Global text mining and development of pharmacogenomic knowledge resource for precision medicine

Understanding patients' genomic variations and their effect in protecting or predisposing them to drug response phenotypes is important for providing personalized healthcare. Several studies have manually curated such genotype-phenotype relationships into organized databases from clinical trial data or published literature. However, there are no text mining tools available to extract high-accuracy information from such existing knowledge. In this work, we used a semiautomated text mining approach to retrieve a complete pharmacogenomic (PGx) resource integrating disease-drug-gene-polymorphism relationships to derive a global perspective for ease in therapeutic approaches. We used an R package, pubmed.mineR, to automatically retrieve PGx-related literature. We identified 1,753 disease types, and 666 drugs, associated with 4,132 genes and 33,942 polymorphisms collated from 180,088 publications. With further manual curation, we obtained a total of 2,304 PGx relationships. We evaluated our approach by performance (precision = 0.806) with benchmark datasets like Pharmacogenomic Knowledgebase (PharmGKB) (0.904), Online Mendelian Inheritance in Man (OMIM) (0.600), and The Comparative Toxicogenomics Database (CTD) (0.729). We validated our study by comparing our results with 362 commercially used the US- Food and drug administration (FDA)-approved drug labeling biomarkers. Of the 2,304 PGx relationships identified, 127 belonged to the FDA list of 362 approved pharmacogenomic markers, indicating that our semiautomated text mining approach may reveal significant PGx information with markers for drug response prediction. In addition, it is a scalable and state-of-art approach in curation for PGx clinical utility

Literature Review of Omicron: A Grim Reality Amidst COVID-19

Coronavirus disease 2019 (COVID-19) first emerged in Wuhan city in December 2019, and became a grave global concern due to its highly infectious nature. The Severe Acute Respiratory Coronavirus-2, with its predecessors (i.e., MERS-CoV and SARS-CoV) belong to the family of Coronaviridae. Reportedly, COVID-19 has infected 344,710,576 people around the globe and killed nearly 5,598,511 persons in the short span of two years. On November 24, 2021, B.1.1.529 strain, later named Omicron, was classified as a Variant of Concern (VOC). SARS-CoV-2 has continuously undergone a series of unprecedented mutations and evolved to exhibit varying characteristics. These mutations have largely occurred in the spike (S) protein (site for antibody binding), which attribute high infectivity and transmissibility characteristics to the Omicron strain. Although many studies have attempted to understand this new challenge in the COVID-19 strains race, there is still a lot to be demystified. Therefore, the purpose of this review was to summarize the structural or virologic characteristics, burden, and epidemiology of the Omicron variant and its potential to evade the immune response

Assessing the Compliance of Dental Clinicians towards Regulatory Infection Control Guidelines Using a Newly Developed Survey Tool: A Pilot Cross-Sectional Study in India

Adherence to the dental practice regulatory guidelines instituted during the COVID- 19 pandemic is essential to minimize the transmission of SARS-CoV-2 strains. Given the lack of a valid and reliable survey tool to assess the adherence to dental practice guidelines, this study aims to develop, validate, and test a survey tool on a pilot sample of dental clinicians practicing in India. A survey tool was developed/validated through a sequential phasic approach: Phase Ideveloping survey using conceptual and literature framework; Phase II: ascertaining its validity and reliability; Phase III: pilot testing; and Phase IV: assessing construct validity by exploratory factor analysis (EFA) on the responses collected in Spring 2021. The EFA was achieved using a traditional unweighted least squares extraction method through a varimax rotation with Kaiser normalization. A six-factor solution with 18 items (with the global reliability of 86%) related to screening, regular infection prevention measures, infection control inside the dental operatory, disinfection of the dental unit, disposal, and other COVID-19-specific preventive measures were extracted. Our sample had higher compliance with regard to providing alcohol-based hand scrubs, providing protective gear to attendees, collecting travel/medical history, and screening patients for COVID-19 symptoms. In contrast, less compliance was observed regarding the use of paperless forms of practice and rubber dams in the operatory. The use of a validated survey tool ensures the collection of reliable and valid data, which can serve as baseline data to measure the uptake and effectiveness of dental practice regulatory guidelines in a clinical setting and community dental health clinics