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Standardizing Clinical Document Names Using the HL7/LOINC Document Ontology and LOINC Codes

Elizabeth S Chen, Genevieve B Melton, Mark E Engelstad, Indra Neil Sarkar
2010 AMIA Annual Symposium Proceedings  
The standardization of clinical document names is an essential first step towards the optimal use, management, and exchange of documents within and across institutions. The HL7/LOINC Document Ontology (DO) is an existing and evolving document standard developed to provide consistent naming of clinical documents and to guide the creation of LOINC codes for clinical notes. The goal of this study was to explore the feasibility and challenges of mapping local clinical document names from two
more » ... tions into the five axes of the DO and then to leverage this mapping for identifying specific LOINC codes. The results indicate that the DO is either adequate or too broad for representing a majority of the document names and that there are LOINC codes available for one- to two-thirds of the names. Through this mapping process, granularity and other issues were revealed that will be valuable for guiding next steps towards effective standardization of clinical document names.
pmid:21346949 pmcid:PMC3041326 fatcat:qm5hqm2uxzelvnwag4ofejhy3i

Attitudes toward prevention of mtDNA-related diseases through oocyte mitochondrial replacement therapy

Kristin Engelstad, Miriam Sklerov, Joshua Kriger, Alexandra Sanford, Johnston Grier, Daniel Ash, Dieter Egli, Salvatore DiMauro, John L.P. Thompson, Mark V. Sauer, Michio Hirano
2016 Human Reproduction  
study question: Among women who carry pathogenic mitochondrial DNA (mtDNA) point mutations and healthy oocyte donors, what are the levels of support for developing oocyte mitochondrial replacement therapy (OMRT) to prevent transmission of mtDNA mutations? summary answer: The majority of mtDNA carriers and oocyte donors support the development of OMRT techniques to prevent transmission of mtDNA diseases. what is known already: Point mutations of mtDNA cause a variety of maternally inherited
more » ... diseases that are frequently disabling and often fatal. Recent developments in (OMRT) as well as pronuclear transfer between embryos offer new potential options to prevent transmission of mtDNA disease. However, it is unclear whether the non-scientific community will approve of embryos that contain DNA from three people. study design, size, duration: Between 1 June 2012 through 12 February 2015, we administered surveys in cross-sectional studies of 92 female carriers of mtDNA point mutations and 112 healthy oocyte donors. participants/materials, setting, methods: The OMRT carrier survey was completed by 92 female carriers of an mtDNA point mutation. Carriers were recruited through the North American Mitochondrial Disease Consortium (NAMDC), the United Mitochondrial Disease Foundation (UMDF), patient support groups, research and private patients followed at the Columbia University Medical Center (CUMC) and patients' referrals of maternal relatives. The OMRT donor survey was completed by 112 women who had donated oocytes through a major in vitro fertilization clinic. main results and the role of chance: All carriers surveyed were aware that they could transmit the mutation to their offspring, with 78% (35/45) of women, who were of childbearing age, indicating that the risk was sufficient to consider not having children, and 95% (87/92) of all carriers designating that the development of this technique was important and worthwhile. Of the 21 surveyed female carriers considering childbearing, 20 (95%) considered having their own biological offspring somewhat or very important and 16 of the 21 respondents (76%) were willing to donate oocytes for research and development. Of 112 healthy oocyte donors who completed the OMRT donor survey, 97 (87%) indicated that they would donate oocytes for generating a viable embryo through OMRT. limitations, reasons for caution: Many of the participants were either patients or relatives of patients who were already enrolled in a research-oriented database, or who sought care in a tertiary research university setting, indicating a potential sampling bias. The survey was administered to a select group of individuals, who carry, or are at risk for carrying, mtDNA point mutations. These individuals are more likely to have been affected by the mutation or have witnessed first-hand the devastating effects of these mutations. It has not been established whether the general public would be supportive of this work. This survey did not explicitly address alternatives to OMRT. wider implications of the findings: This is the first study indicating a high level of interest in the development of these methods among women affected by the diseases or who are at risk of carrying mtDNA mutations as well as willingness of most donors to provide oocytes for the development of OMRT. study funding/competing interest(s): This work was conducted under the auspices of the NAMDC (Study Protocol 7404). NAMDC (U54NS078059) is part of the NCATS Rare Diseases Clinical Research Network (RDCRN). RDCRN is an initiative of the Office of Rare Diseases Research (ORDR) and NCATS. NAMDC is funded through a collaboration between NCATS, NINDS, NICHD and NIH Office of Dietary Supplements.
doi:10.1093/humrep/dew033 pmid:26936885 pmcid:PMC4840023 fatcat:afsakqjihreq3fj2s4nqiqabm4

Navigating the phenotype frontier: The Monarch Initiative [article]

Julie McMurry, Sebastian Kohler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine, Julius Jacobsen (+14 others)
2016 bioRxiv   pre-print
The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease
more » ... ts. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) provides tools for genotype-phenotype analysis, genomic diagnostics, and precision medicine across broad areas of disease. These tools depend on the data integrated through computable phenotypes for cross species comparisons.
doi:10.1101/059204 fatcat:zyuhdhd4tzakfmmjuhkjocmhlq

The Monarch Initiative: Insights across species reveal human disease mechanisms [article]

Christopher Mungall, Julie McMurry, Sebastian Koehler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, TOM CONLIN, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 bioRxiv   pre-print
Once the text is marked up, the user has the option of turning the recognized phenotype terms into a phenotype profile, and performing a profile search, or to link to any of the entity pages identified  ...  are phenotypically similar to Marfan; below each label is its corresponding aggregate similarity score clinical narrative) and perform an automated annotation on this text, with entities in the text marked  ... 
doi:10.1101/055756 fatcat:26ov5gydkvgmxekc5z7yvcqzly

Prevalence of Loss of All Teeth (Edentulism) and Associated Factors in Older Adults in China, Ghana, India, Mexico, Russia and South Africa

Karl Peltzer, Sandra Hewlett, Alfred Yawson, Paula Moynihan, Raman Preet, Fan Wu, Godfrey Guo, Perianayagam Arokiasamy, James Snodgrass, Somnath Chatterji, Mark Engelstad, Paul Kowal
2014 International Journal of Environmental Research and Public Health  
Little information exists about the loss of all one's teeth (edentulism) among older adults in low-and middle-income countries. This study examines the prevalence of edentulism and associated factors among older adults in a cross-sectional study across six such countries. Data from the World Health Organization (WHO's) Study on global AGEing and adult health (SAGE) Wave 1 was used for this study with adults aged 50-plus from China (N = 13,367), Ghana (N = 4724), India (N = 7150), Mexico (N =
more » ... 5), Russian Federation (N = 3938) and South Africa (N = 3840). Multivariate regression was used to assess predictors of edentulism. The overall prevalence of edentulism was 11.7% in the six countries, with India, Mexico, and Russia has higher prevalence rates (16.3%-21.7%) than China, Ghana, and South Africa (3.0%-9.0%). In multivariate logistic analysis sociodemographic factors (older age, lower education), chronic conditions (arthritis, asthma), health risk behaviour (former daily tobacco use, inadequate fruits and vegetable consumption) and other health related variables (functional disability and low social cohesion) were associated with edentulism. The national estimates and identified factors associated with edentulism among older adults across the six countries helps to identify areas for further exploration and targets for intervention.
doi:10.3390/ijerph111111308 pmid:25361046 pmcid:PMC4245614 fatcat:rjlwsvlz75dglldkqwvtwpqxtu

Navigating the Phenotype Frontier: The Monarch Initiative

Julie A. McMurry, Sebastian Köhler, Nicole L. Washington, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 Genetics  
The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease
more » ... ts. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) provides tools for genotype-phenotype analysis, genomic diagnostics, and precision medicine across broad areas of disease.
doi:10.1534/genetics.116.188870 pmid:27516611 pmcid:PMC4981258 fatcat:tqhwmjkc7ze3jnytvuneqedhku

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J.P. Gourdine (+14 others)
2016 Nucleic Acids Research  
Once the text is marked up, the user has the option of turning the recognized phenotype terms into a phenotype profile, and performing a profile search, or to link to any of the entity pages identified  ...  The Monarch annotation service allows a user to enter free text (e.g. a paper abstract or a clinical narrative) and perform an automated annotation on this text, with entities in the text marked up with  ... 
doi:10.1093/nar/gkw1128 pmid:27899636 pmcid:PMC5210586 fatcat:tbsgmbgu4vfmpiwwsenemxj2cm

Mitochondrial diseases in North America

Emanuele Barca, Yuelin Long, Victoria Cooley, Robert Schoenaker, Valentina Emmanuele, Salvatore DiMauro, Bruce H. Cohen, Amel Karaa, Georgirene D. Vladutiu, Richard Haas, Johan L.K. Van Hove, Fernando Scaglia (+23 others)
2020 Neurology: Genetics  
ObjectiveTo describe clinical, biochemical, and genetic features of participants with mitochondrial diseases (MtDs) enrolled in the North American Mitochondrial Disease Consortium (NAMDC) Registry.MethodsThis cross-sectional, multicenter, retrospective database analysis evaluates the phenotypic and molecular characteristics of participants enrolled in the NAMDC Registry from September 2011 to December 2018. The NAMDC is a network of 17 centers with expertise in MtDs and includes both adult and
more » ... ediatric specialists.ResultsOne thousand four hundred ten of 1,553 participants had sufficient clinical data for analysis. For this study, we included only participants with molecular genetic diagnoses (n = 666). Age at onset ranged from infancy to adulthood. The most common diagnosis was multisystemic disorder (113 participants), and only a minority of participants were diagnosed with a classical mitochondrial syndrome. The most frequent classical syndromes were Leigh syndrome (97 individuals) and mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (71 individuals). Pathogenic variants in the mitochondrial DNA were more frequently observed (414 participants) than pathogenic nuclear gene variants (252 participants). Pathogenic variants in 65 nuclear genes were identified, with POLG1 and PDHA1 being the most commonly affected. Pathogenic variants in 38 genes were reported only in single participants.ConclusionsThe NAMDC Registry data confirm the high variability of clinical, biochemical, and genetic features of participants with MtDs. This study serves as an important resource for future enhancement of MtD research and clinical care by providing the first comprehensive description of participant with MtD in North America.
doi:10.1212/nxg.0000000000000402 pmid:32337332 pmcid:PMC7164977 fatcat:h7wkc7ctezdsblraal7qg2itxu

Deep Phenotyping For Patients By Patients: A Plain-Language Medical Vocabulary For Precision Diagnosis

Nicole A. Vasilevsky, Erin D. Foster, Mark E. Engelstad, Leigh Carmody, Matt Might, Chip Chambers, Hugh J.S. Dawkins, Janine Lewis, Maria G. Della Rocca, Michelle Snyder, Cornelius F. Boerkoel, Ana Rath (+21 others)
2018 Zenodo  
This paper describes an effort to increase accessibility of the Human Phenotype Ontology to patients and non-medical experts by adding lay-person synonyms and terminology.
doi:10.5281/zenodo.1168736 fatcat:ah2wg6q5gjdl3mukoeyc2dsjma

Page 757 of Archives of Pathology & Laboratory Medicine Vol. 34, Issue 4 [page]

1942 Archives of Pathology & Laboratory Medicine  
Engelstad (1935) also described damage to pyloric gland cells.  ...  Engelstad (1938). : 22. Regaud and others. Brocq and Oury. Engelstad (1938). Snell and Bollmann. Szego and Rother. 23. Delbet and others. Aue and Ceculin. Wolfer.  ... 

Page 927 of Archives of Pathology & Laboratory Medicine Vol. 34, Issue 5 [page]

1942 Archives of Pathology & Laboratory Medicine  
Engelstad (1934a) stained lungs of his animals for elastic tissue. He described “spreading” of the elastic fibrils as due to inflammatory cell infiltration or to fibrosis (Engelstad, 1934a).  ...  Following heavy irradiation of dogs and shoats, Weigert’s elastic tissue stain demonstrates a marked increase in deep blue or black fibers in the alveolar walls.  ... 

Page 185 of Kansas Medicine Vol. 61, Issue 3 [page]

1960 Kansas Medicine  
Engelstad, what is the usual renal output when there is a low sodium and chloride? Mr. Engelstad: About 500 ml. Dr. Delp: Mr. Ginardi? Mr.  ...  Engelstad, what is the significance of the low sodium and chloride values? Mr. Engelstad: The patient could have had a hypervolemia. Dr. Delp: What would cause him to have a hyper- volemia ? Mr.  ... 

Page 292 of National Union Catalog Vol. 7, Issue [page]

1953 National Union Catalog  
Redaksjon: Helen Engelstad ,et al., Utg. av Norges husflid- og husindustri- a set 0. — boktr., 1950. L van tagaancies and trade —Norway. 1. Title. NK991.E5 5640723 Engelstad, Helen.  ...  FTaSU Engelstad, Carl Fredrik, 1915- ed. Albert Schweitzer erobrer Norge; en liten bok om en stor opplevelse. Redigert av Carl Fredrik Engelstad og Max Tau. Oslo, J.G. Tanum, 1954. 10, ,54; p.  ... 

Page 333 of Archives of Pathology & Laboratory Medicine Vol. 33, Issue 3 [page]

1942 Archives of Pathology & Laboratory Medicine  
We have failed to produce chronic ulcers in rats with roentgen rays despite marked cellular alterations and acute reactions.  ...  . \ similar conclusion was reached by Engelstad* with regard to radiation ulcers in the stomachs of rabbits. He felt that the radiation effect laid the groundwork on which the ulcers later developed.  ... 

Page 676 of AJR, American Journal of Roentgenology Vol. 43, Issue 5 [page]

1940 AJR, American Journal of Roentgenology  
Tt Engelstad, R. B. Ueber die Wirkungen der Réntgenstrahlen auf die Lungen. Acta radiol., suppl. 19, 1934, pp- 1-94- 676  ...  After epidermicidal doses the altera- tions are very pronounced and leave a marked sclerosis, often with bone production. 3.  ... 
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