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1. Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA‐Sequencing

   https://doi.org/10.1002/art.40772  

   Mahendra, Ankit; Yang, Xingyu; Abnouf, Shaza; Adolacion, Jay_R_T; Park, Daechan; Soomro, Sanam; Roszik, Jason; Coarfa, Cristian; Romain, Gabrielle; Wanzeck, Keith; et al (February 2019, Arthritis & Rheumatology)

   ObjectiveTo obtain the comprehensive transcriptome profile of human citrulline‐specific B cells from patients with rheumatoid arthritis (RA). MethodsCitrulline‐ and hemagglutinin‐specific B cells were sorted by flow cytometry using peptide–streptavidin conjugates from the peripheral blood ofRApatients and healthy individuals. The transcriptome profile of the sorted cells was obtained byRNA‐sequencing, and expression of key protein molecules was evaluated by aptamer‐basedSOMAscan assay and flow cytometry. The ability of these proteins to effect differentiation of osteoclasts and proliferation and migration of synoviocytes was examined by in vitro functional assays. ResultsCitrulline‐specific B cells, in comparison to citrulline‐negative B cells, from patients withRAdifferentially expressed the interleukin‐15 receptor α (IL‐15Rα) gene as well as genes related to protein citrullination and cyclicAMPsignaling. In analyses of an independent cohort of cyclic citrullinated peptide–seropositiveRApatients, the expression ofIL‐15Rα protein was enriched in citrulline‐specific B cells from the patients’ peripheral blood, and surprisingly, all B cells fromRApatients were capable of producing the epidermal growth factor ligand amphiregulin (AREG). Production ofAREGdirectly led to increased migration and proliferation of fibroblast‐like synoviocytes, and, in combination with anti–citrullinated protein antibodies, led to the increased differentiation of osteoclasts. ConclusionTo the best of our knowledge, this is the first study to document the whole transcriptome profile of autoreactive B cells in any autoimmune disease. These data identify several genes and pathways that may be targeted by repurposing severalUSFood and Drug Administration–approved drugs, and could serve as the foundation for the comparative assessment of B cell profiles in other autoimmune diseases. 

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2. Keck all sky precision adaptive optics: project overview

   https://doi.org/10.1117/12.2560017  

   Wizinowich, Peter L.; Chin, Jason C.; Correia, Carlos M.; Lu, Jessica R.; Brown, Thomas; Casey, Kelleen; Cetre, Sylvain; Delorme, Jacques-Robert; Gers, Luke; Hunter, Lisa; et al (December 2020, Proceedings of the SPIE)

   Schmidt, Dirk; Schreiber, Laura; Vernet, Elise (Ed.)

   We present the status and plans for the Keck All sky Precision Adaptive optics (KAPA) program. KAPA includes four key science programs, an upgrade to the Keck I laser guide star (LGS) adaptive optics (AO) facility to improve image quality and sky coverage, AO telemetry based point spread function (PSF) estimates for all science exposures, and an educational component focused on broadening the participation of women and underrepresented groups in instrumentation. For the purpose of this conference we will focus on the AO facility upgrade which includes implementation of a new laser, wavefront sensor and real-time controller to support laser tomography, the laser tomography system itself, and modifications to an existing near-infrared tip-tilt sensor to support multiple natural guide star (NGS) and focus measurements. 

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3. A comparison of water quality sensor deployment designs in wadeable streams

   https://doi.org/10.1002/lom3.10452  

   Hensley, Robert; Harrison, Nicolas; Goodman, Keli; Cawley, Kaelin; Litt, Guy; Nance, Bryce; Catolico, Nora (August 2021, Limnology and Oceanography: Methods)

   Abstract The design of infrastructure used for deploying water quality sensors can potentially impact data quality. Despite this, sensor infrastructure design has not been well discussed in the peer‐reviewed literature. Here, we present side‐by‐side measurements from two contrasting designs; a “monopod” consisting of a strut driven into the streambed and a downrigger suspended from an “overhead cable.” We collected measurements over an approximately 6‐month period from two wadeable stream monitoring sites within the National Ecological Observatory Network. In general, we observed minimal differences between measurements, suggesting both designs to be viable options from a data quality perspective under normal operating conditions. However, the monopod design was more susceptible to coming out of the water during low stage and burial by sedimentation. While more expensive and logistically complex to install, the overhead cable design exhibited greater survivability, adjustability, and serviceability. We discuss additional design considerations and potential modifications that we hope will prove useful to other researchers in instrumenting their own sites. 

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4. Poster: Perceived Adversarial Examples

   Man, Yanmao; Li, Ming; Gerdes, Ryan (May 2019, IEEE Symposium on Security and Privacy)

   Adversarial examples in deep learning were first discovered for the digital domain and later effected in the physical domain. In this work, we demonstrate adversarial examples in the perception domain; i.e., adversarial examples that are introduced by compromising the sensing mechanism of an image sensor. Our proposed attack relies on the injection of electromagnetic interference in a remote manner, and does not require physical modifications to the object, which makes the attack easier to launch and harder to detect. 

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5. PTMViz: a tool for analyzing and visualizing histone post translational modification data

   https://doi.org/10.1186/s12859-021-04166-9  

   Chappell, Kevin; Graw, Stefan; Washam, Charity L.; Storey, Aaron J.; Bolden, Chris; Peterson, Eric C.; Byrum, Stephanie D. (May 2021, BMC Bioinformatics)

   Abstract BackgroundHistone 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. ResultsPTMViz 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. ConclusionsHistone modifications play an integral role 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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