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Displaying 76 - 100 of 798

Challenges of Accuracy in Germline Clinical Sequencing Data

July 20, 2021
Author(s)
Justin Zook, Ryan Poplin, Mark DePristo
Physicians are increasingly using clinical sequencing tests to establish diagnoses of patients who might have genetic disorders, which means that accuracy of sequencing and interpretation are important elements in ensuring the benefits of genetic testing

Accurate and Robust Trypan Blue-Based Cell Viability Measurement Using Neural Networks

July 19, 2021
Author(s)
Adele Peskin, Steven Lund, Chenyi Ling, Laura Pierce, Sumona Sarkar, Firdavs Kurbanov, Michael Halter, Joe Chalfoun, John T. Elliott
Trypan blue dye exclusion-based cell viability measurements are highly dependent upon image quality and consistency. In order to make measurements repeatable, one must be able to reliably capture images at a consistent focal plane, and with signal-to-noise

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides

July 15, 2021
Author(s)
Xiaoyu (Sara) Yang, Pedatsur Neta, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion Remoroza, Meghan Burke Harris, Yuxue Liang, Sanford Markey, Stephen E. Stein
Annotating product ion peaks in tandem mass spectra is essential for evaluating spectral quality and validating peptide identification. This task is more complex for glycopeptides and is crucial for the confident determination of glycosylation sites in

Assessment of Serum Total 25 Hydroxyvitamin D Assay Commutability of Standard Reference Materials and College of American Pathologists Accuracy Based Vitamin D (ABVD) Scheme and Vitamin D External Quality Assessment Scheme (DEQAS) Materials: Vitamin D Sta

July 1, 2021
Author(s)
Johanna Camara, Stephen A. Wise, Andrew Hoofnagle, Emma L. Williams, Graham D. Carter, Julia C. Jones, Carolyn Burdette, Grace Hahm, Federica Nalin, Adam J. Kuszak, Joyce M. Merkel, Ramon Durazo-Arvizu, Pierre Lukas, E. Cavalier, Christian Popp, Christian Beckert, Jan Schultess, Glen Van Slooten, Carole Tourneur, Camille Pease, Ravi Kaul, Alfredo Villarreal, Fiona Ivison, Ralf Fischer, Jody M. van den Ouweland, Chung S. Ho, Emmett W. Law, Jean-Nicolas Simard, Renaud Gonthier, Brett Holmquist, Marcelo C. Batista, Heather Pham, Alex Bennett, Sarah Meadows, Lorna Cox, Eugene Jansen, Dilshad A. Khan, Kimberly Robyak, Michael H. Creer, Mark Kilbane, Patrick J. Twomey, James Freeman, Neil Parker, Jinyun Yuan, Robert Fitzgerald, Sohail Mushtaq, Michael W. Clarke, Norma Breen, Christine Simpson, Christopher T. Sempos
An interlaboratory study was conducted through the Vitamin D Standardization Program (VDSP) to assess commutability of Standard Reference Materials® (SRMs) and proficiency testing/external quality assessment (PT/EQA) samples for determination of serum

DNA glycosylase deficiency leads to decreased severity of lupus in the Polb-Y265C mouse model

June 24, 2021
Author(s)
Sesha Paluri, Matthew Burak, Alireza Senenjani, Kelly Carufe, Kaylin Clairmont, Isabel Alvarado-Cruz, Rithy Meas, Michael Kashgarian, Caroline Zeiss, Stephen Maher, Alfred Bothwell, Erdem Coskun, Melis Kant, Pawel Jaruga, Miral M. Dizdar, R S. Lloyd, Joann B. Sweasy
The Polb gene encodes DNA polymerase beta (Pol β), a DNA polymerase that functions in base excision repair (BER) and microhomology-mediated end-joining. The Pol β-Y265C protein exhibits low catalytic activity and fidelity, and is also deficient in

Hydroxyl radical is a significant player in oxidative DNA damage in vivo.

June 15, 2021
Author(s)
Miral M. Dizdar, Barry Halliwell, Amitav Adhikary, Michael Dingfelder
Recent publications have suggested that oxidative DNA damage mediated by hydroxyl radical (.OH) is unimportant in vivo, and that carbonate anion radical (CO3.-) plays the key role. We examine these claims and summarize the evidence that OH does play a key

Ne-22 Ion-Beam Radiation Damage to DNA: From Initial Free Radical Formation to Resulting DNA-Base Damage

June 14, 2021
Author(s)
Melis Kant, Pawel Jaruga, Erdem Coskun, Samuel Ward, Alexander Stark, Thomas Baumann, David Becker, Amitava Adhikary, Michael Sevilla, Miral M. Dizdar
We report on the physicochemical processes and the products of DNA damage involved in Ne-22 ion-beam radiation of hydrated (12±3 H2O/nucleotide) salmon sperm DNA at 77 K. Free radicals trapped at 77 K were identified using electron spin resonance (ESR)

Plasmonic Sensing Studies of a Gas-Phase Cystic Fibrosis Marker in Moisture Laden Air

May 29, 2021
Author(s)
Libin Sun, Drew Hall, Douglas Conrad, Kurt D. Benkstein, Stephen Semancik, Mona Zaghloul
A plasmonic sensing platform was developed as a noninvasive method to monitor gas-phase biomarkers related to cystic fibrosis (CF). The nanohole array (NHA) sensing platform is based on localized surface plasmon resonance (LSPR) and offers a rapid data

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies

May 3, 2021
Author(s)
John Butler, Manuel Fondevila, Carla Santos, Ana Freire, Christopher Phillips, M Lareu, Peter Vallone
A revision of an established 34 SNP forensic ancestry test has been made by swapping the under- performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for

Characterization of extracellular vesicles and artificial nanoparticles with four orthogonal single-particle analysis platforms

April 6, 2021
Author(s)
Emily Mallick, Tanina Arab, Yiyao Huang, Liang Dong, Zhaohao Liao, Zezhou Zhao, Barbara Smith, Norman J. Haughey, Kenneth Pienta, Barbara Slusher, Patrick Tarwater, Juan Pablo Tosar, Angela M. Zivkovic, Wyatt N. Vreeland, Michael E. Paulaitis, Kenneth W. Witwer
We compared four orthogonal technologies for sizing, counting, and phenotyping of extracellular vesicles (EVs) and synthetic particles. The platforms were: single-particle interferometric reflectance imaging sensing (SP-IRIS) with fluorescence

Hydration of Hydrophilic Cloth Facial Coverings Greatly Increases the Filtration Properties for Nanometer and Micrometer-sized Particles

March 8, 2021
Author(s)
Christopher D. Zangmeister, James Radney, Matthew E. Staymates, Edward P. Vicenzi, Jamie Weaver
Filtration efficiencies (FE) of natural, synthetic, and blended fabrics were measured as a function of relative humidity (RH) for particles with mobility diameters between 50 nm and 825 nm. Fabrics were equilibrated at 99 % RH, mimicking conditions

National Institute of Standards and Technology Environmental Scan 2020

February 9, 2021
Author(s)
Heather Evans, Kristen K. Greene, William M. Healy, Elizabeth Hoffman, Kate Rimmer, Anna V. Sberegaeva, Neil M. Zimmerman
The 2020 National Institute of Standards and Technology Environmental Scan provides an analysis of key external factors that could impact NIST and the fulfillment of its mission in coming years. The analyses were conducted through four separate lenses

Chromosome-scale, haplotype-resolved assembly of human genomes

December 7, 2020
Author(s)
Justin Zook, Shilpa Garg, Heng Li
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which

Chapter 4: Oxidatively induced DNA damage: Mechanisms and measurement

November 20, 2020
Author(s)
Miral M. Dizdar, Erdem Coskun, Gamze Tuna, Melis Kant, Pawel Jaruga
Oxidatively induced damage to DNA occurs in living organisms by endogenously or exogenously generated reactive species including free radicals. Mounting evidence suggests that this type of DNA damage plays an important role in the etiology of numerous

A Case Study of Medical Device Wireless Coexistence Evaluation

October 1, 2020
Author(s)
Mohamed Al-Kalaa, Joshua Guag, Seth Seidman, Yao Ma, Jason Coder
This article aims to provide a narrative for addressing wireless coexistence in medical devices to help medical device developers, test engineers, and regulatory affairs personnel throughout the device life cycle. Accordingly, we present a case-study

A NIST-Hosted Virtual Workshop on Measuring SARS-CoV-2 in Wastewater and Fecal Material: A Call for Standards

September 28, 2020
Author(s)
Sandra M. Da Silva, Paulina K. Piotrowski, Christina M. Jones, Stephanie L. Servetas, Nancy J. Lin, Katrice A. Lippa, Scott A. Jackson
The National Institute of Standards and Technology (NIST) has leveraged its expertise in chemical and biological metrology and standards development as well as its strong relationships with stakeholders to host a virtual workshop on June 16, 2020 that

A Diploid Assembly-based Benchmark for Variants in The Major Histocompatibility Complex

September 22, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Chen-Shan Chin, Qiandong Zeng, Alexander Dilthey, Tobias Marschall, Mikko Rautiainen, Erik Garrison, Shilpa Garg
Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5
Displaying 76 - 100 of 798