All posts by Harris

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 conference

Credit: 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.

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…


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

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

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).

del 16 in Acute Myeloid Leukaemia

del 16 in Acute Myeloid Leukaemia (AML) in children: Are the Clinical Implications for Management the Same as for Other Good Risk Cytogenetic Myeloid Leukaemias in Children?

By Marc Hendricks

Recently del 16 has been described in AML in children and adults. According to current guidelines risk stratification for paediatric myeloid leukaemias is based on cytogenetic profiling. Patients with leukaemia with good risk cytogenetic profiles are treated with intensive chemotherapy alone and are not considered candidates for transplantation in first remission. These karyotypes include t(8;21), inv(16), t(16;16) previously described in the association with historical French-American-British M4Eo and t(15;17) in acute promyelocytic leukaemia (APL) along with the other known microvariants.

With the description of the del 16 questions have been raised about whether or not this specific genetic abnormality constitutes a newly discovered good risk variant and whether the same treatment algorithm can be followed as for the other favourable cytogenetic group. The distinction is an important one because it speaks to the need for transplantation to consolidate a remission following intensive chemotherapy: in other words, can transplant be avoided or should children with del16 rather be assigned to a standard risk group and should practitioners then be looking for HLA identical donors to proceed to transplant?

Considering the small number of reported cases there is, as yet, no clear indication that the deletion is interchangeable (as it refers to risk) with inv16 and t(16;16). The source links provided highlight the recent descriptions and the controversial question that it has raised for the management of myeloid leukaemia in children.

Source links: Arthur and Bloomfield (1983),  Rogers et al. (2017)Silva et al. (2004).