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  1. Abstract Background

    Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregularities in histone PTMs can lead to a variety of different diseases including various forms of cancer. Histone modifications are analyzed using high resolution mass spectrometry, which generate large amounts of data that requires sophisticated bioinformatics tools for analysis and visualization. PTMViz is designed for downstream differential abundance analysis and visualization of both protein and/or histone modifications.

    Results

    PTMViz provides users with data tables and visualization plots of significantly differentiated proteins and histone PTMs between two sample groups. All the data is packaged into interactive data tables and graphs using the Shiny platform to help the user explore the results in a fast and efficient manner to assess if changes in the system are due to protein abundance changes or epigenetic changes. In the example data provided, we identified several proteins differentially regulated in the dopaminergic pathway between mice treated with methamphetamine compared to a saline control. We also identified histone post-translational modifications including histone H3K9me, H3K27me3, H4K16ac, and that were regulated due to drug exposure.

    Conclusions

    Histone modifications play an integral rolemore »in the regulation of gene expression. PTMViz provides an interactive platform for analyzing proteins and histone post-translational modifications from mass spectrometry data in order to quickly identify differentially expressed proteins and PTMs.

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  2. Free, publicly-accessible full text available August 1, 2023
  3. Free, publicly-accessible full text available April 1, 2023
  4. Free, publicly-accessible full text available April 1, 2023
  5. Abstract The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020, there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sublineages (B.1.177 and sublineages B.1.177.XX). We collectively call this Janus, and it was eventually replaced by the Alpha (B.1.1.7) variant of concern (VoC), next replaced by Delta (B.1.617.2), which itself might soon be replaced by a fourth pandemic wave consisting of Omicron (B.1.1.529). We observe that splitting up and redefining variant lineages over time, as was the case with Janus and is now happening with Alpha, Delta and Omicron, is not helpful to describe the epidemic waves spreading globally. Only ∼5% of the 30 000 nucleotides of the SARS-CoV-2 genome are found to be variable. We conclude that a fourth wave of the pandemic with the Omicron variant might not be that different from other VoCs, and that we may already have the tools in hand to effectively deal with this new VoC.
  6. Virtual and immersive virtual reality, VR and iVR, provide flexible and engaging learning opportunities, such as virtual field trips (VFTs). Despite its growing popularity for education, understanding how iVR compared to non-immersive media influences learning is still challenged by mixed empirical results and a lack of longitudinal research. This study addresses these issues through an experiment in which undergraduate geoscience students attended two temporally separated VFT sessions through desktop virtual reality (dVR) or iVR, with their learning experience and outcomes measured after each session. Our results show higher levels of enjoyment and satisfaction as well as a stronger sense of spatial presence in iVR students in both VFTs compared to dVR students, but no improvement in learning outcomes in iVR compared to dVR. More importantly, we found that there exists a critical interaction between VR condition and repeated participation in VFTs indicating that longitudinal exposure to VFTs improves knowledge performance more when learning in iVR than through dVR. These results suggest that repeated use of iVR may be beneficial in sustaining students’ emotional engagement and compensating the initial deficiency in their objective learning outcomes compared to other less immersive technologies.

  7. Preserving differential privacy has been well studied under the centralized setting. However, it’s very challenging to preserve differential privacy under multiparty setting, especially for the vertically partitioned case. In this work, we propose a new framework for differential privacy preserving multiparty learning in the vertically partitioned setting. Our core idea is based on the functional mechanism that achieves differential privacy of the released model by adding noise to the objective function. We show the server can simply dissect the objective function into single-party and cross-party sub-functions, and allocate computation and perturbation of their polynomial coefficients t o l ocal p arties. Our method n eeds o nly o ne r ound of noise addition and secure aggregation. The released model in our framework achieves the same utility as applying the functional mechanism in the centralized setting. Evaluation on real-world and synthetic datasets for linear and logistic regressions shows the effectiveness of our proposed method.