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Displaying 1 - 25 of 1090

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

January 24, 2023
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
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

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

October 19, 2022
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
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
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

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

September 16, 2022
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
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
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

Effect of Tribologically-Induced Changes in Surface Termination of Silicon-Containing Diamond-Like Carbon Coatings on the Resistance to Biomolecule Adsorption

August 1, 2022
Cherno Jaye, Daniel A. Fischer, Zixuan Li, Jennings Z. Ye, Jieming Yan, Nicolas Molina, Hsu-Ming Lien, Robert Chrostowksi, Jianliang Lin, Mangolini Mangolini
Silicon-containing diamond-like carbon (DLC) is a class of thin-film materials with excellent mechanical properties, high thermal stability, and good tribological performance over a wide range of environmental conditions. While non-alloyed/non-doped DLCs

NMR and Metabolomics -A Roadmap for the Future

July 23, 2022
Tracey Schock, David Wishart, Leo Cheng, Valerie Copie, Arthur Edison, Hamid Eghbalnia, Jeffrey Hoch, Goncalo Gouveia, Wimal Pathmasiri, Robert Powers, Llyod Sumner, Mario Uchimiya
Metabolomics investigates global metabolic alterations associated with chemical, biological, physiological, or pathological processes. These metabolic changes are measured with various analytical platforms. While liquid chromatography-mass spectrometry (LC

The need for multicomponent gas standards for breath biomarker analysis

July 7, 2022
Kavita Jeerage, Jennifer Berry, Jacolin Murray, Cassie Goodman, Paulina Piotrowski, Christina Jones, Christina Cecelski, Jennifer Carney, Katrice Lippa, Tara Lovestead
Exhaled breath is a non-invasive, information-rich matrix with the potential to diagnose or monitor disease, including infectious disease. Despite significant effort dedicated to biomarker identification in case control studies, very few breath tests are

Computational Study of the Allosteric Effects of p5 on the CDK5-p25 Hyperactivity as Alternative Inhibitory Mechanisms in Neurodegeneration

June 30, 2022
Tejaswi Tammareddy, Walid Keyrouz, Ram D. Sriram, Harish C. Pant, Antonio Cardone, Jeffery B. Klauda
The cyclin-dependent kinase (CDK5) forms a stable complex with its activator p25, leading to the hyperphosphorylation of tau proteins and to the formation of plaques and tangles that are considered to be one of the typical causes of Alzheimer's disease (AD

Evidence that gecko setae are coated with an ordered nanometer-thin lipid film

June 9, 2022
Cherno Jaye, Daniel A. Fischer, Mette Rasmussen, Katinka Holler, Joe Baio, Stanislav Gorb, Tobias Weidner
Motivated by the fascination of gecko adhesion based on the fibrous setae at the tips of their toe pads and their potential for biomimetic applications, the adhesion mechanism has been studied in detail. While the mechanism has been shown to be based on

Reference Material 8376 Microbial Pathogen DNA Standards for Detection and Identification

June 1, 2022
Jason Kralj, Dieter Tourlousse, Monique Hunter, Erica Romsos, Blaza Toman, Peter Vallone, Scott Jackson
Reference Material (RM) 8376 is intended for NGS-based measurements quantitative to the chromosome. A unit of RM 8376 consists of 20 components (A-T, 19 bacteria and 1 human) each containing well-characterized DNA in 10 mmol/L Tris-HCl, 1 mmol/L EDTA pH 8
Displaying 1 - 25 of 1090