diff --git a/docs/cases/PMID_16636245.txt b/docs/cases/PMID_16636245.txt new file mode 100644 index 0000000..119b759 --- /dev/null +++ b/docs/cases/PMID_16636245.txt @@ -0,0 +1,45 @@ +[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 + diff --git a/docs/cases/PMID_24969041.txt b/docs/cases/PMID_24969041.txt new file mode 100644 index 0000000..008dace --- /dev/null +++ b/docs/cases/PMID_24969041.txt @@ -0,0 +1,17 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_27057656.txt b/docs/cases/PMID_27057656.txt new file mode 100644 index 0000000..717fa45 --- /dev/null +++ b/docs/cases/PMID_27057656.txt @@ -0,0 +1,30 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_27435956.txt b/docs/cases/PMID_27435956.txt new file mode 100644 index 0000000..2bdaff3 --- /dev/null +++ b/docs/cases/PMID_27435956.txt @@ -0,0 +1,45 @@ +[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). diff --git a/docs/cases/PMID_27587992.txt b/docs/cases/PMID_27587992.txt new file mode 100644 index 0000000..49c72c6 --- /dev/null +++ b/docs/cases/PMID_27587992.txt @@ -0,0 +1,14 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_28392951.txt b/docs/cases/PMID_28392951.txt new file mode 100644 index 0000000..8acabcd --- /dev/null +++ b/docs/cases/PMID_28392951.txt @@ -0,0 +1,21 @@ +[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. + diff --git a/docs/cases/PMID_29110636.txt b/docs/cases/PMID_29110636.txt new file mode 100644 index 0000000..6ef297e --- /dev/null +++ b/docs/cases/PMID_29110636.txt @@ -0,0 +1,36 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_30034812.txt b/docs/cases/PMID_30034812.txt new file mode 100644 index 0000000..efbab22 --- /dev/null +++ b/docs/cases/PMID_30034812.txt @@ -0,0 +1,30 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_30053862.txt b/docs/cases/PMID_30053862.txt new file mode 100644 index 0000000..bb11d7c --- /dev/null +++ b/docs/cases/PMID_30053862.txt @@ -0,0 +1,32 @@ +[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. \ No newline at end of file diff --git a/docs/cases/PMID_30208878.txt b/docs/cases/PMID_30208878.txt new file mode 100644 index 0000000..e8d670a --- /dev/null +++ b/docs/cases/PMID_30208878.txt @@ -0,0 +1,48 @@ +[source] +pmid = PMID:30208878 +title = GNPTAB c.2404C > T nonsense mutation in a patient with mucolipidosis III alpha/beta: a case report +[diagnosis] +disease_id = OMIM:252600 +disease_label = Mucolipidosis III alpha/beta +[text] +The proband was born of a non-consaguineous, in-vitro fertilization dichorionic twin pregnancy at 36 weeks of gestation. +The father and mother are Han Chinese, aged 30 and 38 years respectively (Fig. 1a). Except for previously treated +maternal Graves’ disease, there was no significant family history including neurodevelopmental delay or metabolic disease. +While the twin brother had a birth weight of 2.50 kg, the proband was small for gestational age with birth weight 1.79 kg, +with length and head circumference all below the 3rd percentile (Fig. 1b). Antenatal and perinatal history was unremarkable. +The proband was discharged on day 16 with body weight of 2.16 kg. +The current photo shows a clear lack of catch-up growth even at four months of age for the proband Note that facial dysmorphism was minimal. +At 24 months of age, the coarsening of facial features, trigonocephaly, flat nasal bridge and prominent eyes became more apparent (left). +The kypho-lordosis, crouched gait with bent knee posture was seen on standing. Claw-hand deformities were seen (right) (d) +Close-up view of the thick claw hand of the patient (left) and pectus carinatum deformity of the chest wall (right) +He was first referred to the authors’ Paediatric out-patient clinic for poor weight gain, microcephaly and increased tone +over all four limbs at five months of age (corrected age of four months). Head circumference and weight were below the third +centile. When reviewed at seven months old, physical examination showed failure to thrive with body weight and height +less than the third centile, head circumference at the third centile, plagiocephaly, and a closed anterior fontanelle. +There were no obvious dysmorphism or neurocutaneous stigmata. Chest, cardiovascular and abdominal examination was normal with no organomegaly. + There was a reducible left inguinal hernia and the genitalia were normal. However, flexion contractures affecting both knees and tight hip adductors were noted. + There was also increase in tone over the lower limbs with brisk deep tendon reflexes. Developmental assessment showed mild gross motor delay. +In view of the abnormal physical findings at the age of seven months, investigations include complete blood count and routine biochemical analysis of liver and renal function were done. + The results were all within age-specific reference intervals. Blood lactate, pyruvate and glucose levels were normal. Thyroid stimulating hormone was not elevated. + Urine cytomegalovirus culture was negative. Urine metabolic screening for ketones, reducing sugars, amino acids, phenylpyruvic acid, tyrosine metabolites, cysteine & homocysteine and keto acids were negative. + DBS metabolic screening found unremarkable patterns of amino acids and acylcarnitines. Skull X-ray and non-contrast magnetic resonance imaging (MRI) of the brain did not + reveal frank radiographic evidence of craniosynostosis or definite abnormal signal intensity in the brain. +Follow up imaging with X-ray and MRI spine at 13 months old showed anterior subluxation of the cervical spine at C1/2, +posterior hemivertebra at L2 and a mild kyphosis. Computed tomography (CT) of the brain at 14 months old showed fusion of +metopic suture and narrowing of sagittal suture. A repeated scan at 21 months old showed craniosynostosis with slightly +deformed skull shape, partial fusion of coronal suture near the vertex, sagittal suture and bilateral lambdoid sutures (Fig. 2a). +Retrospective review of a previous chest X-ray film found mildly widened ribs and scalloped vertebrae (Fig. 2b). +Subsequent regular follow up by the neurologists at 26 months of age showed persistent failure to thrive, +with progressive evolvement of coarse facial features (including prominent eyes, microcephaly with craniosynostosis, +low set ears, thick lips, thick spade-shaped claw hands), musculoskeletal abnormalities (kypho-lordosis, contracture over hip, +knee, elbow and wrist and obvious pectus carinatum) (Fig. 1c) and mild global developmental delay involving the gross motor, fine motor and verbal aspect. +Of note, there was no hepatosplenomegaly, and the child was noted to have microcephaly. +Spot urine testing was performed and found an increased mucopolysaccharide excretion (acid mucopolysaccharide to creatinine ratio of 25.9 mg/mmol, normal: <15 mg/mmol). +No pathological pattern was detected on mucopolysaccharide electrophoresis or oligosaccharide thin-layer chromatography. + + +DBS enzyme activity testing showed increased activity of α-iduronidase (23.96 μM/h, normal: >1.32 μM/h), +iduronate sulfatase (210.78 μM/h, normal: >4.45 μM/h), galactose-6-sulphate sulphatase (6.26 μM/h, normal: >1.02 μM/h), +arylsulfatase B (38.77 μM/h, normal: >3.45 μM/h) and α-hexosaminidase (76.35 μM/h, normal: >1.61 μM/h). +Urinary GAG excretion was normal. While no upper normal limits were cited for the lysosomal enzyme activities by the testing laboratory, +their generalized elevation in the clinical context was suggestive of mucolipidosis [13]. \ No newline at end of file diff --git a/docs/cases/PMID_30296944.txt b/docs/cases/PMID_30296944.txt new file mode 100644 index 0000000..bed4f48 --- /dev/null +++ b/docs/cases/PMID_30296944.txt @@ -0,0 +1,40 @@ +[source] +pmid = PMID:30296944 +title = Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report +[diagnosis] +disease_id = OMIM:604772 +disease_label = Ventricular tachycardia, catecholaminergic polymorphic, 1 +[text] +A 17-year-old Caucasian boy was admitted to our intensive care unit (ICU) after successful +resuscitation by emergency services. While performing running exercise in a fitness center, +he suddenly collapsed. Because neither pulse nor breathing could be detected by the bystanders, +immediate resuscitation was performed. In the first heart rhythm analysis conducted by the paramedics, +ventricular fibrillation (VF) was seen and immediately defibrillated into sinus rhythm. The patient +recovered quickly and was transferred to our ICU by the ambulance service. At admission, the +patient was in hemodynamically stable condition with normal vital signs (heart rate 95/min, +blood pressure 125/79 mmHg, auricular temperature 36.5 °C, respiration 15 breaths/min, oxygen saturation +of 100% on 4-L nasal cannula). The physical examination revealed no abnormal findings. Auscultation of the +heart showed a regular rate and rhythm with normal S1 and S2 and no murmurs or rubs. The breath sounds +of the lungs were equal and clear bilaterally with no wheezes, rhonchi, or rales. The patient was awake +(Glasgow Coma Scale score of 15) and orientated in all aspects. No focal sensory or motor deficits, +aphasia, or inadequate balances were noted in the neurological examination. Deep tendon reflexes and +cranial nerves II through XII were intact. Because there were no cerebral or other sequelae at the +time of hospital admission, we decided not to obtain a cranial computed tomographic scan, +owing to the patient’s young age. When asked about the event, he told us that he had no +symptoms prior to the collapse. However, in the years before, he had syncopated several times +while climbing stairs, playing soccer, and once when he got frightened. A general practitioner +previously performed an exercise ECG, which showed multiple premature beats under submaximal +stress (Fig. 1). As a result, beta-blockers were prescribed (metoprolol succinate 47.5 mg once per day). +Apart from this, the patient had no medical history or prior medication. The patient was a nonsmoker +with no regular alcohol consumption and an unremarkable family, social, and environmental history. +Twelve-lead electrocardiogram obtained during ergometry showing a bigeminus with +right bundle branch block morphology at 80 W. At this point, ergometry was stopped because +recurrent syncopes under physical activity were reported in this patient +At ICU admission, initial medical treatment included the first surface ECG after cardiac arrest, +which showed negative T-waves in V1 and biphasic T-waves in V2 (Fig. 2). The results of blood +tests showed normal findings without signs of cardiac ischemia or metabolic disorders (Table 1). +Respiratory disorders (bronchospasm, aspiration) or neurovascular events seemed to be unlikely +because the physical examination, blood gas analysis, and a pulmonary x-ray showed normal findings. +An echocardiogram revealed normal left ventricular function without wall motion abnormalities, +right heart strain, or valve disease. Additionally, a cardiac magnetic resonance +imaging scan was performed and showed normal findings. \ No newline at end of file diff --git a/docs/cases/PMID_30642278.txt b/docs/cases/PMID_30642278.txt new file mode 100644 index 0000000..7f4961e --- /dev/null +++ b/docs/cases/PMID_30642278.txt @@ -0,0 +1,19 @@ +[source] +pmid = PMID:30642278 +title = Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome +[diagnosis] +disease_id = OMIM:302350 +disease_label = Nance-Horan syndrome +[text] +A 15-year-old boy was admitted to the laboratory of clinical genetics of Peking Union Medical College Hospital for genetic +counseling due to congenital cataracts. In addition to the primary physical characteristic of congenital bilateral nuclear cataracts, +the young patient had a long-narrow face, prominent nose and large anteverted pinnae, screw-driver like incisors, +mild mulberry like molars, one missing maxillary second molar and malocclusion (Fig. 1). Available clinical information +regarding the families is shown in Table 1, and the carrier females lens opacity and vision were unavailable here. +The proband (III:1) and another affected individual (II:5) underwent microincision cataract surgery at the ages of 15 +and 21 years respectively. Available photos before the surgery revealed bilateral lens opacities that heavily affected +the nucleus in the proband (Fig. 1; Fig. 2). Individual II:5 presented with similar facial features including a long narrow face, +mildly anteverted pinnae ear and screw-driver like incisors, mild mulberry like molars and malocclusion (Additional file 1). +Individual II: 5 stated that he was affected by nystagmus, and at the time of recruitment in our study, which might associate with NHS. +However, neither of these individuals had mental retardation or behavioral disturbances. +Their family history revealed no obvious visual defects or dental abnormalities among the rest of the family members. \ No newline at end of file diff --git a/docs/cases/PMID_37619988.txt b/docs/cases/PMID_37619988.txt new file mode 100644 index 0000000..eb2abfc --- /dev/null +++ b/docs/cases/PMID_37619988.txt @@ -0,0 +1,16 @@ +[source] +pmid = PMID:37619988 +title = Compound heterozygous variants in RAB34 in a rare skeletal ciliopathy syndrome +[diagnosis] +disease_id = OMIM:620718 +disease_label = Orofaciodigital syndrome XX +[text] +The affected fetus was the second child of a healthy non-consanguineous Japanese couple. +The pregnancy was initiated by in vitro fertilization procedure, and two fertilized eggs were transferred. +At GA 9+4, the mother was diagnosed with vanishing twins. The ultrasound of the remaining fetus at GA 13+2 +showed multiple abnormalities, including posterior neck edema (nuchal translucency 5.6mm), micrognathia, +low-set ears, auricular hypoplasia, bilateral cleft lip and palate, short extremities and polydactyly, +and atrioventricular septal defect (Supplementary Figure 1). Multiple abnormalities were seen in the follow-up scans and the family opted for termination of pregnancy (TOP) at GA 17+5. The autopsy results were consistent with the ultrasound findings and are summarized in Figure 1. +Postmortem photographs of the affected fetus (TOP GA 17+5). Note bilateral cleft lip and palate, +auricular hypoplasia, microretrognathia, narrow thorax, rhizomelic shortening of the limbs, +bilateral pre- and post-axial polydactyly of hands and feet. (B) Postmortem radiographs. Note handlebar clavicles, mild thoracic narrowing, mildly delayed vertebral ossification, underdeveloped lower part of the ilia, rhizomelic shortening of the long bones and lack of metaphyseal flaring. (C) Magnified photographs of hands. Note 7 digits with preaxial polysyndactyly and postaxial polydactyly of both hands. (D) Magnified photographs of feet. Note 6 digits with preaxial polydactyly of the right foot, and 7 digits with preaxial polydactyly and postaxial polysyndactyly of the left foot. [Colour figure can be viewed at wileyonlinelibrary.com] diff --git a/docs/cases/TEMPLATE.txt b/docs/cases/TEMPLATE.txt index 5cfe629..d56c403 100644 --- a/docs/cases/TEMPLATE.txt +++ b/docs/cases/TEMPLATE.txt @@ -5,6 +5,3 @@ title = disease_id = OMIM: disease_label = [text] - -[text] -optionally multiple vignettes per citation \ No newline at end of file diff --git a/src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/BatchMineCommand.java b/src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/BatchMineCommand.java index 27640e0..6f2758e 100644 --- a/src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/BatchMineCommand.java +++ b/src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/BatchMineCommand.java @@ -6,9 +6,18 @@ import org.monarchinitiative.phenopacket2prompt.mining.FenominalParser; import org.monarchinitiative.phenopacket2prompt.model.PpktIndividual; import org.monarchinitiative.phenopacket2prompt.output.CorrectResult; +import org.monarchinitiative.phenopacket2prompt.output.impl.english.EnglishPromptGenerator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import picocli.CommandLine; +import java.io.BufferedWriter; import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; import java.util.List; import java.util.concurrent.Callable; @@ -16,6 +25,8 @@ mixinStandardHelpOptions = true, description = "Batch Text mine, Translate, and Output phenopacket and prompt") public class BatchMineCommand implements Callable { + private static final Logger LOGGER = LoggerFactory.getLogger(BatchMineCommand.class); + @CommandLine.Option(names={"-d","--data"}, description ="directory to download data (default: ${DEFAULT-VALUE})" ) public String datadir="data"; @@ -47,30 +58,53 @@ public Integer call() throws Exception { if (! hpoJsonFile.isFile()) { System.out.printf("[ERROR] Could not find hp.json file at %s\nRun download command first\n", hpoJsonFile.getAbsolutePath()); } - List individualList = getIndividualsFromTextMining(inDirectory,hpoJsonFile); + // get Individuals from text mining + FenominalParser parser = new FenominalParser(hpoJsonFile, useExactMatching); + List caseBundleList = Utility.getAllCaseBundlesFromDirectory(inDirectory, parser); + List individualList = caseBundleList.stream(). + map(CaseBundle::individual). + toList(); Utility.createDir(output); List correctResultList = Utility.outputPromptsEnglishFromIndividuals(individualList, output); + // OUtput prompts that use the original texts. + EnglishPromptGenerator generator = new EnglishPromptGenerator(); + String queryHeader = generator.queryHeader(); + outputOriginalTextsAsPrompts(queryHeader, caseBundleList); + // output file with correct diagnosis list Utility.outputCorrectTextmined(correctResultList); return 0; } - /** - * Get all of the individual objects by text mining the input files - * @param inDirectory Input directory. Should hold input files formatted for this project (demonstration) - * @param hpoJsonFile File representing hp.json - * @return list of individuals - */ - protected List getIndividualsFromTextMining(File inDirectory, File hpoJsonFile) { - FenominalParser parser = new FenominalParser(hpoJsonFile, useExactMatching); - List caseBundleList = Utility.getAllCaseBundlesFromDirectory(inDirectory, parser); - return caseBundleList.stream(). - map(CaseBundle::individual). - toList(); + private void outputOriginalTextsAsPrompts(String queryHeader, List caseBundleList) { + String textMinedDir = Utility.TEXT_MINED_DIR; + String subdir = "original"; + Path path = Paths.get(textMinedDir, subdir); + Utility.createDir(path.toString()); + for (var cbundle : caseBundleList) { + String prompt = String.format("%s%s", queryHeader, cbundle.caseReport().caseText()); + String fname = String.format("%s%s%s.txt", + path.toAbsolutePath().toString(), + File.separator, + cbundle.caseReport().pmid().replace(":", "_")); + try (BufferedWriter bw = new BufferedWriter(new FileWriter(fname))){ + bw.write(prompt); + + + } catch (IOException e) { + LOGGER.error("Could not write prompt: {}", e.getMessage()); + throw new PhenolRuntimeException(e); + } + } + } + /* + + + private void outputTextmined(FenominalParser parser) { @@ -81,4 +115,6 @@ private void outputTextmined(FenominalParser parser) { // for now, just output one case Utility.outputPromptFromCaseBundle(caseBundleList.getFirst().individual(), output); } + + */ }