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Caufield JH, Liem DA, Garlid AO, Zhou Y, Watson K, Bui AAT, Wang W, Ping P. A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts. J Vis Exp 2018. [PMID: 30295669 PMCID: PMC6235242 DOI: 10.3791/58392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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.
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Affiliation(s)
- John Harry Caufield
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Physiology, University of California, Los Angeles;
| | - David A Liem
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Physiology, University of California, Los Angeles; Department of Medicine/Cardiology, University of California, Los Angeles
| | - Anders O Garlid
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Physiology, University of California, Los Angeles
| | - Yijiang Zhou
- Department of Cardiology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Karol Watson
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Medicine/Cardiology, University of California, Los Angeles
| | - Alex A T Bui
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Radiological Sciences, University of California, Los Angeles; Department of Bioengineering, University of California, Los Angeles; Scalable Analytics Institute (ScAi), University of California, Los Angeles
| | - Wei Wang
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Scalable Analytics Institute (ScAi), University of California, Los Angeles; Department of Bioinformatics, University of California, Los Angeles; Department of Computer Science, University of California, Los Angeles
| | - Peipei Ping
- The NIH BD2K Center of Excellence in Biomedical Computing, University of California, Los Angeles; Department of Physiology, University of California, Los Angeles; Department of Medicine/Cardiology, University of California, Los Angeles; Scalable Analytics Institute (ScAi), University of California, Los Angeles; Department of Bioinformatics, University of California, Los Angeles
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Paterson PG, Grahn BH, Gottschall-Pass KT, Gorecki DK, Semple HA. Postnatal Deficiencies of Zinc and Taurine Alter Electroretinograms, Oscillatory Potentials and Morphology of the Rat Retina. Nutr Neurosci 2016; 2:175-89. [DOI: 10.1080/1028415x.1999.11747276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Ugarte M, Grime GW, Osborne NN. Distribution of trace elements in the mammalian retina and cornea by use of particle-induced X-ray emission (PIXE): localisation of zinc does not correlate with that of metallothioneins. Metallomics 2014; 6:274-8. [DOI: 10.1039/c3mt00271c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ugarte M, Osborne NN, Brown LA, Bishop PN. Iron, zinc, and copper in retinal physiology and disease. Surv Ophthalmol 2013; 58:585-609. [DOI: 10.1016/j.survophthal.2012.12.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 12/09/2012] [Accepted: 12/11/2012] [Indexed: 12/26/2022]
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5
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Abstract
Zinc is an essential trace element required for normal cell growth, development, and differentiation. It is involved in DNA synthesis, RNA transcription, and cell division and activation. It is a critical component in many zinc protein/enzymes, including critical zinc transcription factors. Zinc deficiency/altered metabolism is observed in many types of liver disease, including alcoholic liver disease (ALD) and viral liver disease. Some of the mechanisms for zinc deficiency/altered metabolism include decreased dietary intake, increased urinary excretion, activation of certain zinc transporters, and induction of hepatic metallothionein. Zinc deficiency may manifest itself in many ways in liver disease, including skin lesions, poor wound healing/liver regeneration, altered mental status, or altered immune function. Zinc supplementation has been documented to block/attenuate experimental ALD through multiple processes, including stabilization of gut-barrier function, decreasing endotoxemia, decreasing proinflammatory cytokine production, decreasing oxidative stress, and attenuating apoptotic hepatocyte death. Clinical trials in human liver disease are limited in size and quality, but it is clear that zinc supplementation reverses clinical signs of zinc deficiency in patients with liver disease. Some studies suggest improvement in liver function in both ALD and hepatitis C following zinc supplementation, and 1 study suggested improved fibrosis markers in hepatitis C patients. The dose of zinc used for treatment of liver disease is usually 50 mg of elemental zinc taken with a meal to decrease the potential side effect of nausea.
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Affiliation(s)
| | - Zhanxiang Zhou
- University of North Carolina Greensboro, Greensboro, North Carolina
| | - Matthew Cave
- University of Louisville Medical Center, Louisville, Kentucky
| | - Ashutosh Barve
- University of Louisville Medical Center, Louisville, Kentucky
| | - Craig J. McClain
- Correspondence Author: Craig J. McClain, University of Louisville Medical Center, 550 S Jackson St, ACB 3rd Floor, Louisville, KY 40292, USA,
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Kilic M, Taskesen M, Coskun T, Gürakan F, Tokatli A, Sivri HS, Dursun A, Schmitt S, Küry S. A Zinc Sulphate-Resistant Acrodermatitis Enteropathica Patient with a Novel Mutation in SLC39A4 Gene. JIMD Rep 2011; 2:25-8. [PMID: 23430849 DOI: 10.1007/8904_2011_38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/13/2011] [Accepted: 03/15/2011] [Indexed: 12/13/2022] Open
Abstract
Acrodermatitis enteropathica (AE) is a rare autosomal recessive disorder of zinc deficiency due to an abnormal intestinal zinc transporter. It is characterized by the triad of acral dermatitis, alopecia, and diarrhoea. Once AE is correctly diagnosed, patients are treated with orally administered zinc sulphate. In some patients, relapses occur during adolescence, despite the regular treatment. Here, we discuss the clinical and molecular features of a 13-year-old adolescent girl with acrodermatitis enteropathica who was resistant to high-dose zinc sulphate therapy. We successfully treated the patient with zinc gluconate and vitamin C, and we detected a novel homozygous c.541_551dup (p.Leu186fsX38) mutation in the exon 3 of her SLC39A4 gene.
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Affiliation(s)
- M Kilic
- Department of Pediatrics, Metabolism and Nutrition Unit, Hacettepe University, Ankara, Turkey,
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7
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ZIP2 and ZIP4 mediate age-related zinc fluxes across the retinal pigment epithelium. J Mol Neurosci 2011; 46:122-37. [PMID: 21603979 DOI: 10.1007/s12031-011-9536-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/28/2011] [Indexed: 01/24/2023]
Abstract
Decreases in systemic and cellular levels of zinc (Zn(2+)) during normal aging correlate with several age-related pathologies including age-related macular degeneration. Zn(2+) homeostasis in tissues is not only dependent on dietary intake but also on optimal expression and function of its influx (ZIP) and efflux (ZnT) transporters. We recently showed that many of the Zn(2+) transporters are expressed by the retinal pigment epithelial (RPE) cells. In this study, we present evidence that RPE cells contain less endogenous Zn(2+) with increased aging and transport this ion vectorially with greater transport from the basal to apical direction. Expression of two Zn(2+) influx transporters, ZIP2 and ZIP4, is reduced as a function of RPE age. Gene silencing of ZIP2 and ZIP4 in RPE cells from young donors or their overexpression in cells from older donors confirms that these two transporters are essential in controlling Zn(2+) influx and sequestration in RPE cells. Both transporters are distributed on the basal surface of the RPE where they are likely to control Zn(2+) homeostasis in the outer retina.
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8
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Sadowsky AE. Dermatologic Disorders and the Cornea. Cornea 2011. [DOI: 10.1016/b978-0-323-06387-6.00072-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
The elderly are at nutritional risk as a result of multiple physiological, social, psychological, and economic factors. Elderly persons have a higher incidence of chronic diseases and associated intake of medications that may affect nutrient utilization. Social and economic conditions can adversely affect dietary choices and eating patterns. Physiological functions naturally decline with age, which may influence absorption and metabolism. Loneliness and reluctance to eat may complicate an already marginal situation. This article reviews specific trace metals in relation to the elderly. Our objectives are to provide Dietary Reference Intakes for older adults, to provide information on presenting features and functional consequences of trace metal deficiency, and to discuss potential effects and/or benefits of trace metal supplementation in the elderly.
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Affiliation(s)
- Craig J McClain
- Department of Internal Medicine, University of Louisville Medical Center, 550 S. Jackson Street, ACB 3rd Floor, Louisville, KY 40292, USA.
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10
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Abstract
Experimental evidence exists to suggest that zinc can have positive and negative effects on the physiology of cells depending on the "local" concentration, localisation (extracellular vs. intracellular) and/or state (bound vs. free). The retina contains particularly high amounts of zinc suggesting a pivotal role in the tissue. There is also suggestive evidence that zinc deficiency in humans may result in abnormal dark adaptation and/or age-related macular degeneration. The purpose of this article is to provide an overview of various proposed functions for zinc, particularly in the retina. Endogenous chelatable zinc in the retina is localised mainly to the photoreceptors and retinal pigment epithelial cells. Moreover, the zinc localisation in the photoreceptors varies in dark and light, suggesting a role for zinc in a light-regulated process. Some zinc is also located to other areas of the retina but clearly defined zinc-enriched neurones could not be identified as has been shown to occur in certain areas of the brain. Neurones post-synaptic to zinc-enriched neurones in the brain have been suggested to be particularly vulnerable in ischaemia. The role of zinc in retinal ischaemia has been investigated to determine how it is involved in the process. It would appear that when zinc is administered in low concentrations it generally has a positive effect on an insulted retina as in ischaemia. However, higher concentrations of zinc exacerbates the influence of the insult and also acts as a toxin. Use of zinc supplements in diet must, therefore, be taken with caution.
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Affiliation(s)
- M Ugarte
- Nuffield Laboratory of Ophthalmology, University of Oxford, Walton Street, Oxford OX2 6AW, UK
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11
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Abstract
Zinc, a trace element that influences cell metabolism through a variety of mechanisms, appears to play an integral role in maintaining normal ocular function. This element is present in high concentrations in ocular tissue, particularly in retina and choroid. Zinc deficiency has been shown in a number of species to result in a variety of gross, ultrastructural and electrophysiologic ocular manifestations. The physiological functions for zinc have been studied predominantly in retina and retinal pigment epithelium where zinc is believed to interact with taurine and vitamin A. modify photoreceptor plasma membranes, regulate the light-rhodopsin reaction, modulate synaptic transmission and serve as an antioxidant. Suboptimal zinc status in North America may influence the development and progression of several chronic eye diseases. Zinc supplementation trials and epidemiological studies have produced conflicting results concerning the role of zinc in age-related macular degeneration. Additional well-controlled supplementation trials are indicated to clarify the role of zinc in this disease. Future investigations must also expand our understanding of the mechanisms by which zinc regulates ocular morphology and function.
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Affiliation(s)
- B H Grahn
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
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McEwan NA, McNeil PE, Thompson H, McCandlish IA. Diagnostic features, confirmation and disease progression in 28 cases of lethal acrodermatitis of bull terriers. J Small Anim Pract 2000; 41:501-7. [PMID: 11105789 DOI: 10.1111/j.1748-5827.2000.tb03972.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Lethal acrodermatitis (LAD) is a genetically determined metabolic disease of bull terriers first described in the USA in the 1980s. In this study, the largest so far reported, 28 bull terriers born in the UK were diagnosed as suffering from LAD, and the clinical findings and the progression of the disease with time are described. The main characteristics of LAD are stunting, splayed digits, eating difficulties, skin disease of the face and feet, and increased susceptibility to microbial infections. In older dogs, paronychia, nail disease and hyperkeratosis of the footpads develops, becoming severe in dogs over six months of age. A diagnosis of LAD can be strongly suspected in any bull terrier showing a combination of the aforementioned signs from an early age. Dermatohistopathological demonstration of marked parakeratotic hyperkeratosis is strongly supportive of the diagnosis of LAD and, in association with the typical clinical findings, is sufficient to confirm a diagnosis. Although many of the clinical signs and the pathology of this condition suggest zinc deficiency, the measurement of blood zinc levels as a diagnostic aid is of limited value.
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Affiliation(s)
- N A McEwan
- Division of Small Animal Clinical Studies, University of Glasgow Veterinary School, Bearsden
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13
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Ugarte M, Osborne NN. The localization of free zinc varies in rat photoreceptors during light and dark adaptation. Exp Eye Res 1999; 69:459-61. [PMID: 10504280 DOI: 10.1006/exer.1999.0727] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Depression of the electroretinogram in rats deficient in zinc and taurine during prenatal and postnatal life11This research was funded by the Hospital for Sick Children Foundation Grant XG 93-002 and the Natural Sciences and Engineering Research Council of Canada. K.T. Gottschall-Pass was supported by a Natural Sciences and Engineering Research Council of Canada postgraduate scholarship. J Nutr Biochem 1998. [DOI: 10.1016/s0955-2863(98)00063-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Abstract
Acrodermatitis enteropathica is an inborn error of metabolism resulting in zinc malabsorption and severe zinc deficiency. From personal experience and a literature review the following conclusions were drawn: 1. Symptoms other than dermatitis, vary with age. Diarrhoea, mood changes, anorexia, and neurological disturbance were reported most frequently in infancy. Growth retardation, alopecia, weight loss and recurrent infections were prevalent in toddlers and schoolchildren. Spontaneous remission may occur at adolescence. 2. The severity of symptoms also varies. Intermittent or mild cases of the disease and those presenting with uncommon features such as ophthalmic, cerebral or hepatic involvement, are easily overlooked. In the severe cases this may result in a fatal outcome. If untreated, the overall mortality rate is 20%, being higher in males. 3. The laboratory diagnosis is hazardous. In patients, mean zinc values in serum, urine and hair were ca. 50% of normal levels. There is a 15% overlap with healthy controls; moreover, low zinc levels in serum, urine or hair are also found in other diseases. A more specific test is required. 4. In cases of doubt, in vitro or in vivo zinc absorption tests using radioisotopes (65Zn or 69mZn) may be performed. These appear not to be influenced by other conditions and show less overlap with controls. If such tests are unavailable, the clinical response to 3-30 mumol zinc/kg per day for 5 days may be awaited. This is recommended in infants or children with one or more symptoms of acrodermatitis enteropathica.
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Affiliation(s)
- J P Van Wouwe
- Department of Paediatrics, State University, Leiden, The Netherlands
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