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Bioscience

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Displaying 101 - 125 of 2353

Design and characterization of a protein fold switching network

January 26, 2023
Author(s)
David Travis Gallagher, Biao Ruan, Yanan He, Yingwei Chen, Eun Jung Choi, Yihong Chen, Dana Motabar, Tsega Solomon, Richard Simmerman, Thomas Kauffman, John Orban, Philip Bryan
Protein sequences encoding three common small folds (3-alpha, beta-grasp, and alpha/beta plait) were connected in a network of mutational pathways that intersect at high-identity sequences, termed nodes. The structures of proteins around nodes were

ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics

January 24, 2023
Author(s)
Tobias Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Magnus Palmblad, Ben Neely, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric Deutsch
Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and

Measuring Dimensionality of Cell-Scaffold Contacts of Primary Human Bone Marrow Stromal Cells Cultured on Electrospun Fiber Scaffolds

January 1, 2023
Author(s)
Carl Simon Jr., Peter Bajcsy, Joe Chalfoun, Michael Paul Majurski, Mary C. Brady, Mylene Simon, Nathan Hotaling, Nick Schaub, Allison Horenberg, Piotr Szczypinski, Dongbo Wang, Veronica DeFelice, Soweon Yoon, Stephanie Florczyk
The properties and structure of the cellular microenvironment can influence cell behavior. Sites of cell adhesion to the extracellular matrix (ECM) initiate intracellular signaling that direct cell functions such as proliferation, differentiation and

Deep Learning Image Analysis of Nanoplasmonic Sensors: Toward Medical Breath Monitoring

November 23, 2022
Author(s)
Yangyang Zhao, Boqun Dong, Kurt D. Benkstein, Lei Chen, Kristen L. Steffens, Stephen Semancik
Sensing biomarkers in exhaled breath offers a potentially portable, cost-effective, and noninvasive strategy for disease diagnosis screening and monitoring, while high sensitivity, wide sensing range, and target specificity are critical challenges. We

Prestress in Composite Polymer Gels as a Model for Articular Cartilage

November 2, 2022
Author(s)
Alexandros Chremos, Jack F. Douglas, Peter Basser, Ferenc Horkay
Articular cartilage is a composite gel-like material found in animal and human joints and exhibits a unique load-bearing performance that has been challenging to reproduce in synthetic materials and in molecular dynamics simulations. We investigate a

Sensor Technologies for Quality Control in Engineered Tissue Manufacturing

October 27, 2022
Author(s)
Mary Clare McCorry, Marcie Black, Chrysanthi Williams, Greta Babakhanova, Sumona Sarkar, Nathan Swami, Katherine A. Mirica, Sarah Boermeester, Abbie Underhill
The use of engineered cells, tissues, and organs has the opportunity to change the way injuries and diseases are treated. Commercialization of these groundbreaking technologies has been limited in part by the complex and costly nature of their manufacture

The Influence of Proteoforms: Assessing the Accuracy of Total VDBP Quantification by Proteolysis and LC-MS/MS

October 24, 2022
Author(s)
Lisa Kilpatrick, Roger Bouillon, Clay Davis, Clark Henderson, Andrew N. Hoofnagle, Steven Pauwels, Dirk Vanderschueren, Etienne Waelkens, Hans Wildiers, James H. Yen, Karen W. Phinney
Objectives: Vitamin D-binding protein (VDBP), a serum transport protein for 25-hydroxyvitamin D [25(OH)D], has three common proteoforms which have co-localized amino acid variations and glycosylation. A monoclonal immunoassay was found to differentially
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