreased to 2.0 g/dL, serum creatinine levels increased to 1.29 mg/dL,
+and 24-h urinary protein excretion was 2871 mg/day. Renal ultrasonography revealed increased
+echogenicity of both kidneys with poor differentiation between the peripheral cortex and
+central echogenic complex. At the age of 2 weeks, an open kidney biopsy was performed (Fig. 3).
+Thirty-eight (44%) of 87 glomeruli exhibited segmental lobular collapse and sclerosis,
+and some of the nonsclerotic glomeruli showed features of immature fetal glomeruli.
+Tubules displayed severe focal atrophy and loss. Infiltration of mononuclear cells and fibrosis
+were observed in the interstitium. A follow-up brain MRI at 4 months of age showed the progression of
+diffuse brain atrophy with subarachnoid space widening (Fig. 2b).
+Massive proteinuria persisted and serum creatinine levels began to rise rapidly at the age of 9 months.
+However, the baby received conservative treatment only, including intermittent albumin replacement,
+because the parents did not want immunosuppressive treatment or any other aggressive renal replacement
+therapy. The baby died at the age of 10 months.