Studies
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Joshua M. Peters, Edward B. Irvine, Jacob M. Rosenberg, Marc H. Wadsworth II, Travis K. Hughes, Matthew Sutton, Sarah K. Nyquist, Joshua D. Bromley, Rajib Mondal, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Galit Alter, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Bryan D. Bryson
DOI: https://www.science.org/doi/10.1126/sciadv.adq8229
Intradermal Bacillus Calmette-Guérin (BCG) is the most widely administered vaccine, but it does not sufficiently ...
Huu Tuan Nguyen, Nadia Gurvich, Mark Robert Gillrie, Giovanni Offeddu, Mouhita Humayun, Ellen L. Kan, Zhengpeng Wan, Mark Frederick Coughlin, Christie Zhang, Vivian Vu, Sharon Wei Ling Lee, Seng-Lai Tan, David Barbie, Jonathan Hsu, Roger D. Kamm
Link to Paper: https://www.sciencedirect.com/science/article/abs/pii/S0142961224002655
Abstract: Tumor-associated inflammation drives cancer progression and therapy resistance, often linked to the infiltration of ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: All Metadata, Cell Culture and Tumor Spheroid Creation - Metadata, Device Imaging - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Microfluidic Device Creation - Metadata, Migration Assay Analysis - Data Linked
Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.
Link to Paper: https://doi.org/10.1038/s41564-024-01678-x
Abstract: Antibody features vary ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, FC Receptor Binding Assay - Data Linked, Linear Mixed Model - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata, Titer Assay - Data Linked
Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn
Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3
Immunological ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Library Prep - Metadata, PET-CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Michelle Chen, Elliot I. Corless, Bevin P. Engelward, Timothy M. Swager
Link to Paper: https://pubs.acs.org/doi/full/10.1021/acsomega.4c03959
Agglutination of liquid Janus emulsions creates optical signals that can be detected and quantified. This study reports the detection and quantitation of Interleukin-6 (IL-6) using emulsions functionalized at the water-organic interface with engineered hyperthermophilic affinity proteins (rcSso7d) derived from ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Agglutination Assay - Data Linked, All Metadata, Chemical Synthesis - Metadata, Fourier Transform Infrared Spectroscopy - Data Linked, Gel Permeation Chromatography - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, Pendant Drop Tensiometry - Data Linked
Jessica C. Beard, Chi-Hsien Wang, Arun Sridharan, Robert G. Croy, John M. Essigmann, Timothy M. Swager
Link to Paper: https://doi.org/10.1021/acssensors.4c00927
N-Nitrosamines are contaminants found throughout the environment, including in drinking water, and many nitrosamines are likely potent carcinogens. Correspondingly, there is need for rapid and cost-effective in-field detection methods that can provide timely information about their contamination ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Chemical Synthesis - Metadata, Imaging - Data Linked, Nuclear Magnetic Resonance - Data Linked, Nuclear Magnetic Resonance Analysis - Data Linked, Single-crystal X-ray Crystallography - Data Linked, UV-Vis Spectroscopy - Data Linked, UV-Vis Spectroscopy Analysis - Data Linked
Shu Wang, Amy J Myers, Edward B Irvine, Chuangqi Wang, Pauline Maiello, Mark A Rodgers, Jaime Tomko, Kara Kracinovsky, H. Jacob Borish, Michael C Chao, Douaa Mugahid, Patricia A. Darrah, Robert A. Seder, Mario Roederer, Charles A Scanga, Philana Ling Lin, Galit Alter, Sarah M Fortune, JoAnne L Flynn, Douglas A Lauffenburger
Paper Link: https://doi.org/10.1101/2024.04.13.589359
Link to Model Validation Datasets: https://fairdomhub.org/studies/1198
Abstract: ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Antibody Titer - Data Linked, Antibody Titer Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Model Validation, PET/CT Scan - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
Giovanni S. Offeddu#, Elena Cambria#, Sarah E. Shelton, Kristina Haase, Zhengpeng Wan, Luca Possenti, Huu Tuan Nguyen, Mark R. Gillrie, Dean Hickman, Charles G. Knutson, and Roger D. Kamm
Abstract: Desmoplasia in breast cancer leads to heterogeneity in physical properties of the tissue, resulting in disparities in drug delivery and treatment efficacy among patients, thus contributing to high disease mortality. Personalized in vitro breast cancer models hold ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: Device Creation - Metadata, Device Imaging - Metadata, Imaging Analysis - Data Attached, Tumoroid Formation - Metadata
Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*
Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
Caylin G. Winchell, Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins, Michael Chase, Hannah P. Gideon, Kush V. Patel, Joshua D. Bromley, Andrew W. Simonson, Roisin Floyd-O’Sullivan, Marc Wadsworth, Jacob M. Rosenberg, Rockib Uddin, Travis Hughes, Ryan J. Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A. Scanga, Joshua Mattila, Sarah M. Fortune, Alex K. Shalek, Philana Ling Lin, JoAnne L. Flynn; CD8+ lymphocytes are critical for early ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, DNA Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Attached, Immunohistochemistry - Data Linked, PET/CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Huu Tuan Nguyen, Nicholas Pietraszek, Sarah E. Shelton, Kwabena Arthur, Roger D. Kamm
Link to Paper:
Abstract: Significance: Accurate cell segmentation and classification in 3 dimensional (3D) images are vital for studying live cell behavior and drug responses in 3D tissue culture. Evaluating diverse cell populations in 3D cell culture over time necessitates non-toxic staining methods, as specific fluorescence tags may not be suitable and immunofluorescence ...
Edward B. Irvine, Joshua M. Peters, Richard Lu, Patricia S. Grace, Jaimie Sixsmith, Aaron Wallace, Matthew Schneider, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Esther van Woudenbergh, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Galit Alter, Sarah M. Fortune doi: https://doi.org/10.1101/2022.05.01.490220
Novel vaccination and therapeutic strategies are urgently needed to mitigate the tuberculosis (TB) epidemic. While extensive efforts have focused ...
Submitter: Jake Schissel
Investigation: IMPAcTB
Assays: All Metadata, Antibody Challenge - Metadata, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Survivability Restriction Assay - Data Linked, ELISA - Data Linked, Glycosylation Assay - Data Linked, Library Prep - Metadata, Luminex - Data Linked, Patient Visit - Metadata, Single Cell Clustering Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Extraction - Metadata
Jing Ge, Le P. Ngo, Simran Kaushal, Ian J. Tay, Elina Thadhani, Jennifer E. Kay, Patrizia Mazzucato, Danielle N. Chow, Jessica L. Fessler, David M. Weingeist, Robert W. Sobol, Leona D. Samson, Scott R. Floyd, Bevin P. Engelward,*
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439179/
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have ...
Norah Owiti, Joshua Corrigan, Lee Pribyl, Jennifer Kay, Bevin Engelward
https://doi.org/10.3390/ijms231911776
The comet assay is a versatile assay for detecting DNA damage in eukaryotic cells. The assay can measure the levels of various types of damage, including DNA strand breaks, abasic sites and alkali-sensitive sites. Furthermore, the assay can also be modified to include purified DNA glycosylases so that alkylated and oxidized bases can be detected. The ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Chemical Challenge - Metadata, Comet Chip - Data Linked, Comet Chip Analysis - Data Attached, Tissue Collection - Metadata
Edward B Irvine, Patricia A Darrah, Shu Wang, Chuangqi Wang, Ryan P McNamara, Mario Roederer, Robert A Seder, Douglas A Lauffenburger, JoAnne L Flynn, Sarah M Fortune, Galit Alter
https://doi.org/10.1101/2023.07.31.551245
Altering the route of Bacille Calmette-Guérin (BCG) immunization from low-dose intradermal vaccination to high-dose intravenous (IV) vaccination resulted in a high level of protection against Mycobacterium tuberculosis ( Mtb ) infection, ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis Analysis - Data Linked, Antibody-Dependent NK Cell Activation - Data Linked, Antibody-Dependent NK Cell Activation Analysis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis Analysis - Data Linked, FC Receptor Binding - Data Linked, FC Receptor Binding Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata, Titer Assay - Data Linked, Titer Assay Analysis - Data Linked
Emmanouil Angelidakis, Sophia Chen, Shun Zhang, Zhengpeng Wan, Roger D. Kamm, Sarah E. Shelton
Link to Paper: https://doi.org/10.1002/adhm.202202984
A bidirectional association exists between metastatic dissemination and the hypercoagulable state associated with many types of cancer. As such, clinical studies have provided evidence that markers associated with elevated levels of coagulation and fibrinolysis correlate with decreased patient survival. However, ...
Submitter: Charles Demurjian
Investigation: MetNet
Assays: Cancer Cell Extravasation Analysis - Data Linked, Clot Modeling Analysis - Data Linked, Device Imaging - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Microfluidic Device Creation - Metadata, Permeability Analysis - Data Linked
Lauren Baugh, Brittany A. Goods, Juan S. Gnecco, Yunbeen Bae, Michael Retchin, Constantine N. Tzouanas, Megan Loring, Keith Isaacson, Alex K. Shalek, Douglas Lauffenburger, Linda Griffith
https://www.medrxiv.org/content/10.1101/2022.01.29.22269829v1
Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes ...
Submitter: Charles Demurjian
Investigation: Endometriosis
Assays: All Metadata, DNA Extraction - Metadata, Immunohistochemistry - Data Linked, Linear Mixed Model - Data Linked, Mass Spectrometry Proteomics - Data Linked, Mass Spectrometry Proteomics Analysis - Data Linked, Patient Visit - Metadata, Single Cell Expression Matrix Analysis - Data Linked, Single Cell Sequencing - Data Linked, Tissue Collection - Metadata
Juan S. Gnecco, Alexander Brown, Kira Buttrey, Clara Ives, Brittany A. Goods, Lauren Baugh, Victor Hernandez-Gordillo, Megan Loring, Keith Isaacson, Linda G. Griffith
https://doi.org/10.1101/2021.09.30.462577
The human endometrium undergoes recurring cycles of growth, differentiation, and breakdown in response to sex hormones. Dysregulation of epithelial-stromal communication during hormone cycles is linked to myriad gynecological disorders for which treatments ...
Submitter: Charles Demurjian
Investigation: Endometriosis
Assays: All Metadata, Cell Culture Imaging - Data Linked, Cell Culture and Organoid Generation - Metadata, DNA Extraction - Metadata, Elisa - Data Linked, Gene Expression Analysis - Data Linked, Luminex - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Hannah P.Gideon, Travis K.Hughes, Constantine N.Tzouanas, Marc H.WadsworthII, Ang AndyTu, Todd M.Gierahn, Joshua M.Peters, Forrest F.Hopkins, Jun-RongWei, Conner Kummerlowe, Nicole L.Grant, Kievershen Nargan, Jia YaoPhuah, H. JacobBorish, Pauline Maiello, Alexander G.White, Caylin G.Winchell, Sarah K.Nyquist, Sharie Keanne C.Ganchua, Amy Myers, Kush V.Patel, Cassaundra L.Ameel, Catherine T.Cochran, Samira Ibrahim, Jaime A.Tomko, Lonnie JamesFrye, Jacob ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Immunohistochemistry – Data Linked, Library Creation – Metadata, NHP Necropsy – Metadata, PET-CT Scan Analysis – Data Linked, PET-CT Scan – Data Linked, Patient Visit – Metadata, Single Cell Clustering Analysis – Data Linked, Single Cell Expression Matrix Analysis – Data Linked, Single Cell Sequencing – Data Linked
Haosheng Feng, Shao-Xiong Lennon Luo, Robert G Croy, John M. Essigmann, Timothy M. Swager
https://doi.org/10.1039/D2DT03848J
Cu(I) from tetrakis(acetonitrile)copper(I) hexafluorophosphate ([Cu(MeCN)4]PF6) was complexed with five structurally related phosphines containing N-heterocycles. The interactions between the resulting complexes and some N-nitrosamines were studied using X-ray crystallography as well as emission spectroscopy. Upon complexation, three ...
Submitter: Charles Demurjian
Investigation: MIT SRP
Assays: Absorption and Emission Spectroscopy - Data Linked, Absorption and Emission Spectroscopy Analysis - Data Linked, Chemical Synthesis - Metadata, Crystallography - Data Linked, Electron Paramagnetic Resonance - Data Linked, High Resolution Mass Spectra - Data Linked, High Resolution Mass Spectra Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, X-ray Photoelectron Spectroscopy - Data Linked
Amanda L. Armijo, Pennapa Thongaram, Bogdan I. Fedeles, Judy Yau, Jennifer E Kay, Joshua J. Corrigan, Marisa Chancharoen, Supawadee Chawanthayatham, Leona D. Samson, Sebastian E. Carrasco, Bevin P. Engelward, James G. Fox, Robert G. Croy & John M. Essigmann
DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA ...
