| Literature DB >> 30295669 |
John Harry Caufield1, David A Liem2, Anders O Garlid3, Yijiang Zhou4, Karol Watson5, Alex A T Bui6, Wei Wang7, Peipei Ping8.
Abstract
Clinical case reports (CCRs) are a valuable means of sharing observations and insights in medicine. The form of these documents varies, and their content includes descriptions of numerous, novel disease presentations and treatments. Thus far, the text data within CCRs is largely unstructured, requiring significant human and computational effort to render these data useful for in-depth analysis. In this protocol, we describe methods for identifying metadata corresponding to specific biomedical concepts frequently observed within CCRs. We provide a metadata template as a guide for document annotation, recognizing that imposing structure on CCRs may be pursued by combinations of manual and automated effort. The approach presented here is appropriate for organization of concept-related text from a large literature corpus (e.g., thousands of CCRs) but may be easily adapted to facilitate more focused tasks or small sets of reports. The resulting structured text data includes sufficient semantic context to support a variety of subsequent text analysis workflows: meta-analyses to determine how to maximize CCR detail, epidemiological studies of rare diseases, and the development of models of medical language may all be made more realizable and manageable through the use of structured text data.Entities:
Mesh:
Year: 2018 PMID: 30295669 PMCID: PMC6235242 DOI: 10.3791/58392
Source DB: PubMed Journal: J Vis Exp ISSN: 1940-087X Impact factor: 1.355


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| cancer | Any type of cancer or malignant neoplasm. | II | C00-D49 |
| nervous | Any disease of the brain, spine, or nerves. | VI | G00-G99 |
| cardiovascular | Any disease of the heart or vascular system. Does not include hematological diseases. | IX | I00-I99 |
| musculoskeletal and rheumatic | Any disease of the muscles, skeletal system, joints, and connective tissues. | XIII | M00-M99 |
| digestive | Any disease of the gastrointestinal tract and digestive organs, including the liver and pancreas. | XI | K00-K95 |
| obstetrical and gynecological | Any disease relating to pregnancy, childbirth, the female reproductive system, or the breasts. | XIV; XV | O00-O9A; N60-N98 |
| infectious | Any disease causes by infectious microorganisms. | I | A00-B99 |
| respiratory | Any disease of the lungs and respiratory tract. | X | J00-J99 |
| hematologic | Any disease of the blood, bone marrow, lymph nodes, or spleen. | III | D50-D89 |
| kidney and urologic | Any disease of the kidneys or bladder, including the ureters, as well as the male reproductive organs, including the prostate. | XIV | N00-N53; N99 |
| endocrine | Any disease of the endocrine glands, as well as metabolic disorders. | IV | E00-E89 |
| oral and maxillofacial | Any condition involving the mouth, jaws, head, face, or neck. | XI; XIII | K00-K14; M26-M27 |
| eye | Any condition involving the eyes, including blindness. | VII | H00-H59 |
| otorhinolaryngologic | Any condition of the ear, nose, and/or throat. | VIII | H60-H95; J30-J39 |
| skin | Any disease of the skin. | XII | L00-L99 |
| rare | A special category reserved for reports of rare diseases, defined as those impacting fewer than 200,000 individuals in the United States (see https://rarediseases.info.nih.gov/diseases) |
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| Internal ID | CCR005 | CCR2000 |
| Annotation Date | Mar 2 2018 | Mar 1 2018 |
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| Title | A case of endocarditis. | Ocular histopathology of acrodermatitis enteropathica. |
| Authors | Grant AB;Chang CD | Cameron JD;McClain CJ |
| Year | 2017 | 1986 |
| Journal | World Journal of Medicine and Case Reports | British Journal of Ophthalmology |
| Institution | Department of Medicine, Division of Cardiology, First General Hospital, Boston, Massachusetts, USA | Department of Ophthalmology, University of Minnesota Medical School, Minneapolis, Minnesota 55455 |
| Corresponding Author | Grant AB | Cameron JD |
| PMID | 25555555 | 3756122 |
| DOI | 10.1011/wjmcr.2017.11.001 | NA |
| Link | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9555555/ | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1040795/ |
| Language | English | English |
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| Key Words | brucellosis; endocarditis; mitral valve | NA |
| Demography | 37-year-old male | male child |
| Geographic Locations | Florida; Rio de Janeiro, Brazil | NA |
| Life Style | smoker; drinks alcohol occasionally | NA |
| Family History | third of five children of consanguineous parents; younger brother has chronic eczema | NA |
| Social History | construction worker | NA |
| Medical/Surgical History | history of fatigue | 8 pound 9 ounce (3884 g) product of an uncomplicated, full term pregnancy; in good health until age 1 month when he developed a blistering skin rash on his cheeks; rash spread to involve the skin around the eyes, nose, and mouth; skin lesions were also noted on the abdomen and extremities; diarrhoea and failure to thrive; skin biopsy at that time showed parakeratosis typical of acrodermatitis enteropathica; treated over the next six years with intermittent courses of broad spectrum antibiotics, breast milk, and diodoquin; partially responded; developed total alopecia, intermittent acrodermatitis, and intermittent diarrhoea with suboptimal weight gain; spasticity attributed to central nervous system involvement by the ae had developed by 8 months of age; several episodes of cardiopulmonary arrest at 11 months; lack of co-ordination of his vocal cords; tracheostomy; by age 18 months the child developed searching nystagmus associated with bilateral optic atrophy and slight attenuation of retinal vessels as well as signs of psychomotor retardation; bilateral keratoconjunctivitis; skin rash; second skin biopsy performed at age 3 again showed parakeratosis typical for ae; severe skin rash and diarrhoea; bilateral gross anterior corneal opacities were seen which had completely resolved by the time he was reexamined at age five; frequent infections including otitis media, urinary tract infections, and skin infections |
| Disease System | cardiovascular; infectious | digestive; skin; eye; rare |
| Signs and Symptoms | palpitations and dyspnea in the previous week; presented with lethargy, headache, and chills | severe blepharoconjunctivitis and bilateral anterior corneal vascularisation; severe skin rash and diarrhoea; gram-negative bacterial sepsis; skin lesions typical of acrodermatitis enteropathica, absence of thymic tissue, marked degeneration of the optic nerves, chiasm, and optic tracts and extensive cerebellar degeneration |
| Comorbidity | hypertension; hyperlipidemia | NA |
| Diagnostic Techniques and Procedures | Physical examination; electrocardiography; blood cultures | ocular examination; necropsy |
| Diagnosis | Brucella endocarditis | acrodermatitis enteropathica |
| Laboratory Values | increase in c-reactive protein (9 mg/dl); alkaline phosphatase (250 u/l) | NA |
| Pathology | Brucella melitensis was cultured from blood samples | right and left eyes were similar in appearance; corneal epithelium was reduced in thickness to one to three cell layers of flattened squamous epithelial cells over the entire surface of the cornea; all polarity of the epithelium was lost. bowman's membrane could be identified only in the periphery of the right cornea. no bowman's membrane could be identified in the left cornea. neither degenerative nor inflammatory pannus could be identified in either eye; extensive atrophy of the circular and oblique muscles of the ciliary body; some posterior migration of lens capsular epithelium and early cortical degenerative changes; extensive degeneration of the retinal pigment epithelium throughout the posterior pole; retina was attached and showed mild autolytic changes throughout; some preservation of rod and cone outer segments in the posterior pole, however, these structures were completely lost anterior to the equator; extensive loss of the ganglion cell and nerve fibre layers of both eyes; nearly complete atrophy of the disc and adjacent optic nerve |
| Pharmacological Therapy | gentamycin 240 mg/iv/daily | NA |
| Inverventional Therapy | prosthetic valve replacement | NA |
| Patient Outcome Assessment | recovery was uneventful; discharged home | died in 1971 (age 7) |
| Diagnostic Imaging/Videotape Recording | 2;1;0;1 | 7;0;0;0 |
| Relationship to Other Case Reports | 5555555 | 23430849 |
| Relationship with Clinial Trial | NCT05555123 | NA |
| Crosslink with Database | MedlinePlus Health Information: https://medlineplus.gov/ency/article/000597.htm | HighWire - PDF: http://bjo.bmj.com/cgi/pmidlookup?view=long&pmid=3756122; Europe PubMed Central: http://europepmc.org/abstract/MED/3756122; Genetic Alliance: http://www.diseaseinfosearch.org/result/143 |
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| Funding Source | National Institutes of Health/National Heart, Lung, and Blood Institute | The Minnesota Lions Club; Research to Prevent Blindness; Veterans Administration; Office of Alcohol and Other Drug Abuse Programming of the State of Minnesota |
| Award Number | R01HL123123 (to AG) | NA |
| Disclosures/Conflict of Interest | Dr. Grant is a paid spokesperson for DrugCo. | NA |
| References | 4 | 27 |