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Bioscience

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Displaying 126 - 150 of 1261

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

Semi-automated assembly of high-quality diploid human reference genomes

October 19, 2022
Author(s)
Erich Jarvis, Giulio Formenti, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Kerstin Howe, Karen Miga
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of

compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets

September 29, 2022
Author(s)
Rob Marissen, Jeroen Laros, Josef Rasinger, Madhushri Varunjikar, Ben Neely, Magnus Palmblad
It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected

Report from the NIST Workshop: Launch of the Rapid Microbial Testing Methods Consortium

September 27, 2022
Author(s)
Nancy Lin, Scott Jackson, Stephanie Servetas, Kirsten Parratt, Joy Dunkers, Tara Eskandari, Sheng Lin-Gibson
On September 17, 2020, NIST hosted a virtual workshop to launch the Rapid Microbial Testing Methods (RMTM) Consortium. The RMTM Consortium aims to address the need for measurements and standards to increase confidence in the use of rapid testing for

Population data for 94 identity SNPs in four U.S. population groups

September 23, 2022
Author(s)
Kevin Kiesler, Lisa Borsuk, Becky Steffen, Katherine Gettings, Peter Vallone
The U.S. National Institute of Standards and Technology (NIST) sequenced 1036 human DNA samples from four United States population groups (African American, Asian, Hispanic, and Caucasian) using the ForenSeq DNA Signature Prep Kit with Primer Mix B (DPMB)

Mass Spectral Library Methods for Analysis of Site-Specific N-Glycosylation: Application to Human Milk Proteins

September 16, 2022
Author(s)
Concepcion Remoroza, Meghan Burke Harris, Xiaoyu (Sara) Yang, Sergey Sheetlin, Yuri Mirokhin, Sanford Markey, Dmitrii V. Tchekhovskoi, Stephen E. Stein
We present a mass-spectral library-based method for analyzing site-specific N-linked protein glycosylation. Its operation and utility are illustrated by applying it to both newly measured and available proteomics data of human milk glycoproteins. It

Report on the DHS/NIST Workshop on Standards for an Enduring Capability in Wastewater Surveillance for Public Health (SWWS Workshop)

August 16, 2022
Author(s)
Nancy Lin, Stephanie Servetas, Scott Jackson, Katrice Lippa, Kirsten Parratt, Philip Mattson, Clare Beahn, Mia Mattioli, Sally Gutierrez, Michael Focazio, Ted Smith, Paul Storella, Sarah Wright
Wastewater surveillance is a promising approach to monitor biological and chemical contaminants on a community level in support of public health and safety decisions. Wastewater surveillance has recently been shown highly effective for the early detection

Structural Fingerprinting of siRNA Therapeutics by Solution NMR Spectroscopy

August 4, 2022
Author(s)
Owen Becette, Anh Tran, Jace Jones, John Marino, Robert Brinson
Nucleic acids are an increasingly popular platform for the development of biotherapeutics to treat a wide variety of illnesses, including diseases where traditional drug development efforts have failed. To date, there are 14 short oligonucleotide
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