VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories.

MOTIVATION: Single-cell transcriptomics profiling technologies enable genome-wide gene expression measurements in individual cells but can currently only provide a static snapshot of cellular transcriptional states. RNA velocity analysis can help infer cell state changes using such single-cell transcriptomics data. To interpret these cell state changes inferred from RNA velocity analysis as part of underlying cellular trajectories, current approaches rely on visualization with principal components, t-distributed stochastic neighbor embedding and other 2D embeddings derived from the observed single-cell transcriptional states. However, these 2D embeddings can yield different representations of the underlying cellular trajectories, hindering the interpretation of cell state changes. RESULTS: We developed VeloViz to create RNA velocity-informed 2D and 3D embeddings from single-cell transcriptomics data. Using both real and simulated data, we demonstrate that VeloViz embeddings are able to capture underlying cellular trajectories across diverse trajectory topologies, even when intermediate cell states may be missing. By considering the predicted future transcriptional states from RNA velocity analysis, VeloViz can help visualize a more reliable representation of underlying cellular trajectories. AVAILABILITY AND IMPLEMENTATION: Source code is available on GitHub (https://github.com/JEFworks-Lab/veloviz) and Bioconductor (https://bioconductor.org/packages/veloviz) with additional tutorials at https://JEF.works/veloviz/. Datasets used can be found on Zenodo (https://doi.org/10.5281/zenodo.4632471). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Use of Fitbit Technology Does Not Impact Health Biometrics in a Community of Older Adults.

Introduction: To evaluate if the offering of Fitbit technology led to changes in cardiovascular health metrics in a cohort of older adults. Methods: A retrospective cohort study was developed in two community-embedded health monitoring sites, located in aggregate housing communities for older adults in Westchester County, NY. Participants included older adults (55 years or older) enrolled in the Telehealth Intervention Programs for Seniors (TIPS) initiative, a community-embedded remote patient monitoring initiative. Weekly blood pressure, heart rate, weight, and blood oxygenation were taken on all participants. For participants who accepted a Fitbit Zip device, a weekly step count was also collected. Results: Ninety-four TIPS participants were offered Fitbit technology. Thirty participants accepted the technology and used it for a minimum of 6 months. No significant differences in any of the regularly acquired biometrics were noted between Fitbit users and non-Fitbit users. Across all participants, regardless of Fitbit use, there was a significant decrease in systolic blood pressure (SBP) over time. Conclusions: Neither Fitbit Zip ownership or compliance to Fitbit Zip usage influenced any of the biometrics taken as part of the TIPS. However, participation in the TIPS initiative may have an overall positive effect on SBP in older adults.

CPAP complications after dacryocystorhinostomy: a narrative review.

STUDY OBJECTIVES: Patients with obstructive sleep apnea (OSA) often require the use of a continuous positive airway pressure (CPAP) machine. However, some patients experience issues using CPAP after receiving a dacryocystorhinostomy (DCR) for epiphora. This review aims to assess these complications and the potential interventions. METHODS: A systematic literature search was conducted in March 2023 with the PubMed, EMBASE, Web of Science, and Scopus databases. Since most of the studies were case reports and lacked quantitative results, a narrative review was done. RESULTS: Fourteen studies were included for review, representing 49 patients. During nightly CPAP use, 77.6% (38/49) of patients experienced air regurgitation onto the ocular surface via the tear drainage passage constructed by DCR. The interventions attempted could be categorized into (a) CPAP changes or (b) ophthalmic management. CPAP changes included changing the CPAP mask (successful in 5/6 patients), modifying the pressure or incorporating heated humidifier tubing (2/8 successes), changing the ventilation mode (1/3 successes), and switching to a CPAP alternative (1/2 successes). Ophthalmic management included eye plugs (3/3 successes), eye lubricants (2/6 successes), an eye patch (1/2 successes), and removal of the Lester Jones tube placed during DCR (1/1 successes). After trying these interventions, 36.7% (18/49) of patients continued to experience symptoms and opted to discontinue CPAP therapy. CONCLUSIONS: CPAP related issues after DCR are common and can be difficult to treat. There are a variety of techniques to improve CPAP use and adherence after DCR.

Socratic Artificial Intelligence Learning (SAIL): The Role of a Virtual Voice Assistant in Learning Orthopedic Knowledge.

OBJECTIVE: We hypothesized that learning through multiple sensory modalities would improve knowledge recall and recognition in orthopedic surgery residents and medical students. DESIGN: We developed a virtual study assistant, named Socratic Artificial Intelligence Learning (SAIL), based on a custom-built natural language processing algorithm. SAIL draws from practice questions approved by the American Board of Orthopaedic Surgery and quizzes users through a conversational, voice-enabled Web interface. We performed a randomized controlled study using a within-subjects, repeated measures design. SETTING: Participants first took a pretest to assess their baseline knowledge. They then underwent 10 days of spaced repetition training with practice questions using 3 modalities: oral response, typed response, and multiple-choice. Recall and recognition of the practiced knowledge were assessed via a post-test administered on the first day, first week, and 2 months after the training period. PARTICIPANTS: Twenty-four volunteers, who were medical students and orthopedic surgery residents at multiple US medical institutions. RESULTS: The oral, typed, and multiple-choice modalities produced similar recall and recognition rates. Although participants preferred using the traditional multiple-choice modality to study for standardized examinations, many were interested in supplementing their study routine with SAIL and believe that SAIL may improve their performance on written and oral examinations. CONCLUSIONS: SAIL is not inferior to the multiple-choice modality for learning orthopedic core knowledge. These results indicate that SAIL can be used to supplement traditional study methods. COMPETENCIES: medical knowledge; practice-based learning and improvement.

Adaptive Immune Receptor Distinctions Along the Colorectal Polyp-Tumor Timelapse.

INTRODUCTION: Colorectal cancer (CRC) is the third-most common cancer diagnosed worldwide, with 1.85 million new cases per year. While mortality has significantly decreased due to preventive colonoscopy, only 5% of polyps identified progress to cancer. Studies have found that immunological alterations in other solid tumor microenvironments are associated with worse prognoses. METHODS: We applied an immunogenomics approach to assess adaptive immune receptor gene expression changes that were associated with development of adenocarcinoma, utilizing 79 samples that represented normal, tubular, villous, and tumor colorectal tissue for 32 patients. RESULTS: Results indicated that the number of productive TRD and TRG recombination reads, representing gamma-delta (γδ) T-cells, significantly decreased with progression from normal to tumor tissue. A further assessment of two independent CRC datasets was consistent with a decrease in TRD recombination reads with progression to CRC. Further, we identified three physicochemical parameters for immunoglobulin, complementarity determining region-3 (CDR3) amino acids associated with progression from normal to tumor tissue. CONCLUSIONS: Overall, this study points towards a need for further investigation of γδ T-cells in relation to CRC development; and indicates immunoglobulin CDR3 physicochemical features as potential CRC biomarkers.

Blood-based T cell receptor anti-viral CDR3s are associated with worse overall survival for neuroblastoma.

With the advent of large collections of adaptive immune receptor recombination reads representing cancer, there is the opportunity to further investigate the adaptive immune response to viruses in the cancer setting. This is a particularly important goal due to longstanding but still not well-resolved questions about viral etiologies in cancer and viral infections as comorbidities. In this report, we assessed the T cell receptor complementarity determining region-3 (CDR3) amino acid (AA) sequences, for blood-sourced TCRs from neuroblastoma (NBL) cases, for exact AA sequence matches to previously identified anti-viral TCR CDR3 AA sequences. Results indicated the presence of anti-viral TCR CDR3 AA sequences in the NBL blood samples highly significantly correlated with worse overall survival. Furthermore, the TCR CDR3 AA sequences demonstrating chemical complementarity to many cytomegalovirus antigens represented cases with a worse outcome, including cases where such CDR3s were obtained from tumor samples. Overall, these results indicate a significant need for, and provide a novel strategy for assessing viral infection complications in NBL patients.

Nanoparticle-based targeting of microglia improves the neural regeneration enhancing effects of immunosuppression in the zebrafish retina.

Retinal Müller glia function as injury-induced stem-like cells in zebrafish but not mammals. However, insights gleaned from zebrafish have been applied to stimulate nascent regenerative responses in the mammalian retina. For instance, microglia/macrophages regulate Müller glia stem cell activity in the chick, zebrafish, and mouse. We previously showed that post-injury immunosuppression by the glucocorticoid dexamethasone accelerated retinal regeneration kinetics in zebrafish. Similarly, microglia ablation enhances regenerative outcomes in the mouse retina. Targeted immunomodulation of microglia reactivity may therefore enhance the regenerative potential of Müller glia for therapeutic purposes. Here, we investigated potential mechanisms by which post-injury dexamethasone accelerates retinal regeneration kinetics, and the effects of dendrimer-based targeting of dexamethasone to reactive microglia. Intravital time-lapse imaging revealed that post-injury dexamethasone inhibited microglia reactivity. The dendrimer-conjugated formulation: (1) decreased dexamethasone-associated systemic toxicity, (2) targeted dexamethasone to reactive microglia, and (3) improved the regeneration enhancing effects of immunosuppression by increasing stem/progenitor proliferation rates. Lastly, we show that the gene rnf2 is required for the enhanced regeneration effect of D-Dex. These data support the use of dendrimer-based targeting of reactive immune cells to reduce toxicity and enhance the regeneration promoting effects of immunosuppressants in the retina.

Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data.

Recent technological advancements have enabled spatially resolved transcriptomic profiling but at multi-cellular pixel resolution, thereby hindering the identification of cell-type-specific spatial patterns and gene expression variation. To address this challenge, we develop STdeconvolve as a reference-free approach to deconvolve underlying cell types comprising such multi-cellular pixel resolution spatial transcriptomics (ST) datasets. Using simulated as well as real ST datasets from diverse spatial transcriptomics technologies comprising a variety of spatial resolutions such as Spatial Transcriptomics, 10X Visium, DBiT-seq, and Slide-seq, we show that STdeconvolve can effectively recover cell-type transcriptional profiles and their proportional representation within pixels without reliance on external single-cell transcriptomics references. STdeconvolve provides comparable performance to existing reference-based methods when suitable single-cell references are available, as well as potentially superior performance when suitable single-cell references are not available. STdeconvolve is available as an open-source R software package with the source code available at https://github.com/JEFworks-Lab/STdeconvolve .

Downregulation of Nodal inhibits metastatic progression in retinoblastoma.

Retinoblastoma is the most common intraocular malignancy in children. We previously found that the ACVR1C/SMAD2 pathway is significantly upregulated in invasive retinoblastoma samples from patients. Here we studied the role of an ACVR1C ligand, Nodal, in regulating growth and metastatic dissemination in retinoblastoma. Inhibition of Nodal using multiple short hairpin (shRNAs) in WERI Rb1 and Y79 retinoblastoma cell cultures reduced growth by more than 90%, as determined by CCK-8 growth assay. Proliferation was also significantly inhibited, as found by Ki67 assay. These effects were paralleled by inhibition in the phosphorylation of the downstream effector SMAD2, as well as induction of apoptosis, as we observed more than three-fold increase in the percentage of cells positive for cleaved-caspase-3 or expressing cleaved-PARP1. Importantly, we found that downregulation of Nodal potently suppressed invasion in vitro, by 50 to 80%, as determined by transwell invasion assay (p = 0.02). Using an orthotopic model of retinoblastoma in zebrafish, we found 34% reduction in the ability of the cells to disseminate outside the eye, when Nodal was knocked down by shRNA (p = 0.0003). These data suggest that Nodal plays an important role in promoting growth, proliferation and invasion in retinoblastoma, and can be considered a new therapeutic target for both primary tumor growth and metastatic progression.