CyVerse: Cyberinfrastructure for open science.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

Application of 2D-NMR with room temperature NMR probes for the assessment of the higher order structure of filgrastim.

The higher order structure (HOS) of biotherapeutics is a critical quality attribute that can be evaluated by nuclear magnetic resonance (NMR) spectroscopy at atomic resolution. NMR spectral mapping of HOS can be used to establish HOS consistency of a biologic across manufacturing changes or to compare a biosimilar to an innovator reference product. A previous inter-laboratory study performed using filgrastim drug products demonstrated that two-dimensional (2D)-NMR 1HN-15NH heteronuclear correlation spectroscopy is a highly robust and precise method for mapping the HOS of biologic drugs at natural abundance using high sensitivity NMR 'cold probes.' Here, the applicability of the 2D-NMR method to fingerprint the HOS of filgrastim products is demonstrated using lower sensitivity, room temperature NMR probes. Combined chemical shift deviation and principal component analysis are used to illustrate the performance and inter-laboratory precision of the 2D-NMR method when implemented on room temperature probes.

Use and qualification of primary and secondary standards employed in quantitative ¹H NMR spectroscopy of pharmaceuticals.

Standards are required in quantitative NMR (qNMR) to obtain accurate and precise results. In this study acetanilide was established and used as a primary standard. Six other chemicals were selected as secondary standards: 3,4,5-trichloropyridine, dimethylterephthalate, maleic acid, 3-sulfolene, 1,4-bis(trimethylsilyl)benzene, and 1,3,5-trimethoxybenzene. The secondary standards were quantified using the primary standard acetanilide. A protocol for qualification and periodic checks of these secondary standards was developed, and used for evaluation of the stability of the compounds. Periodic monitoring of purity was performed for several years. The purity was higher than 99% for all secondary standards. All standards maintained the initial purity during the time period of monitoring, with very small variations in purity (0.3-0.4%). The selected secondary standards were shown to be suitable qNMR standards and that periodic requalification of the standards by qNMR ensures reliable analytical results. These standards have been used in our laboratory for compliance testing of pharmaceutical active substances and approved medicinal products as well as for analysis of suspected illegal medicines. In total more than 1000 samples have been tested using both internal and external standardization and examples are given.

Screening of counterfeit corticosteroid in creams and ointments by NMR spectroscopy.

It has been shown that NMR spectroscopy is an effective analytical method to rapidly screen creams and ointments for counterfeit corticosteroids. Extraction and NMR procedures have been developed. Ten over the counter creams and ointments sold in health care shops were screened and two creams were found to contain counterfeited corticosteroids.

Broadening of 1H NMR signals in the spectra of heparin and OSCS by paramagnetic transition metal ions. The use of EDTA to sharpen the signals.

Some signals in the (1)H NMR spectra of heparin and oversulphated chondroitin sulphate (OSCS) are occasionally broad or very broad owing to the presence of paramagnetic metal ions in those polysaccharides. The addition of very small amounts of EDTA to heparin or to OSCS contaminated heparin solutions was needed to obtain normal looking spectra.

Effect of Ca2+ on the 1H NMR chemical shift of the methyl signal of oversulphated chondroitin sulphate, a contaminant in heparin.

The chemical shift of the methyl signal of oversulphated chondroitin sulphate (OSCS) is dependent on the type and concentration of the counterion. When OSCS is present as a contaminant in heparin sodium, the reported methyl 1H chemical shift is 2.15 +/- 0.02 ppm. In this report, a value of 2.18 +/- 0.01 ppm is reported for the OSCS in the presence of Ca2+. The chemical shift of the methyl signal of pure OSCS varies linearly from 2.13 ppm to 2.18 ppm with increasing amounts of Ca2+, until reaching the saturation point of four Ca2+ ions per OSCS disaccharide unit, which contains four sulphate groups (a 1:1 ratio between sulphate groups and Ca2+). This Ca2+ effect can be used for OSCS identification as well as to facilitate quantification.