Bioinformatics
November 2024
Summary: We present ADTGP, an R package that uses Gaussian process regression to correct droplet-specific technical noise in single-cell protein sequencing data. ADTGP improves the interpretability of the data by modeling the distribution of protein expression, conditioned on equal isotype control counts across cells. ADTGP is written in R and needs only the protein raw counts, isotype control raw counts, and a design matrix to run.
View Article and Find Full Text PDFPurpose: Venezia™ is an interstitial brachytherapy applicator for treating advanced cervical and vaginal vault recurrent cancer. However, there are limitations that lead to suboptimal target coverage. 3D printing introduction allows the redesign of Venezia™ for bulky and irregular-shaped tumors.
View Article and Find Full Text PDFRadiotherapy with electrons is commonly applied to the tumor bed after whole-breast radiotherapy following breast conservation surgery for breast cancer patients. However, the radiation dose to adjacent organs-at-risk (OARs) and conformity of planning target volume (PTV) cannot be optimized. In this study, we examine the feasibility of using modulated electron bolus (MEB) to improve PTV conformity and reduce the dose to these OARs.
View Article and Find Full Text PDFUnlabelled: Mutant isocitrate dehydrogenase 1 (IDH1) and IDH2 block the differentiation of acute myeloid leukemia (AML) cells through production of R-2-hydroxyglutarate (R-2-HG). IDH inhibitors can induce differentiation of AML cells by lowering R-2-HG but have limited clinical efficacy as single agents. Here, we performed a genome-wide CRISPR knockout screen in an Idh1-mutated hematopoietic progenitor cell line to identify genes that increased the differentiation response to ivosidenib, an IDH1 inhibitor.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
August 2022
Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a mechanism by which the SARS-CoV-2 virus coopts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-β. We reveal that the SARS-CoV-2 encoded nonstructural protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein.
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