Monthly Archives: August 2020

“Zoom” into data analysis with JupyterLab
Inimary Toby-Ogundeji, PhD
Assistant Professor
University of Dallas

The use of JupyterLab notebook provides a user-friendly method for learning data analysis.  It is easy to work with and also provides a variety of datasets for direct use and case study data discussions.  One example follow-up task that can be used to extend this data analysis activity is performing logistic regression.  An example approach using Firth’s logistic regression method is provided here (  JupyterLab provides a temporary workspace to accomplish basic tasks in R.  One consideration is that it doesn’t maintain the user’s data and/or work once they close the browser.  Analysis performed in JupyterLab cannot be saved to the virtual platform, however files from the work session can be exported out and saved externally.  For users wanting to have the capabilities of saving work sessions and transferring between JupyterLab sessions in a streamlined manner, they can establish a freely available account.

The activity described in this article highlight a user-friendly method to learn some basic data analysis skills.  It is ideal for students with little to no experience in Biostatistics, Bioinformatics or Data Science.  The article provides an opportunity for students to reflect and practice analysis of data collected from biological experiments within an online learning environment.  The activity is suitable for an instructor led session (using an app with screen sharing capabilities). This article provides basic knowledge about how to use R for simple data analysis using the JupyterLab virtual notebook platform.

The goal of this activity is to familiarize the user with the basic steps for importing a data file, retrieval of file contents and generating a histogram using R within a JupyterLab environment.  The workflow steps to accomplish these tasks are outlined below:

  • Access JupyterLab
  • Access “R”
  • Access datasets
  • Perform summary statistics
  • Data visualization

Workflow Step-by-Step instructions and screenshots from JupyterLab

1. Access JupyterLab
a. Login to JupyterLab here:

Home page of JupyterLab Notebook

2. Access “R”

a) Select the (+) symbol at the top left of the JupyterLab screen;

b) Select R

R Console

3. Access the dataset

a) Select the directory titled: “UPMC_cohort”;

b) Identify the filename “meta.csv”.

c) Type data<-read.csv(“meta.csv”,header=TRUE, stringsAsFactors-FALSE)

d) Click run

e) Type data

f) Click run

Dataset from “meta.csv”

4. Perform summary statistics (on variable Cigarette_Pack_Years)

a) Type str(data)

b) Click run

c) Type data$Cigarette_Pack_Years

d) Click run

e) Type summary (data$Cigarette_Pack_Years)

f) Click run

Datatypes for each variable in dataset
Summary statistics

5. Draw a histogram using the “hist” function

a) Type hist(data$Cigarette_Pack_Years, 100, main=”Use of Cigarette (in years)”, xlab=Cigarette Pack Years”, ylab”Frequency”)

b) Click run



R programming-


Dr. Toby holds a PhD in Biomedical Sciences (specialization in Organ Systems Biology) from Ohio State University, College of Medicine. Her postdoctoral training was in Functional Genomics at the FAA-Civil Aerospace Medical Institute in Oklahoma City.  She is currently an Assistant Professor of Biology at University of Dallas.  She teaches several courses including: Human Biology, Bioinformatics and Biostatistics.  She enjoys mentoring undergraduate students and is an active member of The APS. Dr. Toby’s research program at UD is focused on cell signaling consequences that occur at the cellular/molecular interface of lung diseases. She is also leveraging the use of computational methods to assess immune sequencing and other types of high throughput sequencing data as a means to better understand lung diseases.

Evidence-based teaching: when evidence is not enough
Gregory J. Crowther, PhD
Everett Community College

On June 23, Dr. Chaya Gopalan of Southern Illinois University spoke at the APS Institute of Teaching and Learning on the topic of “The Flexibility of Using the Flipped Classroom as a Virtual Classroom During the COVID-19 Pandemic.” The presentation was great — full of empirical data, practical tips, and audience participation.

One of the questions that arose was, assuming that one is flipping a class with video lectures, how long should those video lectures be? I can’t remember what Chaya said about this at the time, but many others used the chat window to weigh in. They mostly argued that shorter is better, with 10-12 minutes being a commonly prescribed upper limit.

The author droning on during a long video lecture.

I had heard this “shorter is better” mantra many times before, and believed that it was well-supported by the literature. Still, I had resisted any impulse to shorten my own videos. I was already generating one video per chapter per course — 50 videos per quarter in all. If I divided each video into four shorter videos, that would be 200 videos per quarter to manage. Couldn’t my students just hit “pause” and take breaks as needed?

Thus, the video-length issue was making me increasingly uncomfortable. I think of myself as an evidence-based teacher, yet I seemed unwilling to go where the evidence was pointing.

Having battled myself to an impasse, I decided to email Chaya. I wrote:

…If you — as an expert flipper who has read the literature and published your own papers on this — were to tell me, “Come on, Greg, the evidence is overwhelming — for the good of your students you just need to make your videos shorter — stop whining and do it!” then I probably would comply. So … what do you think?

Chaya declined to respond with an ultimatum, but she did note that her own videos vary greatly in length — from 8 minutes to an hour! A lot of this variation is topic-specific, she said; some “stories” need to be told as a single chunk, even if it takes longer to do so.

Chaya’s point about chunking the material according to natural breakpoints was exactly what I needed to hear. While the idea of shortening videos because “shorter is better” did not itself inspire me, the idea of finding those breakpoints and reorganizing the material accordingly seemed utterly worthwhile. Maybe this would help my students more easily track their progress within each chapter. And off I went — I was finally ready to shorten my videos!

So, what lessons can be extracted from this bout of navel-gazing?

The thing that jumps out at me is this: my long-held resistance to a fairly mild idea (“make your videos shorter!”) was suddenly overcome not by conclusive new research, but by a subtle shift in perspective. When Chaya made a particular point that happened to resonate with me, I now wanted to make the change that I had been guiltily avoiding for months.

This was — for me, at least — a valuable reminder that, while evidence-based teaching is undoubtedly a good thing, behavior is rarely changed by evidence alone. There’s just no substitute for direct conversations in which open-minded people with shared values can stumble toward a common understanding of something.

It may be slightly heretical for me to say so, but I’ll take a good conversation over a peer-reviewed paper any day.

Greg Crowther teaches human anatomy and physiology at Everett Community College (north of Seattle). He is the co-creator of Test Question Templates, a framework for improving the alignment of biology learning activities and summative assessments.

Protecting yourself means more than a mask; should classes be moved outside?
Mari K. Hopper, PhD
Associate Dean for Biomedical Science
Sam Houston State University College of Osteopathic Medicine

Disruption sparks creativity and innovation. For example, in hopes of curbing viral spread by moving classroom instruction outdoors, one Texas University recently purchased “circus tents” to use as temporary outdoor classrooms.

Although circus tents may be a creative solution… solving one problem may inadvertently create another. Moving events outdoors may be effective in reducing viral spread, but it also increases the skin’s exposure to harmful ultraviolet (UV) radiation from the sun. The skin, our body’s largest organ by weight, is vulnerable to injury. For the skin to remain effective in its role of protecting us from pollutants, microbes, and excessive fluid loss – we must protect it.

It is well known that UV radiation, including UVA and UVB, has deleterious effects including sunburn, premature wrinkling and age spots, and most importantly an increased risk of developing skin cancer.

Although most of the solar radiation passing through the earth’s atmosphere is UVA, both UVA and UVB cause damage. This damage includes disruption of DNA resulting in the formation of dimers and generation of a DNA repair response. This response may include apoptosis of cells and the release of a number of inflammatory markers such as prostaglandins, histamine, reactive oxygen species, and bradykinin. This classic inflammatory response promotes vasodilation, edema, and the red, hot, and painful condition we refer to as “sun burn.”1,2

Prevention of sunburn is relatively easy and inexpensive. Best practice is to apply broad spectrum sunscreen (blocks both UVA and UVB) 30 minutes before exposure, and reapply every 90 minutes. Most dermatologists recommend using SPF (sun protection factor) of at least 30. Generally speaking, an SPF of 30 will prevent redness for approximately 30 times longer than without the sunscreen. An important point is that the sunscreen must be reapplied to maintain its protection.

There are two basic formulations for sunscreen:  chemical and physical. Chemical formulations are designed to be easier to rub into the skin. Chemical sunscreens act similar to a sponge as they “absorb” UV radiation and initiate a chemical reaction which transforms energy from UV rays into heat. Heat generated is then released from the skin.3  This type of sunscreen product typically contains one or more of the following active ingredient organic compounds: oxybenzone, avobenzone, octisalate, octocrylene, homosalate, and octinoxate. Physical sunscreens work by acting as a shield. This type of sunscreen sits on the surface of the skin and deflects the UV rays. Active ingredients zinc oxide and/or titanium dioxide act in this way.4  It’s interesting to note that some sunscreens include an expiration date – and others do not. It is reassuring that the FDA requires sunscreen to retain their original “strength” for three or more years.

In addition to sunscreen, clothing is effective in blocking UV skin exposure. Darker fabrics with denser weaves are effective, and so too are today’s specially designed fabrics. These special fabrics are tested in the laboratory to determine the ultraviolet protection factor (UPF) which is similar to SPF for sunscreen.  A fabric must carry a UPF rating of at least 30 to qualify for the Skin Cancer Foundation’s Seal of Recommendation. A UPF of 50 allows just 1/50th of the UV rays to penetrate (effectively blocking 98%). Some articles of clothing are produced with a finish that will wash out over time. Other fabrics have inherent properties that block UV rays and remain relatively unchanged due to washing (some loss of protection over time is unavoidable) – be careful to read the clothing label.

Some individuals prefer relying on protective clothing instead of sunscreen due to concerns about vitamin D synthesis. Vitamin D activation in the body includes an important chemical conversion stimulated by UV exposure in the skin – and there is concern that sunscreen interferes with this conversion. However, several studies, including a recent review by Neale, et al., concluded that use of sunscreen in natural conditions is NOT associated with vitamin D deficiency.5,6 The authors did go on to note that at the time of publication, they could not find trials testing the high SPF sunscreens that are widely available today (current products available for purchase include SPFs over 100).

Additional concern about use of sunscreens includes systemic absorption of potentially toxic chemicals found in sunscreen. A recent randomized clinical trial conducted by Matta and colleagues investigated the systemic absorption and pharmacokinetics of six active sunscreen ingredients under single and maximal use conditions. Seven Product formulations included lotion, aerosol spray, non-aerosol spray, and pump spray. Their study found that in response to repeat application over 75% of the body surface area, all 6 of the tested active ingredients were absorbed systemically. In this study, plasma concentrations surpassed the current FDA threshold for potentially waiving some of the additional safety studies for sunscreen. The authors went on to note that the data is difficult to translate to common use and further studies are needed. It is important to note that the authors also conclude that due to associated risk for development of skin cancer, we should continue to use sunscreen.

Yet another concern for using sunscreen is the potential for harmful environmental and human health impact. Sunscreen products that include organic UV filters have been implicated in adverse reactions in coral and fish, allergic reactions, and possible endocrine disruption.8,9 In some areas, specific sunscreen products are now being banned (for example, beginning January of 2021, Hawaii will ban products that include oxybenzone and octinoxate). As there are alternatives to the use of various organic compounds, there is a need to continue to monitor and weigh the benefit verses the potential negative effects.

Although the use of sunscreen is being questioned, there is the potential for a decline in use to be associated with an increase in skin cancer. Skin cancer, although on the decline in recent years, is the most common type of cancer in the U.S. It is estimated that more than 3 million people in the United States are diagnosed with skin cancers each year ( Although this is fewer than the current number of Americans diagnosed with COVID-19 (Centers for Disease Control and Prevention, July 20, 2020) – changes in human behavior during the pandemic (spending more time outdoors) may inadvertently result in an increase in the number of skin cancer cases in future years.  

While we responsibly counter the impact of COVID-19 by wearing masks, socially distancing, and congregating outdoors – we must also continue to protect ourselves from damaging effects of the sun. As physiologists, we are called upon to continue to investigate the physiological impacts of various sunscreen delivery modes (lotion, aerosol, non-aerosol spray, and pumps) and SPF formulations. We are also challenged to investigate inadvertent and potentially negative impacts of sunscreen including altered Vitamin D metabolism, systemic absorption of organic chemicals, and potentially adverse environmental and health outcomes.

Again, solving one problem may create another challenge – the work of a physiologist is never done!

Stay safe friends!



  1. Lopes DM, McMahon SB. Ultraviolet radiation on the skin: a painful experience? CNS neuroscience & therapeutics. 2016;22(2):118-126.
  2. Dawes JM, Calvo M, Perkins JR, et al. CXCL5 mediates UVB irradiation–induced pain. Science translational medicine. 2011;3(90):90ra60-90ra60.
  3. Kimbrough DR. The photochemistry of sunscreens. Journal of chemical education. 1997;74(1):51.
  4. Tsuzuki T, Nearn M, Trotter G. Substantially visibly transparent topical physical sunscreen formulation. In: Google Patents; 2003.
  5. Passeron T, Bouillon R, Callender V, et al. Sunscreen photoprotection and vitamin D status. British Journal of Dermatology. 2019;181(5):916-931.
  6. Neale RE, Khan SR, Lucas RM, Waterhouse M, Whiteman DC, Olsen CM. The effect of sunscreen on vitamin D: a review. British Journal of Dermatology. 2019;181(5):907-915.
  7. Matta MK, Florian J, Zusterzeel R, et al. Effect of sunscreen application on plasma concentration of sunscreen active ingredients: a randomized clinical trial. Jama. 2020;323(3):256-267.
  8. Schneider SL, Lim HW. Review of environmental effects of oxybenzone and other sunscreen active ingredients. Journal of the American Academy of Dermatology. 2019;80(1):266-271.
  9. DiNardo JC, Downs CA. Dermatological and environmental toxicological impact of the sunscreen ingredient oxybenzone/benzophenone‐3. Journal of cosmetic dermatology. 2018;17(1):15-19.

    All images from:
    Royalty Free Stock Pictures – Public Domain Images

Prior to accepting the Dean’s positon at Sam Houston State University, Dr Hopper taught physiology and served as the Director of Student Research and Scholarly Work at Indiana University School of Medicine (IUSM). Dr Hopper earned tenure at IUSM and was twice awarded the Trustees Teaching Award. Based on her experience in developing curriculum, addressing accreditation and teaching and mentoring of medical students, she was selected to help build a new program of Osteopathic Medicine at SHSU. Active in a number of professional organizations, Dr. Hopper is past chair of the Chapter Advisory Council Chair for the American Physiological Society, the HAPS Conference Site Selection Committee, and Past-President of the Indiana Physiological Society.