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1. Laboratory tests as short-term correlates of stroke

Author

Michael A. Swiernik, Yang Huang, Trevor Sughrue, and James P. Brody

Subjects
Male, Aging, Neurology, Health records, California, Cohort Studies, 0302 clinical medicine, Heart Rate, 80 and over, Electronic Health Records, 030212 general & internal medicine, Medical diagnosis, Stroke, Aged, 80 and over, General Medicine, Middle Aged, Prognosis, Survival Rate, Cholesterol, Female, Cognitive Sciences, Research Article, Adult, medicine.medical_specialty, Adolescent, HDL, Clinical Neurology, and over, LDL, Young Adult, 03 medical and health sciences, medicine, Humans, Psychiatry, Survival analysis, Retrospective Studies, Aged, Neurology & Neurosurgery, Clinical Laboratory Techniques, Proportional hazards model, business.industry, Cholesterol, HDL, Neurosciences, Cholesterol, LDL, medicine.disease, Blood Cell Count, Brain Disorders, Term (time), Good Health and Well Being, Relative risk, Emergency medicine, Neurology (clinical), business, Blood Chemical Analysis, 030217 neurology & neurosurgery, Forecasting
Abstract

Background The widespread adoption of electronic health records provides new opportunities to better predict which patients are likely to suffer a stroke. Using electronic health records, we assessed the correlation of different laboratory tests to future occurrences of a stroke. Methods We examined the electronic health records of 2.4 million people over a two year time span. These records contained 26,964 diagnoses of stroke. Using Cox regression analysis, we measured whether any one of 1796 different laboratory tests were effectively correlated with a future diagnosis of stroke. Results We identified 38 different laboratory tests that had significant short-term (two year) prognostic value for a future diagnosis of stroke. For each of the 38 laboratory tests we also compiled the Kaplan-Meier survival curve, and relative risk ratio that the test confers. Conclusion Several dozen laboratory tests are effective short-term correlates of stroke. Electronic supplementary material The online version of this article (doi:10.1186/s12883-016-0619-y) contains supplementary material, which is available to authorized users.

Published
2016
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2. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution

Author

Chris R. Gissendanner, Jasper Van Kirk Thompson, Cynthia M. Bauerle, Kobie C. Gordon, Stephanie E. Trapani, Sarah C. R. Elgin, Ching-Chung Ko, Asma Latif, Caitlin E. Peirce, Jeremy S. Harmson, Elvis Nguyen, Jillian M. Walton, Siping He, Lauren L. Rodriguez, Jazmyn J. McCloud, Catherine J. Harmon, Angelica N. Willis, Melissa J. Fritz, Jessica A. Ruby, Michael P. Tokarz, Lisa Deng, Samantha T. Alford, Kathryn M. Sinclair, Victoria G. Hohenstein, Lauren Forbes, Erika F. Simms, Jessica M. Simmons, David A. Zaidins, Anthony T. Tubbs, Tyler M. Fox, Erica J. Puopolo, Garrett V. Hagopian, Hilary M. Whelan, Tina Q. Lu, Rachel Miller, Brandy M. Simpson, Emilie G. Weisser, Theresa W. Wong, Luke J. Peterson, Andrew C. Rose, Chelsea L. Cockburn, Tuajuanda C. Jordan, Daniel A. Russell, Yetta M. Robinson, Justin Z. Knutter, Tin-Yun Tang, Daryl Khaw, Ian Winsten Campbell, Stephen B. Taylor, Arrykka S. Jackson, Zein Al-Atrache, Amanda R. Schott, Samantha C. Wendler, John R. Warner, Sequoia I. Leuba, Steven G. Cresawn, J. Bradley Segal, Hannah S. Wirtshafter, Margaret S. Saha, Christine A. Boyer, Melina Y. Zúniga, Lucia P. Barker, Tamsen Polley, Marcella L. Erb, Anjali Menon, Victoria A. Bradley, Amanda J. Barber, Charles A. Bowman, Kaitlin E. Healy, Molly J. McDonough, Kaylee M. Nicholson, A. Javier Lopez, Andrew A. S. Ang, Erica M. Shepard, Leila Haghighat, Matthew B. Alfano, Manuel Ares, Kathryn Sheldon, Murray A. Katelyn, Alexander G. Anderson, Jeffrey D. Rubin, Larisa A. Kerrigan, Lisa Alexander, Krysta R. Guiney-Olsen, Deborah Jacobs-Sera, Junghee Kim, Rebecca Goldstein, Clark L. Straub, Lianne B. Cohen, Anne Georges, Erin N. Hildebrandt, Angela E. Engelsen, Bridget G. Guiza, Russell D. Green, Paul G. Jasinto, Allison M. Perz, Turi A. Alcoser, Laura Z. Filliger, H. S. Rabinowitz, Christopher D. Shaffer, Kathleen Weston-Hafer, William D. Barshop, Blaire C. Spaulding, Andrew J. Medenbach, Joseph Stukey, Michael J. Resiss, Samuel E. Harvey, Aaron A. Best, Nichols E. Amy, Kevin J. He, Erica C. Jansen, Danielle H. Wang, Katrina Nguyen, Katherine Belfield, Christine E. Schnitzler, Seegren V. Philip, Ian M. Bayles, Belle E. V. English, Graham F. Hatfull, Victor Mac, Barbara J. Taylor, Kathryn E. Loesser-Casey, Ingrid J. Slette, Nathan A. Holz, Rachel E. Pferdehirt, Emilie T. Nguyen, Nicholas Lowery, Agustin Borjon, Bo Zhang, Gail V. Larkin, Lynn O. Lewis, Ellen R. Higinbotham, Kevin W. Bradley, Patrick Ng, Brandon C. Yee, Kurt E. Williamson, Anne M. Campbell, Welkin H. Pope, Roger W. Hendrix, Craig L. Peebles, Jonathan M. Barrett, Brandon K. Morgan, Ericka L. Hufford, Ann M. Findley, Kayla N. Busby, Jonathan W. Shepardson, Breyon R. Dixon, Joe Pogliano, Stephanie Guerra, Robert Sjoholm, Dale J. Schipper, Phillip Wu, Steven M. Caruso, Larissa K. Temple, Yun jeong Yang, Jason H. Ho, Kohana D. Leuba, Judith Savitskaya, Alyssa Carey, Peter M. Hynes, Jonathan W. Jarvik, Jonathan Tsay, Corwin N. Rhyan, Marie D. Anderson, Lyons M. Tatyana, Rebekah D. Chew, Jennifer R. Laroche, Jessica S. Kelsey, Jeffrey Corajod, Keshav Budwal, James Sandoz, Tomas Kasza, Alexander P. Troum, Lindsay A. Parnell, Crystal Estrada, Sahrish Ekram, Shannon Goff, Hannah Wang, Mark H. Forsyth, Lauren N. Broadway, Madav K. Shroff, Zindzi D. George, Dee R. Denver, Grant A. Hartzog, Kimberly R. Davis, Kit Pogliano, Isaac R. Masters, Trevor Sughrue, Courtney A. Long, Vincent J. Huang, Gina M. Hogan, and Roberto Puertas Garcia

Subjects
Genome evolution, Science Policy, Mycobacteriophage, Population, lcsh:Medicine, Genome, Viral, Biology, Microbiology, Genome, 03 medical and health sciences, Virology, education, lcsh:Science, Genome Evolution, 030304 developmental biology, Genetics, Comparative genomics, 0303 health sciences, education.field_of_study, Multidisciplinary, Base Sequence, Geography, Mycobacteriophages, 030306 microbiology, lcsh:R, Genetic Variation, Sequence Analysis, DNA, Genomics, Comparative Genomics, Biological Evolution, United States, 3. Good health, Science Education, Evolutionary biology, Viral evolution, DNA, Viral, lcsh:Q, Mobile genetic elements, Research Article
Abstract

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Published
2011

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