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@@ -23,13 +23,13 @@ fontsize: 14pt
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:::
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-[^1]: Source: https://www.organdonor.gov/statistics-stories/statistics.html
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+[^1]: [organdonor.gov](https://www.organdonor.gov/statistics-stories/statistics.html)
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## Organ transplants are a life-saving treatment
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![Organ donation statistics for the USA in 2018[^2]](graphics/presentation/transplants-organ-CROP-RASTER.png){ height=70% }
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-[^2]: Source: https://www.organdonor.gov/statistics-stories/statistics.html
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+[^2]: [organdonor.gov](https://www.organdonor.gov/statistics-stories/statistics.html)
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## Graft rejection is an adaptive immune response
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@@ -54,7 +54,7 @@ fontsize: 14pt
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![Kidney allograft survival rates in children by transplant year[^3]](graphics/presentation/kidney-graft-survival.png){ height=65% }
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-[^3]: Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)
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+[^3]:[ Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
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## Rejection is treated with immune suppressive drugs
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@@ -90,7 +90,7 @@ animal model for experimental graft rejection treatment
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## Today's focus
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-### Chapter 2
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+### \Large Topic 1: Immune memory
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\Large
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@@ -105,6 +105,8 @@ and memory $\mathsf{CD4}^{+}$ T-cell activation
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## Memory cells are a problem for immune suppression
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+<!-- Need graphics -->
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+
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\large
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Compared to naïve cells, memory cells:
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@@ -118,7 +120,7 @@ Compared to naïve cells, memory cells:
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naïve cells
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* evolve over time to respond even more strongly to their antigen
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-. . .
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+## Memory cells are a problem for immune suppression
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\large
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@@ -177,10 +179,18 @@ Data generated by Sarah Lamere, published in GEO as
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## Finding enriched regions across the genome
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+<!-- Graphic from SICER paper: Fig1 -->
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+<!-- Use one of my IDR example plots for IDR -->
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+
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* Scan across the genome looking for regions with read coverage above
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- background level in each donor using SICER peak caller
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+ background level in each donor using SICER peak caller[^6]
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* Use Irreducible Discovery Rate framework to identify peaks that are
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- called consistently across multiple donors
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+ called consistently across multiple donors[^7]
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+
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+[^6]: [Chongzhi Zang et al. “A clustering approach for identification of enriched domains from histone modification ChIP-Seq data”. In: Bioinformatics 25.15 (2009) doi: 10.1093/bioinformatics/btp340.](https://doi.org/10.1093/bioinformatics/btp340)
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+[^7]: [Qunhua Li et al. “Measuring reproducibility of high-throughput experiments”. In: AOAS (2011)](https://doi.org/10.1214/11-AOAS466)
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+
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+## Finding enriched regions across the genome
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