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2,174 results on '"Lewis, James D."'

1. Indecomposable $K_1$ classes on a Surface and Membrane Integrals

Author

Chen, Xi, Lewis, James D., and Pearlstein, Gregory

Subjects
Mathematics, QA1-939
Abstract

Let $X$ be a projective algebraic surface. We recall the $K$-group $K_{1,\mathrm{ind}}^{(2)}(X)$ of indecomposables and provide evidence that membrane integrals are sufficient to detect these indecomposable classes.

Published
2020
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3. Real Regulators for Products of Elliptic Curves

Author

Chen, Xi and Lewis, James D.

Subjects
Mathematics - Algebraic Geometry, Primary 14C25, Secondary 14F43, 14J28, 14K30
Abstract

Assuming the Kunneth decomposition of the Chow groups of products of general Kummer surfaces, we prove that the Hodge-${\mathcal D}$-conjecture fails for the real regulator $r_{k,1}$ on a product of $n$ general elliptic curves for $2n\ge 3k-1\ge 8$., Comment: 18 pages, to appear in Journal of Mathematical Sciences, The University of Tokyo

Published
2022

5. The Hodge-D-Conjecture fora Product of Elliptic Curves

Author

Ghitza, Alexandru, Lewis, James D., Mansour, Karim, and Silva Jr, Genival Da

Subjects
Mathematics - Algebraic Geometry, 14C35, 14C25, 19E15
Abstract

Let $X/C$ be a general product of elliptic curves. Our goal is to establish the Hodge-D-conjecture for $X$. We accomplish this when $\dim X \leq 5$. For $\dim X \geq 6$, we reduce the conjecture to a matrix rank condition that is amenable to computer calculation., Comment: Errors discovered in paper

Published
2021

10. Yield of Serial Testing for Tuberculosis Exposure in Patients With Inflammatory Bowel Diseases: One Test is Not Enough

Author

Kaur, Manreet, Dassopoulos, Themistocles, Snapper, Scott B., Korzenik, Joshua R., Bohm, Matthew, Raffals, Laura, Poonam, Beniwal-Patel, Hudesman, David, Russ, Kirk, Brook, Loren, Pekow, Joel, Cross, Raymond, Wong, Uni, Bishu, Shrinivas, Bewtra, Meenakshi, Lewis, James D., Duerr, Richard, Saha, Sumona, Caldera, Freddy, Scoville, Elizabeth, Deepak, Parakkal, Ciorba, Matthew, and Lapp, Sean L.

Published
2024
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12. Surgery for Crohn’s Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts

Author

Wolf, Douglas C., Hron, Bridget, Hanson, John S., Mohanty, Sanjib P., Fogel, Ronald P., Levy, L. Campbell, Iskandar, Heba N., Fischer, Monika, Cohen, Benjamin, Swaminath, Arun, Kane, Sunanda, McCabe, Robert P., Jr., Yen, Eugene F., Hanauer, Stephen B., Hudesman, David P., Afzali, Anita, Kelly, Colleen, Weber, John R., Mahadevan, Uma, Herfarth, Hans, Katz, Jeffery, Taleban, Sasha, Rubin, David T., Yachyshyn, Bruce, Reynolds, Gorman J., Gerich, Mark, Dryden, Gerald W., Quezada, Sandra, Higgins, Peter D.R., Shmidt, Eugenia, Lewis, James D., Schwartz, Marc B., Flynn, Ann D., Saha, Sumona, Horst, Sara N., Chiorean, Michael, Green, Patrick D., Scherl, Ellen J., Sandler, Robert, Brotherton, Carol, Albenberg, Lindsey, Valentine, John F., Suskind, David, Meyer, Andrea, Compher, Charlene W., Bewtra, Meenakshi, Kaur, Manreet, Dassopoulos, Themistocles, Snapper, Scott B., Korzenik, Joshua R., Bohm, Matthew, Raffals, Laura, Beniwal-Patel, Poonam, Hudesman, David, Russ, Kirk, Brook, Loren, Pekow, Joel, Cross, Raymond, Wong, Uni, Bishu, Shrinivas, Duerr, Richard, Caldera, Freddy, Scoville, Elizabeth, Deepak, Parakkal, Ciorba, Matthew, Daniel, Scott G., Li, Hongzhe, Hao, Fuhua, Patterson, Andrew D., Hecht, Aaron L., Brensinger, Colleen M., Wu, Gary D., and Bittinger, Kyle

Published
2024
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15. Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry

Author

Kelly, Colleen R, Yen, Eugene F, Grinspan, Ari M, Kahn, Stacy A, Atreja, Ashish, Lewis, James D, Moore, Thomas A, Rubin, David T, Kim, Alison M, Serra, Sonya, Nersesova, Yanina, Fredell, Lydia, Hunsicker, Dea, McDonald, Daniel, Knight, Rob, Allegretti, Jessica R, Pekow, Joel, Absah, Imad, Hsu, Ronald, Vincent, Jennifer, Khanna, Sahil, Tangen, Lyn, Crawford, Carl V, Mattar, Mark C, Chen, Lea Ann, Fischer, Monika, Arsenescu, Razvan I, Feuerstadt, Paul, Goldstein, Jonathan, Kerman, David, Ehrlich, Adam C, Wu, Gary D, and Laine, Loren

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Research, Transplantation, Patient Safety, Pain Research, Emerging Infectious Diseases, Digestive Diseases, Prevention, Adolescent, Adult, Clostridioides difficile, Clostridium Infections, Fecal Microbiota Transplantation, Humans, Inflammatory Bowel Diseases, Irritable Bowel Syndrome, Middle Aged, Prospective Studies, Registries, Treatment Outcome, United States, Young Adult, Risk, Microbiome, Bacteriotherapy, Neurosciences, Paediatrics and Reproductive Medicine, Gastroenterology & Hepatology, Clinical sciences, Nutrition and dietetics
Abstract

Background & aimsFecal microbiota transplantation (FMT) is used commonly for treatment of Clostridioides difficile infections (CDIs), although prospective safety data are limited and real-world FMT practice and outcomes are not well described. The FMT National Registry was designed to assess FMT methods and both safety and effectiveness outcomes from North American FMT providers.MethodsPatients undergoing FMT in clinical practices across North America were eligible. Participating investigators enter de-identified data into an online platform, including FMT protocol, baseline patient characteristics, CDI cure and recurrence, and short and long-term safety outcomes.ResultsOf the first 259 participants enrolled at 20 sites, 222 had completed short-term follow-up at 1 month and 123 had follow-up to 6 months; 171 (66%) were female. All FMTs were done for CDI and 249 (96%) used an unknown donor (eg, stool bank). One-month cure occurred in 200 patients (90%); of these, 197 (98%) received only 1 FMT. Among 112 patients with initial cure who were followed to 6 months, 4 (4%) had CDI recurrence. Severe symptoms reported within 1-month of FMT included diarrhea (n = 5 [2%]) and abdominal pain (n = 4 [2%]); 3 patients (1%) had hospitalizations possibly related to FMT. At 6 months, new diagnoses of irritable bowel syndrome were made in 2 patients (1%) and inflammatory bowel disease in 2 patients (1%).ConclusionsThis prospective real-world study demonstrated high effectiveness of FMT for CDI with a good safety profile. Assessment of new conditions at long-term follow-up is planned as this registry grows and will be important for determining the full safety profile of FMT.

Published
2021

16. Surgery for Crohn’s Disease Is Associated with a Dysbiotic Microbiome and Metabolome: Results from Two Prospective Cohorts

Author

Lewis, James D., primary, Daniel, Scott G., additional, Li, Hongzhe, additional, Hao, Fuhua, additional, Patterson, Andrew D., additional, Hecht, Aaron, additional, Brensinger, Colleen M., additional, Wu, Gary D., additional, Bittinger, Kyle, additional, Wolf, Douglas C., additional, Hron, Bridget, additional, Hanson, John S., additional, Mohanty, Sanjib P., additional, Fogel, Ronald P., additional, Levy, L. Campbell, additional, Iskandar, Heba N., additional, Fischer, Monika, additional, Cohen, Benjamin, additional, Swaminath, Arun, additional, Kane, Sunanda, additional, McCabe, Robert P., additional, Yen, Eugene F., additional, Hanauer, Stephen B., additional, Hudesman, David P., additional, Afzali, Anita, additional, Kelly, Colleen, additional, Weber, John R., additional, Mahadevan, Uma, additional, Herfarth, Hans, additional, Katz, Jeffery, additional, Taleban, Sasha, additional, Rubin, David T., additional, Yachyshyn, Bruce, additional, Reynolds, Gorman J., additional, Gerich, Mark, additional, Dryden, Gerald W., additional, Quezada, Sandra, additional, Higgins, Peter D.R., additional, Shmidt, Eugenia, additional, Lewis, James D., additional, Schwartz, Marc B., additional, Flynn, Ann D., additional, Saha, Sumona, additional, Horst, Sara N., additional, Chiorean, Michael, additional, Green, Patrick D., additional, Scherl, Ellen J., additional, Sandler, Robert, additional, Brotherton, Carol, additional, Albenberg, Lindsey, additional, Valentine, John F., additional, Suskind, David, additional, Meyer, Andrea, additional, Compher, Charlene W., additional, Bewtra, Meenakshi, additional, Kaur, Manreet, additional, Dassopoulos, Themistocles, additional, Snapper, Scott B., additional, Korzenik, Joshua R., additional, Bohm, Matthew, additional, Raffals, Laura, additional, Beniwal-Patel, Poonam, additional, Hudesman, David, additional, Russ, Kirk, additional, Brook, Loren, additional, Pekow, Joel, additional, Cross, Raymond, additional, Wong, Uni, additional, Bishu, Shrinivas, additional, Duerr, Richard, additional, Caldera, Freddy, additional, Scoville, Elizabeth, additional, Deepak, Parakkal, additional, and Ciorba, Matthew, additional

Published
2024
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20. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

Author

Sazonovs, Aleksejs, Stevens, Christine R., Venkataraman, Guhan R., Yuan, Kai, Avila, Brandon, Abreu, Maria T., Ahmad, Tariq, Allez, Matthieu, Ananthakrishnan, Ashwin N., Atzmon, Gil, Baras, Aris, Barrett, Jeffrey C., Barzilai, Nir, Beaugerie, Laurent, Beecham, Ashley, Bernstein, Charles N., Bitton, Alain, Bokemeyer, Bernd, Chan, Andrew, Chung, Daniel, Cleynen, Isabelle, Cosnes, Jacques, Cutler, David J., Daly, Allan, Damas, Oriana M., Datta, Lisa W., Dawany, Noor, Devoto, Marcella, Dodge, Sheila, Ellinghaus, Eva, Fachal, Laura, Farkkila, Martti, Faubion, William, Ferreira, Manuel, Franchimont, Denis, Gabriel, Stacey B., Ge, Tian, Georges, Michel, Gettler, Kyle, Giri, Mamta, Glaser, Benjamin, Goerg, Siegfried, Goyette, Philippe, Graham, Daniel, Hämäläinen, Eija, Haritunians, Talin, Heap, Graham A., Hiltunen, Mikko, Hoeppner, Marc, Horowitz, Julie E., Irving, Peter, Iyer, Vivek, Jalas, Chaim, Kelsen, Judith, Khalili, Hamed, Kirschner, Barbara S., Kontula, Kimmo, Koskela, Jukka T., Kugathasan, Subra, Kupcinskas, Juozas, Lamb, Christopher A., Laudes, Matthias, Lévesque, Chloé, Levine, Adam P., Lewis, James D., Liefferinckx, Claire, Loescher, Britt-Sabina, Louis, Edouard, Mansfield, John, May, Sandra, McCauley, Jacob L., Mengesha, Emebet, Mni, Myriam, Moayyedi, Paul, Moran, Christopher J., Newberry, Rodney D., O’Charoen, Sirimon, Okou, David T., Oldenburg, Bas, Ostrer, Harry, Palotie, Aarno, Paquette, Jean, Pekow, Joel, Peter, Inga, Pierik, Marieke J., Ponsioen, Cyriel Y., Pontikos, Nikolas, Prescott, Natalie, Pulver, Ann E., Rahmouni, Souad, Rice, Daniel L., Saavalainen, Päivi, Sands, Bruce, Sartor, R. Balfour, Schiff, Elena R., Schreiber, Stefan, Schumm, L. Philip, Segal, Anthony W., Seksik, Philippe, Shawky, Rasha, Sheikh, Shehzad Z., Silverberg, Mark S., Simmons, Alison, Skeiceviciene, Jurgita, Sokol, Harry, Solomonson, Matthew, Somineni, Hari, Sun, Dylan, Targan, Stephan, Turner, Dan, Uhlig, Holm H., van der Meulen, Andrea E., Vermeire, Séverine, Verstockt, Sare, Voskuil, Michiel D., Winter, Harland S., Young, Justine, Duerr, Richard H., Franke, Andre, Brant, Steven R., Cho, Judy, Weersma, Rinse K., Parkes, Miles, Xavier, Ramnik J., Rivas, Manuel A., Rioux, John D., McGovern, Dermot P. B., Huang, Hailiang, Anderson, Carl A., and Daly, Mark J.

Published
2022
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27. Push-forwards of Chow groups of smooth ample divisors

Author

Banerjee, Kalyan, Iyer, Jaya NN, and Lewis, James D.

Subjects
Mathematics - Algebraic Geometry, 14C15, 14C20, 15C25, 14C35, 14F42
Abstract

We introduce a homological Lefschetz conjecture on (rational) Chow groups, which can be deduced from some well known conjectures, and illustrate it by a series of key examples. We then prove the injectivity of the push-forward morphism on Chow groups, induced by the closed embedding of the Theta divisor in it's Jacobian $J(C)$. Here $C$ is a smooth irreducible complex projective curve., Comment: Final version, to appear

Published
2018

29. IOIBD Recommendations for Clinical Trials in Ulcerative Proctitis: The PROCTRIAL Consensus

Author

Caron, Bénédicte, Abreu, Maria T., Siegel, Corey A., Panaccione, Remo, Sands, Bruce E., Dignass, Axel, Turner, Dan, Dotan, Iris, Hart, Ailsa L., Ahuja, Vineet, Allez, Matthieu, Ananthakrishnan, Ashwin N., Ghosh, Subrata, Griffiths, Anne M., Halfvarson, Jonas, Kaser, Arthur, Kotze, Paulo G., Koutroubakis, Ioannis E., Lakatos, Peter L., Levine, Arie, Lewis, James D., Magro, Fernando, Mantzaris, Gerassimos J., O’Morain, Colm, Ran, Zhihua, Reinisch, Walter, Rogler, Gerhard, Sachar, David B., Siegmund, Britta, Silverberg, Mark S., Sood, Ajit, Spinelli, Antonino, Steinwurz, Flavio, Tysk, Curt, Yamamoto-Furusho, Jesus K., Schreiber, Stefan, Rubin, David T., Sandborn, William J., Danese, Silvio, and Peyrin-Biroulet, Laurent

Published
2022
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30. Challenges in IBD Research: Environmental Triggers

Author

Ho, Shuk-Mei, Lewis, James D, Mayer, Emeran A, Bernstein, Charles N, Plevy, Scott E, Chuang, Emil, Rappaport, Stephen M, Croitoru, Kenneth, Korzenik, Joshua R, Krischer, Jeffrey, Hyams, Jeffrey S, Judson, Richard, Kellis, Manolis, Jerrett, Michael, Miller, Gary W, Grant, Melanie L, Shtraizent, Nataly, Honig, Gerard, Hurtado-Lorenzo, Andrés, and Wu, Gary D

Subjects
Crohn's Disease, Clinical Research, Digestive Diseases, Autoimmune Disease, Inflammatory Bowel Disease, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Diet, Environmental Exposure, Gastrointestinal Microbiome, Gene-Environment Interaction, Humans, Inflammatory Bowel Diseases, Life Style, Risk Factors, Crohn's disease, ulcerative colitis, environment, exposome, smoking, antibiotic, virus, pollutant, diet, epidemiology, in silico modeling, Crohn’s disease, Clinical Sciences, Gastroenterology & Hepatology
Abstract

Environmental triggers is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, novel technologies, precision medicine and pragmatic clinical research. The Challenges in IBD research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the environmental triggers section is focused on the main research gaps in elucidating causality of environmental factors in IBD. Research gaps were identified in: 1) epidemiology of exposures; 2) identification of signatures of biological response to exposures; and 3) mechanisms of how environmental exposures drive IBD. To address these gaps, the implementation of longitudinal prospective studies to determine disease evolution and identify sub-clinical changes in response to exposures is proposed. This can help define critical windows of vulnerability and risk prediction. In addition, systems biology analysis and in silico modeling were proposed as approaches to integrate the IBD exposome for the identification of biological signatures of response to exposures, and to develop prediction models of the effects of environmental factors in driving disease activity and response to therapy. This research could lead to identification of biomarkers of exposures and new modalities for therapeutic intervention. Finally, hypothesis-driven mechanistic studies to understand gene-environment interactions and to validate causality of priority factors should be performed to determine how environment influences clinical outcomes.

Published
2019

31. Ustekinumab versus adalimumab for induction and maintenance therapy in biologic-naive patients with moderately to severely active Crohn's disease: a multicentre, randomised, double-blind, parallel-group, phase 3b trial

Author

Afzali, Anita, Aitova, Lilia, Aldeguer i Mante, Xavier, Allez, Matthieu, Altorjay, István, Argüelles Arias, Federico, Armuzzi, Alessandro, Augustyn, Monika, Bafutto, Mauro, Barrio, Jesus, Begun, Jakob, Behrend, Clint, Bezemer, Geert, Bonnaud, Guillaume, Brankovic, Marija, Byung, Ik Jang, Calvet Calvo, Xavier, Chachu, Karen, Chebli, Julio Maria Fonseca, Cheon, Jae Hee, Cichoz-Lach, Halina, Clark, Larry, Cummings, Fraser, Dalal, Kunal, Danese, Silvio, De Boer, Nanne, De Lourdes Ferrari, Maria, Désilets, Etienne, Dugalic, Predrag, Duvall, George, Fedorishina, Olga, Filip, Rafal, Flores, Cristina, Fogel, Ronald, Fon, James, Frankel, Michael, Friedenberg, Keith, Fries, Walter, Galina, Vassileva, Gietka, Piotr, Goel, Rishi, Hasselblatt, Peter, Herfarth, Hans, Herszényi, László, Hindryckx, Pieter, Hoentjen, Frank, Horjus Talabur Horje, Carmen, Iduru, Satish, Irving, Peter, Isfort, Robert, Jairath, Vipul, Jones, Michael, Kalimullina, Dilara, Katz, Jeffry, Kaur, Manreet, Khurana, Sunil K, Kim, Joo Sung, Kim, Youngho, Kleczkowski, Dariusz, Knezevic, Slavko, Knoll, Aaron, Korman, Louis Y, Kotzev, Iskren, Kulyapin, Andrey, Lee, Kang Moon, Leemreis, Desiree, Leszczyszyn, Jaroslaw, Limdi, Jimmy, Lissauer, Jack, Loftus, Edward, Malecka-Panas, Ewa, Marshall, John, Mihály, Emese, Milan, Lukas, Monteleone, Giovanni, Nagorni, Aleksandar, Owczarek, Danuta, Palekar, Nichole, Panaccione, Remo, Park, Young Soo, Park, Sang Hyoung, Parra, Rogério, Patai, Árpád, Patel, Kamal, Patel, Bhaktasharan, Pershko, Anatoly, Petrova, Elina, Pineton de Chambrun, Guillaume, Randall, Charles, Riestra Menendez, Sabino, Ritter, Timothy, Rivero, Montserrat, Roblin, Xavier, Rocca, Rodolfo, Romatowski, Jacek, Rydzewska, Grazyna, Saibeni, Simone, Salzberg, Bruce, Sarles, Harry, Saunders, John, Savarino, Edoardo Vincenzo, Serclova, Zuzana, Shchukina, Oksana, Siegel, Jonathan, Soofi, Najm, Sparrow, Miles, Stokesberry, David, Suiter, Daniel, Svorcan, Petar, Tkachev, Alexander, Tsonev, Nikolay, Tünde, Kristóf, Ulbrych, Jan, Vanasek, Tomas, Varga, Márta, Vermeire, Severine, Vicente Lidon, Raquel, Weiss, Michael L, Wesley, Emma, Winstead, Nathaniel, Wojcik, Katarzyna, Wypych, Joanna, Zaltman, Cyrla, Zdena, Zadorova, Sands, Bruce E, Irving, Peter M, Hoops, Timothy, Izanec, James L, Gao, Long-Long, Gasink, Christopher, Greenspan, Andrew, Hanauer, Stephen B, Kuehbacher, Tanja, Lewis, James D, Loftus, Edward V, Jr, Mihaly, Emese, Scherl, Ellen, Shchukina, Oksana B, and Sandborn, William J

Published
2022
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37. Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome

Author

Chassaing, Benoit, Compher, Charlene, Bonhomme, Brittaney, Liu, Qing, Tian, Yuan, Walters, William, Nessel, Lisa, Delaroque, Clara, Hao, Fuhua, Gershuni, Victoria, Chau, Lillian, Ni, Josephine, Bewtra, Meenakshi, Albenberg, Lindsey, Bretin, Alexis, McKeever, Liam, Ley, Ruth E., Patterson, Andrew D., Wu, Gary D., Gewirtz, Andrew T., and Lewis, James D.

Published
2022
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38. Rationally Equivalent Points On Hypersurfaces In ${\mathbb P}^n$

Author

Chen, Xi, Lewis, James D., and Sheng, Mao

Subjects
Mathematics - Algebraic Geometry, 14C15, 14C25
Abstract

We prove a conjecture of Voisin that no two distinct points on a very general hypersurface of degree $2n$ in ${\mathbb P}^n$ are rationally equivalent., Comment: 57 pages

Published
2017

39. Specialization of cycles and the K-theory elevator

Author

del Angel, Pedro Luis, Doran, Charles, Iyer, Jaya, Kerr, Matt, Lewis, James D., Müller-Stach, Stefan, and Patel, Deepam

Subjects
Mathematics - Algebraic Geometry, 14C25, 19E15, 14C30
Abstract

A general specialization map is constructed for higher Chow groups and used to prove a "going-up" theorem for algebraic cycles and their regulators. The results are applied to study the degeneration of the modified diagonal cycle of Gross and Schoen, and of the coordinate symbol on a genus-2 curve., Comment: 45 pages, 1 figure; minor revision

Published
2017

41. American Gut: an Open Platform for Citizen Science Microbiome Research

Author

McDonald, Daniel, Hyde, Embriette, Debelius, Justine W, Morton, James T, Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A, Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, Goldasich, Lindsay DeRight, Dorrestein, Pieter C, Dunn, Robert R, Fahimipour, Ashkaan K, Gaffney, James, Gilbert, Jack A, Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A, Janssen, Stefan, Jeste, Dilip V, Jiang, Lingjing, Kelley, Scott T, Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V, Metcalf, Jessica L, Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T, Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S, Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Jin, Spector, Timothy, Swafford, Austin D, Thackray, Varykina G, Thompson, Luke R, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, Mann, Allison E, Amir, Amnon, Frazier, Angel, Martino, Cameron, Lebrilla, Carlito, Lozupone, Catherine, Lewis, Cecil M, Raison, Charles, Zhang, Chi, Lauber, Christian L, Warinner, Christina, Lowry, Christopher A, Callewaert, Chris, Bloss, Cinnamon, Willner, Dana, Galzerani, Daniela Domingos, Gonzalez, David J, Mills, David A, Chopra, Deepak, Gevers, Dirk, Berg-Lyons, Donna, Sears, Dorothy D, Wendel, Doug, Lovelace, Elijah, Pierce, Emily, TerAvest, Emily, Bolyen, Evan, Bushman, Frederic D, Wu, Gary D, Church, George M, Saxe, Gordon, Holscher, Hanna D, Ugrina, Ivo, German, J Bruce, Caporaso, J Gregory, Wozniak, Jacob M, Kerr, Jacqueline, Ravel, Jacques, Lewis, James D, Suchodolski, Jan S, Jansson, Janet K, Hampton-Marcell, Jarrad T, and Bobe, Jason

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Medical Biochemistry and Metabolomics, Human Genome, Microbiome, Genetics, Clinical Research, 4.1 Discovery and preclinical testing of markers and technologies, citizen science, microbiome, American Gut Consortium
Abstract

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

Published
2018

42. Enterotypes in the landscape of gut microbial community composition.

Author

Costea, Paul I, Hildebrand, Falk, Arumugam, Manimozhiyan, Bäckhed, Fredrik, Blaser, Martin J, Bushman, Frederic D, de Vos, Willem M, Ehrlich, S Dusko, Fraser, Claire M, Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B, Knights, Dan, Lewis, James D, Ley, Ruth E, Ochman, Howard, O'Toole, Paul W, Quince, Christopher, Relman, David A, Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M, Wu, Gary D, Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, and Bork, Peer

Subjects
Gastrointestinal Tract, Animals, Humans, Bacteria, RNA, Ribosomal, 16S, Bacterial Typing Techniques, Biodiversity, Metagenome, Metagenomics, Gastrointestinal Microbiome, Human Genome, Genetics, Clinical Research, Microbiology, Medical Microbiology
Abstract

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.

Published
2018

49. Risk of Acute Liver Injury With Antiretroviral Therapy by Viral Hepatitis Status

Author

Gowda, Charitha, Newcomb, Craig W, Liu, Qing, Carbonari, Dena M, Lewis, James D, Forde, Kimberly A, Goldberg, David S, Reddy, K Rajender, Roy, Jason A, Marks, Amy R, Schneider, Jennifer L, Kostman, Jay R, Tate, Janet P, Lim, Joseph K, Justice, Amy C, Goetz, Matthew Bidwell, Corley, Douglas A, and Re, Vincent Lo

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Liver Disease, HIV/AIDS, Rare Diseases, Prevention, Digestive Diseases, Chronic Liver Disease and Cirrhosis, Emerging Infectious Diseases, Clinical Research, Hepatitis, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, antiretroviral, drug-induced liver injury, hepatotoxicity, HIV, HIV., Clinical sciences, Medical microbiology
Abstract

BackgroundThe risk of hepatotoxicity with antiretroviral therapy (ART) remains unknown. We determined the comparative risk of acute liver injury (ALI) for antiretroviral drugs, classes, and regimens, by viral hepatitis status.MethodsWe followed a cohort of 10 083 human immunodeficiency virus (HIV)-infected persons in Kaiser Permanente Northern California (n = 2099) from 2004 to 2010 and the Veterans Aging Cohort Study (n = 7984) from 2004 to 2012. Within the first year of ART, we determined occurrence of (1) liver aminotransferases >200 U/L and (2) severe ALI (coagulopathy with hyperbilirubinemia). We used Cox regression to determine hazard ratios (HRs) with 95% confidence intervals (CIs) of endpoints among initiators of nucleos(t)ide analogue combinations, antiretroviral classes, and ART regimens, all stratified by viral hepatitis status.ResultsLiver aminotransferases >200 U/L developed in 206 (2%) persons and occurred more frequently among HIV/viral hepatitis-coinfected than HIV-monoinfected persons (116.1 vs 20.7 events/1000 person-years; P < .001). No evidence of differential risk was found between initiators of abacavir/lamivudine versus tenofovir/emtricitabine among coinfected (HR, 0.68; 95% CI, .29-1.57) or HIV-monoinfected (HR, 1.19; 95% CI, .47-2.97) groups. Coinfected patients had a higher risk of aminotransferases >200 U/L after initiation with a protease inhibitor than nonnucleoside reverse-transcriptase inhibitor (HR, 2.01; 95% CI, 1.36-2.96). Severe ALI (30 events; 0.3%) occurred more frequently in coinfected persons (15.9 vs 3.1 events/1000 person-years; P < .001) but was too uncommon to evaluate in adjusted analyses.ConclusionsWithin the year after ART initiation, aminotransferase elevations were infrequently observed and rarely led to severe ALI. Protease inhibitor use was associated with a higher risk of aminotransferase elevations among viral hepatitis-coinfected patients.

Published
2017

50. Simplicial Abel-Jacobi maps and reciprocity laws

Author

Gil, Jose Ignacio Burgos, Kerr, Matt, Lewis, James D., and Lopatto, Patrick

Subjects
Mathematics - Algebraic Geometry, 14C25, 14C30, 14C35
Abstract

We describe an explicit morphism of complexes that induces the cycle-class maps from (simplicially described) higher Chow groups to rational Deligne cohomology. The reciprocity laws satisfied by the currents we introduce for this purpose are shown to provide a clarifying perspective on functional equations satisfied by complex-valued di- and trilogarithms., Comment: 51 pages, 1 figure; appendix by Burgos Gil added

Published
2015

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