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Bowel habits, faecal microbiota and faecal bile acid composition of healthy adults consuming fruit pomace fibres: two-arm, randomised, double-blinded, placebo-controlled trials
- Celeste Alexander, Mary Brauchla, Kristen D. Sanoshy, Traci M. Blonquist, Grace N. Maloney, Eunice Mah, Kathleen Kelley-Garvin, Oliver Chen, DeAnn J. Liska, Jin-E Shin, Thomas W. Boileau, Kelly S. Swanson
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- Journal:
- British Journal of Nutrition / Volume 130 / Issue 1 / 14 July 2023
- Published online by Cambridge University Press:
- 14 September 2022, pp. 42-55
- Print publication:
- 14 July 2023
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Dietary fibre modulates gastrointestinal (GI) health and function, providing laxation, shifting microbiota, and altering bile acid (BA) metabolism. Fruit juice production removes the polyphenol- and fibre-rich pomace fraction. The effects of orange and apple pomaces on GI outcomes were investigated in healthy, free-living adults. Healthy adults were enrolled in two double-blinded, crossover trials, being randomised by baseline bowel movement (BM) frequency. In the first trial, subjects (n 91) received orange juice (OJ, 0 g fibre/d) or OJ + orange pomace (OJ + P, 10 g fibre/d) for 4 weeks, separated by a 3-week washout. Similarly, in the second trial, subjects (n 90) received apple juice (AJ, 0 g fibre/d) or AJ + apple pomace (AJ + P, 10 g fibre/d). Bowel habit diaries, GI tolerance surveys and 3-d diet records were collected throughout. Fresh faecal samples were collected from a participant subset for microbiota and BA analyses in each study. Neither pomace interventions influenced BM frequency. At Week 4, OJ + P tended to increase (P = 0·066) GI symptom occurrence compared with OJ, while AJ + P tended (P = 0·089) to increase flatulence compared with AJ. Faecalibacterium (P = 0·038) and Negativibacillus (P = 0·043) were differentially abundant between pre- and post-interventions in the apple trial but were no longer significant after false discovery rate (FDR) correction. Baseline fibre intake was independently associated with several microbial genera in both trials. Orange or apple pomace supplementation was insufficient to elicit changes in bowel habits, microbiota diversity or BA of free-living adults with healthy baseline BM. Future studies should consider baseline BM frequency and habitual fibre intake.
7 - Perspective: Biodiversity and the (data) beast
- from Part II - Next Generation Biodiversity Science
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- By Holly M. Bik, University of California Davis Genome Center, USA, W. Kelley Thomas, University of New Hampshire, USA
- Edited by Peter D. Olson, Natural History Museum, London, Joseph Hughes, University of Glasgow, James A. Cotton
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- Book:
- Next Generation Systematics
- Published online:
- 05 June 2016
- Print publication:
- 16 June 2016, pp 154-174
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Summary
Introduction
The challenges faced in the analysis of high-throughput sequencing data are discussed so frequently that the issues have become palpable stereotypes. Phrases such as ‘data deluge’, ‘hockey stick graph’ and ‘bioinformatics bottleneck’ are ubiquitous to the point of spawning an internet bingo card of overused sound bytes for audiences to check off during seminars (http://bit.ly/wYNxrF). Yet for all the discussion of these challenges, the dialogue about potential solutions is ignored or wildly speculative. In the sequencing world, the game is changing and no one knows how to make the next play. Computational pipelines progress slowly compared to the pace of sequencing technology, with each new platform requiring updated iterations of code and new empirical tests of error rates and data formats.
In spite of the myriad challenges left to surmount, high-throughput sequencing has already transformed and accelerated the pace of biodiversity research. Our current bioinformatic capabilities have been hard-won: characterizing and grappling with fundamentally different sequencing chemistries and order-of-magnitude-increases in file size have required substantial initial investments. The infancy of high-throughput fields means that the current biological insights are rudimentary compared to the sophisticated, complex analyses that will become available over the next decade. Yet by simply investigating ecosystems from a new perspective (genome-scale and community-level exploration, versus the narrower genetic and taxonomic questions previously necessitated by lower throughput Sanger sequencing), we have instantly gained a transformative view of biodiversity and ecological processes. These fledgling insights are already unprecedented, and the steadily increasing breadth of computational tools continues to widen our capacity for integrative data analysis.
The birth and death of sequencing technologies
Researchers impact sequencing technology almost as much as sequencing technology drives research. The platform currently in vogue may quickly fall out of fashion when a better (and cheaper) option hits the market. Biomedical applications drive the market and design for sequencers, with many large-scale sequencing centres focusing their resources on clinical applications (BGI@UCDavis, the Broad Institute), or species of agricultural or economic importance (BGI's facilities in China). Although many ‘megasequencing’ projects focused on biodiversity are now underway (Table 7.1), more fundamental and blue-skies research questions are inherently at the mercy of the technology and protocols favoured across biomedical fields. The dominance of BGI and the falling cost of sequencing are also prompting a reshuffling of long-term visions for many core facilities.
El Paso Housing Sector Econometric Forecast Accuracy
- Thomas M. Fullerton, Jr., Brian W. Kelley
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- Journal:
- Journal of Agricultural and Applied Economics / Volume 40 / Issue 1 / April 2007
- Published online by Cambridge University Press:
- 26 January 2015, pp. 385-402
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There is comparatively little empirical evidence regarding the accuracy of regional housing sector forecasts. Much of the recent analysis conducted for this topic is developed for housing starts and indicates a relatively poor track record. This study examines residential real estate forecasts previously published for El Paso, TX using a structural econometric model. Model coverage is much broader than just starts. Similar to earlier studies, the previously published econometric predictions frequently do not fare very well against the selected random walk benchmarks utilized for the various series under consideration.
DNA Base Identification by Electron Microscopy
- David C. Bell, W. Kelley Thomas, Katelyn M. Murtagh, Cheryl A. Dionne, Adam C. Graham, Jobriah E. Anderson, William R. Glover
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- Journal:
- Microscopy and Microanalysis / Volume 18 / Issue 5 / October 2012
- Published online by Cambridge University Press:
- 09 October 2012, pp. 1049-1053
- Print publication:
- October 2012
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Advances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.
Contributors
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- By Aakash Agarwala, Linda S. Aglio, Rae M. Allain, Paul D. Allen, Houman Amirfarzan, Yasodananda Kumar Areti, Amit Asopa, Edwin G. Avery, Patricia R. Bachiller, Angela M. Bader, Rana Badr, Sibinka Bajic, David J. Baker, Sheila R. Barnett, Rena Beckerly, Lorenzo Berra, Walter Bethune, Sascha S. Beutler, Tarun Bhalla, Edward A. Bittner, Jonathan D. Bloom, Alina V. Bodas, Lina M. Bolanos-Diaz, Ruma R. Bose, Jan Boublik, John P. Broadnax, Jason C. Brookman, Meredith R. Brooks, Roland Brusseau, Ethan O. Bryson, Linda A. Bulich, Kenji Butterfield, William R. Camann, Denise M. Chan, Theresa S. Chang, Jonathan E. Charnin, Mark Chrostowski, Fred Cobey, Adam B. Collins, Mercedes A. Concepcion, Christopher W. Connor, Bronwyn Cooper, Jeffrey B. Cooper, Martha Cordoba-Amorocho, Stephen B. Corn, Darin J. Correll, Gregory J. Crosby, Lisa J. Crossley, Deborah J. Culley, Tomas Cvrk, Michael N. D'Ambra, Michael Decker, Daniel F. Dedrick, Mark Dershwitz, Francis X. Dillon, Pradeep Dinakar, Alimorad G. Djalali, D. John Doyle, Lambertus Drop, Ian F. Dunn, Theodore E. Dushane, Sunil Eappen, Thomas Edrich, Jesse M. Ehrenfeld, Jason M. Erlich, Lucinda L. Everett, Elliott S. Farber, Khaldoun Faris, Eddy M. Feliz, Massimo Ferrigno, Richard S. Field, Michael G. Fitzsimons, Hugh L. Flanagan Jr., Vladimir Formanek, Amanda A. Fox, John A. Fox, Gyorgy Frendl, Tanja S. Frey, Samuel M. Galvagno Jr., Edward R. Garcia, Jonathan D. Gates, Cosmin Gauran, Brian J. Gelfand, Simon Gelman, Alexander C. Gerhart, Peter Gerner, Omid Ghalambor, Christopher J. Gilligan, Christian D. Gonzalez, Noah E. Gordon, William B. Gormley, Thomas J. Graetz, Wendy L. Gross, Amit Gupta, James P. Hardy, Seetharaman Hariharan, Miriam Harnett, Philip M. Hartigan, Joaquim M. Havens, Bishr Haydar, Stephen O. Heard, James L. Helstrom, David L. Hepner, McCallum R. Hoyt, Robert N. Jamison, Karinne Jervis, Stephanie B. Jones, Swaminathan Karthik, Richard M. Kaufman, Shubjeet Kaur, Lee A. Kearse Jr., John C. Keel, Scott D. Kelley, Albert H. Kim, Amy L. Kim, Grace Y. Kim, Robert J. Klickovich, Robert M. Knapp, Bhavani S. Kodali, Rahul Koka, Alina Lazar, Laura H. Leduc, Stanley Leeson, Lisa R. Leffert, Scott A. LeGrand, Patricio Leyton, J. Lance Lichtor, John Lin, Alvaro A. Macias, Karan Madan, Sohail K. Mahboobi, Devi Mahendran, Christine Mai, Sayeed Malek, S. Rao Mallampati, Thomas J. Mancuso, Ramon Martin, Matthew C. Martinez, J. A. Jeevendra Martyn, Kai Matthes, Tommaso Mauri, Mary Ellen McCann, Shannon S. McKenna, Dennis J. McNicholl, Abdel-Kader Mehio, Thor C. Milland, Tonya L. K. Miller, John D. Mitchell, K. Annette Mizuguchi, Naila Moghul, David R. Moss, Ross J. Musumeci, Naveen Nathan, Ju-Mei Ng, Liem C. Nguyen, Ervant Nishanian, Martina Nowak, Ala Nozari, Michael Nurok, Arti Ori, Rafael A. Ortega, Amy J. Ortman, David Oxman, Arvind Palanisamy, Carlo Pancaro, Lisbeth Lopez Pappas, Benjamin Parish, Samuel Park, Deborah S. Pederson, Beverly K. Philip, James H. Philip, Silvia Pivi, Stephen D. Pratt, Douglas E. Raines, Stephen L. Ratcliff, James P. Rathmell, J. Taylor Reed, Elizabeth M. Rickerson, Selwyn O. Rogers Jr., Thomas M. Romanelli, William H. Rosenblatt, Carl E. Rosow, Edgar L. Ross, J. Victor Ryckman, Mônica M. Sá Rêgo, Nicholas Sadovnikoff, Warren S. Sandberg, Annette Y. Schure, B. Scott Segal, Navil F. Sethna, Swapneel K. Shah, Shaheen F. Shaikh, Fred E. Shapiro, Torin D. Shear, Prem S. Shekar, Stanton K. Shernan, Naomi Shimizu, Douglas C. Shook, Kamal K. Sikka, Pankaj K. Sikka, David A. Silver, Jeffrey H. Silverstein, Emily A. Singer, Ken Solt, Spiro G. Spanakis, Wolfgang Steudel, Matthias Stopfkuchen-Evans, Michael P. Storey, Gary R. Strichartz, Balachundhar Subramaniam, Wariya Sukhupragarn, John Summers, Shine Sun, Eswar Sundar, Sugantha Sundar, Neelakantan Sunder, Faraz Syed, Usha B. Tedrow, Nelson L. Thaemert, George P. Topulos, Lawrence C. Tsen, Richard D. Urman, Charles A. Vacanti, Francis X. Vacanti, Joshua C. Vacanti, Assia Valovska, Ivan T. Valovski, Mary Ann Vann, Susan Vassallo, Anasuya Vasudevan, Kamen V. Vlassakov, Gian Paolo Volpato, Essi M. Vulli, J. Matthias Walz, Jingping Wang, James F. Watkins, Maxwell Weinmann, Sharon L. Wetherall, Mallory Williams, Sarah H. Wiser, Zhiling Xiong, Warren M. Zapol, Jie Zhou
- Edited by Charles Vacanti, Scott Segal, Pankaj Sikka, Richard Urman
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- Book:
- Essential Clinical Anesthesia
- Published online:
- 05 January 2012
- Print publication:
- 11 July 2011, pp xv-xxviii
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