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1. Genetic classification of populations using supervised learning.

Author

Michael Bridges, Elizabeth A Heron, Colm O'Dushlaine, Ricardo Segurado, International Schizophrenia Consortium (ISC), Derek Morris, Aiden Corvin, Michael Gill, and Carlos Pinto

Subjects
Medicine, Science
Abstract

There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

Published
2011
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4. INTEGRATING EARTHEN BUILDING MATERIALS AND METHODS INTO MAINSTREAM CONSTRUCTION

Author

Vivian Loftness, Lola Ben-Alon, Kent A. Harries, Michael Bridges, and Erica Cochran Hameen

Subjects
Engineering, Architectural engineering, Environmental Engineering, 010504 meteorology & atmospheric sciences, business.industry, Geography, Planning and Development, 0211 other engineering and technologies, Public Health, Environmental and Occupational Health, 02 engineering and technology, Building and Construction, Management, Monitoring, Policy and Law, 01 natural sciences, Architecture, Mainstream, 021108 energy, business, 0105 earth and related environmental sciences, General Environmental Science, Civil and Structural Engineering, Nature and Landscape Conservation
Abstract

Earthen Building Materials and Methods (EBMM) exhibit excellent environmental, health, indoor air quality and affordability benefits. Despite these advantages, EBMM are not yet broadly implemented in mainstream construction. The main barriers and gaps to implementing earthen construction are analyzed through 126 survey responses and 10 in-depth interviews of a range of experts and end-users, and possible solutions to overcoming these barriers are presented. Specifically, the research indicates that according to earthen construction experts and potential homeowners, inability or difficulty in obtaining building permits is the strongest barrier to implementation. Additionally, existing technical data and environmental assessments must be synthesized and enumerated in order to support decision makers in advancing earthen building policy.

Published
2020
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7. Contributors

Author

Heather Appling, Katherine Bendix, Donna M. Bowers, Michael Bridges, J. Douglas Call, Kevin Carroll, Tzurei Chen, Kevin K. Chui, Bradley Conner, Jonathan Day, Susan Ann Denninger, Todd DeWees, Carol Pierce Dionne, Joan E. Edelstein, Eric Folmar, Tabitha D. Galindo, Tamara Gravano, Patrick D. Grimm, Jeremy E. Hilliard, Ethan A. Hood, Heather Jennings, Milagros \\'Millee\\' Jorge, Géza F. Kogler, Theresa E. Leahy, Michelle M. Lusardi, Sharidy MacCord, Kimberly Leigh Malin, Tyler Manee, Olfat Mohamed, Kelly J. Negley, Andrea Oberlander, E. Annemarie, Elicia Pollard, Benjamin K. Potter, John Rheinstein, Daniel A. Riddick, Daniel H. Riddick, Julie D. Ries, S. Tyler Shultz, Susan Spaulding, Melissa Thacker, Eddie J. Traylor, Susan H. Ventura, R. Scott Ward, Brian J. Wilkinson, Joshua Thomas Williams, Christopher K. Wong, and Sheng-Che Yen

Published
2020
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8. Management of Conditions Associated With Aging and Older Adults Using Therapeutic Electromagnetic Energy

Author

Kevin K. Chui, Jeremy Hilliard, and Michael Bridges

Subjects
030203 arthritis & rheumatology, Gerontology, 03 medical and health sciences, 0302 clinical medicine, business.industry, Rehabilitation, Medicine, Physical Therapy, Sports Therapy and Rehabilitation, Narrative, CINAHL, Geriatrics and Gerontology, business, 030217 neurology & neurosurgery
Abstract

Objective:To assess the effectiveness of therapeutic electromagnetic energy in the management of conditions associated with an aging and older adult population.Methods:A systematic review of literature from 2008 to 2018 was completed in PubMed, CINAHL, and Science Direct. We also reviewed sources to

Published
2018
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9. Introduction

Author

E. Michael Bridges, Ian D. Hannam, L. Roel Oldeman, Frits W.T. Penning de Vries, Sara J. Scherr, and Samran Sombatpanit

Published
2019
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11. Saturation Recovery EPR and Nitroxide Spin Labeling for Exploring Structure and Dynamics in Proteins

Author

Zhongyu, Yang, Michael, Bridges, Michael T, Lerch, Christian, Altenbach, and Wayne L, Hubbell

Subjects
Models, Molecular, Protein Conformation, Electron Spin Resonance Spectroscopy, Animals, Humans, Proteins, Spin Labels, Algorithms
Abstract

Experimental techniques capable of determining the structure and dynamics of proteins are continuously being developed in order to understand protein function. Among existing methods, site-directed spin labeling in combination with saturation recovery (SR) electron paramagnetic resonance spectroscopy contributes uniquely to the determination of secondary and tertiary protein structure under physiological conditions, independent of molecular weight and complexity. In addition, SR of spin labeled proteins was recently demonstrated to be sensitive to conformational exchange events with characteristic lifetimes on the order of μs, a time domain that presents a significant challenge to other spectroscopic techniques. In this chapter, we present the theoretical background necessary to understand the capabilities of SR as applied to spin labeled proteins, the instrumental requirements, and practical experimental considerations necessary to obtain interpretable data, and the use of SR to obtain information on protein: (1) secondary structure via solvent accessibility measurements, (2) tertiary structure using interspin distance measurements, and (3) conformational exchange.

Published
2015

12. The effect of medical student feedback about resident teaching on resident teaching identity: a randomized controlled trial

Author

David, Yuan, Michael, Bridges, Frank J, D'Amico, and Stephen A, Wilson

Subjects
Male, Students, Medical, Social Identification, Attitude of Health Personnel, Teaching, Humans, Internship and Residency, Female, Single-Blind Method, Family Practice, Education, Medical, Undergraduate, Feedback
Abstract

Residents often teach medical students, other residents, and patients. However, few residents get feedback about their teaching. This study's objective was to determine if feedback from medical students increases resident teaching identity.This was a stratified, single blinded, randomized controlled trial of an educational intervention. Residents were stratified based on year of residency and then randomized to receive feedback by medical students or not. Medical students evaluated resident teaching effectiveness by ranking resident ability to apply the five microskills for clinical teaching and to role model being an effective clinician. Residents were surveyed to determine their level of teacher identity before and after the intervention. Allocation concealment and intention to treat principles were used.All residents (n=32) that met inclusion criteria participated with complete response rate to both pre-intervention and post-intervention surveys. There was no difference in teaching identity between residents who received feedback and those who did not, except in one subscale of the Teacher Identity Scale-global teaching identity, where residents who received medical student feedback scored lower.There was no difference between intervention and control group in resident teaching identity over time. The residents found feedback important. This was a randomized controlled trial with strong methodology that helps advance understanding of the importance of medical student feedback on resident teaching.

Published
2014

13. Observing the Evolution of the Universe

Author

James Aguirre, Alexandre Amblard, Amjad Ashoorioon, Carlo Baccigalupi, Amedeo Balbi, Bartlett, J. G., Nicola Bartolo, Dominic Benford, Mark Birkinshaw, Jamie Bock, Dick Bond, Julian Borrill, Franois Bouchet, Michael Bridges, Emory Bunn, Erminia Calabrese, Christopher Cantalupo, Ana Caramete, Carmelita Carbone, Suchetana Chatterjee, Sarah Church, David Chuss, Carlo Contaldi, Asantha Cooray, Sudeep Das, Francesco de Bernardis, Paolo de Bernardis, Gianfranco de Zotti, Delabrouille, J., Xavier Dsert, F., Mark Devlin, Clive Dickinson, Simon Dicker, Matt Dobbs, Scott Dodelson, Olivier Dore, Jessie Dotson, Joanna Dunkley, Maria Cristina Falvella, Dale Fixsen, Pablo Fosalba, Joseph Fowler, Evalyn Gates, Walter Gear, Sunil Golwala, Krzysztof Gorski, Alessandro Gruppuso, Josh Gundersen, Mark Halpern, Shaul Hanany, Masashi Hazumi, Carlos Hernandez-Monteagudo, Mark Hertzberg, Gary Hinshaw, Christopher Hirata, Eric Hivon, Warren Holmes, William Holzapfel, Wayne Hu, Johannes Hubmayr, Kevin Huffenberger, Kent Irwin, Mark Jackson, Andrew Jaffe, Bradley Johnson, William Jones, Manoj Kaplinghat, Brian Keating, Reijo Keskitalo, Justin Khoury, Will Kinney, Theodore Kisner, Lloyd Knox, Alan Kogut, Eiichiro Komatsu, Arthur Kosowsky, John Kovac, Lawrence Krauss, Hannu Kurki-Suonio, Susana Landau, Charles Lawrence, Samuel Leach, Adrian Lee, Erik Leitch, Rodrigo Leonardi, Julien Lesgourgues, Andrew Liddle, Eugene Lim, Michele Limon, Marilena Loverde, Philip Lubin, Antonio Magalhaes, Davide Maino, Tobias Marriage, Victoria Martin, Sabino Matarrese, John Mather, Harsh Mathur, Tomotake Matsumura, Pieter Meerburg, Alessandro Melchiorri, Stephan Meyer, Amber Miller, Michael Milligan, Kavilan Moodley, Michael Neimack, Hogan Nguyen, Dwyer, Ian O., Angiola Orlando, Luca Pagano, Lyman Page, Bruce Partridge, Timothy Pearson, Hiranya Peiris, Francesco Piacentini, Lucio Piccirillo, Elena Pierpaoli, Davide Pietrobon, Giampaolo Pisano, Levon Pogosian, Dmitri Pogosyan, Nicolas Ponthieu, Lucia Popa, Clement Pryke, Christoph Raeth, Subharthi Ray, Christian Reichardt, Sara Ricciardi, Paul Richards, Graca Rocha, Lawrence Rudnick, John Ruhl, Benjamin Rusholme, Claudia Scoccola, Douglas Scott, Carolyn Sealfon, Neelima Sehgal, Michael Seiffert, Leonardo Senatore, Paolo Serra, Sarah Shandera, Meir Shimon, Peter Shirron, Jonathan Sievers, Kris Sigurdson, Joe Silk, Robert Silverberg, Eva Silverstein, Suzanne Staggs, Albert Stebbins, Federico Stivoli, Radek Stompor, Naoshi Sugiyama, Daniel Swetz, Andria Tartari, Max Tegmark, Peter Timbie, Matthieu Tristram, Gregory Tucker, Jon Urrestilla, John Vaillancourt, Veneziani, M., Licia Verde, Joaquin Vieira, Scott Watson, Benjamin Wandelt, Grant Wilson, Edward Wollack, Mark Wyman, Amit Yadav, Giraud-Héraud, Y., Olivier Zahn, Matias Zaldarriaga, Michael Zemcov, Jonathan Zwart, APC - Cosmologie, AstroParticule et Cosmologie (APC (UMR_7164)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), APC - Gravitation (APC-Gravitation), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Max-Planck-Institut für Gravitationsphysik ( Albert-Einstein-Institut ) (AEI), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Max-Planck-Institut für Gravitationsphysik ( Albert-Einstein-Institut ) (AEI), Physique Corpusculaire et Cosmologie - Collège de France (PCC), Collège de France (CdF)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Collège de France (CdF)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-AstroParticule et Cosmologie (APC (UMR_7164)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7), PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Max-Planck-Institut für Gravitationsphysik ( Albert-Einstein-Institut ) (AEI), and Bartlett, James

Subjects
[SDU.ASTR.CO] Sciences of the Universe [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Cosmology and Nongalactic Astrophysics (astro-ph.CO), [PHYS.ASTR.CO] Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], [SDU.ASTR.CO]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Astrophysics::Instrumentation and Methods for Astrophysics, FOS: Physical sciences, Astrophysics::Earth and Planetary Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, Cosmology and Extragalactic Astrophysics, Astrophysics, Astrophysics::Galaxy Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

How did the universe evolve? The fine angular scale (l>1000) temperature and polarization anisotropies in the CMB are a Rosetta stone for understanding the evolution of the universe. Through detailed measurements one may address everything from the physics of the birth of the universe to the history of star formation and the process by which galaxies formed. One may in addition track the evolution of the dark energy and discover the net neutrino mass. We are at the dawn of a new era in which hundreds of square degrees of sky can be mapped with arcminute resolution and sensitivities measured in microKelvin. Acquiring these data requires the use of special purpose telescopes such as the Atacama Cosmology Telescope (ACT), located in Chile, and the South Pole Telescope (SPT). These new telescopes are outfitted with a new generation of custom mm-wave kilo-pixel arrays. Additional instruments are in the planning stages., Science White Paper submitted to the US Astro2010 Decadal Survey. Full list of 177 author available at http://cmbpol.uchicago.edu

Published
2009

15. Chapter 10: Defeating the Developer's Dilemma

Author

Michele DiPietro, Michele DiPietro, Susan A. Ambrose, Michael Bridges, Anne Fay, Marsha C. Lovett, Marie Kamala Norman, Michele DiPietro, Michele DiPietro, Susan A. Ambrose, Michael Bridges, Anne Fay, Marsha C. Lovett, and Marie Kamala Norman

Abstract

To Improve the Academy: A Journal of Educational Development: vol. 27, (dlps) 17063888.0027.014, http://hdl.handle.net/2027/spo.17063888.0027.014, This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. Please contact mpub-help@umich.edu to use this work in a way not covered by the license.

Published
2009

16. Importance of the extra-cellular matrix in the long term, anchorage dependent growth of cell line CHO Kl

Author

Michael Bridges, Carol Gebert, and Peter P. Gray

Subjects
chemistry.chemical_classification, Insulin, medicine.medical_treatment, Contact inhibition, Biology, Cell biology, Extracellular matrix, Cell metabolism, Biochemistry, chemistry, Cell culture, Transferrin, medicine, Cell shape, Autocrine signalling
Abstract

Growth of the CHO Kl cell line in serum free media has been reported for some years. Insulin, transferrin and selenium supplementation to the basal media is sufficient for some applications, but control of the extra cellular matrix (ECM) is critical for long term, anchorage dependent growth. Due to the autocrine nature of the ECM and its relationship with cell culture parameters, control and optimisation is difficult. Identification of links between surface properties of the substratum, cell-cell contact inhibition, cell metabolism, growth rate, ECM secretion and cell shape have both highlighted the importance of the ECM and provided a framework for the further development of long term serum free culture.

Published
1994
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