Article
Multidisciplinary Sciences
Simon Johannes Gairing, Peter Robert Galle, Joern Markus Schattenberg, Karel Kostev, Christian Labenz
Summary: Portal vein thrombosis (PVT) is associated with a higher incidence of bone fractures, particularly in women and patients aged 51-60. The association between PVT and bone fractures is maintained regardless of whether the patients have liver cirrhosis or not.
Article
Gastroenterology & Hepatology
Marjolaine Ngollo, Kevin Perez, Nassim Hammoudi, Yuri Gorelik, Marc Delord, Claire Auzolle, Hugo Bottois, Dominique Cazals-Hatem, Madeleine Bezault, Stephane Nancey, Benjamin Pariente, Xavier Treton, Mathurin Fumery, Anthony Buisson, Nicolas Barnich, Philippe Seksik, Shai S. Shen-Orr, Lionel Le Bourhis, Matthieu Allez
Summary: The study identified several biological pathways in surgical ileal mucosa specimens associated with an increased risk of disease recurrence. Integration of the JAK/STAT and mitochondrial dysfunction pathways in the clinical model improved the prediction of post-operative recurrence.
JOURNAL OF CROHNS & COLITIS
(2022)
Article
Gastroenterology & Hepatology
Songsoo Yang, Christopher Prien, Xue Jia, Tracy Hull, David Liska, Scott R. Steele, Amy L. Lightner, Michael Valente, Stefan D. Holubar
Summary: Redo ileocolic resection for recurrent Crohn's disease is associated with increased overall morbidity but not anastomotic leak.
DISEASES OF THE COLON & RECTUM
(2023)
Article
Gastroenterology & Hepatology
Songsoo Yang, Christopher Prien, Xue Jia, Tracy Hull, David Liska, Scott R. Steele, Amy L. Lightner, Michael Valente, Stefan D. Holubar
Summary: Redo ileocolic resection for recurrent Crohn's disease is associated with increased overall morbidity but not anastomotic leak. Factors such as age, comorbidities, medications, and fistulizing disease may affect the surgical outcomes.
DISEASES OF THE COLON & RECTUM
(2023)
Article
Cell Biology
Jiho Sohn, Lu Li, Lixia Zhang, Robert J. Genco, Karen L. Falkner, Herve Tettelin, Aryn M. Rowsam, Dominic J. Smiraglia, Jan M. Novak, Patricia I. Diaz, Yijun Sun, Keith L. Kirkwood
Summary: This study found that periodontal disease (PD) is associated with the severity and progression of Crohn's disease (CD). PD is associated with increased levels of Haemophilus parainfluenzae strains in patients with CD. Oral inoculation of Haemophilus parainfluenzae induces strain-dependent intestinal inflammation in murine models of inflammatory bowel disease, which is associated with increased intestinal interferon-g (IFN-g)+ CD4+ T cells and disruption of the host hypusination pathway. Overall, this study establishes the strain-specific pathogenic role of Haemophilus parainfluenzae in intestinal inflammation and highlights the potential effect of PD on intestinal colonization by pathogenic Haemophilus parainfluenzae strains in patients with CD.
Article
Gastroenterology & Hepatology
G. Luglio, L. Pellegrini, A. Rispo, F. P. Tropeano, N. Imperatore, G. Pagano, A. Amendola, A. Testa, G. D. De Palma, F. Castiglione
Summary: About 25% of CD patients develop post-operative complications, and factors such as pre-operative management and surgery duration are associated risk factors.
INTERNATIONAL JOURNAL OF COLORECTAL DISEASE
(2022)
Article
Endocrinology & Metabolism
Martine Paquette, Sophie Bernard, Alexis Baass
Summary: This study found that patients with DBL have a significantly higher risk of ASCVD and PVD compared to normolipidemic controls, as well as a higher risk of PVD compared to patients with FH. Adequate screening for DBL is vital to improve the clinical care and prevent the development of ASCVD in these patients.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Clinical Neurology
Melanie P. Jensen, Benjamin Meir Jacobs, Ruth Dobson, Sara Bandres-Ciga, Cornelis Blauwendraat, Anette Schrag, Alastair J. Noyce
Summary: Lower lymphocyte count is associated with an increased risk of subsequent Parkinson's disease. Other blood markers, such as reductions in eosinophil counts, monocyte counts, and C-reactive protein, may also be related to increased disease risk, but only the association with lower lymphocyte count remains robust. Mendelian randomization analysis suggests a potential causal relationship between lower lymphocyte count and Parkinson's disease risk.
ANNALS OF NEUROLOGY
(2021)
Article
Gastroenterology & Hepatology
Marzieh Akhlaghpour, Talin Haritunians, Shyam K. More, Lisa S. Thomas, Dalton T. Stamps, Shishir Dube, Dalin Li, Shaohong Yang, Carol J. Landers, Emebet Mengesha, Hussein Hamade, Ramachandran Murali, Alka A. Potdar, Andrea J. Wolf, Gregory J. Botwin, Michelle Khrom, Bana Int IBD Genetics, Ashwin N. Ananthakrishnan, William A. Faubion, Bana Jabri, Sergio A. Lira, Rodney D. Newberry, Robert S. Sandler, R. Balfour Sartor, Ramnik J. Xavier, Steven R. Brant, Judy H. Cho, Richard H. Duerr, Mark G. Lazarev, John D. Rioux, L. Philip Schumm, Mark S. Silverberg, Karen Zaghiyan, Phillip Fleshner, Gil Y. Melmed, Eric A. Vasiliauskas, Christina Ha, Shervin Rabizadeh, Gaurav Syal, Nirupama N. Bonthala, David A. Ziring, Stephan R. Targan, Millie D. Long, Dermot P. B. McGovern, Kathrin S. Michelsen
Summary: In this study, a genetic association was found between perianal Crohn's disease (pCD) and a mutation in the CFB gene, which impairs its function and contributes to the occurrence and development of pCD in patients with Crohn's disease.
Article
Cardiac & Cardiovascular Systems
Sandro Ninni, David Dombrowicz, Tanya Kuznetsova, Rocio Vicario, Vance Gao, Olivier Molendi-Coste, Joel Haas, Eloise Woitrain, Augustin Coisne, Annette E. Neele, Koen Prange, Lisa Willemsen, Samy Aghezzaf, Stamatina Fragkogianni, Amine Tazibet, Laurent Pineau, James Robert White, Jerome Eeckhoute, Mohamed Koussa, Henri Dubrulle, Francis Juthier, Jerome Soquet, Andre Vincentelli, Jean-Louis Edme, Menno de Winther, Frederic Geissmann, Bart Staels, David Montaigne
Summary: This study aimed to evaluate the potential impact of hematopoietic somatic mosaicism (HSM) on preoperative blood and myocardial myeloid cells and explore its effect on postoperative outcomes. The results showed a significant association between HSM and the risk of atrial fibrillation, as well as an exaggerated inflammatory response following surgery. Therefore, assessing HSM may be beneficial in the personalized management of patients in the perioperative period.
JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Jingrong Weng, Xutao Lin, Xi Chen, Yu-fan Liang, Yu-cheng Xu, Jia-wei Cai, Peng-cheng Lu, Yuming Rong, Yifeng Zou, Lixin Zhu
Summary: This study found that the prognosis of L4-EGD phenotype may be better than that of the Non-L4-EGD phenotype in patients with Crohn's disease.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Anesthesiology
Ahmad Mohammad Ismail, Rebecka Ahl, Maximilian Peter Forssten, Yang Cao, Per Wretenberg, Tomas Borg, Shahin Mohseni
Summary: Continued beta-blocker therapy is associated with a significant reduction in mortality risk within the first year following hip fracture surgery.
ANESTHESIA AND ANALGESIA
(2021)
Article
Biochemistry & Molecular Biology
Hyo Won Ahn, Zelia F. Worman, Arianna Lechsinska, Lindsay M. Payer, Tongguang Wang, Nasir Malik, Wenxue Li, Kathleen H. Burns, Avindra Nath, Henry L. Levin
Summary: Transposable elements (TEs) may contribute to the risk of neuropsychiatric diseases by affecting gene expression and regulation.
Article
Rheumatology
Daisy Vedder, Martijn Gerritsen, Michael T. Nurmohamed, Ronald F. van Vollenhoven, Christian Lood
Summary: The study revealed elevated levels of neutrophil activation markers, MPO and calprotectin, in gout patients compared to healthy controls. These markers were associated with various risk factors for cardiovascular disease, including hyperlipidemia, hypertension, and diabetes. Furthermore, the presence of a neutrophil activation signature was strongly linked to an increased 10-year risk of cardiovascular mortality in these patients.
Article
Surgery
Vivian L. Wang, Anahita D. Jalilvand, Anand Gupta, Jennwood Chen, Chaitanya Vadlamudi, Kyle A. Perry
Summary: In this retrospective study, it was found that smokers and non-smokers who underwent LARS surgery had similar outcomes in terms of symptom resolution, PPI cessation rates, and satisfaction with the surgery.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2021)
Article
Rheumatology
Sicong Huang, Tianrun Cai, Brittany N. Weber, Zeling He, Kumar P. Dahal, Chuan Hong, Jue Hou, Thany Seyok, Andrew Cagan, Marcelo F. DiCarli, Jacob Joseph, Seoyoung C. Kim, Daniel H. Solomon, Tianxi Cai, Katherine P. Liao
Summary: This study found that elevated inflammation early in the diagnosis of rheumatoid arthritis (RA) was associated with heart failure, specifically heart failure with preserved ejection fraction (HFpEF). The association was not observed with heart failure with reduced ejection fraction (HFrEF). This finding suggests a window of opportunity for prevention of HFpEF in RA patients.
ARTHRITIS CARE & RESEARCH
(2023)
Article
Biology
Xuan Wang, Layla Parast, Larry Han, Lu Tian, Tianxi Cai
Summary: Identifying effective surrogate markers is crucial for improving clinical trial efficiency. Replacing long-term outcomes with shorter-term and/or cheaper surrogate markers can shorten study duration and reduce costs. However, methods for combining multiple markers to construct a composite marker with improved surrogacy are limited.
Article
Gastroenterology & Hepatology
William Yuan, Jayson S. Marwaha, Shana T. Rakowsky, Nathan P. Palmer, Isaac S. Kohane, David T. Rubin, Gabriel A. Brat, Joseph D. Feuerstein
Summary: Population-scale analysis reveals patterns in prescribing trends for ulcerative colitis management, including earlier use of biologics, associations of step-up therapy with higher corticosteroid exposure, and association of combination therapy with positive patient outcomes.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Urology & Nephrology
James A. Diao, Gloria J. Wu, Jason K. Wang, Isaac S. Kohane, Herman A. Taylor, Hocine Tighiouart, Andrew S. Levey, Lesley A. Inker, Neil R. Powe, Arjun K. Manrai
Summary: The newly recommended 2021 CKD-EPI creatinine-based eGFR equation may result in substantial changes to recommended care for US patients of all racial and ethnic groups.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Statistics & Probability
Xinzhou Guo, Waverly Wei, Molei Liu, Tianxi Cai, Chong Wu, Jingshen Wang
Summary: In this study, a new data analysis pipeline and statistical methodology were introduced to address the limitations of previous research on the association between statin usage and the risk of developing type II diabetes. The study found that females with high genetic risk for diabetes are the most vulnerable subgroup for developing diabetes after taking statins.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Article
Mathematical & Computational Biology
Layla Parast, Tianxi Cai, Lu Tian
Summary: The primary benefit of identifying a valid surrogate marker is the ability to use it in a future trial to test for a treatment effect with shorter follow-up time or less cost. However, previous work has shown potential heterogeneity in the utility of surrogate markers. Therefore, ignoring this heterogeneity may lead to inaccurate conclusions about the treatment effect. This article introduces a novel test that accounts for the heterogeneity in surrogate marker utility.
STATISTICS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Byorn W. L. Tan, Bryce W. Q. Tan, Amelia L. M. Tan, Emily R. Schriver, Alba Gutierrez-Sacristan, Priyam Das, William Yuan, Meghan R. Hutch, Noelia Garcia Barrio, Miguel Pedrera Jimenez, Noor Abu-el-rub, Michele Morris, Bertrand Moal, Guillaume Verdy, Kelly Cho, Yuk-Lam Ho, Lav P. Patel, Arianna Dagliati, Antoine Neuraz, Jeffrey G. Klann, Andrew M. South, Shyam Visweswaran, David A. Hanauer, Sarah E. Maidlow, Mei Liu, Danielle L. Mowery, Ashley Batugo, Adeline Makoudjou, Patric Tippmann, Daniela Zoeller, Gabriel A. Brat, Yuan Luo, Paul Avillach, Riccardo Bellazzi, Luca Chiovato, Alberto Malovini, Valentina Tibollo, Malarkodi Jebathilagam Samayamuthu, Pablo Serrano Balazote, Zongqi Xia, Ne Hooi Will Loh, Lorenzo Chiudinelli, Clara-Lea Bonzel, Chuan Hong, Harrison G. Zhang, Griffin M. Weber, Isaac S. Kohane, Tianxi Cai, Gilbert S. Omenn, John H. Holmes, Kee Yuan Ngiam
Summary: This retrospective observational study analyzed data from 12,891 COVID-19 patients and found that age, severe COVID-19, severe acute kidney injury (AKI), and ischemic heart disease were associated with worse mortality outcomes. The severity of AKI was associated with poorer kidney function recovery, while the use of remdesivir was associated with better recovery. In patients without chronic kidney disease, age, male sex, severe AKI, and hypertension were associated with post-AKI kidney function impairment. COVID-19-associated AKI was also linked to higher mortality and worse long-term kidney function recovery.
Article
Computer Science, Information Systems
Jacqueline Honerlaw, Yuk-Lam Ho, Francesca Fontin, Jeffrey Gosian, Monika Maripuri, Michael Murray, Rahul Sangar, Ashley Galloway, Andrew J. Zimolzak, Stacey B. Whitbourne, Juan P. Casas, Rachel B. Ramoni, David R. Gagnon, Tianxi Cai, Katherine P. Liao, J. Michael Gaziano, Sumitra Muralidhar, Kelly Cho
Summary: The development of phenotypes using electronic health records is a resource-intensive process. The Department of Veterans Affairs (VA) has developed a standard for phenotype metadata collection, called CIPHER, which improves upon existing methods by capturing algorithm context and validation approach. This standard is applicable across healthcare systems and is currently used in the largest healthcare system in the United States.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Letter
Biochemistry & Molecular Biology
Harrison G. Zhang, Jacqueline P. Honerlaw, Monika Maripuri, Malarkodi Jebathilagam Samayamuthu, Brendin R. Beaulieu-Jones, Huma S. Baig, Sehi L'Yi, Yuk-Lam Ho, Michele Morris, Vidul Ayakulangara Panickan, Xuan Wang, Griffin M. Weber, Katherine P. Liao, Shyam Visweswaran, Bryce W. Q. Tan, William Yuan, Nils Gehlenborg, Sumitra Muralidhar, Rachel B. Ramoni, Isaac S. Kohane, Zongqi Xia, Kelly Cho, Tianxi Cai, Gabriel A. Brat, James R. Aaron, Giuseppe Agapito, Adem Albayrak, Giuseppe Albi, Mario Alessiani, Anna Alloni, Danilo F. Amendola, Francois Angoulvant, Li L. L. J. Anthony, Bruce J. Aronow, Fatima Ashraf, Andrew Atz, Paul Avillach, Paula S. Azevedo, James Balshi, Brett K. Beaulieu-Jones, Douglas S. Bell, Antonio Bellasi, Riccardo Bellazzi, Vincent Benoit, Michele Beraghi, Jose Luis Bernal-Sobrino, Melodie Bernaux, Romain Bey, Surbhi Bhatnagar, Alvar Blanco-Martinez, Clara-Lea Bonzel, John Booth, Silvano Bosari, Florence T. Bourgeois, Robert L. Bradford, Gabriel A. Brat, Stephane Breant, Nicholas W. Brown, Raffaele Bruno, William A. Bryant, Mauro Bucalo, Emily Bucholz, Anita Burgun, Tianxi Cai, Mario Cannataro, Aldo Carmona, Charlotte Caucheteux, Julien Champ, Jin Chen, Krista Y. Chen, Luca Chiovato, Lorenzo Chiudinelli, Kelly Cho, James J. Cimino, Tiago K. Colicchio, Sylvie Cormont, Sebastien Cossin, Jean B. Craig, Juan Luis Cruz-Bermudez, Jaime Cruz-Rojo, Arianna Dagliati, Mohamad Daniar, Christel Daniel, Priyam Das, Batsal Devkota, Audrey Dionne, Rui Duan, Julien Dubiel, Scott L. DuVall, Loic Esteve, Hossein Estiri, Shirley Fan, Robert W. Follett, Thomas Ganslandt, Noelia Garcia-Barrio, Lana X. Garmire, Nils Gehlenborg, Emily J. Getzen, Alon Geva, Tobias Gradinger, Alexandre Gramfort, Romain Griffier, Nicolas Griffon, Olivier Grisel, Alba Gutierrez-Sacristan, Larry Han, David A. Hanauer, Christian Haverkamp, Derek Y. Hazard, Bing He, Darren W. Henderson, Martin Hilka, Yuk-Lam Ho, John H. Holmes, Chuan Hong, Kenneth M. Huling, Meghan R. Hutch, Richard W. Issitt, Anne Sophie Jannot, Vianney Jouhet, Ramakanth Kavuluru, Mark S. Keller, Chris J. Kennedy, Daniel A. Key, Katie Kirchoff, Jeffrey G. Klann, Isaac S. Kohane, Ian D. Krantz, Detlef Kraska, Ashok K. Krishnamurthy, Sehi L'Yi, Trang T. Le, Judith Leblanc, Guillaume Lemaitre, Leslie Lenert, Damien Leprovost, Molei Liu, Ne Hooi Will Loh, Qi Long, Sara Lozano-Zahonero, Yuan Luo, Kristine E. Lynch, Sadiqa Mahmood, Sarah E. Maidlow, Adeline Makoudjou, Alberto Malovini, Kenneth D. Mandl, Chengsheng Mao, Anupama Maram, Patricia Martel, Marcelo R. Martins, Jayson S. Marwaha, Aaron J. Masino, Maria Mazzitelli, Arthur Mensch, Marianna Milano, Marcos F. Minicucci, Bertrand Moal, Taha Mohseni Ahooyi, Jason H. Moore, Cinta Moraleda, Jeffrey S. Morris, Michele Morris, Karyn L. Moshal, Sajad Mousavi, Danielle L. Mowery, Douglas A. Murad, Shawn N. Murphy, Thomas P. Naughton, Carlos Tadeu Breda Neto, Antoine Neuraz, Jane Newburger, Kee Yuan Ngiam, Wanjiku F. M. Njoroge, James B. Norman, Jihad Obeid, Marina P. Okoshi, Karen L. Olson, Gilbert S. Omenn, Nina Orlova, Brian D. Ostasiewski, Nathan P. Palmer, Nicolas Paris, Lav P. Patel, Miguel Pedrera-Jimenez, Emily R. Pfaff, Ashley C. Pfaff, Danielle Pillion, Sara Pizzimenti, Hans U. Prokosch, Robson A. Prudente, Andrea Prunotto, Victor Quiros-Gonzalez, Rachel B. Ramoni, Maryna Raskin, Siegbert Rieg, Gustavo Roig-Dominguez, Pablo Rojo, Paula Rubio-Mayo, Paolo Sacchi, Carlos Saez, Elisa Salamanca, Malarkodi Jebathilagam Samayamuthu, L. Nelson Sanchez-Pinto, Arnaud Sandrin, Nandhini Santhanam, Janaina C. C. Santos, Fernando J. Sanz Vidorreta, Maria Savino, Emily R. Schriver, Petra Schubert, Juergen Schuettler, Luigia Scudeller, Neil J. Sebire, Pablo Serrano-Balazote, Patricia Serre, Arnaud Serret-Larmande, Mohsin Shah, Zahra Shakeri Hossein Abad, Domenick Silvio, Piotr Sliz, Jiyeon Son, Charles Sonday, Andrew M. South, Anastasia Spiridou, Zachary H. Strasser, Amelia L. M. Tan, Bryce W. Q. Tan, Byorn W. L. Tan, Suzana E. Tanni, Deanne M. Taylor, Ana I. Terriza-Torres, Valentina Tibollo, Patric Tippmann, Emma M. S. Toh, Carlo Torti, Enrico M. Trecarichi, Yi-Ju Tseng, Andrew K. Vallejos, Gael Varoquaux, Margaret E. Vella, Guillaume Verdy, Jill-Jenn Vie, Shyam Visweswaran, Michele Vitacca, Kavishwar B. Wagholikar, Lemuel R. Waitman, Xuan Wang, Demian Wassermann, Griffin M. Weber, Martin Wolkewitz, Scott Wong, Zongqi Xia, Xin Xiong, Ye Ye, Nadir Yehya, William Yuan, Alberto Zambelli, Harrison G. Zhang, Daniela Zoller, Valentina Zuccaro, Chiara Zucco
Article
Psychiatry
Yi-han Sheu, Jiehuan Sun, Hyunjoon Lee, Victor M. Castro, Yuval Barak-Corren, Eugene Song, Emily M. Madsen, William J. Gordon, Isaac S. Kohane, Susanne E. Churchill, Ben Y. Reis, Tianxi Cai, Jordan W. Smoller
Summary: This study finds that applying machine learning models to clinical data can outperform clinicians in suicide risk stratification. The researchers use a landmark model framework, aligned with clinical practice, and a large electronic health record database to predict suicide-related behaviors. The models developed using this approach achieve high predictive performance across different prediction windows and settings.
PSYCHIATRY RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Matthew B. A. McDermott, Brendan Yap, Peter Szolovits, Marinka Zitnik
Summary: Designing methods to induce explicit and deep structural constraints in latent space at the sample level is an open problem in NLP-derived methods. McDermott and colleagues propose a pre-training framework imposing such constraints and demonstrate its advantages over existing methods. They investigate the problem of how pre-training methods impose relational structure in induced per-sample latent spaces and introduce a framework that enables a comprehensive understanding. The empirical studies confirm the theoretical analyses and lead to consistent improvements in various tasks.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Jun Wen, Xiang Zhang, Everett Rush, Vidul A. Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J. Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P. Liao, Marinka Zitnik, Tianxi Cai
Summary: Predicting molecule-disease indications and side effects can be enhanced by comprehensively mining semantic dependencies between molecules, diseases, and diseases. This study introduces a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP), which incorporates clinical semantics from electronic health records (EHR) of 12.6 million patients. M2REMAP achieves significant improvements in prediction performance on indications and side effects by combining multimodal molecule representation and disease semantic embedding.
Meeting Abstract
Clinical Neurology
Wen Zhu, Chenyi Chen, Lili Zhang, Elizabeth Walker, Shruthi Venkatesh, Fujun Zhang, Ferhan Qureshi, Tamara Hoyt, John Foley, Zongqi Xia
Meeting Abstract
Clinical Neurology
Shruthi Venkatesh, Claire Riley, Amar Dhand, Nandini Doshi, Katelyn Kavak, Elle Levit, Christopher Perrone, Bianca Weinstock-Guttman, Erin Longbrake, Philip De Jager, Zongqi Xia