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 (https://bit.ly/31gb7vG). 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
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.
Karen L. Sweazea, PhD, FAHA Arizona State University
As faculty, we often find ourselves juggling multiple responsibilities at once. Although many of us are interested in adding hands-on or other activities to our classes, it can be difficult to find the time to develop them. This is where more advanced students who have already taken the class or graduate students can help.
A couple of summers ago I requested the help of an extra teaching assistant in my Animal Physiology course. The role of the position I was requesting was unique as I was not seeking a student to help with grading or proctoring exams. Rather, the role of this student was to help develop in-class activities that would enhance the learning experience of students taking the course.
For each lesson, the special graduate student TA was tasked with finding an existing (ex: https://www.lifescitrc.org/) or creating a new activity that could be implemented in the classroom during the last 10-20 minutes of each session, depending on the complexity of the activity. This enabled me to begin converting the course into a flipped classroom model as students enrolled in the course were responsible for reading the material ahead of time, completing a content comprehension quiz, and coming to class prepared to discuss the content and participate in an activity and/or case study. Special TAs can also assist with developing activities for online courses.
While the benefits of having such a TA for the faculty are clear, this type of experience is also beneficial to both the TA as well as the students enrolled in the course. For the TA, this experience provides an opportunity to develop their own teaching skills through learning to develop short lesson plans and activities as well as receiving feedback from the faculty and students. For the students, this is a great way to build cultural competence into the course as TAs are often closer in age to the students and may better reflect the demographics of the classroom. Cultural competence is defined by the National Education Association as “the ability to successfully teach students who come from a culture of cultures other than our own.” Increasing our cultural competency, therefore, is critical to student success and is something that we can learn to address. Having special TAs is just one way we can build this important skill.
Karen Sweazea is an Associate Professor in the College of Heath Solutions at Arizona State University. Her research specializes in diabetes and cardiovascular disease. She received her PhD in Physiological Sciences from the University of Arizona in 2005 where her research focused on understanding glucose homeostasis and natural insulin resistance in birds. Her postdoctoral research was designed to explore how poor dietary habits promote the development of cardiovascular diseases.
Dr. Sweazea has over 40 publication and has chaired sessions and spoken on topics related to mentoring at a variety of national and local meetings. She has additionally given over 10 guest lectures and has developed 4 graduate courses on topics related to mentoring and professional development. She has mentored or served on the committees for undergraduate, master’s, and doctoral students and earned an Outstanding Faculty Mentor Award from the Faculty Women’s Association at Arizona State University for her dedication towards mentoring.
My students, like me, enjoy a challenge. Occasionally this challenge comes in the form of staying on track, using our lab time efficiently to achieve the learning outcomes and staying engaged with the material. There are specific topics that we cover in our undergraduate human anatomy and physiology course, such as the skeletal system, that had become a little dry over time. Classes occasionally included students sitting at desks looking disinterestedly at disarticulated bones glancing at their lab manual and then checking their phones. I felt that the students were not getting enough out of our laboratory time and weren’t nearly as excited as I was to be there!
With other faculty members I recently devised some new laboratory activities that include a series of quests that closely resemble a mental obstacle course, to try to encourage engagement with the material and make our learning more playful and memorable. There may also be some healthy competition along the way.
I teach an undergraduate two semester combined anatomy and physiology course, in which I lead both the lecture and laboratory portions. Students who are enrolled in this course are majoring in Biology, Neuroscience, Public Health and Health Promotions. Many of the enrolled students are destined for graduate school programs such as Medicine, Nursing, Physical Therapy, Physicians Assistant and PhD Programs. An example of the quest format we used recently in a bone laboratory is described here.
The Quests
The laboratory is set up with multiple quest stations that each represent a multi-step task on areas within the overarching laboratory topic. All of the tasks are designed to enable students to achieve the learning outcomes of the laboratory in an engaging way. The quest stations are designed to encourage the students to physically move around the laboratory in order to interact with other students, touch the exhibits, explore case studies, complete illustrations and build models. Each student begins with a quest guide which provides instructions and upon which they take notes, answer questions and complete drawings. Students move at their own pace and work in self-selected pairs or groups of three. They are able to ask for assistance at any stage of a quest from either of two faculty members present.
Clinical case studies
Because of the students’ interest in patient care, we use clinical case studies as a major component of the obstacle course. X-ray images of a variety of pathological conditions as well as healthy individuals challenged students’ ability to identify anomalies in bone structure and surgery outcomes. The images that we used included a skull of a newborn showing clearly the fontanelles, an example of osteoporosis and joint replacement surgery. Students are required to identify anatomical location of the image as well as any anomalies, pathology or points of interest. Because of the student demographic of this class, many of them are destined to enter healthcare professions, they are particularly interested in this quest and are invested in solving the mystery diagnoses.
The Creative Part
Illustrations
An example of a student’s histological drawing.
The coloring pencils and electric pencil sharpener have come into their own in the laboratory and like Grey’s Anatomy illustrator Henry Vandyke Carter created before them, amazing anatomically accurate drawings are appearing on the page. Histology has been a particularly challenging aspect of our course for students with little previous exposure to sectioned specimens. In an attempt to allow students to really process what they are looking at and reflect on the tissue function I have asked students to draw detailed images of the histological specimens, label cell types and reflect on specific cell functions. This exercise aims to elevate the student’s ability to look closely at histological specimens and gain a better understanding of what they are observing and contemplate specific cell function.
Another quest involves categorizing bones and making illustrations of them, making note of unique identifying features and their functions.
3-D Modeling
Student synovial joint models with notes on function
Reminiscent of scenes from my three year old’s birthday party, I brought out the modeling clay and tried to stifle the reflex instruction to “don’t mix the colors”! Students were tasked with creating a 3-dimensional model of structures such as synovial joints. This is a particularly successful exercise in which students work with colored modeling clay to construct models of joints and label parts of the joint and describe the function of each part. This allows students to consider the relationship between the structure and function and move beyond looking at two-dimensional images from their textbooks and lecture slides. Students submit images of their completed models to the faculty for successful completion of the quest.
Other quest stations that were part of this particular laboratory session included Vertebrae Organizing, Mystery Bone Identification and Bone Growth Mechanisms.
One of the primary things that I learned from this exercise was that designing game-like scenarios in the classroom is far more enjoyable and entertaining for me as well as for the students, a win-win scenario. Overall from the perspective of the teaching faculty, the level of engagement was significantly increased compared with previous iterations of the class. The quality of the work submitted was high and in addition, this quest-based laboratory design is suitable for a wide range of topics and activities. I am currently designing a muscle physiology laboratory in a similar format that will include an electromyogram strength and cheering station as well as a sliding filament muscle contraction student demonstration station. In reflection I feel that my personal quest to find a novel and interesting way for the students to learn about bones was successful. Now onto the next quest……
Sarah Knight Marvar received her BSc in Medical Science and
PhD in Renal Physiology from the University of Birmingham, UK. Sarah is
currently a Senior Professorial Lecturer and Assistant Laboratory Director in
the Biology Department at American University in Washington DC. Sarah teaches
undergraduate Anatomy and Physiology, general biology classes as well as a
Complex Problems class on genetic modification to non-majors as part of the AU
Core program. Sarah’s research interests include using primary research
literature as a teaching tool in the classroom, open educational resources and
outreach activities.
Alice R. Villalobos, BS, PhD Texas Tech University
As teachers we hope students remember and apply all the physiology they learned in our class. However, many undergraduate students hope simply to get through this semester of physiology and their other courses. They dread the amount of material and that ‘so many things go on in the body at one time.’ I asked myself what could be integrated into lecture or lab to help students better learn material in class, study more effectively on their own and ideally, improve recall when taking exams. Around this time, I attended a teaching workshop focused on short activities and simple tools that could be incorporated into lectures to facilitate learning and recall. One tool was the ‘bumper sticker’.
Similar to an actual bumper sticker, the teaching bumper sticker is a short memorable phrase or slogan that encapsulates a thought, principle, or concept. In this case, a bumper sticker helps students learn and remember a concept or principle. In all areas of life, we use short sayings or one-liners often of unknown derivation that convey a profound or funny, classic or clever, instructional or encouraging thought. ‘Righty tighty, lefty loosey.’ means turn the screw to right to tighten and left to loosen. “I before E except after C.” with the addendum, “… and in words, such as protein or weight.” Could bumper stickers work in a physiology course? I already borrowed “Water follows sodium; sodium doesn’t follow water.” from my undergraduate professor. We all develop short phrases while working on lectures, reading physiology papers and books, or on the fly during lecture.
Recently, I began using bumper stickers in a more organized manner. I took a sheet of lined paper, wrote ‘Bumper Stickers for A&P-II’ on the top, and made plenty of copies. On the first day of class I discussed tips to improve learning and study habits. I explained the bumper sticker was a teaching/learning tool and gave each student a sheet. I admitted it was an experiment, but my intention was to give them short phrases to refer to and contemplate when studying on their own or spark a memory on an exam. That very day we started glycolysis. The first bumper sticker was “You must spend an ATP to make ATP.” I explained the first step in glycolysis is phosphorylation, using a phosphate from ATP. Despite some initial skepticism, bumper stickers caught on and helped many students.
Rather than repeating your explanation verbatim, students must accurately explain concepts to themselves and others in their own words. When students study with a partner or in groups, they can refer back to the bumper sticker along with lecture notes, diagrams and textbook to explain the respective concept to each other in their own words and peer-correct. When students are teaching each other, they are truly ‘getting it’. Granted, it is essential that students use more exact and scientific vocabulary to describe a mechanism or concept, as is true for any discipline. For most students this won’t happen the very first time they explain the concept. Learning physiology or any subject is a process; developing the vocabulary is part of that process. A memorable bumper sticker is a prompt for stimulating discussion – verbal communication in the context of learning a given physiological mechanism and developing the vocabulary of physiology.
There is no established technique for the initial delivery of a bumper sticker phrase. However, its two-fold purpose as a teaching/learning tool is to help students understand and remember a concept; thus, the phrase and initial proclamation must be memorable. Based on my hits and misses, here are several tips. First, keep it short, ideally 10 words or less. Second, timing is key. Similar to a joke, timing is important but varies with topic and teaching style. Some use the phrase as a teaser to introduce a topic; others use it to summarize key points. Third, be as direct as possible and capture students’ full attention. Some write the phrase on the board or slide and make an announcement, “Listen up. Write this down.” Fourth, look directly at your students and state the phrase clearly with meaning, effective voice inflection, dramatic tone, appropriate pause, facial expression, hand gesturing, and/or a little physical comedy. Fifth, use accurate and scientific terms to explain the meaning of the phrase as it applies to the physiological concept. This is absolutely critical. Left to interpretation, students might misunderstand the actual physiological concept.
Bumper stickers for better study and testing strategies
*Use common sense at all times, especially on test day.* At times, students forget obvious and intuitive things. For example, when applying Boyle’s Law to respiration, don’t forget to breathe. I remind students that lung volume and intrapulmonary pressure will change such that when we inhale air flows in, and when we exhale air flows out. Physical laws applied to physiological mechanisms explain relationships among different components of a mechanism, e.g., the pressure of a quantity of gas to its volume. I assure them, they can and will learn the fundamental physics on which Boyle’s law is based, but keep it simple and remember – when you inhale air flows in, when you exhale air flows out.
*Understand the question, before you answer it.* My PhD advisor shared this pearl of wisdom before my qualifying exam. I encourage students to calmly, slowly and deliberately read the entire question. On any multiple choice or essay exam, they must be certain of what is being asked, before answering a question. Do not stop reading the question until you come to a period, question mark or exclamation point. Students are concerned about wasting precious time. Slowing down just a bit to answer correctly is worth the time and decreases the odds of second guessing or having to go back to the question. I make another pitch for reading the text book. It is a way to practice reading calmly and deliberately and catching differences in font or formatting, e.g., print style, italics, bold, underline, that may indicate key terms for an exam question.
Bumper stickers for general principles in physiology
*Enough, but not too much.* Many students think every physiological end point is maintained at a constant value. I explain that various parameters are regulated such that they gently fluctuate within a narrow range. Plasma sodium must be ‘enough’; if it drops too low osmolarity decreases. If sodium is ‘too much’, osmolarity increases; plasma volume increases; blood pressure increases. If an endpoint falls below range, regulatory mechanisms bring it back up into range; should it increase above normal range, regulatory mechanisms bring it back down into range.
*It’s not a mathematical equation; it’s a relationship.* Many students confess they are ‘really bad at math’ or ‘hate math’. CO, MAP, renal clearance, alveolar ventilation rate – all math. Understanding and passing physiology requires math. I tell students math describes physiological relationships between different factors that regulate or dictate a given endpoint, similar to interactions and relationships among friends or a team. Actual equations represent precise relationships, e.g., CO = HR x SV. In that case, cardiac output will increase and decrease in direct proportion to heart rate and stroke volume. Then there is Poiseuille’s Equation. Students are not required to memorize that equation, but they must learn and apply the principles of the equation: F α DP, F α1/R and F α r4. I clarify the α symbol means ‘in proportion to’, not equals. I repeat, ‘It’s not a mathematical equation; it’s a relationship.” I suggest they view a as a hug, and embrace the dependence of blood flow on the pressure gradient, vascular resistance, and the luminal radius. The 4 means when radius changes even just a little, flow changes a lot! I provide a more technical explanation of how blood flow can decrease significantly with gentle vasoconstriction and increase with gentle vasodilation; this showcases the essential regulatory role of vascular smooth muscle. This particular bumper sticker serves to remind them math is critical to our understanding of physiology and hopefully, ease their anxiety. More math awaits in respiratory physiology, and they revisit and apply F αDP, F α1/R and F α r4 to air flow.
*Know what abbreviations mean, and don’t make up abbreviations.* I explain the names of hormones, especially, are rich in information. These names indicate source, stimulus for release, and mechanism of action. For example, atrial natriuretic peptide, ANP, is a peptide hormone secreted from atrial tissue when plasma volume increases that increases urine output (-uretic) and sodium (natri-) excretion. Not too creative, but self-explanatory. Couple it with “Water follows sodium …”; problem solved.
Bumper stickers for chronological order or sequence
For many cellular and organ mechanisms, there is a strict chronological order of events. During the cardiac cycle, there is a distinct chronological order for each of several different phenomena that occur simultaneously and interdependently. I use bumper stickers to teach a basic concept of cardiac physiology that help students learn the cardiac cycle – the electrical~mechanical relationship. First, I show the entire Wiggers diagram and explain it tracks the series of interrelated electrical and mechanical events as they occur in the same timeline of one heartbeat. I assure them we will take one panel at a time and pull it altogether at the end. I start with the relationship of the ECG to the 4 ventricular phases, using a set of bumper sticker phrases that I write on the board. We review the electrical events of P (atrial depolarization), QRS (ventricular depolarization) and T (ventricular repolarization) deflections. Then, I say, “Pay attention. Write down each phrase.”
*Electrical then mechanical.* I explain emphatically that first an electrical signal is transmitted and received, then the atrial or ventricular muscle responds. In the cardiac cycle, electrical events P, QRS, and T each precede atrial or ventricular responses.
*Depolarizeàcontract. Repolarizeàrelax.* I explain depolarization triggers contraction; repolarization leads to relaxation. P wave signals atrial contraction; QRS complex signals ventricular contraction; T wave signals ventricular relaxation.
*Depolarizeàcontractàincrease pressure. Repolarizeàrelaxàdecrease pressure.* I remind them changes in pressure gradients across the atrioventricular and semilunar valves determine whether valves open or close and consequently, whether blood flows into or out of the ventricle. Depolarization leads to ventricular contraction and in turn, an increase in pressure; repolarization leads to ventricular relaxation and in turn, a decrease in pressure.
*The AV valve is the fill valve; the semilunar valve is the ejection valve.* A student thought of this phrase! She explained, “When the AV valve – tricuspid or mitral – is open during diastole, the ventricle fills with blood from the atrium. When the semilunar valve – pulmonary or aortic – is open during systole, blood is ejected.” In that moment I thought my work as a teacher was done; my student is teaching herself and others. I give her full credit, but use her bumper sticker. I further explain when the ventricle relaxes and pressure drops below the atrial pressure, the AV valve will open, and blood enters the ventricle; when it contracts ventricular pressure exceeds atrial pressure and the AV valve closes; as it continues to contract, eventually ventricular pressure exceeds aortic pressure, the aortic valves opens, and blood is ejected into the aorta.
Bumper stickers might not be the right tool for every teacher, student, or topic, or be appropriate for undergraduate versus graduate course. If you decide to implement this tool, you might not have a bumper sticker for every basic or general physiology concept or mechanism or a set of bumper stickers for every organ system. You might only use a bumper sticker phrase once or twice in a whole semester. When used appropriately, they truly can make a difference. On the other hand – if how you teach is working just fine and your students are getting it – then all I have to say is, “If it ain’t broke, don’t fix it!”
Alice Villalobos received her Bachelors of Science in biology from Loyola Marymount University and her PhD in comparative physiology from the University of Arizona-College of Medicine. For the past several years, she has taught Anatomy & Physiology-II and Introduction to Human Nutrition in the Department of Biology at Blinn College and guest lectured at Texas A&M University on the topics of brain barrier physiology and heavy metal toxicology. She recently relocated to Texas Tech University to join the Department of Kinesiology & Sport Management where she teaches Physiological Nutrition for Exercise.
Fernanda Klein Marcondes Associate Professor of Physiology Biosciences Department Piracicaba Dental School (FOP), University of Campinas (UNICAMP)
Educational games may help students to
understand Physiology concepts and solve misconceptions. Considering the topics
that have been difficult to me during my undergraduate and graduate courses,
I’ve developed some educational games, as simulations and noncompetitive activities.
The first one was the cardiac cycle puzzle. The puzzle presents figures of
phases of the cardiac cycle and a table with five columns: phases of cardiac
cycle, atrial state, ventricular state, state of atrioventricular valves, and state
of pulmonary and aortic valves. Chips are provided for use to complete the
table. Students are requested to discuss which is the correct sequence of
figures indicating the phases of cardiac cycle, complete the table with the
chips and answer questions in groups. This activity is performed after a short
lecture on the characteristics of cardiac cells, pacemaker and plato action
potentials and reading in the textbook. It replaces the oral explanation from
the professor to teach the physiology of the cardiac cycle.
I also developed an educational game
to help students to understand the mechanisms of action potentials in cell
membranes. This game is composed of pieces representing the intracellular and
extracellular environments, ions, ion channels, and the Na+-K+-ATPase
pumps. After a short lecture about resting membrane potential, and textbook
reading, there is the game activity. The students must arrange the pieces to
demonstrate how the ions move through the membrane in a resting state and
during an action potential, linking the ion movements with a graph of the action
potential. In these activities the
students learn by doing.
According to their opinions, the
educational games make the concepts more concrete, facilitate their
understanding, and make the environment in class more relaxed and enjoyable.
Our first studies also showed that the educational games increased the scores
and reduced the number of wrong answers in learning assessments. We continue to
develop and apply new educational games that we can share with interested
professors, with pleasure.
Luchi KCG, Montrezor LH, Marcondes FK. Effect of an educational game on university students´
learning about action potentials. Adv Physiol
Educ., 41 (2): 222-230, 2017.
Cardozo LT, Miranda AS, Moura MJCS, Marcondes FK. Effect of a puzzle on the process of students’
learning about cardiac physiology. Adv Physiol
Educ., 40(3): 425-431, 2016.
Marcondes FK, Moura MJCS, Sanches A, Costa R, Lima PO, Groppo FC, Amaral
MEC, Zeni P, Gaviao KC, Montrezor LH. A puzzle used to teach the cardiac
cycle. Adv Physiol Educ., 39(1):27-31, 2015.
Fernanda Klein Marcondes received her Bachelor’s Degree in Biological Sciences at University
of Campinas (UNICAMP), Campinas – SP, Brazil in 1992. She received her Master
in Biological Sciences (1993) and PhD in Sciences (1998). In 1995 she began a
position at Piracicaba Dental School, UNICAMP, where she is an Associate
Professor of Physiology and coordinates studies of the Laboratory of Stress.
She coordinates the subjects Biosciences I and II, with integration of
Biochemistry, Anatomy, Histology, Physiology and Pharmacology content in the Dentistry
course. In order to increase the interest, engagement and learning of students
in Physiology classes, she combines lectures with educational games, quizzes,
dramatization, discussion of scientific articles and group activities. Recently
she started to investigate the perception of students considering the different
teaching methodologies and the effects of these methodologies on student
learning.
Lynn Cialdella Kam, PhD, MA, MBA, RDN, CSSD, LD Case Western Reserve University
Creating a Community with Faceless Students
As I enjoy the last bit of summer “break”, I am grappling with how I connect with my students if I never see them. This is not the first time teaching online. In fact, I did it back in the day before it was popular and I had really thought about how to teach. However, a core element of my teaching now is to develop a sense of community and engage students in experiential learning experiences. Online courses makes this more challenging than courses held in the traditional face-to-face classroom setting.
My Dreams of Online Teaching
As I create elaborate videos with animation and careful editing for each class, I envision I am the next Steven Spielberg of online teaching – and my students are at the edge of their seats taking in every second. Exchanges between students follow such as:
Student 1: “You know the part where Dr. Kam talked about the role leptin plays in bone health, I was just blown away!”
Student 2: “I know, and it is so cool — it is called an adipokine. I can’t wait for the next episode!”
Student 3: “Hey, do you all want to come over to my apartment for a Binge-Watching Party? We can start with the first episode and then watch the new one together!”
Student 1 and 2: “Yeah, let’s do it.”
The Reality
Online learning makes it challenging for students to get to know me and each other – and my guess is most students are likely multitasking while they watch the video. So, do I have to change my teaching philosophy and succumb to the faceless environment? I decide the answer is “No” and want to share with you three simple ideas of how I intend to bring online off of virtual reality into real life.
Zoom In for a Meet and Greet: At the beginning of each semester, I offer my students a chance to stop by my office for a “Meet and Greet”. This is a short session where I talk with the student maybe 10 to 15 mins and learn a little about their interest, goals, and concerns. Zoom is an easy way to set up a meeting with a student virtually (reference below). For free, you can have unlimited one on one meetings.
Student Led Discussion: I often engage my students in small group experiential learning activities. With online courses, I have used discussion boards in the past where I posed a question or post an article to discuss. However, this semester, each student in my online class will take a turn at leading a discussion. I have given them the broad theme like “Obesity and Genetics”, and they are then tasked with posing a compelling question and/or thought. The discussion will be open for a week. At the end of the week, the student leader will write up and share a short recap of key points made during the discussion.
Game Time with Kahoot!: Kahoot! is a game-based platform that can be used to create quizzes and/or challenges that students can take using their phone or computer. You can set it up so a student can challenge another student to a dual of the minds or have a quiz that the student can take on their own for self-assessment.
Looking for other ideas?
Tools are out there for students to create their own podcast, video, diagrams, or pretty much anything that you can imagine. Here are some resources for you to explore:
Images displayed in the post are rightfully owed and licensed from Creative Commons.
Lynn Cialdella Kam
joined CWRU as an Assistant Professor in Nutrition in 2013. At CWRU, she is
engaged in undergraduate and graduate teaching, advising, and research. Her
research has focused on health complications associated with energy imbalances
(i.e. obesity, disordered eating, and intense exercise training). Specifically,
she is interested in understanding how alterations in dietary intake (i.e.,
amount, timing, and frequency of intake) and exercise training (i.e., intensity
and duration) can affect the health consequences of energy imbalance such as
inflammation, oxidative stress, insulin resistance, alterations in
macronutrient metabolism, and menstrual dysfunction. She received her PhD in
Nutrition from Oregon State University, her Masters in Exercise Physiology from
The University of Texas at Austin, and her Masters in Business Administration
from The University of Chicago Booth School of Business. She completed her postdoctoral
research in sports nutrition at Appalachian State University and is a licensed
and registered dietitian nutritionist (RDN).
Monica J. McCullough, PhD Western Michigan University, Department of Biological Sciences
After attending the 2018 APS – ITL conference for the first time,
I walked away with so many actionable ideas to implement in my large classes.
One valuable experience was practicing active learning techniques as part of a
session. “Doing” helps many to learn much more than “hearing” about best practices.
I not only learned much from the active sessions offered at APS-ITL but
transferred that experience into my own classroom upon returning.
I decided to try a semester-long project for my Intro to Bio for
majors, modifying a project I learned about from Dr. Beth Beason-Abmayr (http://advan.physiology.org/content/41/2/239) from
Rice University. Dr. Beason-Abmayr introduced ‘The Fictitious Animal
Project’ during her session at APS-ITL as one she uses in her Vertebrate
Physiology for non-bio majors, averaging around 30 students per semester.
During her session at APS-ITL, we divided into groups, ranging from 2-10,
and mimicked the project. I instantly saw the value of this activity and had to
add it to my teaching repertoire. Dr.
Beason-Abmayr’s project was to create a fictitious animal that had certain
physiological characteristics. Students had categories, such as cardiovascular
system, respiratory system, that were randomly selected and answer sets of
questions that students would answer about the integration of them, including
benefits and trade-offs for the fictitious animal. They completed
scheduled homework sets after topics were discussed in class. The students
worked in groups and would present their creations to the class with drawings
of their animals. What really piqued my interest was that since students had to
create an animal that does not exist in nature, they couldn’t just Google it to
create this project, and the potential to bring out their ingenuity to the
design.
Since I was going to teach biological form and function the
upcoming Fall, and mind you for the first time, I thought I’d start with this
semester-long project for 290 students, which were primarily freshmen. A major
component that I wanted to maintain was the student presentations, as this is
an important skill for these budding scientists. Obviously, the logistics to
maintain this was the first decision, and when factoring in around 75 groups (averaging
4 students per group), I decided that the group presentations would span a
total of 4 days at the end of the semester, in a gallery-style presentation.
Presenters would line the room with their visual aid and the rest of the class
would visit each group with designated rubrics. (Presentation
Rubric) Additionally, the individual group members would submit a peer
evaluation of their group mates at the end of the day of their presentation. (Group
Peer Evaluation). My next modification was to adapt the category options so that
the students would create a species that yielded both plant and animal
components, as we would be learning about both. There were 5 overall
anatomical/physiological categories, including size, circulation, sensory
environmental interaction, structure and motility. These
too would be randomized with the use of Google by “rolling the dice” to assign
each characteristic. (Project
directions) I continued with Dr. Beason-Abmayr’s project checkpoint of
homework sets throughout the semester where students work on a subset of the
categories and continue to build their species, as we learn about the topics in
class. Each group submitted electronically to Dropbox, and allow time for
feedback with rubrics. (HW set
1 rubric example) To end, there was a final wrap-around short answer portion on
the final exam where students described each category and how it was
incorporated with their own species. This allowed
me to check for individual understanding of the project as we all know some
group projects allow for ‘moochers’ to do and understand little.
For me, this project is a keeper. It helped reinforce the
essential concepts during the semester and practice soft skills needed to excel
in the workforce. It was exciting to see how some students really embraced the
project, including creating a costume of their species, 3-D print outs, live
plants they’ve modified and sculptures. While difficult, there were also some
group conflicts that did occur, yet, these emerging adults were able to work
through their differences. A key factor to this was each group developing their
own contract at the very beginning of the semester and was open for adjustments
for the duration of the semester. (Team
Contract) The big take-away for me is, it is worth the risk to try
something new in the classroom, no matter how large or small the size. This
project helped student gains with the material, and practice throughout the
semester. As an educator, I feel it is pivotal to find ways that help our
students feel confident with the material and keep them curious and innovative.
Just as at the top presentations at our conference, doing
science makes concepts stick much more than just hearing about it.
Monica
J. McCullough, PhD joined as a Faculty Specialist in the Department of
Biological Sciences and Western Michigan University in 2016, prior to which she
was faculty at Adrian College. She currently teaches large introductory
courses, including Anatomy, Physiology and Biological Form and Function. Dr.
McCullough received her BS and PhD from Western Michigan University and studied
regulation of neurotrophic factors. Dr. McCullough has 4 young children and has
found a great interest in doing science demo’s in her elementary children’s’
classrooms.
Teaching a large (nearly 400 students), introductory survey course in human anatomy and physiology is a lot like trying to hit a constantly moving target. Once you work out a solution or better path for one issue, a new one takes its place. You could also imagine a roulette wheel with the following slots: student-faculty ratios, student preparation, increasing enrollments, finite resources, limited dissection specimen availability (e.g., cats), textbook prices, online homework, assessment, adaptive courseware, core competencies, learning outcomes, engagement, supplemental instruction, prerequisites, DFW rates, teaching assistants, Dunning Kruger effect, open educational resources, GroupMe, student motivation, encouraging good study habits, core concepts, aging equipment … and the list goes on.
If the ball lands on your slot, are you a winner or loser?
Before getting ahead of myself, I need to provide an overview of A&P at the University of Mississippi. Fall semesters start with 390 students enrolled in A&P I within one lecture section, 13 lab sections at 30 students each, anywhere from 10-13 undergraduate teaching assistants, 2 supplemental instruction (SI) leaders, and at least six, one-hour SI sessions each week. The unusual class size and number of lab sections is the result of maxing out lecture auditorium as well as lab classroom capacities. I am typically the only instructor during the fall (A&P I) and spring (A&P II) terms, while a colleague teaches during the summer terms. The two courses are at the sophomore-level and can be used to fulfill general education requirements. There are no prerequisites for A&P I, but students must earn a C or better in A&P I to move on to A&P II. Approximately one-third of the students are allied health (e.g., pre-nursing) and nutrition majors, one-third are exercise science majors, and the remaining one-third of students could be majoring in anything from traditional sciences (e.g., Biology, Chemistry, etc.) to mathematics or art.
The university supports a Supplemental Instruction program through the Center for Excellence in Teaching and Learning (https://cetl.olemiss.edu/supplemental-instruction/). The SI program provides an extra boost for students in historically demanding courses such as freshman biology, chemistry, physics, accounting, etc. SI leaders have successfully passed the courses with a grade of B or better, have been recommended to the program by their professors, agree to attend all lectures for the courses in which they will be an SI leader, and offer three weekly, one-hour guided study sessions that are free to all students enrolled in the course. SI leaders undergo training through Center for Excellence in Teaching and Learning and meet weekly with the course professor. Students who regularly attend SI sessions perform one-letter grade higher than students who do not attend SI sessions.
It can be as easy for an instructor to be overwhelmed by the teaching side of A&P as it is for the student to be overwhelmed by the learning side! I know that a major key to student success in anatomy and physiology courses is consistent, mental retrieval practice across multiple formats (e.g., lectures, labs, diagrams, models, dissection specimens, etc.). The more a student practices retrieving and using straightforward information, albeit a lot of it, the more likely a student will develop consistent, correct use. Self-discipline is required to learn that there are multiple examples, rather than one, of “normal” anatomy and physiology. However, few students know what disciplined study means beyond reading the book and going over their notes a few times.
To provide a model for disciplined study that can be used and implemented by all students, I developed weekly study plans for A&P I and II. These study plans list a variety of required as well as optional activities and assignments, many of which are completed using our online courseware (Pearson’s Mastering A&P) and include space for students to write completion dates. If students complete each task, they would spend approximately 10 out-of-class hours in focused, manageable activities such as:
Completion of active learning worksheets that correlate to learning outcomes and can be used as flashcards.
Practice assignments that can be taken multiple times in preparation for lecture exams and lab practicals.
Self-study using the virtual cadaver, photographic atlas of anatomical models, interactive animations of physiological processes, virtual lab experiments, and dissection videos.
Regular graded assignments aligned with course learning outcomes.
Weekly study plans are also useful during office visits with students. I can easily assess student progress and identify changes for immediate and long-term improvement. An advantage of using online courseware to support course objectives is the ability to link various elements of the courses (e.g., lecture, lab, SI sessions, online homework, group study, and self-study) with a consistent platform.
All of this sounds like a great sequence of courses, doesn’t it? Yet, the target has kept moving and the roulette wheel has kept spinning. Imagine for the story within this blog that the roulette ball has landed on “using adaptive courseware to improve supplemental instruction.”
In 2016 the University of Mississippi was one of eight universities chosen by the Bill and Melinda Gates Foundation with support of the Association for Public and Land-Grant Universities to increase the use of adaptive courseware in historically demanding general education courses. Thus, began the university’s PLATO (Personalized Learning & Adaptive Teaching Opportunities) Program (https://plato.olemiss.edu/). The PLATO grant provides support for instructors to effectively incorporate adaptive courseware into their courses and personalize learning for all affected students. Administrators of the grant were particularly supportive of instructors who could use adaptive courseware to support the SI sessions. This challenge was my personal roulette ball.
I decided to use diagnostic results from Mastering A&P graded homework assignments to prepare for weekly meetings with SI leaders. Diagnostic data on percent of University of Mississippi students correctly answering each question as well as percent of UM students answering incorrect options are compared to the global performance of all Mastering A&P users. For each question incorrectly answered by more than 50% of the students, I write a short (4-6 sentences) explanation of where students are making errors in expressing or using their knowledge and how to prevent similar errors in the future. I then searched for active learning activities and teaching tips associated with the challenging questions from the LifeSciTRC (https://www.lifescitrc.org/) and Human Anatomy and Physiology Society (HAPS; https://www.hapsweb.org/) websites. I specifically search for active learning exercises that can be conducted in a small, group setting using widely available classroom resources (e.g., white board, sticky notes, the students, etc.).
By using online courseware diagnostics, selecting focused learning activities, and communicating regularly with SI leaders, I was able to create value and unique learning opportunities for each student. The SI session format has been extremely well-received by the students and they immediately see the purpose in the study session experience. The best part is that it takes me only 30-40 minutes each week to write up explanations for the diagnostics and find the best learning activities.
I would say that we are all winners with this spin of the wheel.
Carol Britson received her B.S. from Iowa State University and her M.S. and Ph.D. from the University of Memphis. She has been in the Department of Biology at the University of Mississippi for 22 years where she teaches Vertebrate Histology, Human Anatomy, Introductory Physiology, and Human Anatomy and Physiology I and II. In 2018 she received the University of Mississippi Excellence in Teaching award from the PLATO (Personalized Learning & Adaptive Teaching Opportunities) Program supported by the Association of Public and Land-Grant Universities and the Bill and Melinda Gates Foundation.
Society has moved into the age of virtual reality. This computer-generated trend has wide-sweeping implications in the classroom. Specific to anatomy, impressive 3D modeling programs permit students to dissect simulated bodies pixel by pixel. It is exciting and often more cost-effective. Virtual dissection, without doubt, can play a significant role in the current learning environment. However, as stated by Rene Descartes, “And so that they might have less difficulty understanding what I shall say about it, I should like those who are unversed in anatomy to take the trouble, before reading this, of having the heart of a large animal with lungs dissected before their eyes (for it is in all respects sufficiently like that of a man)”. This idea leads me to my argument; there is no replacement for the real thing.
We as teachers must incorporate a variety of learning tools for a student to truly understand and appreciate anatomical structure. Anatomical structure also needs to be related to physiological function. Is there anyone reading this that has not repeated the mantra “form determines function” hundreds or thousands of times during their teaching? The logistical and financial restrictions to human cadavers, necessitates the frequent incorporation of chemically preserved specimens into our laboratory curriculum. Course facilitators often employ a cat or a pig as a substitute for the human body. I am not advocating against the use of preserved specimens or virtual programs for that matter (and kudos to my fellow facilitators who have learned the arduous techniques required to dissect a preserved specimen). However, it is my opinion that it is a time consuming assignment with limited educational end points. Not to mention the rising specimen costs and limited vendor options. The cost of a preserved cat is now ~$40, while the average cost of a live mouse is only ~$5. Two very important components necessary to understand the concept that form determines function are missing from preserved specimens (even cadavers). These two components are: texture and color. With respect to color, the tissues of preserved specimens are subtle variations of gray, completely void of the Technicolor show of the living organism. Further, texture differences are extremely difficult to differentiate in a preserved specimen. Compare this to a fresh or live specimen and the learning tools are innumerable. You might argue that mice are much smaller, but dissecting microscopes can easily enhance the dissection and in my experience far outweigh the noxious experience of dissecting a chemically preserved organism.
To further convince you of the value of dissecting fresh tissue I would like to present a couple of examples. First, why is the color of tissue important? One of the most important bodily pigments is hemoglobin. Hemoglobin, as we all know, is the pigment that gives blood its red color. Therefore the color of a tissue often reflects the level of the tissue vascularity and often (but of course not always) in turn the ability of that tissue to repair or regenerate. Simply compare the color of the patellar tendon (white) to the red color of the quadriceps. Muscles being highly vascularized have a much greater ability to regenerate than non-vascular connective tissue such as the patellar tendon. In addition, muscles contain myoglobin, a red protein very similar to hemoglobin. Two clear examples of teaching opportunities that would be missed with the traditional use of preserved specimens.
Texture is completely lost with chemical preservation as tissues become hardened and rubbery. My students are always blown away by the fact you can completely eliminate the overall structure of the brain by pressing it between their two fingers. The tactile experience of holding the delicate brain allows students to explore how form begets function begets pathology. Traumatic brain injury (TBI) has become a hot topic in our culture. We no longer see children riding bicycles without helmets, the National Football League has new rules regarding tackle technique and my 8-year-old soccer player is penalized for headers during game play. What better way to educate a new generation of students just how delicate nervous tissue is than by having them “squash” a mouse brain? Regardless, of the amazing skull that surrounds the brain and the important fluid in which it floats, a hit to the head can still result in localized damage and this tactile experience emphasizes this in a way no virtual dissection could ever accomplish.
Finally, I would like to discuss a topic close to my heart that does require a non-preserved large animal specimen. The function of arteries and veins is vastly different based on the structure of elastic or capacitance vessels, respectively. For example, the deer heart allows easy access to the superior or inferior vena cava (veins that are thin and easily collapsed) and the aorta (thick and elastic artery) permitting valuable teaching moments on vessel structural variability for divergent physiological function. These structures on a preserved specimen are usually removed just as they enter the heart making them very difficult to evaluate.
These are just some elementary examples. Numerous concepts can be enhanced with the added illustrations of texture and color. When presented with both options, my students always choose the fresh tissue! The wonder and excitement of handling fresh tissue has become a hallmark of our Anatomy and Physiology course and is regularly mentioned as student’s favorite example of hands-on learning in the classroom.
I have to end this with a special shout-out to my dear lab adjunct Professor Elizabeth Bain MSN, RN. Liz has made access to deer heart and lungs an easy task for me.
April Carpenter, PhD is an Assistant Professor in the Health and Exercise Physiology Department at Ursinus College. She received her PhD in Molecular and Cellular Physiology at Louisiana State University Health Sciences Center and completed two postdoctoral fellowships at the Hospital for Special Surgery in New York and Cincinnati Children’s Hospital Medical Center. Her research interests include the molecular regulation of endothelial function and its impact on all phases of skeletal muscle injury. Dr. Carpenter currently teaches Anatomy and Physiology, Research Methods and a new Pathophysiology course.
As a scientist and educator over the years, I have had the good fortune and pleasure to write and edit many manuscripts and documents, especially in collaborations with mentors, colleagues, and students. As most of us in the business know, writing doesn’t always come easy. It is often very challenging to convey information, thoughts, and ideas in a coherent and straightforward manner, and leave little room for misinterpretation, confusion, and ambiguity. In addition, it can be hard to convey excitement in writing. Writing is an art and deserves time and effort to create a masterpiece. Realistically though, time is rarely on our side for routinely creating works of art. However, we should still try!
Writing for me is work in progress, but very enjoyable. I know that I can always improve. Consequently, I seek better and more creative ways to express myself. I certainly wasn’t always enthusiastic about writing. Graduate students and postdoctoral fellows please take note! As a graduate student writing my early manuscripts, I would often string a few sentences together that seemed reasonable and whisper to myself, “This is close and good enough.” It rarely was. My doctoral mentor, Dr. Walter F. Boron (presently at Case Western Reserve University) almost always caught those good enough sentences when we sat together meticulously reviewing every sentence when editing a manuscript. This experience was humbling, yet highly educational, and certainly one of the high points of my graduate school years. I have continued this tradition in my own lab— enduring the occasional sighs of annoyance from my students.
The extra effort in writing can be a wonderful and rewarding experience. Many helpful resources are available. Don’t be afraid to pull out that composition/grammar book when needed. I am particularly fond of The Random House Handbook (1), which remains dust-free on my office bookshelf. Also, make use of that Thesaurus tab in Microsoft® Word! Finally, learn from the creativity of others in their writing prose, sentence structure, and expression usage.
I leave you with a list of some of my favorite writing points and guides from over the years.
I acquired most of these from my former advisor, Dr. Boron; I owe him a great deal of gratitude. I also used Ref. 1 to supplement my understanding. Write on and become my fellow artists!
1. Tell a story with the goal of exciting your readers (yes, even with a scientific manuscript).
2. Assemble outlines.
3. Write rather than stare at a blank screen/page for too long. You can always edit a mess later.
4. Edit exhaustively, but spaced out over time.
5. Get input from others.
6. Scrutinize every sentence.
7. Ask the following for every sentence:
“Does it say what I want it to say?”
“How can I make it clearer and/or shorter?”
8. Write active sentences. For example, “Compound X caused effect Y” is better than, “The effect Y was caused by compound X.”
Writing active sentences also holds when citing the work of others. For example, “Smith et al. showed that…” is stronger than, “It has been shown that… (Smith et al.).”
9. Use parallel construction in multi-part sentences. For example, “Compound X caused an increase in Y, and Compound A caused a decrease in B.”
Use parallel construction for multiple sentences that are clearly linked. For example, if you are making three points and you start the first sentence with, “First,…,” then you should have a “Second,…” and a “Third,…”
10. Give the direction of an effect whenever possible. Using the example above, “Compound X caused an increase in Y” is better than, “Compound X had an effect on Y.” Sentences should be as informative as possible.
11. Use present tense when discussing a universal truth.
12. Be consistent in using declarative or non-declarative statements in main headings, in-line headings, figure legends, etc. throughout a body of work.
13. Be careful assigning an action to an inanimate object such as an experimental result. For example, “Experiment X showed Y.” Did the experiment really perform an action?
14. Use caution when starting a sentence with This or These. The reference needs to be clear.
15. Use then in if/then statements. Many writers leave out the then. For example, “If you add media A, then the cells will die” flows better than, “If you add media A the cells will die.” If you use if in an if/then sentence, then hunt for the expected then.
16. Use more gerunds, which are refreshingly active. For example, “Applying X increased Y” is more appealing than, “Application of X increased Y.”
17. Experiment with less frequently used forms of punctuation, e.g., the semicolon and em dash. It’s fun!
18. Don’t confuse that and which clauses. That is used in a restrictive clause to understand sentence meaning. Which is used in a nonrestrictive clause to present additional information; which follows a comma.
19. Use because instead of since in many cases. Since refers to time.
20. Minimize split infinitives. Some will argue with me on this one. For example, “to argue incessantly” is better than, “to incessantly argue.” It is sometimes difficult to avoid splitting up to-base verb pairs because they then sound clumsy. Some will reason that a split is acceptable in those cases. My Father’s response: “No. Rewrite the sentence.”
21. Be careful with generic terms such as numerous, many, variety of, etc. Ask yourself, “Is the term accurate? How many exactly?” Consider giving an appropriate example to the reader.
22. Use respectively sparingly. For example, “The results from experiments A, B, and C were 5.6, 8.9, and 4.3, respectively” is hard to follow and tedious. A good general rule: Avoid sentences that require the reader to match up terms in different parts of the sentence.
23. Remember the neither…nor combination.
24. Know the difference between i.e. and e.g.
25. Consider abandoning the old-fashioned, two-space rule between sentences that was popular with typewriter use. We’re in the age of computers with line justification.
Mark O. Bevensee, PhD is an Associate Professor in the Department of Cell, Developmental & Integrative Biology at the University of Alabama at Birmingham. His laboratory focuses on studying the cellular and molecular physiology of acid-base transporters involved in regulating intracellular pH in health and disease. Dr. Bevensee also teaches— primarily cell and renal physiology to graduate and professional students. He has served as the Director of the Renal Module for medical students since 2006, and currently serves as the Co-Director & Interim Director of the Master of Science in Biomedical and Health Sciences post-baccalaureate program. He is a member of many education committees, including the Medical Education Committee of the University of Alabama School of Medicine. He serves on the editorial board of Advances in Physiology Education (American Physiological Society, APS) and Medical Science Educator (International Association of Medical Science Educators, IAMSE), as well as the Membership committee of IAMSE. He has been a member of the APS for over 20 years, and is the newly elected Awards Councilor of the Cell and Molecular Physiology Section (CaMPS) Steering Committee of the APS.
Reference:
1. Crews, F. C. (1992). The Random House Handbook, 6th Ed. McGraw-Hill, Inc., New York.
