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Writing a Doctoral Thesis

How to Write Your Ph.D

By Elisabeth Pain on April 30, 2018

Shared by Amanda Edwards

Writing a doctoral thesis—the culmination of years of research work—can be a daunting endeavor. But learning from those who have already tackled this task can help you make the process a little smoother. Science Careers asked recent graduates and current students to reflect on their experiences and what did—and didn’t—work for them.

How did you structure your thesis and approach writing it? How long did it take?

In my department, theses must be no longer than 175 pages plus front matter and appendices. They can be written in either the so-called “traditional thesis format,” which largely consists of a general introduction, a literature review, an overall description of the materials and methods, a presentation of all the results, and a general discussion—or in “manuscript format,” where the main chapters are written as standalone publishable articles between a general introduction and discussion. For my thesis, which I started writing just a couple of months ago, I have chosen the manuscript format.
– Leslie Holmes, Ph.D. candidate in biology at Queen’s University in Kingston, Canada

I wasn’t given any specific guidelines on the format or content. The most common advice at my university back in Italy was to look at an older thesis and put together something similar. I had published several papers, so I reorganized them into one coherent and logical story—writing a general background introduction, a chapter introducing my research topic more specifically, a description of the common instrumentation and data analysis, several adapted chapters presenting the original work of my research, and a general conclusion. Altogether, my dissertation was approximately 150 pages. The actual writing took 2 months—the time I had before the final submission deadline. I guess I managed to write it because I had to, the alternative being to fail the Ph.D.
– Eleonora Troja, associate research scientist in astrophysics at the University of Maryland in College Park who works at NASA’s Goddard Space Flight Center in Greenbelt, Maryland

In the Netherlands, where I did my Ph.D., theses are commonly structured as an introduction, four chapters of original research work, and a summarizing discussion. Work that is already published or has been submitted does not need to be rewritten. I was quite lucky to have published two research papers and a review of my field that served as the introduction, and I was revising another manuscript that I had submitted to a journal. This meant that I only had to write one more research chapter and the summarizing discussion, which made the total time and effort to complete my thesis manageable. I started by making a very general outline with all my chapter titles. After getting approval from my supervisor, I made a more detailed outline for the two chapters I had left to write. This was especially helpful for the research manuscript. At the time, my co-author (another Ph.D. student) and I were still acquiring and analyzing the data. The outline helped us with our figures, although some of them started as mock figures that were completed later. Altogether my thesis was 135 pages, which is quite average for a Ph.D. thesis at my institution, and it took me approximately 150 working hours over a couple of months.
– Anoek Zomer, postdoctoral fellow in cancer biology at the University of Lausanne in Switzerland and the Ludwig Institute for Cancer Research

My thesis had to be written in publishable chapters. I had a hard time keeping the chapters short enough for manuscript submissions, so at the time of defense my thesis—which consisted of three chapters plus an overall abstract for introduction—was 125 pages, but it ended up being trimmed after that. I focused on producing several manuscript-ready chapters rather than trying to include all the research work that I did. I first organized my data and results into a storyboard by printing all my graphs and laying them out on a giant table. This strategy helped me see how the pieces fit together, which results would be in or out, the best way to display the data, and where the chapter breaks should be. It also helped me identify a few gaps that needed to be filled back in the lab. Altogether it took about 1 year, including a couple months of maternity leave in the early stages, to write the whole thing.
 Sarah Gravem, postdoctoral scholar in marine ecology at Oregon State University in Corvallis

I decided to write my entire dissertation from scratch. I was already working on two manuscripts for journal submission, but both were collaborations, so it made more sense, and it was also easier, to tell the story of my Ph.D. just by itself. I wrote up my scientific results in four different chapters, with additional chapters for the introduction, materials and methods, and conclusion. For each of the results chapters, I went back to my original experiments and computational results to verify the findings and regenerated the figures and tables as required. I made a lot of notes and flowcharts describing what should go into each chapter to guide me during the writing, which later also helped me provide a quick overview at the beginning of each chapter and crosscheck information at the end of the writing process. As I completed the whole thing, I was quite surprised at how much I had written. My thesis was nearly 300 pages, and I almost got concerned about examiners having to read them all. But the “real thesis” was only about 180 pages, with the remainder being appendices, including my two manuscripts under review, references, and lists of figures and tables. I spent about 6 months putting it all together, using the 4-year duration of my stipend as a hard deadline to push myself to finish.
– Katharina F. Heil, research associate in computational neuroscience at the University of Edinburgh in the United Kingdom

My writing got squeezed into a two-and-a-half-week gap between the end of a major research project and my defense date, which had been chosen 6 months earlier. Luckily, my department allows students to use published papers as dissertation chapters and I had published regularly during my Ph.D., so all I really needed to write was my introduction. I chose to put together a brief history of my field. This required tracking down and reading a whole bunch of historical papers. Then I jotted down every thought I had on the subject, producing a bullet list of elements I wanted to cover, logical connections between ideas, references, and even just catchy phrases. Then I made a first attempt to compile all these thoughts into some structured text, focusing on whether I had sufficient material to support my points and how well they flowed. After that, I focused on honing the phrasing itself, using online resources such as spell checkers and grammar books as English is my second language, followed by a final overall polish. With all the figures and numerous supplementary materials, my thesis—which I’ve just successfully written, defended, and submitted—ended up being over 200 pages, which is within the norm in our department.
– Anton Goloborodko, postdoctoral fellow in theoretical biophysics at the Massachusetts Institute of Technology in Cambridge

Who did you get help or feedback from? How involved was your principal investigator (PI)?

When it comes to theses, I find that no one is as helpful as former grad students from your group. When I reached out to our lab’s alumni for advice, they helped me understand the overall process of thesis writing, estimate the time it would take to complete different parts, and watch out for potential pitfalls. I also downloaded and skimmed through their theses to get a feel for what the final product was supposed to look like. My PI had been heavily involved in writing each of the papers that went into my thesis, so the need for his input was less critical. Nonetheless, before sitting down to write, I had a conversation with him in which we figured out what the main theme of my thesis should be and which papers to use. Then when the time came to polish my thesis, many of my friends and colleagues, and my wife, who is also a biophysicist, provided invaluable advice.
– Goloborodko

I sent each chapter’s methods and results to all my committee members so that we could make sure that the science was complete before I dug into the key scientific messages. My PI made sure we were in touch and made himself available for questions. He also was an excellent and very thorough editor—having somebody who will rip your writing apart and help you trim and organize is critical. Nearer the end, my fellow graduate students also helped me cut a lot of words.
– Gravem

My PI got involved a couple of times: At the beginning when I asked him for advice about how to put a thesis together, and at the end for the final reading of the draft. But I still felt totally lost. So when my best friend told me that he was going to visit his adviser to discuss how to write his thesis, I did not hesitate to tag along. His adviser clarified the expectations of the graduating commission, gave us some useful suggestions, and reassured us that all would be OK. That meeting helped me feel less overwhelmed and more confident. A senior colleague of mine, who was an expert adviser for Ph.D. students at another university, also offered his help, and he reviewed every single chapter of my thesis. I would deal with the revisions while he was moving on to the next chapter, which made it much more manageable and saved a lot of time. At that time, I badly needed someone to tell me that I wasn’t doing something totally wrong or stupid.
 Troja

I sent my chapters to my PI one by one as I finished writing them. At times, I would get some feedback relatively straight away by email or through Skype; other times, I would need to send one or two reminders. Setting deadlines for myself, and letting my PI know about them, made me more accountable and helped me stick to my schedule. When I needed concrete tips on specific aspects of the thesis and my PI was really busy, I would just stop by his office. At times, all I needed was a quick “Yes, you are moving in the right direction” to keep going. I also sent individual chapters to people whom I knew had an interest in my research, mainly for proofreading, and I tried to find native English speakers to help me with grammar and spelling. I notified them all ahead of time so that they would have some flexibility on when and how to give me feedback.
– Heil

I was lucky to have a very caring supervisor who literally always had his door open. However, I tried to only request his input when I felt that critical decisions had to be made, for example when I had finished an outline or a chapter. He provided feedback mainly through track changes added to my drafts, which I found very convenient. When I received his input, I tried to deal with the revisions immediately, leaving the comments that required more work for later. By tackling the quick revisions first, I felt that I was making progress, which helped me stay motivated.
– Zomer

How did you make time and mental space to work on your thesis?

To focus on my writing, I had to stop most of my research, though I still performed some minor tasks that did not require significant time and concentration, such as launching computer calculations. Regarding work-life balance, my wife and I have an informal pact that we try not to work after dinner and on weekends. Without proper rest, productivity just drops and you end up feeling miserable. I can’t say that this pact was enforced during the thesis writing period, but even in the most intense times, we did get out of town at least once a week for a walk in nearby parks and nature reserves to decompress.
– Goloborodko

During the entire writing period, I kept some other work-related activities going. Especially at the beginning, I remained active as a teaching assistant. Working with students was a nice distraction from my thesis, and it was motivating to see that my work was useful and appreciated by others, especially during unrewarding writing times. I also worked on other research projects in parallel and went to several international conferences and a summer school on citizen science. These activities not only offered a welcome break from the thesis, but also reminded me of how important and interesting my research was. I also made sure to stay active to keep up my positive energy. Going to the gym always brought me back to writing with a clear mind and a healthier feeling. Sometimes I would try to arrange coffee breaks with friends to reward myself with a piece of cake and good company. Other times, planning to visit a museum or try a new restaurant helped me keep going by giving me a nice event to look forward to.
– Heil

I stopped doing most of my fieldwork about a year and a half before my thesis was due, which was about the same time my son was born. After my maternity leave, I spent 6 to 8 hours a day writing from home, with my baby on my lap or sleeping next to me. Once he was in day care at 7 months old, I went to coffee shops nearby so that I could pop over and nurse him at lunchtime. Several times a day, I practiced the Pomodoro Technique where I’d set the timer for 45 minutes and not do anything but write—no emails, no social media, no other tasks. If I thought of something I needed to do, I wrote it down for later. In addition to combining writing with motherhood, other aspects of work-life balance were also extremely important to me. I didn’t work most weekends, and I made sure I got outside and exercised or had some fun every day. Letting go of guilt about not working was key. Feeling bad doesn’t get you anywhere, and it just makes the experience unenjoyable for you and the people you love or live with.
– Gravem

Early on, it really helped to take a few days away from the lab and just write. I took advantage of the fact that my parents were on holiday and spent a week in their house. I set realistic daily deadlines, and if I met those I treated myself with a little reward, like a short run through the forest or an evening picnic with an old friend. That week proved very productive, and I came back motivated to get the rest of my writing and experiments done. After I returned, I made sure to continue doing some fun activities without necessarily having to achieve something first, as I realized that I should not be too hard on myself. Going for a run between writing spells, for example, allowed me to get some distance from my thesis and helped me to maintain perspective and generate new ideas. But these activities tended to be spontaneous—I didn’t want to put too much on my schedule so that I could continue writing when I was in the flow.
– Zomer

Emotionally, what was the thesis writing process like?

It was really hard, but I did enjoy it. Writing can feel like a very long, lonely tunnel, but the more you practice, the easier it gets.
– Gravem

Starting with the easy task of reformatting my published articles allowed me to make a large amount of progress quickly and feel in control of the writing process while reducing the stress of the approaching deadline. I had a harder time with my thesis introduction, though I really enjoyed digging through the history of my field. I was even happy that I had to do it—this way, I could prioritize it over other tasks. But the extensive reading made writing much more challenging than I expected, and the tight deadline made it less enjoyable. Almost until the very end, I felt like the task was overly ambitious. To reduce stress at that stage, I kept reminding myself that it was a unique chance to focus on the history of research instead of the research itself.
– Goloborodko

Writing my thesis was for sure an experience that I enjoyed. This was the moment when I was finally putting together all my work of the last 5 years, and I was proud of it.
– Zomer

I guess a good work-life balance would have been important; too bad I did not maintain it. All I could feel was panic. For 2 months, I basically did nothing besides writing my thesis and applying for jobs. When I needed a break from the thesis, I switched to my job applications. This was one of the most miserable times of my academic career. Luckily, at the end I got the postdoc I wanted, which made me forget all the stress and frustration.
– Troja

My Ph.D., including the writing period, was an emotional roller coaster. It wasn’t always easy, but remembering that every little effort brings you closer to your final goal is crucial to just keep going and survive emotionally. And while writing was daunting at times, I also found it motivating to see just how much research I had done.
– Heil

I’m only at the beginning stages of my writing, but it has been enjoyable so far. This is probably because I will finally have something tangible out of my Ph.D., which is immensely encouraging!
– Holmes

Do you have any further advice about how to make thesis writing as smooth as possible?

My general recommendation is don’t start at the last minute and don’t underestimate the time it will take. A thesis is not only about the science, but also about how to present it. Even though I had published papers containing a lot of material ready to be included in the thesis, I still had to put a lot of effort and time into reformatting the text, and I even had to improve or update some figures. If I could go back in time, I would start writing my thesis in my first year rather than leaving all the work for the last year. The introductory chapters explaining your subject matter can be written before having any data, and in retrospect, I had all the scientific results to write two-thirds of my thesis before the beginning of my last year.
– Troja

When I was studying for orals in my second year, I was very organized about writing my notes and archiving relevant papers, which proved super helpful when writing my thesis. It was also very helpful that in the first few years of my Ph.D. I had written dozens of grant proposals, which gave me an early opportunity to think about how to present the big picture, as well as some text that I could use as a starting point.
– Gravem

The acknowledgments section, and the time it takes, shouldn’t be overlooked. I saw it as my best chance to sum up the nonscientific part of my Ph.D. and express my gratitude to everyone who helped me along the way, and finding the right words took me several days. I chose to leave it until after my defense, when I could write at a much more relaxed pace during the few weeks I had to edit my thesis.

Beware of perfectionism. A doctoral thesis concludes a major part of one’s life and there is a tendency to want to make it flawless. In my case, a non-negotiable deadline provided an effective remedy. Other projects or life events may also impose deadlines. If you’re not facing looming deadlines, self-imposed time limits for individual chapters would probably work.

Regarding technical aspects, my department provides a LaTeX template, which was very helpful. It enforces structured writing and deals with all the formatting so that you can focus on content. For example, it handles numbering, so you don’t have to update figure numbers every time you insert or delete a figure. And because LaTeX is based on plain text format, I don’t have to worry about not being able to open my thesis file a decade from now. LaTeX requires a certain amount of technical expertise, but this can be overcome with a little effort and Googling.

I am also a big fan of cloud services. I used an online LaTeX editor called Overleaf that allowed me to easily share drafts with my supervisor. I started with a free account, and once I reached the storage limits I paid a tiny fee for 1 month of a “Pro” account. I was also happy to discover that Mendeley, the cloud-based literature management software I have been using for the last decade, integrated easily with Overleaf—although Mendeley did break the night before submission, extending my workday to 6 a.m.
– Goloborodko

Try to figure out when your most productive times of the day are. Also, something that I unfortunately learned the hard way is to leave yourself a roadmap before walking away from your writing, especially if it’s going to be for more than a day. Write yourself a note about thoughts and ideas or the findings and questions that you were pondering in your last work session so that you can immediately pick up where you left off. As for the writing itself, I attended some writing boot camps that helped me get started. I also read some books on writing. One that I’d recommend in particular is The Scientist’s Guide to Writing.
– Holmes

Printing out substantial parts of my writing and leaving a bit of time before reading them allowed me to efficiently proofread and adjust things. And when the writing was not going as well as expected, I switched to the figures or formatting. That way, I could still feel that I was moving forward. Even though you may often feel as though progress is very, very slow, focus on just trying to add a little bit of improvement to your thesis every hour and every day.
– Heil

Source link: Pain (2018).

Overcoming ‘PhD Blues’

Harness the Power of Groups to Beat the ‘PhD Blues’

By Karra Harrington on July 4, 2018

Shared by Amanda Edwards

Doctoral students can use writing meet-ups to overcome isolation and depression — and boost their motivation, says Karra Harrington.

Illustration of group discussion

Credit: Adapted from Viktoria Kurpas/Shutterstock

Feelings of depression, anxiety and isolation are so common during a PhD programme that some have dubbed the experience ‘the PhD blues’. As a PhD student and practising psychologist, I wanted to try to reduce the impact of the blues on my fellow students and on me.

I decided to plan a regular meet-up with my student peers, in which we could write up our theses together. My hope was that it would establish deep social connections and help us to cope with some of the challenges of our PhD programmes.

I had attended Shut Up and Write! writing groups, which involve short ‘sprints’ of writing with breaks in between. Everyone works silently during the sprints and socializes during the breaks. These groups helped me to manage my productivity and motivation — but I had no sense of connection with my fellow writers. Often, participants would check e-mails or take a walk during breaks. And different people attended each session, which made it hard to get to know each other and to build connections. Any conversations were superficial and perfunctory.

For my group, I wanted to use the breaks to create supportive networks and to share ideas on how to overcome challenges. Ultimately, I wanted to create a community in which participants could learn from and support each other while also feeling productive and making progress on their theses.

I first needed to find participants. I reached out to students involved with the Cooperative Research Centre for Mental Health, an Australian research consortium based in Melbourne that aims to further mental-health research through collaboration. Students in the consortium work across research areas, institutions and geographical locations. Such diversity meant that relationships developed among students who would not usually interact regularly. It also meant that we could use the sessions to expand our networks and gain fresh perspectives on common challenges.

I launched the meet-up almost two years ago, and it has been a huge success, with a regular attendance of six to ten students every month. Our sessions are done in person and through videoconferencing, and include two to three hours of writing, as well as discussions on how to find mentors, structure thesis drafts or balance family life with completing a PhD. I facilitate each session, and group members raise topics according to their needs and interests. Members say that they feel accountable to the group, and that this motivates them and limits procrastination. They also check in with each other between sessions.

Interaction zone

Bringing together students from different institutions, and creating a space in which they could interact, was challenging. The videoconferencing helps members who can’t get to campus — they feel engaged with their peers and less isolated. The meet-ups help me, too: I often have limited contact with other people during my working day. A regularly scheduled time to meet with others and discuss my science gives me a break from the isolation and is something to look forward to every month.

It took some time to build trust in the group so that everyone felt comfortable participating in the discussions. As facilitator, I keep discussions on track and relevant, encourage quieter group members to speak up and provide opportunities for those participating through videoconferencing to contribute. These efforts help to establish a sense of fairness and equality in the group.

Illustration of group discussion with video conferenceCredit: Adapted from Viktoria Kurpas/Shutterstock

The consistency of attendance by core group members is important because it helps participants to build relationships, thereby fostering a sense of safety and trust within each session. Group members say that they value having opportunities to connect with other PhD students and share their experiences, and that the group has helped them to maintain their motivation and sense of well-being.

Along the way, I’ve realized the importance of setting clear expectations using ground rules. Our ground rules are based on respect and confidentiality, and include speaking one at a time, listening to each other, not talking during writing sessions and maintaining confidentiality on all issues that we discuss in the group. All group members agree to stick to the rules, and the facilitator helps to enforce them.

As our group continued to meet and members started to open up about challenges that they faced, we found that the ground rules became even more valuable, because they helped to promote a sense of safety and encouraged useful exchanges between members. I found that it was also useful to make the group’s purpose — to manage productivity and well-being — explicit from the start. On signing up to join, members know immediately what to expect. We use the Pomodoro Technique, which involves blocks of writing, breaks for discussion and goal setting, to manage our productivity. At the start of each session, we share our individual goals with each other; and during the discussion breaks, we check with one another on our progress towards our goals.

For some group members, this was a new way of working and it took some time to get used to. But the fact that we made it clear from the start why we had adopted this way of working helped new members to understand and to agree to try out these techniques. Members say they’ve found that the group helps them to set aside quality writing time, and that the structure of the sessions enables them to make progress on their thesis even when they are struggling with motivation.

The peer-mentoring aspect gives everyone a space in which to ask questions and to share what they know. A group member might, for example, seek advice about conference networking while also providing guidance on a data-analysis technique. By creating opportunities for members to ask for support and advice, the sessions help everyone to feel more hopeful and to identify proactive steps that they can take to overcome challenges. The opportunity to help others and to share knowledge provides everyone with a sense of empowerment and the ability to recognize their own strengths and expertise.

Our discussions help to normalize the challenges of PhD studies and remind us to celebrate our successes. We wanted to share the benefits of the group with other PhD students, and so we’ve developed our model into a programme called Write Smarter: Feel Better. We have created guidelines for group sessions and training materials for group facilitators. These cover things such as how to build trust, and how to help the group reach agreement on ways in which members should interact with each other. Australia’s University of Melbourne and Edith Cowan University are now testing the programme, with evaluations planned for completion by the end of this year.

At both universities, PhD students volunteer for the role of facilitator. We worked with the universities to develop strategies to support PhD students in this role; these included providing first-aid training in mental health and arranging for a university staff member to be a support contact. Importantly, although the universities offer support, the sessions remain led by PhD students and for PhD students.

Creating this meet-up group has been one of the most rewarding aspects of my PhD experience. I have learnt so much from organizing and facilitating the sessions, and now have a solid peer network. I have been able to gain insights on my research and career that I wouldn’t have had if I had stuck to working on my own or only with lab peers. To paraphrase Maya Angelou, my goal is not only to survive, but to thrive — with passion, compassion, humour and style — and my meet-up is helping me to do exactly that.

Nature 559, 143-144 (2018)

doi: 10.1038/d41586-018-05589-w

Source link: Harrington (2018).

Predatory Publishing Practices

Potential Predatory and Legitimate Biomedical Journals: Can You Tell the Difference? A Cross-Sectional Comparison 

By  Amanda Edwards

The Internet has transformed scholarly publishing, most notably, by the introduction of open access publishing. Recently, there has been a rise of online journals characterized as ‘predatory’, which actively solicit manuscripts and charge publications fees without providing robust peer review and editorial services. We carried out a cross-sectional comparison of characteristics of potential predatory, legitimate open access, and legitimate subscription-based biomedical journals.

We identified 13 evidence-based characteristics by which predatory journals may potentially be distinguished from presumed legitimate journals. These may be useful for authors who are assessing journals for possible submission or for others, such as universities evaluating candidates’ publications as part of the hiring process. More information about the publication pitfalls can be found in the source link below.

Source link: Shamseer et al. (2018).

Are You the Ironman or Wonder Woman of the Science?

Can a PhD save the world?

By  Loosely Translated on May 16, 2018

Shared by Amanda Edwards

I, like so many of us, always wanted to be a superhero. As a child, I dreamed of being Ironman. I was going to be a genius billionaire playboy   philanthropist who would bring about world peace, save the world from alien invasions and use my technology to develop cleaner sources of energy. I was also going to fly and shoot beams out of my hands!

My dream changed as I got older. In high school, I went from wanting to be like Ironman with the suit to wanting to be a virologist in a hazmat suit curing Ebola in West Africa. At the start of my postgraduate career, I went from wanting to be a virologist in West Africa to being a mycologist studying the fungi that kill trees. I pursued a PhD to help the world!

BOOM_the scientist_2

Now that I’m here, I feel like my research won’t have as much impact as someone else researching safer energy or a vaccine for HIV. In truth, many PhDs probably don’t think their work matters or that they are making a REAL difference.

Number of PhDs awarded in the USIf you look at the number of PhDs in the United States between 1957 and 2016, you’ll see an almost tenfold increase in the number of doctorates awarded—a trend that exists in many other countries too. While there are more people walking around with PhDs today than there were in the 1950s, it hasn’t helped solve any of the major problems facing the world in 1957 or today. War, inequality, climate change, biodiversity loss and clean energy were all problems in 1957 and are still today (in some cases, even worse). If we adopt an extremely simplistic view, it would seem that all the PhDs in the world are not having much of an impact. That makes me feel worse. Fortunately, it’s a very simplistic view.

We understand a lot more about the world today than we did in 1957. The purpose of a PhD, among other things, is to generate knowledge. Knowledge drives humanity forward; it doesn’t matter if it comes from studying the migratory patterns of birds, assessing the importance of cultural heritage in the 21st century, or developing a new vaccine for HIV. All this research generates knowledge which allows us to understand ourselves, our world and the universe better. And this knowledge is the starting point to effect change and growth. Because, in the right hands, knowledge can be used to change policy, improve education, create technology that makes the world a better place.

Jane Goodall summed it up perfectly: “Only if we understand, will we care. Only if we care, will we help. Only if we help shall all be saved.”

So, this knowledge – however big, however small – has to reach beyond the thesis. If you think of the size of our global problems – migration, war, disease, climate change — science communication and engagement with society has never been more important. But it’s a difficult road, trying to communicate science to non-scientists…

Bill-Nye-Saves-the-World

Even someone like Bill Nye the Science Guy battles. His show, “Bill Nye Saves the World,” which debuted in 2017, seeks to tackle the anti-science sentiment in the US by educating through entertainment. It has been met with a lot of criticism (obviously) and hasn’t received the wonderful ratings it was looking for.  Niel deGrasse Tyson’s show, “Cosmos: A Spacetime Odyssey,” was Emmy nominated and praised for its success (mainly amongst space enthusiasts). Tyson won the Public Welfare Medal from the National Academy of Sciences for the show and its promotion of science. Unfortunately, it only reached 1.3% of all U.S. householdsScientists seem to be famous among scientists and science enthusiasts, which is not a large enough part of the population or a part we need to be communicating more with.

science communication wrong_2

We can’t expect a handful of scientists to do all the communicating. To draw in a larger audience, we need to speak to a more diverse audience, of different races, religions, countries, political views, etc. To do that, we need very diverse scientists to present science issues that unite global audiences around shared values and what we can do to address them. Here lies an opportunity to become the next science hero, like Lee BergerJill Farant or Nox Makunga… only better, a science superhero. Become the Ironman or Wonder Woman of the science universe and use your PhD powers for good. Talk and help save the world.

Source link: SAYAS BLOG (2018).

CancerSEEK: A Novel Blood Cancer Test

A Blood Test That Can Detect Eight Common Cancer Types

By Ramadhani Chambuso

A newly invented blood test called CancerSEEK® can detect eight common cancer types, possibly even before symptoms appear. The test works through assessment of the levels of circulating proteins and mutations in cell-free DNA in the peripheral blood of the individual.

The designed multi-analytic blood test was applied in the US to 1,005 patients with non-metastatic, clinically detected cancers of the ovary, liver, stomach, pancreas, oesophagus, colorectal, lung, or breast. CancerSEEK® tests were positive in a median of 70% of the eight cancer types. Furthermore, the sensitivity ranges from 69% to 98% for five types of cancer (ovary, liver, stomach, pancreas, and oesophagus). The specificity of CancerSEEK® was greater than 99% and only 7 of 812 healthy controls scored positive. However, the estimated total sensitivity of CancerSEEK® was 55% among all eight cancer types.

The cost of the test is estimated to be less than $500, which is comparable or lower than other screening tests for single cancers, for example, colonoscopy. Currently, there are no screening tests available for average-risk individuals for cancers of ovary, liver, stomach, pancreas, and oesophagus.

This is an advanced stage for screening for cancers which identifies people with the disease when it is in its earliest stages and more treatable conditions with non-invasive procedures.

Source: Cohen et al. (2018).

Fusobacterium nucleatum and Colorectal Cancer

Oral Bacteria Found Predominantly Associated with Human Colorectal Cancer Cells

By Ramadhani Chambuso

The same oral commensal bacterium and gum disease pathogen called Fusobacterium nucleatum was found to be predominantly associated with primary human colorectal cancer cells and even in distant metastatic lesions, a study published in 2017 on the journal Science, reports. Furthermore, it was proven in mice with colon cancer that after treatment with antibiotics, Fusobacteruim load, cancer cell proliferation and overall tumour growth, all were reduced, which indicates that this organism may play a crucial role in colon cancer development.

Despite other studies suggesting the possible pro-tumorigenic role of Fusobacterium which may include modulation of host immune response to cancer cells and further enhancement of tumour cell invasion in colon cancer pathogenesis, this new study was scientifically able to show the correlation between decrease in Fusobacterium load and the decreased in rate of tumour growth and improved overall patient survival.

Although it is not clear yet if good oral hygiene would probably add advantage to preventive measures to colorectal cancer outcome, these scientists recommended the use of antibiotic Metronidazole, Fusobacterium–specific antimicrobial agents or phage therapy concurrently in colon cancer treatment. This is because broad-spectrum antibiotics may risk other gut microbial balance and did not show any additional effects on tumour growth control in their study.

Source: Bullman et al. (2017), Mima et al. (2015).

Hormonal Contraception and Breast Cancer

Hormonal Contraceptives may Increase a Woman’s Risk of Breast Cancer

By Ramadhani Chambuso

The risk of breast cancer was elevated among women who used hormonal contraceptives than among women who had never used them before, a study suggests, published in December, 2017 on the top journal in human Medicine, New England Journal of Medicine.

The study was done in Denmark, followed up 1.8 million women for 10.9 years who used hormonal birth control methods and only 11,517 cases of breast cancer occurred. Furthermore, when compared with women who have never used any hormonal control pills, the risk of breast cancer increased up to 38% depending on duration of use from less than 1 year to more than 10 years in all forms of hormonal contraception methods such as the pills, injections or hormone releasing-Intra Uterine Devices (IUDs).

However, the overall absolute increased risk in breast cancers diagnosed among current and recent users of any hormonal contraceptive was 13%, approximately 1 extra breast cancer for every 7690 women using hormonal contraception for 1 year.

Although these findings sound scary, on the other hand, the risk is somehow similar to the breast cancer risk contributed by physical inactivity, excessive weight gain, or alcohol consumption. However, all these extra contributing factors for breast cancer risk were not excluded in this study.

In contrary, oral contraceptives use, prevents more cancers than it causes. For example, it is known to reduce the risk of ovarian cancer, endometrial cancer and there is a strong suggestion that they may also reduce the risk of colorectal cancer.

In my opinion, this should be weighed against the clear benefits of hormonal contraception use that go beyond the obvious advantages of preventing unwanted pregnancies. In addition, the search for new hormonal contraceptives that do not elevate breast cancer risk or use of copper IUDs should be alternatively emphasized.

Source:  Mørch et al. (2017).

32nd International Papillomavirus Conference: Call for Abstracts

WELCOME TO IPVC 2018 
IN CONJUNCTION WITH AOGIN 2018
Join us for the 32nd International Papillomavirus Conference, to be held October 2-6 in Sydney, Australia. Australia has been at the forefront of HPV research from key innovations in immunology and vaccine development through to the implementation of large scale vaccination initiatives and an upcoming imminent transition to HPV-based cervical screening. We are also very pleased to be co-hosting the meeting with AOGIN, and plan a strong regional focus on HPV control in the Asia-Pacific Region.

Our conference theme is ‘Towards Global Control of HPV Disease’ and through workshops, invited lectures, and oral and poster sessions presenting the latest research results, the conference will cover papillomavirus (PV)-related topics from basic science to global health impact. We will be paying special attention to HPV control in populations that are most vulnerable to HPV disease worldwide, including those in Low and Middle Income Countries and Indigenous communities.

Read the welcome letter here.

Relive our outstanding 2017 Conference in Cape Town, South Africa with our photo gallery!

Discover Australia’s most beautiful city from the iconic Sydney Opera House to the sparkling blue harbour, exhilarating entertainment, delicious restaurants and historic heritage.

> See all pictures > Learn more
SHARE YOUR RESEARCH

ABSTRACT SUBMISSION IS NOW OPEN
Submit your latest work for the chance to present your research during the upcoming
IPVC 2018 conference.

NEW! The number of abstract topics has nearly doubled this year.
Choose from 5 main categories:

  • Basic research
  • Clinical research
  • Public health / epidemiology
  • High resource settings
  • Low and middle income (LMIC) settings

> View the full list here

Submit your abstract

Research Journey

My Cancer Research Journey as a Story

By Ramadhani Chambuso

In clinical medicine, researchers believe that HIV/HPV co-infected women progress relatively rapidly to invasive cervical cancer.

But then, I thought that may be too general because others do not progress to the invasive disease regardless of their CD4 T cell counts or Anti-Retroviral drug use.

Therefore, what I did, was to find out if host immunity and molecular genetic variations with HIV/HPV co-infection may influence early cervical cancer development. Interestingly, I have discovered that specific immune genes in combination with HIV/HPV co-infection may influence cervical cancer development in South African Women.

Conclusively, these results enlighten our insight to the disease development, add new knowledge to the existing theories in Clinical Oncology and may change the screening and management of the disease to focus or target more on individualized molecular genetic variations for cervical carcinogenesis.

Paediatric Brain Tumours

Advances in our Understanding of Paediatric Brain Tumours

By Marc Hendricks

Massive advances have been made in the last forty years in paediatric oncology. The best example of this is in acute lymphoblastic leukaemia (ALL) which is the most frequently diagnosed malignancy in children and which in the early 1970s was almost uniformly fatal. Today in developed nations the overall survival for ALL tops 80%, in some countries as high as 90%. Almost every other solid paediatric tumour has followed suit except for paediatric brain tumours, which despite comprising a third of all tumours seen by paediatric oncologists, was the group in which arguably there was the slowest progress by comparison.

Recently however, the advent of molecular mapping of paediatric brain tumours has transformed the landscape of our conventional ideas of risk stratifying children with brain tumours which traditionally was built on the prospect of resectability of the primary tumour, the presence or absence of metastatic disease and the histology of the tumour.

The two most recent examples which best demonstrate this seismic shift in our understanding of paediatric brain tumours is undoubtedly the new molecular risk stratification groups which have emerged in paediatric medulloblastoma (Kool et al., 2012Taylor et al., 2012) and the removal of the term primitive neuroectodermal tumour (PNET) from the WHO classification, following emerging studies from Sturm et al. (2016) revealing multiple molecular sub-types amongst tumours traditionally described as PNETs. Using DNA methylation profiling, the investigators were able to demonstrate amongst other things four distinct new categories of tumour each with its own recurring genetic alterations, histopathological signature and clinical characteristics.

This technology is unravelling almost faster than therapeutic interventions can keep up as new risk groups and sub-groups are identified through cutting edge laboratory work. International clinical trial groups have been quick to follow on the heels of these discoveries by incorporating molecular categorisation into new treatment protocols in order to learn more about the optimal management of these tumours. In addition, similar technologies are now being used in other groups of brain tumours with the hope that more can be learned particularly about tumours, which up to now have eluded clinicians, surgeons and radiation oncologists. This, in concert with advances in surgical and radiotherapeutic techniques, brings with it renewed hope that a new era in paediatric brain tumour management has dawned.

Source links: Kool et al. (2012)Taylor et al. (2012)Sturm et al. (2016).