BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data.

Recent surges in large-scale mass spectrometry (MS)-based proteomics studies demand a concurrent rise in methods to facilitate reliable and reproducible data analysis. Quantification of proteins in MS analysis can be affected by variations in technical factors such as sample preparation and data acquisition conditions leading to batch effects, which adds to noise in the data set. This may in turn affect the effectiveness of any biological conclusions derived from the data. Here we present Batch-effect Identification, Representation, and Correction of Heterogeneous data (BIRCH), a workflow for analysis and correction of batch effect through an automated, versatile, and easy to use web-based tool with the goal of eliminating technical variation. BIRCH also supports diagnosis of the data to check for the presence of batch effects, feasibility of batch correction, and imputation to deal with missing values in the data set. To illustrate the relevance of the tool, we explore two case studies, including an iPSC-derived cell study and a Covid vaccine study to show different context-specific use cases. Ultimately this tool can be used as an extremely powerful approach for eliminating technical bias while retaining biological bias, toward understanding disease mechanisms and potential therapeutics.

Pleural fluid cytology in prompt diagnosis of pleuro-pulmonary nocardiosis masquerading as COVID-19.

Introduction: There are few reports of nocardial infections among the Indian population. We report this case because of its rarity and unique presentation and to highlight the role of cytology in diagnosis. Case Details: A 74-year-old woman presented with fever and chest pain of a duration of 15 days. In view of the coronavirus disease (COVID) pandemic, she was given steroids. She developed breathlessness and was referred to a tertiary care hospital. Her pleural fluid cytology showed filamentous bacteria. A diagnosis of nocardia was confirmed by culture. Discussion: Nocardiosis refers to the localized or disseminated infection caused by filamentous aerobic bacteria of the genus Nocardia. The clinical presentation of nocardiosis is highly variable. In our case, clinical misdiagnosis as COVID-19 and steroid treatment would have caused deterioration of nocardiosis. Conclusion: All patients with pulmonary symptoms should be thoroughly evaluated before considering a diagnosis of COVID-19. Pleural fluid cytology can be of help in the diagnosis of nocardiosis.