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3. Density Deconvolution with Normalizing Flows

Author

Dockhorn, Tim, Ritchie, James A., Yu, Yaoliang, and Murray, Iain

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

Density deconvolution is the task of estimating a probability density function given only noise-corrupted samples. We can fit a Gaussian mixture model to the underlying density by maximum likelihood if the noise is normally distributed, but would like to exploit the superior density estimation performance of normalizing flows and allow for arbitrary noise distributions. Since both adjustments lead to an intractable likelihood, we resort to amortized variational inference. We demonstrate some problems involved in this approach, however, experiments on real data demonstrate that flows can already out-perform Gaussian mixtures for density deconvolution., Comment: Appearing at the second workshop on Invertible Neural Networks, Normalizing Flows, and Explicit Likelihood Models (ICML 2020), Virtual Conference. 8 pages, 6 figures, 5 tables

Published
2020

5. Scalable Extreme Deconvolution

Author

Ritchie, James A. and Murray, Iain

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

The Extreme Deconvolution method fits a probability density to a dataset where each observation has Gaussian noise added with a known sample-specific covariance, originally intended for use with astronomical datasets. The existing fitting method is batch EM, which would not normally be applied to large datasets such as the Gaia catalog containing noisy observations of a billion stars. We propose two minibatch variants of extreme deconvolution, based on an online variation of the EM algorithm, and direct gradient-based optimisation of the log-likelihood, both of which can run on GPUs. We demonstrate that these methods provide faster fitting, whilst being able to scale to much larger models for use with larger datasets., Comment: Appearing at the Second Workshop on Machine Learning and the Physical Sciences (NeurIPS 2019), Vancouver, Canada

Published
2019

7. Grams ME, Sang Y, Ballew SH, et al, for the Chronic Kidney Disease Prognosis Consortium. Predicting timing of clinical outcomes in patients with chronic kidney disease and severely decreased glomerular filtration rate. Kidney Int. 2018;93:1442–1451

Author

Astor, Brad, Appel, Lawrence J, Levin, Adeera, Tang, Mila, Djurdjev, Ognjenka, Navaneethan, Sankar D, Jolly, Stacey E, Schold, Jesse D, Nally, Joseph V, Wheeler, David C, Emberson, Jonathan, Townend, John, Landray, Martin, Feldman, Harold I, Hsu, Chi-yuan, Lash, James P, Kalra, Philip A, Ritchie, James P, Maharajan, Raman, Middleton, Rachel J, O’Donoghue, Donal J, Eckardt, Kai-Uwe, Schneider, Markus P, Köttgen, Anna, Kronenberg, Florian, Bärthlein, Barbara, Chang, Alex R, Green, Jamie A, Kirchner, H Lester, Ho, Kevin, Marks, Angharad, Black, Corri, Prescott, Gordon J, Fluck, Nick, Nakayama, Masaaki, Miyazaki, Mariko, Yamamoto, Tae, Yamada, Wang, Angela Yee-Moon, Cheung, Sharon, Wong, Sharon, Chu, Jessie, Wu, Henry, Garg, Amit X, McArthur, Eric, Nash, Danielle M, Shalev, Varda, Chodick, Gabriel, Blankestijn, Peter J, Wetzels, Jack FM, van Zuilen, Arjan D, van den Brand, Jan A, Levey, Andrew S, Inker, Lesley A, Sarnak, Mark J, Tighiouart, Hocine, Zhang, Haitao, Stengel, Benedicte, Metzger, Marie, Flamant, Martin, Houillier, Pascal, Haymann, Jean-Philippe, Rios, Pablo G, Mazzuchi, Nelson, Gadola, Liliana, Lamadrid, Verónica, Sola, Laura, Collins, John F, Elley, C Raina, Kenealy, Timothy, Moranne, Olivier, Couchoud, Cecile, Vigneau, Cecile, Brunskill, Nigel J, Major, Rupert W, Shepherd, David, Medcalf, James F, Kovesdy, Csaba P, Kalantar-Zadeh, Kamyar, Molnar, Miklos Z, Sumida, Keiichi, Potukuchi, Praveen K, Heerspink, Hiddo JL, de Zeeuw, Dick, Brenner, Barry, Carrero, Juan Jesus, Gasparini, Alessandro, Qureshi, Abdul Rashid, Elinder, Carl-Gustaf, Visseren, Frank LJ, van der Graaf, Yolanda, Evans, Marie, Stendahl, Maria, Schön, Staffan, Segelmark, Mårten, Prütz, Karl-Göran, Naimark, David M, Tangri, Navdeep, and Mark, Patrick B

Subjects
Renal and urogenital, Chronic Kidney Disease Prognosis Consortium, Clinical Sciences, Urology & Nephrology
Abstract

The Chronic Kidney Disease (CKD) Prognosis Consortium is a collaborative author of the above-mentioned article. The CKD Prognosis Consortium investigators/collaborators are as follows: • African American Study of Kidney Disease and Hypertension (AASK): Brad Astor, Lawrence J. Appel; Canadian Study of Prediction of Death, Dialysis and Interim Cardiovascular Events (CanPREDDICT): Adeera Levin, Mila Tang, Ognjenka Djurdjev; Cleveland Clinic CKD Registry Study (CCF): Sankar D. Navaneethan, Stacey E. Jolly, Jesse D. Schold, Joseph V. Nally Jr.; Chronic Renal Impairment in Birmingham (CRIB): David C. Wheeler, Jonathan Emberson, John Townend, Martin Landray; Chronic Renal Insufficiency Cohort Study (CRIC): Harold I. Feldman, Chi-yuan Hsu, James P. Lash, Lawrence J. Appel; Chronic Renal Insufficiency Standards Implementation Study (CRISIS): Philip A. Kalra, James P. Ritchie, Raman Maharajan, Rachel J. Middleton, Donal J. O'Donoghue; German Chronic Kidney Disease Study (GCKD): Kai-Uwe Eckardt, Markus P. Schneider, Anna Köttgen, Florian Kronenberg, Barbara Bärthlein; Geisinger Health System: Alex R. Chang, Jamie A. Green, H. Lester Kirchner, Kevin Ho; Grampian Laboratory Outcomes, Morbidity and Mortality Studies – 2 (GLOMMS2): Angharad Marks, Corri Black, Gordon J. Prescott, Nick Fluck; Gonryo Study: Masaaki Nakayama, Mariko Miyazaki, Tae Yamamoto, Gen Yamada; Hong Kong CKD Studies: Angela Yee-Moon Wang, Sharon Cheung, Sharon Wong, Jessie Chu, Henry Wu; Ontario Institute for Clinical Evaluative Sciences, Provincial Kidney, Dialysis and Transplantation program (ICES KDT): Amit X. Garg, Eric McArthur, Danielle M. Nash; Maccabi Health System: Varda Shalev, Gabriel Chodick; Multifactorial Approach and Superior Treatment Efficacy in Renal Patients with the Aid of a Nurse Practitioner (MASTERPLAN): Peter J. Blankestijn, Jack F.M. Wetzels, Arjan D. van Zuilen, Jan A. van den Brand; Modification of Diet in Renal Disease Study (MDRD): Andrew S. Levey, Lesley A. Inker, Mark J. Sarnak, Hocine Tighiouart; Nanjing CKD Network Cohort Study (Nanjing CKD): Haitao Zhang; NephroTest Study (NephroTest): Benedicte Stengel, Marie Metzger, Martin Flamant, Pascal Houillier, Jean-Philippe Haymann; National Renal Healthcare Program – Uruguay (NRHP-URU): Pablo G. Rios, Nelson Mazzuchi, Liliana Gadola, Verónica Lamadrid, Laura Sola; New Zealand Diabetes Cohort Study (NZDCS): John F. Collins, C. Raina Elley, Timothy Kenealy; Parcours de Soins des Personnes Agées (PSPA): Olivier Moranne, Cecile Couchoud, Cecile Vigneau; Primary-Secondary Care Partnership to Prevent Adverse Outcomes in Chronic Kidney Disease (PSP CKD): Nigel J. Brunskill, Rupert W. Major, David Shepherd, James F. Medcalf; Racial and Cardiovascular Risk Anomalies in CKD Cohort (RCAV): Csaba P. Kovesdy, Kamyar Kalantar-Zadeh, Miklos Z. Molnar, Keiichi Sumida, Praveen K. Potukuchi; Reduction of Endpoints in Non-insulin Dependent Diabetes Mellitus with the Angiotensin II Antagonist Losartan (RENAAL): Hiddo J.L. Heerspink, Dick de Zeeuw, Barry Brenner; Stockholm CREAtinine Measurements Cohort (SCREAM): Juan Jesus Carrero, Alessandro Gasparini, Abdul Rashid Qureshi, Carl-Gustaf Elinder; Second Manifestations of ARTerial Disease Study (SMART): Frank L.J. Visseren, Yolanda van der Graaf; Swedish Renal Registry CKD Cohort (SRR CKD): Marie Evans, Maria Stendahl, Staffan Schön, Mårten Segelmark, Karl-Göran Prütz; Sunnybrook Cohort: David M. Naimark, Navdeep Tangri; West of Scotland CKD Study: Patrick B. Mark, Jamie P. Traynor, Colin C. Geddes, Peter C. Thomson.• CKD Prognosis Consortium Steering Committee: Alex R. Chang, Josef Coresh (Chair), Ron T. Gansevoort, Morgan E. Grams, Anna Köttgen, Andrew S. Levey, Kunihiro Matsushita, Mark Woodward, Luxia Zhang.• CKD Prognosis Consortium Data Coordinating Center: Shoshana H. Ballew (Assistant Project Director), Jingsha Chen (Programmer), Josef Coresh (Principal Investigator), Morgan E. Grams (Director of Nephrology Initiatives), Lucia Kwak (Programmer), Kunihiro Matsushita (Director), Yingying Sang (Lead Programmer), Aditya Surapaneni (Programmer), Mark Woodward (Senior Statistician).• Kidney Disease Improving Global Outcomes (KDIGO) Controversies Conference on Prognosis and Optimal Management of Patients with Advanced CKD: Kai-Uwe Eckardt (Conference Co-Chair), Brenda R. Hemmelgarn (Conference Co-Chair), David C. Wheeler (KDIGO Co-Chair), Wolfgang C. Winkelmayer (KDIGO Co-Chair), John Davis (CEO), Danielle Green (Managing Director), Michael Cheung (Chief Scientific Officer), Tanya Green (Communications Director), Melissa McMahan (Programs Director).

Published
2018

8. Evans M, Grams ME, Sang Y, et al., for the Chronic Kidney Disease Prognosis Consortium. Risk factors for prognosis in patients with severely decreased GFR. Kidney Int Rep. 2018;3:625–637

Author

Astor, Brad, Appel, Lawrence J, Levin, Adeera, Djurdjev, Ognjenka, Tang, Mila, Navaneethan, Sankar D, Jolly, Stacey E, Schold, Jesse D, Nally, Joseph V, Wheeler, David C, Emberson, Jonathan, Townend, John, Landray, Martin, Feldman, Harold I, Hsu, Chi-yuan, Lash, James P, Kalra, Philip A, Ritchie, James P, Maharajan, Raman, Alderson, Helen, Lane, Beverly, Eckardt, Kai-Uwe, Schneider, Markus P, Köttgen, Anna, Kronenberg, Florian, Bärthlein, Barbara, Chang, Alex R, Green, Jamie A, Kirchner, H Lester, Ho, Kevin, Marks, Angharad, Black, Corri, Prescott, Gordon J, Fluck, Nick, Nakayama, Masaaki, Miyazaki, Mariko, Yamamoto, Tae, Yamada, Wang, Angela Yee-Moon, Cheung, Sharon, Wong, Sharon, Chu, Jessie, Wu, Henry, Shalev, Varda, Chodick, Gabriel, Blankestijn, Peter J, Wetzels, Jack FM, van Zuilen, Arjan D, van den Brand, Jan A, Levey, Andrew S, Inker, Lesley A, Sarnak, Mark J, Tighiouart, Hocine, Zhang, Haitao, Stengel, Benedicte, Rios, Pablo G, Mazzuchi, Nelson, Gadola, Liliana, Lamadrid, Verónica, Sola, Laura, Collins, John F, Elley, C Raina, Kenealy, Timothy, Moranne, Olivier, Couchoud, Cecile, Vigneau, Cecile, Brunskill, Nigel J, Major, Rupert W, Shepherd, David, Medcalf, James F, Kovesdy, Csaba P, Kalantar-Zadeh, Kamyar, Molnar, Miklos Z, Sumida, Keiichi, Potukuchi, Praveen K, Heerspink, Hiddo JL, de Zeeuw, Dick, Brenner, Barry, Carrero, Juan Jesus, Barany, Peter, Qureshi, Abdul Rashid, Elinder, Carl-Gustaf, Visseren, Frank LJ, van der Graaf, Yolanda, Evans, Marie, Stendahl, Maria, Schön, Staffan, Segelmark, Mårten, Prütz, Karl-Göran, Naimark, David M, Tangri, Navdeep, Mark, Patrick B, Traynor, Jamie P, Geddes, Colin C, Thomson, Peter C, and Coresh, Josef

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Renal and urogenital, Good Health and Well Being, Chronic Kidney Disease Prognosis Consortium, Biomedical and clinical sciences, Health sciences
Abstract

[This corrects the article DOI: 10.1016/j.ekir.2018.01.002.].

Published
2018

15. Harmonization of Busulfan Plasma Exposure Unit (BPEU): A Community-Initiated Consensus Statement

Author

McCune, Jeannine S., Quinones, Christine M., Ritchie, James, Carpenter, Paul A., van Maarseveen, Erik, Yeh, Rosa F., Anasetti, Claudio, Boelens, Jaap J., Hamerschlak, Nelson, Hassan, Moustapha, Kang, Hyoung Jin, Kanda, Yoshinobu, Paci, Angelo, Perales, Miguel-Angel, Shaw, Peter J., Seewaldt, Victoria L., Savani, Bipin N., Hsieh, Angela, Poon, Betsy, Mohty, Mohamad, Pulsipher, Michael A., Pasquini, Marcelo, and Dupuis, L. Lee

Published
2019
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17. Phase 1 Open-Label Dose Escalation Trial for the Development of a Human Bacillus Calmette-Guérin Challenge Model for Assessment of Tuberculosis Immunity In Vivo.

Author

Blazevic, Azra, Edwards, Rachel L, Xia, Mei, Eickhoff, Christopher S, Hamzabegovic, Fahreta, Meza, Krystal A, Ning, Huan, Tennant, Janice, Mosby, Karla J, Ritchie, James C, Girmay, Tigisty, Lai, Lilin, McCullough, Michele, Beck, Allison, Kelley, Colleen, Edupuganti, Srilatha, Kabbani, Sarah, Buchanan, Wendy, Makhene, Mamodikoe K, and Voronca, Delia

Subjects
CLINICAL trial registries, TUBERCULOSIS, IMMUNITY, INTRADERMAL injections, IMMUNE response
Abstract

Background A controlled human infection model for assessing tuberculosis (TB) immunity can accelerate new vaccine development. Methods In this phase 1 dose escalation trial, 92 healthy adults received a single intradermal injection of 2 × 106 to 16 × 106 colony-forming units of Bacillus Calmette-Guérin (BCG). The primary endpoints were safety and BCG shedding as measured by quantitative polymerase chain reaction, colony-forming unit plating, and MGIT BACTEC culture. Results Doses up to 8 × 106 were safe, and there was evidence for increased BCG shedding with dose escalation. The MGIT time-to-positivity assay was the most consistent and precise measure of shedding. Power analyses indicated that 10% differences in MGIT time to positivity (area under the curve) could be detected in small cohorts (n = 30). Potential biomarkers of mycobacterial immunity were identified that correlated with shedding. Transcriptomic analysis uncovered dose- and time-dependent effects of BCG challenge and identified a putative transcriptional TB protective signature. Furthermore, we identified immunologic and transcriptomal differences that could represent an immune component underlying the observed higher rate of TB disease incidence in males. Conclusions The safety, reactogenicity, and immunogenicity profiles indicate that this BCG human challenge model is feasible for assessing in vivo TB immunity and could facilitate the vaccine development process. Clinical Trials Registration NCT01868464 (ClinicalTrials.gov). [ABSTRACT FROM AUTHOR]

Published
2024
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18. Introduction

Author

Bordegoni, Monica, primary, Gupta, Satyandra K, additional, and Ritchie, James M., additional

Published
2021
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21. Phase 1 Open-Label Dose Escalation Trial for the Development of a Human Bacillus Calmette-Guérin Challenge Model for Assessment of Tuberculosis Immunity In Vivo

Author

Blazevic, Azra, primary, Edwards, Rachel L, additional, Xia, Mei, additional, Eickhoff, Christopher S, additional, Hamzabegovic, Fahreta, additional, Meza, Krystal A, additional, Ning, Huan, additional, Tennant, Janice, additional, Mosby, Karla J, additional, Ritchie, James C, additional, Girmay, Tigisty, additional, Lai, Lilin, additional, McCullough, Michele, additional, Beck, Allison, additional, Kelley, Colleen, additional, Edupuganti, Srilatha, additional, Kabbani, Sarah, additional, Buchanan, Wendy, additional, Makhene, Mamodikoe K, additional, Voronca, Delia, additional, Cherikh, Sami, additional, Goll, Johannes B, additional, Rouphael, Nadine G, additional, Mulligan, Mark J, additional, and Hoft, Daniel F, additional

Published
2023
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23. A framework for the development of effective anti-metastatic agents

Author

Anderson, Robin L., Balasas, Theo, Callaghan, Juliana, Coombes, R. Charles, Evans, Jeff, Hall, Jacqueline A., Kinrade, Sally, Jones, David, Jones, Paul S., Jones, Rob, Marshall, John F., Panico, Maria Beatrice, Shaw, Jacqui A., Steeg, Patricia S., Sullivan, Mark, Tong, Warwick, Westwell, Andrew D., and Ritchie, James W. A.

Published
2019
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24. Haptic Virtual Reality DFMA - A Case Study

Author

Read, Avery, Ritchie, James, Lim, Theodore, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Barbic, Jernej, editor, D'Cruz, Mirabelle, editor, Latoschik, Marc Erich, editor, Slater, Mel, editor, and Bourdot, Patrick, editor

Published
2017
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29. Safely reducing haemodialysis frequency during the COVID-19 pandemic

Author

Lodge, Michelle Da Silva, Abeygunaratne, Thilini, Alderson, Helen, Ali, Ibrahim, Brown, Nina, Chrysochou, Constantina, Donne, Rosie, Erekosima, Ibi, Evans, Philip, Flanagan, Emma, Gray, Simon, Green, Darren, Hegarty, Janet, Hyde, Audrey, Kalra, Philip A., Lamerton, Elizabeth, Lewis, David, Middleton, Rachel, New, David, Nipah, Robert, O’Donoghue, Donal, O’Riordan, Edmond, Poulikakos, Dimitrios, Rainone, Francesco, Raman, Maharajan, Ritchie, James, Sinha, Smeeta, Wood, Grahame, and Tollitt, J.

Published
2020
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37. To Facilitate or Not? Understanding the Role of the Teacher in Using a Serious Game

Author

Baalsrud Hauge, Jannicke, Lim, Theodore, Ritchie, James, Kalverkamp, Matthias, Bellotti, Francesco, Ribeiro, Claudia, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, and De Gloria, Alessandro, editor

Published
2015
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39. Additional Tables and Figures from A Cancer Research UK First Time in Human Phase I Trial of IMA950 (Novel Multipeptide Therapeutic Vaccine) in Patients with Newly Diagnosed Glioblastoma

Author

Rampling, Roy, primary, Peoples, Sharon, primary, Mulholland, Paul J., primary, James, Allan, primary, Al-Salihi, Omar, primary, Twelves, Christopher J., primary, McBain, Catherine, primary, Jefferies, Sarah, primary, Jackson, Alan, primary, Stewart, Willie, primary, Lindner, Juha, primary, Kutscher, Sarah, primary, Hilf, Norbert, primary, McGuigan, Lesley, primary, Peters, Jane, primary, Hill, Karen, primary, Schoor, Oliver, primary, Singh-Jasuja, Harpreet, primary, Halford, Sarah E., primary, and Ritchie, James W.A., primary

Published
2023
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41. Diagnostic performance of cardiac Troponin I for early rule-in and rule-out of acute myocardial infarction: Results of a prospective multicenter trial

Author

Storrow, Alan B., Christenson, Robert H., Nowak, Richard M., Diercks, Deborah B., Singer, Adam J., Wu, Alan H.B., Kulstad, Erik, LoVecchio, Frank, Fromm, Christian, Headden, Gary, Potis, Tracie, Hogan, Christopher J., Schrock, Jon W., Zelinski, Daniel P., Greenberg, Marna R., Ritchie, James C., Chamberlin, Janna S., Bray, Kurtis R., Rhodes, Daniel W., Trainor, Deirdre, Holmes, Dawn, and Southwick, Paula C.

Published
2015
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42. Absolute and relative changes (delta) in troponin I for early diagnosis of myocardial infarction: Results of a prospective multicenter trial

Author

Storrow, Alan B., Nowak, Richard M., Diercks, Deborah B., Singer, Adam J., Wu, Alan H.B., Kulstad, Erik, LoVecchio, Frank, Fromm, Christian, Headden, Gary, Potis, Tracie, Hogan, Christopher J., Schrock, Jon W., Zelinski, Daniel P., Greenberg, Marna R., Christenson, Robert H., Ritchie, James C., Chamberlin, Janna S., Bray, Kurtis R., Rhodes, Daniel W., Trainor, Deirdre, and Southwick, Paula C.

Published
2015
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