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JOURNAL ARTICLE
Daniel Yoo, Gillian Divard, Marc Raynaud, Aaron Cohen, Tom D Mone, John Thomas Rosenthal, Andrew J Bentall, Mark D Stegall, Maarten Naesens, Huanxi Zhang, Changxi Wang, Juliette Gueguen, Nassim Kamar, Antoine Bouquegneau, Ibrahim Batal, Shana M Coley, John S Gill, Federico Oppenheimer, Erika De Sousa-Amorim, Dirk R J Kuypers, Antoine Durrbach, Daniel Seron, Marion Rabant, Jean-Paul Duong Van Huyen, Patricia Campbell, Soroush Shojai, Michael Mengel, Oriol Bestard, Nikolina Basic-Jukic, Ivana Jurić, Peter Boor, Lynn D Cornell, Mariam P Alexander, P Toby Coates, Christophe Legendre, Peter P Reese, Carmen Lefaucheur, Olivier Aubert, Alexandre Loupy
In kidney transplantation, day-zero biopsies are used to assess organ quality and discriminate between donor-inherited lesions and those acquired post-transplantation. However, many centers do not perform such biopsies since they are invasive, costly and may delay the transplant procedure. We aim to generate a non-invasive virtual biopsy system using routinely collected donor parameters. Using 14,032 day-zero kidney biopsies from 17 international centers, we develop a virtual biopsy system. 11 basic donor parameters are used to predict four Banff kidney lesions: arteriosclerosis, arteriolar hyalinosis, interstitial fibrosis and tubular atrophy, and the percentage of renal sclerotic glomeruli...
January 16, 2024: Nature Communications
#22
JOURNAL ARTICLE
Teresa Irianto, Udo S Gaipl, Michael Rückert
Cancer can affect all human organs and tissues and ranks as a prominent cause of death as well as an obstruction to increasing life expectancy. A notable breakthrough in oncology has been the inclusion of the immune system in fighting cancer, potentially prolonging life and providing long-term benefits. The concept of "immunotherapy" has been discussed from the 19th and early 20th centuries by Wilhelm Busch, William B. Coley and Paul Ehrlich. This involves distinct approaches, including vaccines, non-specific cytokines and adoptive cell therapies...
2024: International Review of Cell and Molecular Biology
#23
Brian D Williamson, R Yates Coley, Clarissa Hsu, Courtney E McCracken, Andrea J Cook
No abstract text is available yet for this article.
January 15, 2024: Prevention Science: the Official Journal of the Society for Prevention Research
#24
JOURNAL ARTICLE
Nicholas David, Wenhao Sun, Connor W Coley
No abstract text is available yet for this article.
May 2023: Nature computational science
#25
REVIEW
Priyanka Raghavan, Brittany C Haas, Madeline E Ruos, Jules Schleinitz, Abigail G Doyle, Sarah E Reisman, Matthew S Sigman, Connor W Coley
Models can codify our understanding of chemical reactivity and serve a useful purpose in the development of new synthetic processes via, for example, evaluating hypothetical reaction conditions or in silico substrate tolerance. Perhaps the most determining factor is the composition of the training data and whether it is sufficient to train a model that can make accurate predictions over the full domain of interest. Here, we discuss the design of reaction datasets in ways that are conducive to data-driven modeling, emphasizing the idea that training set diversity and model generalizability rely on the choice of molecular or reaction representation...
December 27, 2023: ACS Central Science
#26
JOURNAL ARTICLE
Danielle Kipnis, Alissa Pacheco, Dalina Delfing, Nia Toomer-Mensah, Chelsea E Macpherson, Jamie Rieger, Anita Parker, R Bernard Coley, Denise Coley, Hiral Shah, Lori Quinn
No abstract text is available yet for this article.
February 2024: Parkinsonism & related Disorders
#27
JOURNAL ARTICLE
Gregory E Simon, Susan M Shortreed, Eric Johnson, Zimri S Yaseen, Marc Stone, Andrew D Mosholder, Brian K Ahmedani, Karen J Coleman, R Yates Coley, Robert B Penfold, Sengwee Toh
PURPOSE: Observational studies assessing effects of medical products on suicidal behavior often rely on health record data to account for pre-existing risk. We assess whether high-dimensional models predicting suicide risk using data derived from insurance claims and electronic health records (EHRs) are superior to models using data from insurance claims alone. METHODS: Data were from seven large health systems identified outpatient mental health visits by patients aged 11 or older between 1/1/2009 and 9/30/2017...
December 19, 2023: Pharmacoepidemiology and Drug Safety
#28
Megan N Guerin, TreVaughn Ellis, Mark J Ware, Alexandra Manning, Ariana Coley, Ali Amini, George Chung, Kristin C Gunsalus, John R Bracht
In this study we report a naturally evolved temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the full mitochondrial genome sequence of this organism, and show through dN/dS analysis statistically robust evidence of positive selection in H...
December 7, 2023: bioRxiv
#29
Avril K Coley, Chenyue Lu, Amaya Pankaj, Matthew J Emmett, Evan R Lang, Yuhui Song, Katherine H Xu, Nova Xu, Bidish K Patel, Abhijit Chougule, Linda T Nieman, Martin J Aryee, Cristina R Ferrone, Vikram Deshpande, Joseph W Franses, David T Ting
PURPOSE: Dysregulation of viral-like repeat RNAs are a common feature across many malignancies that are linked with immunological response, but the characterization of these in hepatocellular carcinoma (HCC) is understudied. In this study, we performed RNA in situ hybridization (RNA-ISH) of different repeat RNAs, immunohistochemistry (IHC) for immune cell subpopulations, and spatial transcriptomics to understand the relationship of HCC repeat expression, immune response, and clinical outcomes...
December 5, 2023: bioRxiv
#30
JOURNAL ARTICLE
Hao Zhang, Randy S Haun, Francois Collin, Clarissa Cassol, Johnathan O H Napier, Jon Wilson, Samar Hassen, Kerime Ararat, Christie Boils, Nidia Messias, Tiffany N Caza, L Nicholas Cossey, Shree Sharma, Josephine M Ambruzs, Nikhil Agrawal, Grigoriy Shekhtman, Wenlan Tian, Titte Srinivas, Kunbin Qu, Robert N Woodward, Christopher P Larsen, Steven Stone, Shana M Coley
Gene expression profiling (GEP) from formalin-fixed paraffin-embedded (FFPE) renal allograft biopsies is a promising approach for feasibly providing a molecular diagnosis of rejection. However, large-scale studies evaluating the performance of models using NanoString platform data to define molecular archetypes of rejection are lacking. We tested a diverse retrospective cohort of over 1400 FFPE biopsy specimens, rescored according to Banff 2019 criteria and representing ten of 11 UNOS regions, using the Banff Human Organ Transplant (B-HOT) panel from NanoString and developed a multi-class model from the gene expression data to assign relative probabilities of four molecular archetypes: No Rejection, Antibody-Mediated Rejection (ABMR), T cell-Mediated Rejection (TCMR), and Mixed Rejection...
December 11, 2023: Laboratory Investigation; a Journal of Technical Methods and Pathology
#31
JOURNAL ARTICLE
Gregory E Simon, Maricela Cruz, Jennifer M Boggs, Arne Beck, Susan M Shortreed, R Yates Coley
OBJECTIVE: The authors examined whether machine-learning models could be used to analyze data from electronic health records (EHRs) to predict patients' responses to antidepressant medications. METHODS: EHR data from a Washington State health system identified patients ages ≥13 years who started an antidepressant medication in 2016 in a community practice setting and had a baseline Patient Health Questionnaire-9 (PHQ-9) score of ≥10 and at least one PHQ-9 score recorded 14-180 days later...
December 5, 2023: Psychiatric Services: a Journal of the American Psychiatric Association
#32
JOURNAL ARTICLE
Tracy A Blusewicz, Katherine P Coley, Robert D Moore, John R Miklos
INTRODUCTION: Lichen sclerosus (LS) is a chronic, distressing, inflammatory process that has a huge impact on quality of life in women. Uncontrolled vulvar LS can lead to chronic symptoms of itching and pain and can lead to anatomic changes, scarring, and elevated risk of cancer. First-line therapy with corticosteroids is often not successful in controlling symptoms, especially over the long term. This is the first study to review the effects of bipolar radiofrequency (RF) with microneedling to treat the vaginal and vulvar symptoms of LS...
December 1, 2023: Surgical Technology International
#33
Liam Hudson, Jeremy W Mason, Matthias V Westphal, Matthieu J R Richter, Jonathan R Thielman, Bruce K Hua, Christopher J Gerry, Guoqin Xia, Heather L Osswald, John M Knapp, Zher Yin Tan, Praveen Kokkonda, Ben I C Tresco, Shuang Liu, Andrew G Reidenbach, Katherine S Lim, Jennifer Poirier, John Capece, Simone Bonazzi, Christian M Gampe, Nichola J Smith, James E Bradner, Connor W Coley, Paul A Clemons, Bruno Melillo, C Suk-Yee Hon, Johannes Ottl, Christoph E Dumelin, Jonas V Schaefer, Ann Marie E Faust, Frédéric Berst, Stuart L Schreiber, Frédéric J Zécri, Karin Briner
No abstract text is available yet for this article.
November 21, 2023: Nature Communications
#34
JOURNAL ARTICLE
Candice Roufosse, Maarten Naesens, Mark Haas, Carmen Lefaucheur, Roslyn B Mannon, Marjan Afrouzian, Nada Alachkar, Olivier Aubert, Serena M Bagnasco, Ibrahim Batal, Chris O C Bellamy, Verena Broecker, Klemens Budde, Marian Clahsen-Van Groningen, Shana M Coley, Lynn D Cornell, Darshana Dadhania, Anthony J Demetris, Gunilla Einecke, Alton B Farris, Agnes B Fogo, John Friedewald, Ian W Gibson, Catherine Horsfield, Edmund Huang, Syed A Husain, Annette M Jackson, Jesper Kers, Željko Kikić, Amanda Klein, Nicolas Kozakowski, Helen Liapis, Massima Mangiola, Robert A Montgomery, Brian Nankinvell, Desley A H Neil, Peter Nickerson, Marion Rabant, Parmjeet Randhawa, Leonardo V Riella, Ivy Rosales, Virginie Royal, Ruth Sapir-Pichhadze, Pinaki Sarder, Minnie Sarwal, Carrie Schinstock, Mark Stegall, Kim Solez, Jeroen van der Laak, Chris Wiebe, Robert B Colvin, Alexandre Loupy, Michael Mengel
The XVIth Banff Meeting for Allograft Pathology was held in Banff, Alberta, Canada, from September 19 to 23, 2022, as a joint meeting with the Canadian Society of Transplantation. In addition to a key focus on the impact of microvascular inflammation and biopsy-based transcript analysis on the Banff Classification, further sessions were devoted to other aspects of kidney transplant pathology, in particular T cell-mediated rejection, activity and chronicity indices, digital pathology, xenotransplantation, clinical trials, and surrogate endpoints...
November 4, 2023: American Journal of Transplantation
#35
JOURNAL ARTICLE
Jeremy W Mason, Yuen Ting Chow, Liam Hudson, Antonin Tutter, Gregory Michaud, Matthias V Westphal, Wei Shu, Xiaolei Ma, Zher Yin Tan, Connor W Coley, Paul A Clemons, Simone Bonazzi, Frédéric Berst, Karin Briner, Shuang Liu, Frédéric J Zécri, Stuart L Schreiber
Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry...
November 2, 2023: Nature Chemical Biology
#36
JOURNAL ARTICLE
A A Coley, A Landry, R J van den Hoogen, D D McNutt
Theories of gravity based on teleparallel geometries are characterized by the torsion, which is a function of the coframe, derivatives of the coframe, and a zero curvature and metric compatible spin-connection. The appropriate notion of a symmetry in a teleparallel geometry is that of an affine symmetry. Due to the importance of the de Sitter geometry and Einstein spaces within General Relativity, we shall describe teleparallel de Sitter geometries and discuss their possible generalizations. In particular, we shall analyse a class of Einstein teleparallel geometries which have a 4-dimensional Lie algebra of affine symmetries, and display two one-parameter families of explicit exact solutions...
2023: European Physical Journal. C, Particles and Fields
#37
JOURNAL ARTICLE
Brian D Williamson, R Yates Coley, Clarissa Hsu, Courtney E McCracken, Andrea J Cook
In research assessing the effect of an intervention or exposure, a key secondary objective often involves assessing differential effects of this intervention or exposure in subgroups of interest; this is often referred to as assessing effect modification or heterogeneity of treatment effects (HTE). Observed HTE can have important implications for policy, including intervention strategies (e.g., will some patients benefit more from intervention than others?) and prioritizing resources (e.g., to reduce observed health disparities)...
October 28, 2023: Prevention Science: the Official Journal of the Society for Prevention Research
#38
JOURNAL ARTICLE
Tianyi Jin, Connor W Coley, Alfredo Alexander-Katz
We unveil a unified view on the effect of side chains on the glass transition temperatures ( T g ) in polymer melts by using molecular dynamics simulations, density functional theory calculations, and available experimental data. We use acrylates as a model system and evaluate the effect of n -alkyl side chains on T g . We find that backbone dihedral angle fluctuations follow established patterns due to sterics, as expected. However, we also find that the dihedral angle orthogonal to the backbone, which normally is neglected when discussing the effect on T g , introduces a secondary rotational degree of freedom which strongly impacts T g ...
October 27, 2023: ACS Macro Letters
#39
JOURNAL ARTICLE
Alexander T Williams, Jing Chen, Kayesha Coley, Chiara Batini, Abril Izquierdo, Richard Packer, Erik Abner, Stavroula Kanoni, David J Shepherd, Robert C Free, Edward J Hollox, Nigel J Brunskill, Ioanna Ntalla, Nicola Reeve, Christopher E Brightling, Laura Venn, Emma Adams, Catherine Bee, Susan E Wallace, Manish Pareek, Anna L Hansell, Tõnu Esko, Daniel Stow, Benjamin M Jacobs, David A van Heel, William Hennah, Balasubramanya S Rao, Frank Dudbridge, Louise V Wain, Nick Shrine, Martin D Tobin, Catherine John
Thyroid hormones play a critical role in regulation of multiple physiological functions and thyroid dysfunction is associated with substantial morbidity. Here, we use electronic health records to undertake a genome-wide association study of thyroid-stimulating hormone (TSH) levels, with a total sample size of 247,107. We identify 158 novel genetic associations, more than doubling the number of known associations with TSH, and implicate 112 putative causal genes, of which 76 are not previously implicated. A polygenic score for TSH is associated with TSH levels in African, South Asian, East Asian, Middle Eastern and admixed American ancestries, and associated with hypothyroidism and other thyroid disease in South Asians...
October 23, 2023: Nature Communications
#40
JOURNAL ARTICLE
Sascha Dublin, Mikael Anne Greenwood-Hickman, Leah Karliner, Clarissa Hsu, R Yates Coley, Leonardo Colemon, Anna Carrasco, Deborah King, Andrea Grace, Sei J Lee, Judith M E Walsh, Tyler Barrett, Jia Broussard, Umesh Singh, Abisola Idu, Kristine Yaffe, Malaz Boustani, Deborah E Barnes
BACKGROUND: About half of people living with dementia have not received a diagnosis, delaying access to treatment, education, and support. We previously developed a tool, eRADAR, which uses information in the electronic health record (EHR) to identify patients who may have undiagnosed dementia. This paper provides the protocol for an embedded, pragmatic clinical trial (ePCT) implementing eRADAR in two healthcare systems to determine whether an intervention using eRADAR increases dementia diagnosis rates and to examine the benefits and harms experienced by patients and other stakeholders...
October 17, 2023: Contemporary Clinical Trials
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