Whether you are preparing a literature review for your thesis, a journal article, or grant application here are a few tips to help you get started and stay organized:
Determine what information you need.
Why are you searching the literature? Are you developing a research project and want to know what has been published about your topic? Are you interested in literature on a particular method? Are you preparing a grant application or manuscript to submit to a journal? The answers to these questions will help you decide where to search, and whether or not the information that you find is what you need.
Develop a focused question.
If you enter a few words, or a phrase, into a database, then you are likely to retrieve either a very large or very small number of results. Developing a focused research question helps you construct a search strategy that will retrieve a precise set of results. If you have a complex topic, then you may have multiple questions (and searches).
Choose your resources.
Once you have determined what information you need and developed a focused question, then you are ready to choose your resources. Choosing which resources to search can be overwhelming. While PubMed is often a good place to start, think about where, and by whom, information about your topic is likely to be published, and what type of information you need (e.g. journal articles, conference proceedings, patents). What disciplines might have a perspective on your topic? What organizations, associations, institutes, companies or agencies investigate issues related to your topic?
Bibliographic databases, such as PubMed and Web of Science Core Collection, are organized collections of references to published literature (e.g. journal articles, conference abstracts, books). When you are deciding which database(s) to search, consider the subjects, dates, and types of literature the database covers, as well as the search platform. For example, MEDLINE, the database that is the principal component of PubMed, is also available through the Ovid search platform. While PubMed and Ovid MEDLINE are similar, small differences in the content and search features of these two databases means that you will retrieve different results. See the Sackler School Biomedical Sciences Research Guide for a list of biomedical database, or ask me!
Create personal accounts.
You may think that you are finally ready to start searching. Not quite. Create a personal account with the databases, or platforms (e.g. Ovid, Web of Science), that you plan to search. A personal account allows you to save searches and sets of results, and receive email notifications when new results matching your search criteria become available. Unfortunately, you have to create a separate accounts for each database or platform, but it is a good idea to do so for the resources that you use frequently. At the very least, I suggest that you create a My NCBI account, which is the personal account associated with PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein. See the March 2016, May 2016, summer 2016 and December 2016 PubMed Tip of the Month posts for more information on creating and using a My NCBI account.
Use a citation manager.
Choose a citation manager before you embark on a literature review. Citation managers allow you to organize and store your own collection of references, and insert formatted citations and bibliographies into documents. Contact me (firstname.lastname@example.org) if you need assistance selecting or using a citation manager.
Document your search methods.
Get into the habit of documenting the parameters of your search, including: the databases that you searched; the platform on which you searched (e.g. Ovid, Web of Science, etc.); years covered by the database; complete search strategies; any limits applied, such as year, age, language; and the date on which you ran the searches. While this information is not typically required for a manuscript (unless, of course, you are doing a systematic review, meta-analysis or scoping review), or grant application, a literature search is part of your research and should be recorded as you would any other experiment. Doing so saves you considerable time and effort if you need to replicate the search in the future.
If you have limited information about a journal article (e.g. author name and year of publication), then PubMed’s Single Citation Matcher may help you locate the article. Accessible from the PubMed homepage, this tool does exactly what its name implies: it matches citation information to PubMed records. Single Citation Matcher can quickly narrow your search to records that match the information you have.
In a remarkable display of bipartisanship, the Senate passed HR 34 and President Obama signed the 21st Century Cures Act into law on Dec. 13, 2016. The original bill was introduced and sponsored by Rep. Suzanne Bonamici (D-OR) on Jan 2015 and garnered co-sponsors from both sides of the aisle, including the support of Rep. Lamar Smith (R-TX), Chairman of the House Committee on Space, Science and Technology. The House approved the original bill in Oct 2015 and after a year on the Senate floor where the bill underwent several amendments proposed by both Democrats and Republicans, the Senate approved the bill on Dec 6 2016 and passed the bill on to President Obama to be signed into law.
This law is meant to accelerate drug development and bring cutting edge treatment to patients, revise the current status of mental health research and treatment for disorders, with a strong focus on the current opioid crisis sweeping across the nation. The law is also of significant importance to biomedical scientists as it will expand funding for certain fields, keeping in line with the Precision Medicine Initiative launched in 2015. More specifically, the Cures act will provide funding for specific NIH innovation projects such as the Precision Medicine Initiative ($4.5 billion through FY 2026), the BRAIN initiative ($1.51 billion through FY 2026), the Cancer Moonshot project ($1.8 billion through FY 2023) and the Regenerative Medicine (stem cells) program (30$ mn through FY 2026). In addition, this law will stimulate innovative research by awarding investigators with the Eureka Prize for “significant advances” or “improving health outcomes”. The law also seeks to promote new researchers through its Next Generation of Researchers Initiative, an attempt to solve the postdoc crisis in academia. As a response to the lack of women and underrepresented minorities in STEM fields, the law also contains provisions that will attract and retain such scientists in “priority research areas”. Finally, to further encourage early-stage researchers, the law authorizes the establishment of programs to help in the repayment of student loans and raises the cap on the repayment assistance available to the researchers.
Besides ensuring funding for biomedical research, this law aims to address privacy concerns brought up by experts regarding patient information in the era of precision medicine (for more details, check out our analysis of the precision medicine initiative). Under this law, certificates of confidentiality will be provided to all NIH-funded researchers whose studies involve collection of sensitive patient information. This information will be withheld by the NIH, but can be accessed upon requests filed under the Freedom of Information Act. On the other hand, in order to make sure data sharing is made easier for scientists, this law will allow NIH to break out of red tape and regulations that obstruct scientists from attending scientific meetings and sharing data.
Despite the generally positive reception of the Cures Act by NIH officials and research scientists, the bill was not without its critics. The principal criticism of the final product is that it constitutes a handout to pharmaceutical and medical device companies by substantially weakening the FDA’s regulatory check on bringing new treatments into the clinic.
For example, Sydney Lupkin and Steven Findlay point to the$192 million worth of lobbying collectively expended by over a hundred pharmaceutical, medical device, and biotech companies on this and related pieces of legislation. The goal of this lobbying, Lupkin and Findlay assert, was to give the FDA “more discretion” in deciding how new drugs and other treatments gain approval for clinical use – presumably saving a great deal of money for the companies that develop them. Adding weight to their assertion is the fact that President Trump isreportedly considering venture capitalist Jim O’Neill for FDA commissioner. Mr. O’Neill isstrongly supported by libertarian conservatives who see FDA regulations as inordinately expensive and cumbersome, so it seems reasonable to worry about how Mr. O’Neill would weigh safety against profit in applying his “discretion” as head of the FDA. On the other hand, under a wise and appropriately cautious commissioner with a healthy respect for scientific evidence, we might hope that maintaining high safety standards and reducing thecurrent staggering cost of drug development are not mutually exclusive.
Additionally, Dr. David Gorskiwrites of one provision of the Cures Act that appears to specifically benefit a stem-cell entrepreneur whoinvested significantly in a lobbying firm pushing for looser approval standards at the FDA. Once again, it is not unreasonable to suspect that there is room to reduce cost and bureaucratic red tape without adversely impacting safety. And in fairness to the eventual nominee for FDA commissioners, previous commissionershave not been universally praised for their alacrity in getting promising treatments approved efficiently… at least, not within the financial sector. Still, the concerns expressed by medical professionals and regulatory experts over the FDA’s continued intellectual autonomy and ability to uphold rigorous safety standards are quite understandable, given the new administration’senthusiasm for deregulation.
It appears that this law will also allow pharmaceutical companies to promote off-label use of their products to insurance companies without holding clinical trials. Additionally, pharma companies can utilize “data summaries” instead of detailed clinical trial data for using products for “new avenues”. It is possible that these provisions were created with the NIH basket trials in mind (details here). However, as Dr. Gorski argues, without clinical trial data, off label use of drugs will be based on “uncontrolled observational studies”, which, while beneficial for pharma companies, are risky for patients from the perspective of patient advocacy groups. These fears are not without evidence – a recent article from STAT describes how the off-label use of Lupron, a sex hormone suppressor used to treat endometriosis in women and prostate cancer in men, is resulting in a diverse array of health problems in 20-year olds who received the drug in their puberty.
Another “Easter egg”, albeit unpleasant, awaits scientists and policy-makers alike. Buried in Title V of the law is a $3.5 bn cut on Human and Health Services’ Prevention and Public Health fund, without a proper explanation added to such an act. Given the outcry on the lack of public health initiatives in the Precision Medicine Initiative, one is again left to wonder why 21st century cures are focusing only on treatment and drug development and not on policies directed towards promoting public health and prevention of diseases.
In conclusion, the implementation of this law will largely depend on the current administration. With the NIH budget for FY2017 still up in the air, the confirmation of nominees still hanging in balance, this law is far from being implemented. Based on the provisions, it appears that overall biomedical funding will be boosted in particular fields, designated “priority research areas”. However, it shouldn’t fail an observant reader that this bill also seems to allow pharma companies a higher chance to exploit the consumers. It, therefore, still remains a question of whose priorities (consumers/patients vs. investors/corporations) are being put forward first and the answer, in our humble opinion, will be determined by a dialogue between the people and the government.
This month I present, for your reading pleasure, excerpts from my interview with Nafis Hasan from CMDB. Nafis and I had a remarkably wide-ranging conversation covering existential philosophy, cultural differences between Bangladesh and the US, the exquisite symmetry between ecology and cell biology, and current controversies in carcinogenesis research. I can only hope to capture in the space below a mere whisper of his deeply-considered intellectual convictions and passion for social justice. Fortunately, Nafis has also authored an editorial on Science Activism in this very issue, and I strongly urge you, dear reader, to check that out next!
AH: Where did you grow up?
NH: I grew up in the house that my father and his brothers built in Dhaka, Bangladesh, and moved to the U.S. when I was 18. Most of my dad’s siblings and their families lived with us in Dhaka. As kids, we didn’t really have the notion of “privacy” for the longest time: the elders would each get a room and the kids would sleep in the living room on a big mattress. My cousins and I would all get into trouble at the same time… it was fun!
AH: Have you had any opportunities to travel around the States?
NH: For F1 visa (student visa) holders, you have a 3-month window where you have to find a job or get into school. After graduating from Lafayette College [in Easton, Pennsylvania], I thought, “If I have to leave the country, I might as well see it.” So when one of my friends said, “Let’s do a road trip,” I said “Let’s do it!” We started from Pennsylvania, went down to Virginia, our first stop was Shenandoah – I had actually never been camping before that, it was all a very new experience. We had two American kids, a Colombian kid, and a kid from South Africa… It was very liberating, and I started to see the country as it really is. At the same time, on the road, I was interviewing for jobs. I remember doing a job interview [by video phone] at a McDonalds in Idaho. I borrowed a shirt from one of my friends who dresses nicer than I do, since the interviewer could only see the top half of me… Over the course of two months, I think I applied to 200 jobs. Finally, I ended up getting a research tech job at Thomas Jefferson University in Philly.
AH: What was it like adjusting to American culture?
NH: When I came to America, I had no idea what to expect, I had only heard things from my cousins who came here for college and what was on TV. One thing that I had in my mind was that I was going to try and meet as many people of different nationalities as I can. But there was a big cultural divide, how they grew up versus how I grew up. I think the road trip really helped me to understand the diversity of American people and especially during these times when people are so polarized, I reach out to that experience. We grew up seeing this version of America as the land of opportunity, the land of freedom, but America is not the government, is not their foreign policy, is not the consumerism that has taken over the world… America is more about the people that you meet here, and that’s how I see the country. America encapsulates the dichotomy of homogeneity versus heterogeneity, and I think that’s so beautiful.
AH: When did you begin to discover your interest in biology research?
NH: In Bangladesh I went to a private school that taught everything in English. The division of sciences starts in 7th grade, and biology was definitely the most interesting to me. At the same time, I was caught up in the process of deconstructing my religious identity, because I was reading biology which has hard facts about how your body works, which calls into question how life was created… I found that more fascinating than having a set answer imposed by some superior being.
AH: How did you choose your field of study for grad school, and why is it so interesting?
NH: I started reading a lot of scientific nonfiction, presenting cancer as a very complex biological phenomenon, which was fascinating to me. I also had a solid foundation in breast cancer by the time I applied for grad school and I wanted to pursue that… I had seen lots of tumors, but no mammary glands. The more I learn about the mammary gland, the more I am fascinated by it. It develops throughout life: initially it’s just a branched structure that looks like sticks; when you get pregnant, it almost flowers, with grape-like clusters that come up through alveologenesis and these alveoli then revert back to the branched structure after weaning. It’s comparable to how trees shed leaves in the Fall, except in reverse: this course of nature – the seasons that you see – the same dynamic is there in animal tissue. And all of this is happening through the lifetime, after the majority of the organs are already fully developed!
AH: What is one of the big challenges or controversies in your field at the moment?
NH: Traditionally, cell culture is done in two dimensions, on plates that are usually plastic – and plastic is not a natural substrate for cells to grow on, so you can’t recapitulate the same 3D environment where the cells are growing inside an organism. You can either try to mimic the natural environment as much as possible, or try to make a scaffold that is biocompatible… Cells need to be able to manipulate their environment, just as the environment should be able to provide them with physical or chemical cues to make them grow or organize in certain ways. Our lab has a very organic approach to it: we do 3D cultures in type 1 collagen, the predominant structural protein found in the mammary gland stroma. We believe that “organicism is greater than reductionism.” This is where we’re at odds with a lot of others in the cancer field, where reductionism is still the predominant philosophy. And we’re not saying it’s bad! It’s just insufficient to explain carcinogenesis.
Science is often thought of as a monolithic entity, but it is actually a complex composition of a discipline, an institution, and a community, all focused on finding truth and knowledge in data and the natural world. Science as a community consists of people of all ethnicities and from all socioeconomic classes; talent is found everywhere, and we as scientists do not and should not limit our number to those with a privileged pedigree. Science as an institution is a pillar of modern society, supporting and enabling growth and progress previously impossible to achieve. Science as a discipline is an investigative practice that demands rigor, critical analysis, and substantive evidence to support the conclusions that we draw from the data. Science as a discipline to formulate theory may be apolitical, but as an institution and a community that is an integral part of modern civic society, science cannot simply be an idle observer. Atrocities have been committed in the name of science when the idea of the pure monolith prevails and is exploited by political regimes to suppress minorities, such as the Tuskegee syphilis experiments and Nazi human trials. However, science has also been used to fight for the welfare of all people and to resist such regimes: Rachel Carson, Albert Einstein, Linus Pauling, Max von Laue all used their privilege as scientists to fight for justice and the greater good. While the scientific discipline provides a path for pure theory, we are human, each with our own biases that guide our investigation, influence our analysis, and may even blind us to the truth. Ultimately, the application of scientific theory to society bears the imprint of our ideas and our biases, and we as a community bear responsibility for the results. It is therefore imperative that we distinguish the apolitical discipline of science from the institution and community of science, which are a part of civic society and inherently political. We currently hold privileged positions in society that are at risk in the contemporary political climate. The defense of science is our moral and civic duty. Furthermore, in defending ourselves, we should also take a stand to give a voice to those who cannot do so for themselves.
This is not a temporary issue. Trump is not the only President who has or will challenge evidence-based policy and threaten the scientific community. However, it is crucial that we take action now because the dangers of climate change are imminent and we cannot afford to deny it anymore. Therefore, it is imperative that scientists come forward to educate and communicate with the public in a language and tone sufficient to start a dialogue. We start by communicating with each other, educating each other about our work. From there, we communicate and educate our family members and relatives, our friends, our communities and beyond. This has to be a grassroots movement – no top-down policy will fix the scientific literacy issue and lead American society toward a future where policies are based on hard evidence as opposed to blind faith. This is how we can give back to the public, who provide the majority of funding for our work, and ensure that science does not belong to an elite population, but in the hands and minds of the people.
This is why we are calling on you, each and every scientist, ranging from technicians to postdocs, graduate students to faculty, to action. Educate and communicate with your science. Explain why it is necessary. Even if you talk to just one person a day, that can make a difference. That is where we start. If you want to do more, organize. Rally behind policymakers who heed scientific evidence and will champion such causes. Volunteer at high schools and colleges. Take part in science festivals. Celebrate science and its achievements sans the elitism. It is not about funding, or whose research is more important. It is about making science accessible to the masses, who have tirelessly supported and benefited from our work for decades and will continue to do so. It is about rescuing science from the clutches of political partisanship. It is about freedom to communicate our science, the protection of our community, and the advancement of our society.
For too long academics have been cooped up in their self-imposed exclusive isolation from the masses. For too long we have assumed that Science exists in a vacuum. We cannot afford this axiom anymore. We have to consider the social, political, and economic forces that affect the direction of scientific research. We have a moral and civic duty to fight for what is right and to prevent the use of science to advance fascist ideology. The time to take action is now.
Here are some resources to help you take action in the short term –
Above all, talk to your family. Talk to your friends. Tell them about your work and explain why it is necessary for science to overcome partisan politics. Help educate the younger generation on the importance of scientific research. And last but not least, thank them for their support for your work.If you know of any other actions/events taking place to support Science, please let us know by leaving a comment on this post.