Category Archives: Literature Review

Deconstructing the Written Comprehensive Exam

We've all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.

We’ve all felt like this at some point leading up to comprehensive exams. Photo from Flickr user Jixar, used under CC license.

This article appeared in its original form at Gradhacker.org on March 22, 2013.

The dreaded written comprehensive exam. Many graduate students will have to pass some form of comprehensive exam at some point in their program. This can often include putting together a multi-page grant-style project proposal. Putting one of these together for the first time can be a daunting process if you are unprepared. But have no fear, there are ways to make crafting a solid document far less painful and even somewhat enjoyable.

Now at this point I have to mention that this advice will be most relevant for students preparing an exam on their own projects in the style of an NIH grant. However, this basic approach can apply to putting together any large proposal for your project.

Write down your outline: This will be the skeleton of your whole document. What are the absolute key points that you want to address? In the case of a grant style document, pick out your three aims first so that they address your three highest priorities. Once you get your main points set, start fleshing out your sub-aims in order of the most important questions in each aim. It’s a good idea to get the outline set before you begin writing since it becomes more difficult to rearrange material effectively once it is written long-form.

Find the gaps in your subject knowledge: Now that you’ve got your outline it’s time to find the holes in your knowledge of the topic. Do as much as much of a literature review as you have time for. Start early if you can because it has been observed that prolonged contact with material leads to better learning than cramming at the last minute and will help you in dealing with the finer points of your material later on.

There is a limit to how much of a review is helpful for you, though. At a certain point too many citations will bog you down and will no longer add to your proposal; so make sure to use citations judiciously.

Write a full first draft as fast as you can: It doesn’t have to be pretty at first, you just need something to edit. The easiest way I’ve found to write these is to sit down with a copy of your outline and start writing down your ideas as they sound in your head, no matter how far that is from formal language*.  This can help find remaining gaps in the proposal which become visible as you get full ideas on paper.

(*I approached my own exam this way and the first draft of my proposal was HORRIBLE, but it did give me something to edit and helped me find the areas that I needed to fill in with further literature review. Now, at least 10 drafts later, I have something that I will be proud to turn in today. It was much easier having a rough document early on in the process to work with than trying to put it all together at the very end. )

Leave it alone:  Now that you’ve spent this much time thinking about, reading about, and writing out this draft you’re probably somewhat sick of it, to say the least (I know I was). This is the perfect time to put it away for a day or two. Go do something else that you enjoy and will take your mind off of the work. This serves two purposes: it helps you maintain your sanity by taking some time off to recharge, and helps you come back to edit the draft with a fresh perspective.

Keep editing and writing separate: Now that you have a first draft it may be tempting to edit and write in significant changes at the same time. Be careful with this, as you may get trapped in a loop where you’re spending too much time editing new material as you write instead of getting the new ideas fully on paper. Reserve your first read through to editing only and observe any remaining gaps that you have in the proposal.  After the first full read through and any additional literature review it’s time to write in new edits.

While straightforward and fairly simple, it can be helpful to have guidelines in mind while writing something as large as a comprehensive exam proposal. This can help take some of the dread out of the process so that you can enjoy the opportunity to put your own ideas together. As graduate students, a good deal of our work involves writing and communicating our ideas clearly

If you have the time, I also highly recommend reading “The Science of Scientific Writing” by George D. Gopen and Judith A. Swan. This is an extremely helpful article that focuses on how readers will read your document and tips on how to make scientific writing more understandable for a wide variety of audiences.

Do you have any advice for the written comprehensive exam? Please share it in the comments section below.

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Filed under General, Gradhacker Posts, Graduate School, Literature Review

Designer immunity, vectored immunoprophylaxis and the future of medicine

Antibody Molecule

Antibody Molecule (Photo credit: sc63)

 

One of my very favorite aspects of being a scientist is being right on the cutting edge of modern research. I have the pleasure of working in an environment where new discoveries are made daily that span from the mundane to the revelatory. Today I want to take the time to write about a recent paper that for me came to my attention that falls solidly in the revelatory category.

 

 

This 2012 Nature paper by Balazs et al is a great example of modern virology in combination with immunology is being used in novel ways to combat different health issues. Read on to see how this group used a viral vector to give mice protective immunity against HIV infection. Continue reading

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Filed under HIV/AIDS, Immunology, Literature Review, Rational Drug Design, Vaccines, Viral Disease

In through the backdoor: How controlled viral replication can be immunologically advantageous

When a B cell encounters its triggering antige...

(Photo credit: Wikipedia)

It may surprise many of you to know that some vaccines currently being used are actually composed of a living virus that actively replicates in your body in order to generate immunity. I’ve written about one of these live vaccines before on this site: the oral polio vaccine (OPV). These are effective vaccines that mount a long-term adaptive immunity to the pathogen in question.  This is done by immune cells that break down the virus and present small parts known as antigens to immature immune cells, which then mature in response to the antigen and are then capable of mounting an immune response to this same challenge in the future.

A recent paper to come out has shown one way that these live but attenuated viruses can be capable of generating such an effective immune response in vivo. Read on to see a potentially novel mechanism in generating an adaptive immune response to cytopathic viruses. Continue reading

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Filed under Immunology, Literature Review, Vaccines

New Training for the New Science

There has been a growing concern among scientists on how to train the next generation of researchers. This last month I came into contact with an article by Ferric C. Fang and Arturo Casadevall in Microbe magazine titled Reforming Science as well as the editorial Next-generation training in Nature. As a young researcher just beginning what I hope will be a lifelong career in the sciences this article hits on so many areas that need to be addressed. Three points in this article stood out to me and I wanted to address them from the perspective of someone who is just starting out and looking for training opportunities that will prepare me to work in the modern scientific field. These areas are the broadening of the scope of knowledge of new PhD trainees, a realignment of the culture to support quality of work over quantity, as well as the call to generate more flexible career pathways for young scientists in order to prevent attrition from the sciences. Continue reading

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Filed under General, Graduate School, Literature Review, Social Outreach

Mining host functions in search of novel treatments: APOBEC3G and retroviruses

English: Diagram of the HIV virus.

Diagram of  HIV virus. (Photo credit: Wikipedia)

Hello Readers! My apologies for the unexpected hiatus as preliminary exams and the end of the semester have occupied the bulk of my time recently. I thought I would make the most of the situation and post the written portion that I’ve recently completed as it is an interesting subject I was unaware of until recently. Studies in this area may lead to future treatments for retroviral infections such as human immunodeficiency virus 1 (HIV-1), the infectious agent responsible for acquired immune deficiency syndrome (AIDS) by showing exactly how the host protein APOBEC3G exerts an antiviral effect against this virus in the cell. Continue reading

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Filed under HIV/AIDS, Literature Review, Rational Drug Design