dence for under-represented minority students; and make other small changes such as moving the final from the first day of finals at 7:30 AM to a later time when students are shown to have greater success. A long-term goal is to hire a professor of practice in statistics for continued leadership and research in statistical education at UNM.
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No workshop fee. Food and caffeine contribution: $10-15. Math & Stat event link.
I'm going to host an R Package Development R-Hack-a-Pack one-day workshop on Friday 8/17 from 10-5. This is like a "hack-a-thon", but, instead of tackling a dataset analysis, the goal is to learn and use the skills to package R code. The first hour or so will cover the basic ideas of packaging code using modern tools such as RStudio, devtools, and usethis. The rest of the day is intended as a protected time where you can turn your code into a package. We'll cover the basics of creating a package, package testing, writing vignettes, and using github (and CRAN) for version control and making your package available.
If you already have a set of functions that you load with script("my_functions.R"), then you're an afternoon away from making a great package.
If you have a large script with repeated code, then you can start by turning the repeated code into functions, package those functions, and write a short vignette to perform the same analysis using your package.
If you have an idea for a new package to develop, bring that idea with you and we can consider trying to develop it during the workshop.
My project is to package all the code and data for my two-semester data analysis course while I'm not helping others.
If you would like to volunteer to be a helper during the day for logistical issues, please email me directly. It would be nice to have lunch and an afternoon coffee break with a snack.
Read an Rmd file, update existing prefixed code chunks, and renumber.
Review the input and output files to see how the chunk header names have been updated. Below is an example of the two Rmd files in the vignette. test_in.Rmd was read in and test_out.Rmd was created. The chunk headers are shown below from each file.
O'Connor's algorithm overview is the order of parts to write that I'm using as a basis below. Baldwin's order is slightly different and indicated in each citation. [caption id="" align="aligncenter" width="240"] Overview of the formulation of a scientific manuscript. (O'Connor)[/caption] 1. Figures/Tables "Construction of first-draft figures and tables based on data is the critical first step toward preparation of an outline for the manuscript." (O'Connor) "Paste the figures and tables on a wall in their approximate order of appearance. This will provide the skeleton from which to begin the construction of a more detailed outline and draft." (O'Connor) "Write a first draft of figure legends. Make each legend's opening sentence into a figure title to describe the variables compared." (O'Connor) "The entire story of your paper should be comprehensible from this abstract and the figures and tables." (2b. Baldwin) "Each figure should illustrate at least one important take-home message of your paper and ideally be understandable in 30 seconds to an uninformed scientific reader." (Baldwin) Caption: "the first sentence should summarize the main point of the figure." "The entire figures should be fully comprehensible from the figure caption." "Table legends should include only a stand-alone first sentence." (Baldwin) For more on figures, see our chapter in the 4th ed of the "Handbook of Psychophysiology". 2. Summary Statements "These important statements are conclusions summarizing the major contributions of the manuscript to the scientific community. Use short rigid statements usually containing cause/effect words." (O'Connor) 3. Scientific Audience Identify the scientific audience and journals. (O'Connor) 4. Materials and Methods "Write the materials and methods section to supplement and explain the figure legends." (O'Connor) "Write while you are still conducting experiments." (1.+4. Baldwin) 5. Re-evaluate Data "For each figure and table, make a note of which summary statement it addresses." (O'Connor) 6. Results "Once each figure and table has a legend describing the mathematical variables compared, then the first sentence of each results paragraph is simply the results of this comparison." (O'Connor) "The Results section should highlight all of the conclusions that you can draw from your data." (3. Baldwin) 7. Discussion/Conclusions "Convert by logical arguments the relations of mathematical variables stated in the results section into mechanistic interpretations of cause and effect. Simply restate the data relation from each results paragraph and convert each to mechanistic conclusions." (O'Connor) Table 1 (O'Connor) gives examples of results words for data relations vs. discussion words for logic and mechanism. "The discussion should start with a paragraph which succinctly states your motivation, and the conclusions that you draw from your data that do not require discussion and ends with an introduction to the weaker conclusions that you would like to draw, but do require discussion." "The following paragraphs should discuss the conclusions that you would like to draw from your data, but require discussion because the inferences are indirect, or your data or the data in the literature are contradictory." "The last paragraph should summarize all major conclusions from the discussion of your results and indicate future research directions." (6. Baldwin) 8. References This is taken care of by a reference manager with well-curated reference data and style file. 9. Introduction "First, summarize the subject and review the literature to allow the reader to (i) understand the statements in the Results and Discussion, (ii) understand how the statements fit into the extant scientific body of knowledge, and (iii) Understand that the conclusions are indeed novel, the next step in the knowledge of the subject." (O'Connor) "Write the last paragraph of the Introduction first; this should be an abbreviated road map of the question that you are addressing and the means by which you answered the question" (5. Baldwin) "Circle all of the words and concepts that you used in this last paragraph that need to be introduced and elaborated on in preceding paragraphs of the Introduction. In this way, you will be reverse engineering the entire Introduction from your last paragraph." (Baldwin) Remove the fluff. 10. Title "The title should be a positive statement from the summary statements." (O'Connor) 11. Conclusion Paragraph "In this paragraph, restate the logical conclusions and explain why these conclusions are important, how they will influence future thinking in this and other fields. In the introduction, these conclusions were the next step. Now discuss the future based on the conclusions in this manuscript or an alternative path to further substantiate the validity of your conclusions. Also, state the relevance of results in the present manuscript to other fields." (O'Connor) 12. Abstract "Use the abstract in general terms to describe the most important points in the work." (O'Connor) "Write a rough draft of the abstract … to create the roadmap of the logic of the results and conclusions that you will be developing." (2b. Baldwin) 13. Revise, revise, revise. Erase your memory of your writing and see it fresh.
Thanks thesaurus.com. When you can't find the phrase to get you started, start with "70 useful sentences for academic writing" by Luiz Otávio Barros.
apply both to extend current models in the application to fMRI brain imaging data.
Continue UNM 100-level statistics and mathematics education initiatives to understand factors influencing student success and find strategies to increase success.
Richard Wilson book page includes purchasing details. Six and a half years ago we called for contributions. Now we contribute this book back to the FolkMADS community.
In Vivo Inhibition of miR-155 Promotes Recovery after Experimental Mouse Stroke Ernesto Caballero-Garrido, Juan Carlos Pena-Philippides, Tamar Lordkipanidze, Denis Bragin, Yirong Yang, Erik Barry Erhardt, and Tamara Roitbak. The Journal of Neuroscience, 35(36), pdf, 12446-12464 Online: September 9, 2015 http://www.jneurosci.org/content/35/36/12446.short?sid=d532fe0d-f727-4729-8f7c-ab2cf8a1e7f7 DOI: 10.1523/JNEUROSCI.1641-15.2015 Abstract A multifunctional microRNA, miR-155, has been recently recognized as an important modulator of numerous biological processes. In our previous in vitro studies, miR-155 was identified as a potential regulator of the endothelial morphogenesis. The present study demonstrates that in vivo inhibition of miR-155 supports cerebral vasculature after experimental stroke. Intravenous injections of a specific miR-155 inhibitor were initiated at 48 h after mouse distal middle cerebral artery occlusion (dMCAO). Microvasculature in peri-infarct area, infarct size, and animal functional recovery were assessed at 1, 2, and 3 weeks after dMCAO. Using in vivo two-photon microscopy, we detected improved blood flow and microvascular integrity in the peri-infarct area of miR-155 inhibitor-injected mice. Electron microscopy revealed that, in contrast to the control group, these animals demonstrated well preserved capillary tight junctions (TJs). Western blot analysis data indicate that improved TJ integrity in the inhibitor-injected animals could be associated with stabilization of the TJ protein ZO-1 and mediated by the miR-155 target protein Rheb. MRI analysis showed significant (34%) reduction of infarct size in miR-155 inhibitor-injected animals at 21 d after dMCAO. Reduced brain injury was confirmed by electron microscopy demonstrating decreased neuronal damage in the peri-infarct area of stroke. Preservation of brain tissue was reflected in efficient functional recovery of inhibitor-injected animals. Based on our findings, we propose that in vivo miR-155 inhibition after ischemia supports brain microvasculature, reduces brain tissue damage, and improves the animal functional recovery. SIGNIFICANCE STATEMENT In the present study, we investigated an effect of the in vivo inhibition of a microRNA, miR-155, on brain recovery after experimental cerebral ischemia. To our knowledge, this is the first report describing the efficiency of intravenous anti-miRNA injections in a mouse model of ischemic stroke. The role of miRNAs in poststroke revascularization has been unexplored and in vivo regulation of miRNAs during the subacute phase of stroke has not yet been proposed. Our investigation introduces a new and unexplored approach to cerebral regeneration: regulation of poststroke angiogenesis and recovery through direct modulation of specific miRNA activity. We expect that our findings will lead to the development of novel strategies for regulating neurorestorative processes in the postischemic brain.