Health InformaticsRutgers, The State University of New Jersey65 Bergen Street, Room 171Newark, NJ 07101-1709

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Preparing Your Graduate Project

Slide 1: Publicity Poster

Slide 2: Good morning! I’m Jim Parmentier, an Adjunct Associate Professor here in the Biopharma program, and this is a webinar to prepare you to plan and complete your Graduate Project. The Graduate Project is a graduation requirement in the Clinical Trial Sciences track of the MS degree here at UMDNJ. Thank you for coming tonight. I’ve planned this talk to last about one hour. If it runs into Baby Bath time, and you have to leave, ….don’t worry. We recording the session, and you can finish watching at some later time. And, for that same reason, I’m going to go fairly quickly…so don’t take notes. Just sit back and think with me about things that will help you research and prepare your Graduate Project.

Slide 3: Aspects to Consider: Here are some aspects to consider when you first begin to think about your Graduate Project.

Note that it starts and ends with some administrative responsibilities that you need to worry about. Some paperwork is needed before your begin your work….and some more is important near or after the end of the project. Let’s see where you can find those responsibilities.

Slide 4: Go to the Biopharma website > and to General Information > Fill out the Graduate Project Fieldwork Initiation Form > that’s a live link.Fax or email it to your Advisor

Tell us what kind of experience you are looking for, …tell us what contacts you may have that might help place you where you could do some fieldwork , and how far you are willing to travel, and your availability. Note that if you are working full time, your choice of placements will be limited. This same form is necessary, and the beginning, if you are planning to do a literature-based project.

Slide 5: If you are already registered, you’ll be able to get to this site on Moodle. Here’s a screen grab of the website. (“Screen grab” means that this page isn’t live…..it’s just a picture). But if you go there and scroll down you will see a section that is specific to the MS in Clinical Trial Sciences. And there you can read all about the administrative work….and so we don’t have to discuss that anymore.

Slide 6: So, in this slide…we are left with four topics. Next, for today’s discussion, let’s carve off that fourth topic. Oral presentation is a somewhat different skill that writing….and it requires some different forms of teaching (…on my part) and learning (….on your part) to get good at it. The topic of your Oral Presentation will be the same as the topic of your Written Presentation, and once you develop a story to tell I and others on the Biopharma faculty will help you learn how to present it orally. So, let’s defer that for right now…..NSP

Slide 7: Now we’ve trimmed it down to a workable problem. Let’s focus on these three elements right here.

The first thing I want to remind you is that the Graduate Project requirement comes at the end of your UMDNJ career…..not at the beginning, and by the time you reach it you have all the tools you need to do these four things.

You will have read many scientific papers in the course of your training. You will have written not a few scientific papers of your own, and had them critiqued by your professors. You may have taken the courses that UMDNJ offers in Research Design (IDST6400) or Technical Writing (BPHE6800). And certainly you have watched and listened to a lot of oral presentations….like this one. You know what learning styles bore you…..and what ones interest you. You know what writing styles work best for you….that best help you learn something. So it is those styles and skills that you now want to incorporate into your own work as you prepare your Graduate Project. Basically, you’re going to learn about something interesting….and then you’re going to tell someone else all about it. NSP Slide 8: So, we begin here.

Now, to a great extent, it will be the question that you ask that will determine1) The types of evidence you will need to answer the question.

2) the scope of your evidence, or literature search, and, in some cases, 3) whether you will even find a meaningful answer.

Slide 9: So, what makes a good research question? Slide 10: Well, the foundation of a good research question is always someone saying…

Slide 11: ”There has to be a better way to do this!”

So, let’s dissect that statement a little bit.

Slide 12: “The word “this” means we are talking about an action, or a problem, or a thing. I mean, seriously, what else can it be? We aren’t interested in questions of philosophy. We don’t want to deal here with topics such as “Is public health valuable?” or “Should nurses wear white coats?” We want to explore some tangible topic that is related to your educational or your professional experiences while you were here at UMDNJ.

Slide 13: Now what can we say about something being a “better way”. In most cases, that means that we are going to be comparing some things. It means discussing a change that you saw, or that you created….which you might do in a laboratory-based project…...or something you propose or suggest should happen in the area of the topic you are researching. It may be historical…..like the history and development of FDA regulations regarding anti-obesity drugs, or active….. like creating a database of regulatory guidelines that you compiled for your company to use in its Reg Affairs office. You should be writing about “a better way”. Slide 14: Finally, in this slide, I have bolded the word “has”…for emphasis. It indicates the frustration of not knowing. It means that it is important to you…that you really care about this. If it is important to you, chances are it has also been important to other people, and so you stand a good chance of finding some literature on the topic.

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A good example of this connection is….about two years ago, the father of a student in our program had been told he needed a hip replacement and, frankly, he was frightened to undergo the surgery. His daughter undertook to research the history, the techniques, the requirements for, and the safety and efficacy of having a hip replacement. She did a good job….and we both learned a lot about the topic. The amount of information available to you on the topic is going to be directly related to how important the topic is to other people. …. NSP

Slide 15: Now, those three requirements will help you make a topic choice….but they also impose some boundaries or restrictions on what you might choose. Would you, for example, choose a research question such as …. Will bungee jumping help heal lower back pain? The question may interest you…..but there’s probably not a lot of work being done in the area. Probably not a good Graduate Project choice. NSP

Slide 16: How about a topic like…..Should fire engines be painted red?

Well, it turns out there is some public health literature on this….and the question is apparently what Fox News likes to call “unsettled science”. Maybe people say they see the yellow fire truck better, and will get out of the way. Possibly people who are red-blue colorblind will also see them better, but most of us old guys recognize the red ones faster, especially at a distance, because that’s how they were painted when I was a kid. But for your Graduate Project….probably not a good choice. Slide 17: Here are some things that may help you choose. In choosing a good research question we want to select one to which we use apply some principles of good research design.

1) It should be answerable: That means the question must be circumscribed…it can’t be open-ended. It should present you with a recognizable path for discovery. Data on its answer should be available, and you should at least know where to start looking for it.

2) It should be relevant: It should be meaningful to someone….not just to the small group of your friends who also like bungee jumping. We should be working on topics in which many other people are interested in the outcome too. Maybe patients….maybe insurance agencies, if your topic has economic ramifications ….or maybe regulatory authorities. Hopefully, it will also be interesting and relevant to you as well…..or, if not relevant, well, then derived from your own curiosities. So, be sure to pick something that you are interested in. Also, that will make the project much more fun.

3) It should be feasible: The question of feasibility is not as important in for a literature-based research project as it is for a laboratory or a clinical research project….but still it should be considered. Can you do this……and more importantly, can you get it done in a 15-16 week semester, which is the amount of time most of you will have to do it. For example, if you wanted to investigate some of the regulatory policies of the SFDA….the Sino Food and Drug Administration…then you probably would want already to have special access to the government literature from China and be able to read them in the original form. Perhaps you do have some special sources, or special skills. What I’m really saying here is…try to match your project to your skills and interests.

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Finally, you should know that there is a lot of literature available on research design, and on the question of how to select and plan a research topic. I show two examples here…..the book on the left, on Pfizeer’s book on Evidence-Based Medicine, is the text that’s used in IDST6400. The book on the right, by Leslie Portnoy, is focused on Nursing Research. Send me an email if you want to know more about either one of them.

Slide 18: More ways to approach your search for a topic…..here is how NIH defines clinical research questions, in its own instructional material. It considers them to come in four types:

Diagnosis: to what degree is a particular test a valid and reliable predictor of a clinical condition.Etiology: what is the cause of a specific clinical condition?Therapy: how effective is an intervention (….a treatment)? What are the benefits and harms? How does it compare to other types of intervention (or no intervention)?Prognosis: what is the likely effect of an intervention (treatment) on the patient’s future condition (health, life-span, quality of life, etc.)

Slide 19: CEBM….the Center for Evidence Based Medicine, in Oxford, divides it up pretty much the same way…

Frequency (prevalence or incidence): how often does a particular disease occur?DiagnosisPrognosisTherapyBenefits, Common Harms and Rare Harms

These examples …from NIH and CEBM…are fairly simple, because they are strictly clinical questions. For a literature based project, the focus of your research question can go beyond whether a non-complex therapy is likely to work for a particular type of patient, and when it does, then evidence analysis can become substantially more complicated

Slide 20: So…here’s an example of a question you might study….a pretty simple one. It involves the connection between the presence of hormones and incidence of hot flashes.

Among perimenopausal women, what is the effect of using hormone replacement therapy with drug X (versus no treatment) to reduce the incidence of hot flashes?

This is likely to be fairly straightforward…..there’s probably not a lot of other experimentally uncontrollable factors interfering with the relationship.

Slide 21: But how about this question?

Among school age children, how effective are specialized school-based physical activity programs (compared to standard programs) in bringing about weight loss?

It seems deceptively similar…..but we know that childhood weight loss is an extremely complex phenomenon that depends on genetics, and family factors, and peer pressure, and diet, and activity

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level, and community level factors, and even institutional policies. For example, does the child’s school schedule or encourage an exercise period?

So, simple versus complex does NOT mean:

That the research is easier or less expensive, or that the question has to be complicated.Simple versus complex refers to how many causal factors are involved and the nature of their relationships.

Standard evidence analysis is pretty good for answering simple questions. It’s not so good for answering complex questions (even when they look simple).

So, let me say it again…..whether or not you come up with a meaningful answer may hinge on whether you ask the question in the right way.

However, there are some tricks that can help you find information on your chosen question. And that can help you refine, or focus your question. There is a process….and we call it PICO. Slide 22: PICO is a mnemonic that reminds us to break down a good question into its important components. You’ve heard about this already, or will hear about it, in BPHE5310…..and it’s also discussed in IDST6400, so I won’t spend too much time on it here.

P - What are the relevant characteristics of the patient, the population, or the group: e.g., sex, age, race, primary problem, medical history

I – the Intervention. What happens to the patient (e.g., exposure to asbestos dust) or what is to be done (e.g., treatment or diagnostic test)? “…, or what is the effectiveness of using drug X…”

C – Comparison . (Note: not all questions will have comparisons)

O - You’ve GOT to have specific, concrete, measurable outcomes.

As an example….you don’t want to say “what is this person’s “health”?. Instead, you say, “what is this person’s “systolic blood pressure measurement” or his “5 year mortality”.

Instead of “what is their “psychological outlook or attitude” ….ask …“what is their score on the Hamilton Depression Scale”, or their “score on the Health Related Quality of Life tool”. And, instead of “improvement” try “weight lost” or “decrease in blood serum cholesterol”.

Slide 23: So let’s try applying PICO principles to our two questions. Here’s a re-write of the first one…color-coded to the PICI principles.Slide 24: And, here’s the second one. So, you see, it is doable. It just takes some thought and some practice, and I’m sure you’ll all get used to it over time. So, let’s proceed.Slide 25: Finally, before we leave this important first step of choosing a research topic, I’ve put a list of suggested Graduate Project topics up on the IDST6980 website, which you can review at your leisure. Slide 26: Now, on to Part 2 – How to search the medical literature.

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First off, you want to get your information right from the horse’s mouth. (For some of you who may be unfamiliar with that phrase, it means that you want to read original sources.)

The phrase actually is early business terminology. Horses were an important and expensive investment. Unscrupulous horse traders would often mix salt in with their feed stock the day before a big horse show, thus making them thirsty….. and an animal that has a belly swollen full of water looks fatter and sleeker and younger and stronger to a potential buyer. But if you look at the horse’s teeth you can get a pretty good measure of its age and the general condition of its health. So….you always want to get your information straight from the horse’s mouth.

OK. That was a diversion. But, we all know that a great many people in the pharmaceutical industry make a living by writing reviews and commentary on selected topics….and some of those can be quite helpful, particularly as you are getting started on a topic. But for this project you want to seek out and read originally conducted research material. You don’t want to just read blogs…..and you don’t want to read just Wikipedia and other internet sources…..and you don’t just want to read the abstracts of papers you find….(which is a point I’ll expand on in some upcoming slides). And, you don’t want to base your Graduate Project solely on an interview with your Grandmother who thinks she needs a hip replacement because she has trouble riding her exercise bicycle. Maybe there’s another problem for her hip pain. Slide 27: So, here are some requirements to keep in mind about the information you want to find in the world’s medical literature.

1) It must be relevant . This means that the documents you find must apply to the question you want to answer. Or at least some component of that document should be applicable.

2) It must be reliable and accessible . This means it must have been generated by sources you can identify and trust, and it must be made available to other readers….that is, you must be able to reference it. In addition, while not explicitly mentioned on the slide, but relevant to the point, is the fact that the information you work with should be current. Up-to-date. That’s part of what makes it reliable.

3) Finally, it must be interpretable. This means that you must be able to understand what you are reading and be able to relate it to your own topic and interests. Documents with statistics you don’t understand, or papers about topics you don’t have the background knowledge to appreciate, may require considerable effort on your part before they are usable. It’s all all doable, of course….but it may take time to get yourself up to speed in the field. In the end, you need to know your stuff….so don’t pick a topic that is beyond your understanding.

Slide 28: Now to be really comfortable with medical literature searching you need to know something about aggregators (such as OVID-SP, EMBASE, and EBSCO Host), and how they differ from databases (such as the non-proprietary database MEDLINE, and the proprietary database EMBASE [via Elsevier].

You need to know how to navigate PubMed, which is the abstract search service provided by the National Center for Biotechnology Information). You ought to understand Boolean and Command-line search techniques and, finally, you should understand how MEDLINE works….that is, its formatting and

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the basis by which chooses the MeSH settings….that is, the Medical Subject Headings… that get assigned to each article. How do you do that?

Slide 29: Well, one way is to listen to Carol Mitchell, who is presently teaching BPHE6310 and has given a presentation on the topic each year in that course for the past three semesters. Here is a link a Blackboard Collaborate session that she presented in the Spring 2012 course. It explains all the topics I listed on the previous slide, and much more, and will provide you with the practical tools you need to be able to search the literature.

Slide 30: But before you run off to view that webinar ….and because some of you won’t do it anyway, let me briefly describe the basics of PubMed and how to use it.

This is the splash page for PubMed….a search engine that is maintained and updated by NCBI…the National Center for Biotechnology Information. PubMed accesses MEDLINE, which is one of several literature databases available to you. MEDLINE was developed by the National Library of Medicine in the 1950’s and early ‘60’s. It monitors a great many medical journals. Published articles from around the world get scanned daily and uploaded into the system. PubMed lets you sort through all of them and pick out what interests you. On the screen you can see links to tutorials on how to use PubMed, and how to generate specific types of searches, such as Clinical Queries or Clinical Trials (…that’s a link to clinicaltrials.gov)…or how to get all this information on your mobile device or e-reader. If you were to scroll down the active website you would see links to many more medical resources within NIH and the US Government, and also to private organizations that share their information freely with the public. This includes genome maps, protein sequences, taxonomies and much more.

Now member that PubMed only gives you abstracts. It doesn’t give you full papers. However, it gives you the references to full papers, so you can go look them up in any library you wish, including UMDNJ. And our UMDNJ library has a great many holdings in the primary topic areas that interest us here in the Biopharma program. So, let’s make sure we understand how our own library works.

Slide 31: The UMDNJ library provides free access to several databases, including MEDLINE. There are many databases….some of which are quite specific. For example, PSYCH deals primarily with psychological topics. Our library also has several aggregators…..such as OVID. Aggregators access several different databases. My guess is that for the choice of topics and the level of effort we expect from you in preparing your Graduate Project, PubMed will be able to yield all the references that you will need to know, and you will be able to find all you need in the UMDNJ Library. And it’s all free. This ought not to be the hardest part of your project effort.

This is a slide that Carol made…you can see her name up there on the upper left of the screen. Basically, it is a four-click process from your login page….to the “My Apps” icon…then to the library icon…then to “electronic journals”…and there you see an empty bar where you type in the name of the journal you want to search. From that point on, you use the search procedures that are provided by whatever journal you go to.

So, now that we know about PubMed…..and we know how to search for something specific in our own library…. let’s go back to PubMed and I’ll show you how these two entities can be directly linked …so

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you can have one-click access from a PubMed abstract to the full text of any published article in the UMDNJ holdings.

Now, I should first say that our live UMDNJ librarians will work with you to access holdings that the library doesn’t directly own. But you should understand that if you locate articles that are in our own library it becomes ridiculously easy, as well as cheap….like, free…..to get them. Briefly, here’s how it’s done.

Slide 32: First, you need to get a NCBI account. You click on the circled link in the upper right hand corner, and fill out the tab that pops up. Once you have an account, you can have it forever….and you can keep it open all the time. You get a big file cabinet on the NCBI server in which you can save all your search results and download them later. You can sort them into different folders…. you can save the search patterns you used to find them, …..you can search the search patterns…..and it’s all free. There’s no reason not to have one if you are in the Biopharma program.

OK. The next step is to link your account in PubMed with your login to UMDNJ. Slide 33: Here is a list of the steps …… don’t write it down. I didn’t take the time to create slides for each step, but you can get the list later, right from this slide set. Consider it part of your early experimentation with PubMed. However, I will show you the reverse process….which is pretty cool in itself. Now this only works if you already have an account in PubMed.

So, first you open your PubMed account open and leave it open. Then go back to the UMDNJ library.

Slide 34: Go back to the UMDNJ library page ….but this time click on “our Campus Libraries”.

Slide 35: There in the lower left is a menu selector called “Find Articles in….”. You see I’ve selected PubMed. In the bar next to PubMed, type in “Name [au] AND NAME [JOURNAL]” of whatever it is you are looking for. Using the correct syntax is important, but you’ll learn that easily from a tutorial once you’ve signed in and created an account.

For this example, I’m going to type in my name and the JOURNAL OF ONCOLOGY. Then hit the return key.

Slide 36: …and …voila…you will be taken to the abstract of my latest publication, as it is listed in PubMed. Now hit the icon that says “Find it in UMDNJ” … there in the upper right…. Slide 37: and Bingo! ….. you will be taken directly to the full article.

Slide 38: Now let’s ask ourselves another question. How much work should you put into the literature search phase of your Graduate Project? Typically, the big organizations that create systematic reviews charge about $100,000 for a systematic review, including a meta-analysis. Such reviews take anywhere from 6 to 18 months to complete, and may consider perhaps 50+ sources. The commercial organizations that do these searches have entire teams working on a single review.

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You’ll need to be realistic about what you can accomplish in 15 weeks.

If your initial searches fall way outside your own “target” number (…by more or by less)…then you’ll need to change your search process. You need to use an iterative approach. You may need to reformulate your question ……. expand or contract it.

Instead of studying the relationship between aroma therapy and stress…..you might just limit it to the effects of lavender.

If you want to write about clinical trials in the US using human embryonic stem cell therapies…..well, be aware that the field is still in its infancy. The NIH website only lists two of them as ongoing…..both having to do with the treatment of macular degeneration. So you won’t find much. So, maybe you should expand your topic to include pluripotent non-embryonic stem cells……or, include material from other countries where embryonic stem cell research isn’t prohibited……or, write about the regulatory guidelines in this area….or, write about the ethical aspects of this topic. My point is…..in the research phase of your project work you should be prepared to alter your emphasis depending on the results of your research. This is an iterative process….you should be prepared to go through a research cycle several times, each time incorporating what you’ve just learned into what you already know. That’s how science is done.

1. The first ACT trial is testing the safety of hESC-derived retinal cells to treat patients with an eye disease called Stargardt's Macular Dystrophy (SMD).

2. The second ACT trial is testing the safety of hESC-derived retinal cells to treat patients with age-related macular degeneration.

Slide 39: OK….now your literature searching is done, or at least well-started…..it’s time to start thinking about the writing phase of your work. We want to talk about….

Slide 40: ….Technical Writing. ….and the buzzword here is COMMUNICATION!

Slide 41: I want to begin this section with a quote I came across just this past weekend. I’m reading this book, by Stacy Schiff, the year that Benjamin Franklin he spent living in Paris. It was 1776….he had been sent there by the Continental Congress to try and convince Louis XVI, the 22-yr old King of France to send weapons, or clothing, or ships, and maybe even soldiers….by going back to war again with England…they had just finished the 7-Years War 16 years ago….and there were many young noblemen who wanted to cover themselves again with glory….anything that would help General Washington and his struggling Army win our freedom. The Colonial government didn’t have much money to spend on this, but they did have a lot of extra land, and they could offer exclusive trading rights, and landing rights for certain ships…..that they were willing to swap that for material support. So, among his many other duties, Franklin was besieged daily by merchants and sea captains and military officials and all sorts of schemers who wanted a piece of the action. And the documents they sent to him for approval ….basically they were grant proposals…some in English, some in French….were, for the most part, atrocious. And…..one day, in great frustration,

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Slide 42: …he delivered the following lesson to one particularly obnoxious applicant…..and he said… Whoever writes to a stranger…

Slide 43: “Whoever writes to a stranger should observe three points; 1) That what he proposes be practicable; 2) His proposition should be made in explicit terms, so as to be easily understood; 3) What he desires should in itself be reasonable. Hereby he will give a favorable expression of his understanding and create a desire of further acquaintance. Now it happens that you were negligent in all these points.”

So, that was 236, to be exact. And it’s still true today.

Slide 44: Under the umbrella term of Technical Writing we include a series of specific document types…each of which has some particular features that are important to consider. Examples of these include INDs and NDAs, Investigator Brochures, and grant applications,….and review articles, laboratory notebooks, and marketing reports, and book chapters…and even smaller things like resumes, and personnel reports…even lectures, like this one…..have certain structural components, and it helps to know what they are and use them properly. Many of us write out our lectures, so that we don’t forget things we want to say …. and because having a structure makes it easier for a speaker to present material … and for a listener to follow it.

As you might expect, there are some basic techniques for Good Writing that apply to all forms of the writing we do. We don’t have time to discuss them all in this hour, but I’ll put some resources on the Graduate Project webpage that cover most of them. Here are two I particularly like. Perelman’s Mayfield Handbook, there on the left….and the Little Red Writing Book, by Brandon Royal, shown on the right.

Slide 45: So here are some general principles that apply to all types of expository writing….and often to fictional writing as well.

The first says….that until you know what you are writing about, you probably shouldn’t spend too much time writing about it. Read, take notes, talk to people, scribble out some early thoughts, make an outline…..but the actual writing is best done once you know you have something you want to say. You don’t have to have it perfectly formed in your mind to start writing…. But you do need to have some sort of idea, flow, or structure to work with. If you are an experimentalist, it’s probably not too useful to do too much writing about the results and implications of your data until you’ve finished gathering and thinking about that data. The same is true for literature research topics.

The second point helps you decide how to position your article. How detailed should it be? How much background do you need to include so that your chosen audience will understand it?

My suggestion, for your Graduate Project, is to aim your story at your student peer group. By that, I mean, aim it to intelligent folks who are willing to put some effort into understanding you…. but who probably won’t know as much as you will about the topic by the time you are done with it. Don’t feel you need to write to research scientists who are actively working in your selected field. But don’t dumb it down to a high school level, either. Smiley faces and humorous asides…..they’re not needed. This is

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formal writing, intended to teach persons who have a background in science and research about an area that may be new to them.

Finally, the over-riding concept of Good Writing Practice is to be clear….to be complete….and to be easily understood. Usually, that means explaining things in a simple manner. And so, with that in mind, I want to talk for a few minutes about the concept of writing a Journal Article. This is one of those document types that has a proud and distinctive history, and part of that distinctiveness has developed in order to achieve the goal stated there in #3.

Slide 46: The macro-view of an article is quite straight forward. It is basically U-shaped… beginning with a general description of the topic or problem and then taking a deep dive into the details of your work….and then coming back up again to explain how your data and conclusions relate to, or change, or overthrow, or more generally ….how they affect the broader world from which you started. As an example, I often find it possible to read and understand the first few paragraphs of a paper, and then perhaps the concluding comments, even if the central body of the work….let’s say a work in physics, astronomy or many areas of medicine…that central body may be lost to me. If the paper is well written it will relate to something I know and frequently enough so that I can figure out if I really need or want to learn the jargon, the mathematics, or the underlying physiology of the topic of the paper.

Slide 47: Now the next thing to know is that this U-shaped structure has been codified by the world’s library association, and has been given the acronym of IMRAD…which stands for Introduction, Methods, Results, And Discussion. And you can read a history of this codification in the 2004 article by Sollaci and Pereira that I’ve noted on the slide. It is the IMRAD format that I think you will find most useful for writing your Graduate Project.

Slide 48: Now I get to tell another story. The history of journals is really quite fascinating….and on this slide are some references to the topic. Prior to the mid-17th century new ideas spread slowly, mostly by scholars as they traveled about from one place to another, usually among the universities of the time. Printing had been available for 150 years, but books were heavy and expensive. But letters were not. Letters, carried by horse-drawn wagons or by riders, were a reliable way to exchange of information as long as the amounts were small. Soon well-connected men of science, and engineering, began circulating digests of their work and discoveries within their cities…and among cities….and that concept led to the idea of a periodic publication…a journal…a collection of writings that might be followed regularly by interested persons.

Slide 49: The first two such journals both appeared in 1665. The French contribution was the Journal des Sçavans […later renamed Journal des Savants] .... and it tried to cover all fields of knowledge. That same year, the Royal Society of London began publishing Philosophical Transactions. The focus of this collection was strictly on science…..which was then called natural philosophy…hence the title. Each month now for 348 years the Royal Society has published its Philosophical Transactions … there’s a link to its most recent offering…. http://rstb.royalsocietypublishing.org and you can get it for free at the UMDNJ Library site. Early scientific papers were usually written in the form of a letter, with the experimental details or techniques intermingled with background information and conclusions. Peer review procedures were set up quite early, because the journal organizers realized that some filtering was necessary.

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http://www.nuffieldtrust.org.uk/publications/difficult-balance-editorial-peer-review-medicineAnd the questions asked by these early reviewers….such as is the manuscript original, important, and interesting? Is the data valid? are the conclusions justified by the data? is the writing clear? is it new and is it true?”

….these encouraged the development of a more structured form …….in the 19 th century it carried an overall organization known as “theory—experiment—discussion”…..and, three-quarters through the 20 th

century….that is, in 1978…the International Committee of Medical Journal Editors formally adopted the IMRAD structure and set up rules for how authors, editors, peer reviewers and publishers would handle these papers. If you go to their website you can find the specific authorship criteria for most English-language journals. While there are some variations on font and such, they all follow IMRAD, and you should too.

Slide 50: So, with all that as background, how do we begin? Well, let’s begin at the beginning…with the Introduction. Slide 51: The purpose of an introduction is to familiarize and orient your readers. Don’t hide your main point or save it until the end of the paper.

Here are three steps you can follow….think of each one as a “move” you can make that will have a particular effect on the reader. Let’s look at them closer.

Slide 52: Broadly sketch out where the subject of your article will fall. What is the “Big Picture?” Here are some ways to do that….you obviously don’t have to do them all.· Point out the importance of the general subject· Make generalizations about the subject· Review items of previous research

Slide 53: Next, justify to the reader how your article will contribute to that topic area. There are several ways to do this.· Maybe there is a gap in the existing research database or interpretation · Maybe you have some question about the value or accuracy of existing research or current thinking· Make a counter-claim, i.e. assert something contrary to expectations· Indicate that your work is following, or expand an accepted path of previous research

Slide 54: State what your particular article will accomplish in relation to your statement in #2. Give the reader a sense of how your text will proceed. Follow these steps…

· State the research that was done…· State the principal findings —what the reader can expect to know by the time he or she gets to the

end of the article· Indicate the basic structure of the article —what will appear in it and in what order

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By constructing an introduction along these lines, you ensure that your reader has enough information to follow your text and make use of the information it contains.

One other tip on Introductions….which also applies to Abstracts…..don’t write them until you have written most of the rest of the article, or at least until you know pretty well what you are planning to say in the rest of the article.

Slide 55: Next, we want to ask what goes into the Methods section of your Graduate Project. Well, it will really depend on what type of report you are writing. If you are doing experimental work, or public health survey work, or something that requires the tools and processes to meet your stated objectives, then this is easy. This section is particularly important in real journal publications….that are meant for peer groups in other institutions. This is because knowledgeable readers will read it very carefully. They will want to judge how well you have designed and used the problem-solving process …whether you used some new piece of equipment or a well-established technique….or perhaps a new test series or sequence of exposures. Many will go right to this section to begin their study of your work. They may want to test your methodology against results in their own laboratories. For a real publication, these people are your primary readers. All others…the curious, the hesitant, the exploring….they are of less concern to you here. They may have to struggle through on their own. Your job is to be clear, accurate, and succinct. And, since whatever you are writing about is what you have been thinking about now for many months, this generally isn’t a hard section to write. You already know your stuff. Here’s where you begin to tell your story. What are some of the pitfalls of writing a Methods section? One is providing too little or too much information. Too little and it looks like you’re hiding something. Too much would be describing methods that are already published. That’s not necessary. Just cite them. Similarly, describing experimental procedures that didn’t produce the data you are about to present …even if they were good experiments…is usually unnecessary. Obviously, if you’re doing a literature review you are selecting which sources to include and which to not include….you have to be the one to decide what is most helpful to the story you are telling. Slide 56: The Results Section presents the data that your Methods Section produced, and it answers the question(s) that you established in your Introduction Section. It is where you describe the information that you generated….either in your lab work, if you are doing an experimental project….or in your library research, if you are doing a literature study. Note that "description" is not "interpretation”…that will come later. At this point you want the reader to understand what you found in your research.

There is one important aspect of “interpretation” that you do need to take into consideration in the Results Section of the paper. You have to decide which data or information to display or discuss, and that itself a form of interpretation. Your choice will reflect an inevitable bias that surrounds all of this process. You just have to do it honestly and well. We don’t have the time now to get into a discussion of “intellectual property” and “selection bias” …..but I do think that the effort could be compared pretty well to that of a miner panning for gold in a Rocky Mountain stream. Nuggets of information are there in your data. You have to point them out to the reader. One last point on presenting Results. There are two characteristics of your research efforts that compete for their right to be included in your document.

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First ….not everything you read about is worth reporting, and

Second……you may not know the full meaning or implications of all your data.

The former argues for exclusion…the latter for inclusion. In writing a real-life publication, you may want to keep some of your story back for a later publication, or for a different audience. But you also may want to put out good solid findings that you don’t fully understand on the hope that someone else may recognize what they mean. Also, some readers will want to re-analyze your data themselves rather than accept the description or interpretation that you present, and you need to give them that opportunity.

Slide 57: The Discussion Section. The comments on this slide are sufficient unto themselves. ● Summarize the findings you presented in the Results Section ● Cite supporting literature. Tie your work back into the larger body of research in the area. ● Explain discrepancies you noticed between your findings and any previous reports. . ● Point out shortcomings of your work and define any unsettled points. ● Discuss the implications of your work and, if you can, suggest what should be done now that we know what we now know. Now, if you write something about global warming you may not necessarily be called upon also to propose solutions to the problem….but here is where you get to amplify, and puff up a bit…you have already made your scientific contributions. That’s the data on which you’ll be judged. Here you can do some ….though perhaps not wild….. speculation. You may also want to provide a summary or a conclusion about the work’s importance, depending on whether or not you plan to have a formal section entitled Conclusion.

Slide 58: Before we leave this point, let’s just acknowledge something here…..the Discussion Section IS hard to write.

It requires knowledge, and perspective, and thought. OK… you’ll probably have the knowledge because you’ll have done more reading on your chosen topic than anyone else in your peer group. And you’re quite capable of thought, or you wouldn’t have gotten into our program in the first place. But, at your present stage of development in the profession, you may not have much perspective on the problem…..and see how your topic or your discovery relates to the BIG PICTURE. That's not a mistake. That's an opportunity to take your first draft….remember, we’re still talking about your first draft, right? … You fully intend to re-work and revise it in the coming days and weeks. So here is an opportunity to take your first draft and go talk with someone else who may be able to give you some insight. Your advisor….or a colleague….or, at times, and perhaps, even asking someone who you don’t know to look over your work.

Slide 59: Writing The Conclusion. Here is where you analyze your own work and compare it to the work of others. Here is where you talk about future work. Remember that science is a conveyor belt, always moving forward, often replacing itself. Draw conclusions… make suggestions, for your own work or for the work of others. It’s not considered good form to actually say that you intend to give up on this

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line of work…, even if you didn’t discover something earth-shattering. There’s value in being optimistic. Someone may want to follow up on it, even if you don’t. You never know.

Slide 60: In the original draft of this section, which I first prepared for a lecture in BPHE6800, the course in Regulatory Writing for Submissions and Publications, I had several slides on the value and importance and techniques of using well-designed diagrams and figures and illustrations in your papers. In the interests of time, I’ve trimmed most of that out of this talk but you should at least consider a few aspects of the topics. Here are some reasons why we use Tables and Figures:

• to condense large amounts of information and to simplify complex findings such as morphology, pathological findings, experimental designs, models or apparatus.

• to convince your readers of your findings, by showing them some significant data. (Other data may appear in appendices or other attachments).

• to focus attention on certain findings, in particular, the relationships between values• to tell a story

Both tables and figures should be numbered, and both should have brief, informative titles that aren’t sentences, and make them clear enough so that the data is understandable without having to look at the text. And don't use tables and graphs to present the same data. The Best Practices in this area have changed and are continuing to change rapidly. Tables are expensive and take of space in a paper journal …. and print editors used to edit them severely to save money. But space isn’t a problem online, and there is real value in having all the pertinent data available directly to the reader. But the basic rules of writing still apply…..you want to write so that you won’t be misunderstood. And tables and figures and illustrations are very much a part of that process.

Slide 61: And I know it’s getting later, but I do want to show you this.

This is a revised drawing of a map designed made by Charles Joseph Minard, a civil engineer born in Dijon, France in 1781. Minard spent his career working on dams, canals and bridge projects throughout Europe, and he had a strong interest in mapmaking and the graphic presentation of data. In 1861, fifty years after the Napoleonic era, he prepared this map. It portrays the hardships and losses suffered by Napoleon's army in the Russian campaign of 1812.

Beginning in June, when the French army crossed the Polish-Russian border, on the left, the thickness of the tan band corresponds to the size of the army at each recorded position along its advance. Harassed but never confronted by the Russian Army, which cut Napoleon’s supply lines and devastated the countryside as they retreated, the army had shrunk by 2/3’s when it finally reached Moscow. Czar Nicholas finally engaged Napoleon at Borodino Field, in late November, and then abandoned the city…but not before the panicked citizens had fled, taking whatever supplies they had with them, and burning the wooden city. Nicholas refused to negotiate and finally, in October, with winter coming on, Napoleon headed home. The path of his retreat is depicted by the lower, black band. Minard displays the retreat line and relates it to temperature and the date in the table below.

The graph displays the following six variables, all in a single two-dimensional image: the size of the Army. the direction the army was traveling, and where units split off and rejoined; the location of the army, near specific cities, at various dates, as it retreated …..

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the geographical co-ordinates …its latitude and longitude…as it moved. the temperature along the path of the retreat ….

For his temperatures, Minard used a different scale than what we use today….but at its lowest point, the recorded temperature compared to 37 degrees below zero. It was one of the worst winters in memory. This map has been called by illustrators the single most informational graphic image ever developed. You can see it more accurately at the website noted on the slide:

http://cartographia.wordpress.com/2008/04/30/napoleons-invasion-of-russia

Slide 62: Writing an Abstract: In an abstract you address "What is the report about?". You do it in miniature and without too much detail.

□ Every abstract has a little: □ Introduction □ Methods □ Results □ Discussion □ Conclusion In fact, if you’ve done it right, the abstract is just a mini-Introduction, just as the Introduction is a mini-article. I hope you’re beginning to notice a pattern here. Being able to condense your efforts into a short summary is a real skill…it isn’t easy.

Finally, the abstract is the part of your paper that will be the most widely read…and on which most search engines will concentrate. Slide 63: References Our final topic is about referencing. Here’s a book you should read….you can download it for free from the website noted there. Referencing is our community’s standard way of acknowledging sources of information. References allow the reader to find the sources that you used, so that they can go see for themselves if that work was done properly, or if there were related ideas in the referenced study that would be useful for them to know. In addition to acknowledging your sources, referencing supports and defines your own contribution to the topic and it shows that you have read widely in the area.

Now, in all areas of study, there are broad aspects of any tropic that are known as “common knowledge”. These are facts, or dates, or events or other information that someone working in the area would be expected to know. In your case, since you aren’t expected to know everything…or even very much about these topics before you began researching them….you probably don’t have a lot of “common knowledge” about them, so you will want to err on the side of doing more rather than less referencing. Ideally, you should, reference where you got an idea…..and how you came by a particular study…or found some useful data to present, whether it’s in numbers or in case studies or in regulatory documents. Quotes should be referenced, of course…..as are paraphrases and projections, unless you are the one making those projections.

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Slide 64: Types of References There generally are two types of references….(1) in text references, and (2) the making of bibliographies and/or a reference list. How to do these things is described in the book I just showed you, and in many other places, including some shown on this slide. Please do look at what the UMDNJ library has for you on the topic…...and decide early on which style you intend to follow in your own paper, because you will want to collect that information as you do your background reading. JAMA is good for journals….APA is good for Graduate projects. There are software programs like EndNote that can help you…..and the whole topic has gotten rather complex since the introduction of the internet. We don’t have time to go into all the details today, but it is worth some of your study time to learn how. For today, I’ll be happy if I have impressed on you the need to cite your sources and give credit to those who have thought about your topic in the many years before you became interested in it.

Slide 65: So…there you have it….. from Research Topics to Results to References….and everything in between. Everything you need to find and tell your story clearly to the world. Here’s how one painter chose to render this art of communication ….because that’s really what we’ve been talking about here this evening…..how do we communicate ideas from one person to another.

Here you see two ships crossing paths out on the ocean. The one bearing down on us might be many months out of port on a voyage that could last several years. That’s the WR Grace, out of Bath, Maine, and the signal flags flying from her starboard shroud read Report Me All Well. That’s the title of this painting by Charles Robert Patterson, and it hangs in the Maine Maritime Museum, in Bath. Only later does your eye see the intended recipient of her communication…..far off in the distance, but perhaps headed home…and perhaps carrying that important message to the families and, yes, to the investors, that wait there for the Grace’s return. Report Me All Well……So Far So Good……We’re Still Here …… don’t forget about us.

Slide 66: Giving Clear Instructions You have all been very patient, and I thank you for your time. I hope my story made sense to you. Writing is hard work, but it is central to our success in this, and in many other professions. The Graduate Project, here in the Biopharma Program, is an opportunity to develop your scientific writing skills while you still are among friends … who will help and support you through the process. It’s meant to be both a learning exercise and an original contribution to your chosen field. And it’s well worth doing and it’s worth doing well.

Just remember … write it so that you can’t be mis-understood!

Thanks…………………….jp

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