Category: Emma Kampouraki

by Emma Kampouraki

For thousands of years, the only true driving force of life on Earth has been evolution. Among the population of every species, only those with the strongest characteristics survive, leading them to selectively pass on these characteristics to their ascendants, in an attempt to adapt better to the changing environment.

Humans, having evolved as a result of the same process, are now taking nature as an example for the construction of their own habitat. Recently, I had the opportunity to meet the Founder and Director of Innovation at Biohm in a Pint of Science event. Biohm could – and may – have been derived from the combination of bio and home; otherwise construction using natural materials. Mostly considered as waste nowadays, organic matter is well re-used in nature, through a process facilitated by decomposers; organisms that break down dead or decaying organisms, absorbing nutrients for their own growth and development. Could we do the same with our homes?

Ehab Sayed from Biohm says yes. The company collects organic waste and holistically sustainable natural materials (which sometimes include organisms, for example fungi) and turns them into building materials, which are satisfactorily durable and stable for a number of years before they are replaced (for free) with new ones. Durability is mainly down to the specific material or mixture of materials used, and stability depends on the particular structures constructed. Their novel and revolutionary construction system is called Triagomy and is basically the way they assemble the materials together which gives them great stability and the ability to be self-assembled. The team consists of researchers, engineers, architects and experts in circular economy and sustainability. The perfect blend for green buildings and the advent of the recycled construction industry.

If we can convince ourselves to think out of the box, use what we have effectively and respect the environment as a priority, we will ultimately facilitate and speed up evolution in our own habitat. Evolution will bring growth and better adaptation. More importantly, it will solve the problems of plastic pollution, waste management, toxic construction materials and deteriorating health in Earth’s ageing population.

 

Declaration: This is a non-sponsored blog, inspired by a novel idea for a circular economy and recycle, facilitated by scientific knowledge.

 

 

by Emma Kampouraki

Earlier this week, I attended a very successful seminar in the School of Pharmacy Newcastle University. Entitled ‘Optimising medications for people with limited life expectancy’, this seminar could only be a great opportunity to find out about factors affecting our prescribing culture, not only in the UK, but in western world in general.

Basically, the main point of the speaker Dr Adam Todd, Reader in Pharmaceutical Public Health, School of Pharmacy was to showcase the current evidence on surplus medication prescribed for elderly people with late stage diseases with limited life expectancy according to predictions of clinicians. De Todd had extensive experience in lung cancer patients who have been prescribed medication ‘for life’, which at some point lose their purpose and should be discontinued. However, no clinician or pharmacist would easily review the medication list of those patients unless an adverse drug reaction or change in their clinical response appeared. In many cases, patients are under the impression that they really shouldn’t discontinue any medication, without understanding of the actual effect of the particular drug to their bodies. Therefore, even if the need to discontinue a specific therapy is pointed out to them, their lack of education doesn’t allow them to accept the proposal as a positive change, but rather return to a different prescriber with the desire to leave with a prescription for the exact same drug.

Guidelines fail to consider situations like this and they don’t provide recommendations on discontinuation of a medication if its mostly preventative nature is no longer useful for the patients and could only continue reducing their quality of life. Healthcare professionals are not aware of the consequences of unnecessary medication for the patient either. Therefore, the vicious circle continues and leaves those who understand the problem with the only option to raise awareness in scientific conferences and informal chats.

With all current information and guidance available about prescribing, is it time to look the other way and reduce the load of polypharmacy that heavily strikes the elderly population and costs millions to the NHS each year? The change is in front of us; we just have to learn and go with it.

by Emma Kampouraki

Publishing research results in scientific journals is crucial for research dissemination within the scientific community. The impact and quality of a research project can be demonstrated by the journal it is published in. For all research projects, as long as they are scientifically sound, legitimate and well designed, there is a journal that is appropriate. However, sometimes we aim high and without taking into account the competition in the field and the scope of the target journal, which can be very disappointing at times. In order to avoid a potential rejection, there are certain steps to be followed.

1. Identify a few target journals in advance

The main factors to consider when choosing journals is not only the impact factor, but also the scope of the journals of interest. For example, a specific haematology journal might not accept a manuscript about the pharmacology of an anticoagulant drug in vitro. It is always good to aim higher, but it might take more time to identify a journal that meets your criteria. On the other hand, if the manuscript gets rejected you’d have to repeat the steps all over again. However, the worst case scenario is your manuscript is rejected before getting to reviewers, in which case, you would have no clue what to improve before re-submitting to another journal. If you do get through to reviewers, and the rejection comes as a result of their comments, then this is your opportunity to use the feedback and improve your manuscript to hit another top journal.

2. Format your manuscript according to author guidance of the journal

Paying close attention to the journal’s guidelines for submission shows the dedication, the attention to detail and the professionalism all good quality journals will look for in their authors. If you can’t be bothered to read their 10-page guidance and even identify the category your manuscript falls in, then don’t expect to get a positive response back.

3. Write a good cover letter

Your letter to the editor should be polite, professional and succinct. Dedicate enough time to make sure that, firstly, there are no typos and, secondly, it contains a good answer as to why your manuscript is relevant to the journal and what is the overall impact of your research. The stronger the impact you (and your results) can demonstrate, the more time the editor will spend on your abstract, hence you’re more likely to reach the review stage.

4. Submit according to the guidance (pay submission fees)

Some high impact journals may ask for a fee, but don’t be put off by that. Follow the steps, spend some time to review the final version of your manuscript, to upload all necessary documentation and tick all those boxes appropriately. Again, the editor will use the information submitted to inform the selection of reviewers, if they are happy with the first impression of your work.

Even if you do get a rejection, which happens in nine out of ten cases, there is nothing wrong with resubmitting to a new journal. The process will start over again, but you’ll certainly find things to improve. After all, your confidence and belief in your own research output is a necessary ingredient of your academic life.

by Emma Kampouraki

While a vast proportion of our knowledge about drugs focuses on the mechanism of action, the indications and the adverse events that may appear, we are still at an early stage to understand fully the interaction between drugs and our genetic background. It is well established that such interaction is present and has a great impact on the response of patients to a number of commonly used prescription medication.

After the observation of substantial differences between patients’ responses, while receiving the same treatment, it became apparent that the “one size fits all” design is not effective anymore. Vogel in 1959, described the term ‘pharmacogenetics’ as the field that studies the way in which one single change in a gene influences the response to a drug. However, after the completion of the Human Genome project in 2003, the term ‘pharmacogenomics’ was used to describe the influence of the whole genome to the drug response. Pharmacogenetics is a subspecialty of Pharmacogenomics and does not require whole genome sequencing, whereby analysis of all the genes is performed. The two terms are often used interchangeably, but this sometimes can cause confusion.

The importance of pharmacogenetics is also reflected in the recent clinical trials. There is an increasing interest to study how drug responses are affected by patients’ genetic variations as demonstrated by the 1060 studies about pharmacogenetics or pharmacogenomics to date.

There are numerous examples of drugs that are influenced by certain genes, either regarding their pharmacodynamics or pharmacokinetics. One important gene that encodes a microsomal liver enzyme from the P450 complex is CYP2D6. As shown in 1970, this gene affects the elimination of debrisoquine, an antihypertensive drug. People carrying certain alleles (i.e. versions) of this gene have altered elimination rates and therefore different duration of action.

Also, certain alleles of the NAT2 gene lead to the production of less N-acetyltransferase which causes slower acetylation and elimination in patients and side effects from the longer stay of the drug in the blood circulation.

Similarly, suxamethonium, a general anaesthetic, can cause prolonged apnoea in patients with defects in BCHE gene producing low activity of the enzyme that normally breaks down suxamethonium. Primaquine, a drug against malaria, has been shown to cause acute haemolysis in patients with G6PD enzyme deficiency.

The most important example is that of warfarin. This anticoagulant drug has a very narrow therapeutic window, causing serious, potentially lethal side effects after small instabilities in its levels. The dose for each patient has been proven to be dependent on two genes, CYP2C9 that affects the elimination by metabolising the S- enantiomer of warfarin and VKORC1, the actual target enzyme that warfarin inhibits.

In fact, FDA updated the drug labelling in 2007, recommending very specific dose adjustments after genetic testing of these two genes in combination.

In order to organise the information from the studies, a database was created, called PharmaGKB, which can easily facilitate the acquisition of information among researchers and clinicians and the actual clinical implementation of pharmacogenetics.

So, what exactly are the benefits from translating pharmacogenetic information into clinical practice? In a study of 2008, it was estimated that over one fourth of commonly prescribed drugs have some type of genetic information that could be used in medicine. It is possible to predict interactions between drugs, potential side-effects and individualization of treatment, such as informed choice of drugs or dosage as in the case of warfarin.

Currently, several kits for pharmacogenetic testing for warfarin are commercially available with their cost continuously decreasing, making genetic testing easier than ever before. In Freeman Hospital, Newcastle upon Tyne, such a kit utilises literally a droplet of patient blood and provides the genetic analysis result within 40 minutes after a fully automated run.

A more personalized design of new drugs, especially in population level, can be achieved using the different allele frequencies in genes that are important for drug activity and metabolism. This way, each population would receive more appropriate drugs schemes for its most prevalent genetic changes. Although there is a great number of challenges in this field, including ethics and concern about potential access to the data, which can be partially addressed by the advances of technology, the benefits are many and the cost-effectiveness of the implementation of pharmacogenetics is reported in many studies. The field of pharmacogenetics has therefore a lot to offer to the scientific and medical community.

by Emma Kampouraki

You should know {react} by now. If you are reading this, you’ve seen the magazine somewhere on campus, online, or you are even a fan of our blog. Be that as it may, you should have realized what {react} is trying to add to your everyday lives; a splash of science mixed with attractive design and high quality of photos.

But how did we end up there? Well, that’s an interesting story because no one is greatly confident to answer. {react} was born from a team of PhD students and a few members of staff who dreamed of a science magazine that would target a wide range of audiences, help people learn more about science, and most of all encourage students write more about science and the process of publication. {react} was soon much appreciated by the student community and, although this fluctuates, {react} often seems unable to accommodate the numerous interesting articles it receives for every issue. Then, the blog was created. It would be a pity for those articles to stay hidden in a hard drive.

A magazine would never come together without the co-operation of a big team that literally does everything from scratch. If you look at previous issues of {react}, the style slightly changes to reflect the influence of new members in the design team as well as popular demand for certain types of articles (such as research articles, as opposed to interviews). A large part of the character of {react} is its design. Another important bit is the articles themselves. And how these end up in print, is a long story.

To cut this story short, the call for proposals is announced by the team via social media, posters across campus, word of mouth and e-mail newsletters. When the deadline closes and according to the number of submissions received, we normally go through the process of reviewing the 150-word proposals and selecting the ones that reach our standards in terms of quality and fit with the pre-announced theme. Authors are then contacted with clear guidelines on how to produce their full-length articles. A sub-editor is allocated who can guide them through the process of reviewing the article and making the necessary changes to meet our publication standards. The design team comes last to format the magazine in such way that will be appealing to reach and enjoyable to read.

As in every team, we need a proper hierarchy system to ensure all needs are met within certain timeframes. This also ensures that messages are properly communicated and tasks are co-ordinated. The editor(s) organize the meetings and provide the team with guidelines and information. At the same time, the team makes decisions democratically. Positions in the committee include the sub-editors, the blog manager(s), the design team, the copy editor and the editor(s). These roles are allocated on a voluntary, first come, first serve basis during our recruitment events or training workshops. PhD students are preferred for the committee due to the nature of the magazine and to offer training opportunities for skills development; however, we have had Master students help out as well.

Issue 11 has just been published and will be available soon, both online and in print, available across campus and at most major student spots in Newcastle. It is the result of hard work, team effort and co-ordination of a great number of authors, reviewers and sub-editors. We couldn’t be prouder for this issue as it encompasses a variety of scientific topicsfrom different fields, which makes it more inclusive than ever. Join us in our training events to learn more about the magazine and, if you fancy, join our team to help bring science closer to the many audiences {react} targets and to celebrate the results of team work by a team of PhD students.

• Current call for proposals ongoing under theme “Limits”, deadline 14th September, 150-word article proposal to be sent to react.mag.team@gmail.com
  
• Upcoming training workshops:

Meet the {react} team – 12th November 2018

Meet the team behind our student-led science magazine, and learn how you can contribute as a writer, editor or designer

{react} training day – 20th February 2019

Join us for a suite of training sessions in science writing and communication delivered by experts in the fields of public engagement, science journalism and design

by Emma Kampouraki

Over the last couple of centuries, we have faced rapid and unprecedented urbanisation. Cities comprise of a complicated urban system which can easily break down as a result of both external and internal factors.

In an attempt to study the system of a system and understand how a city operates, we have to go the traditional way and do what drives scientific research over time; observe! An observatory is more likely to be a keyword for astronomy; nevertheless, it is also a useful concept when trying to collect observations about our cities. Our observations in turn help us generate the data needed to understand how one system impacts the other system, for example in the interaction of transport, electricity and drainage. In the desert of our knowledge about cities, making evidence-based decisions seems like a sci-fi scenario. We normally ‘try stuff without having data’ and we then have to deal with our disappointment and a few thousand pounds -if not more- wasted. At the same time, politics and various short-term requirements drive policies that stay in place longer than their optimum lifespan.

With this in mind, researchers from Newcastle University, as part of the Urban Observatory Programme of the University and the national UKCRIC observatory programme through the CORONA project, have installed as many as 200 air pollution monitoring sensors fitted with CCTV cameras (that take up to 2000 observations per minute) around Newcastle. This compares to a devastating figure of only 35 sensors in London.

The sensors record more than 60 variables of air pollution, wind, people and movement, all day and night. As expected, before and after an event, the image of air pollution that is received can be markedly different. However, the function of the sensors is highly dependant on a number of other systems, the most critical of which is the availability of network for data transmission. And here comes the take of lamppost; urban monitoring is hard, owned by councils and managed by other stakeholders. The question of reliability is of course always relevant; damp and gaps in data are some of the major issues to be resolved.

As Philip James, Senior Lecturer in GIS pointed out, ‘’smart cities are not a done deal. Sensors cost a lot, mainly for maintenance, and context is always more important than just data.’’

The Air Quality Directive takes account of guidelines from the World Health Organisation. It sets certain limits and information requirements for several pollutants to help countries address and prioritise the harmful effects of pollution. For nitrogen dioxide (NO₂) the Air Quality Directive sets the annual mean concentration levels of NO₂ limit value at 40μg/m³ for the protection of human health.

Over a ‘pint of science’, we learnt with real examples that city monitoring is a great way to not only learn more about the urban environment we have constructed, but also assess biodiversity and raise citizen awareness. Smart cities have more than sensors, for example smart bins, but we’ve still got time for improvement.

By Emma Kampouraki

Exam and writing-up periods are the worst, we all admit that. Especially when the weather starts making our days brighter and our mood better. So many interesting and pleasant things to do, so little time… What shall we do with the unpleasant ones, though? Follow me to explore 8 ways to make the most out of your time of study.

1. Prepare your notes early

I’ve always found myself panicked when starting studying for an exam. I was that student who would keep a notebook for one module and it would end up having notes for multiple modules (or even recipes). So, it used to take me 2 days to sort out what’s relevant and what’s not.

This is not a good example, so don’t follow my rule! If you are like me, tackle the issue early, always carry some blank notebooks or sheets with you, or start early! Before the end of the term, start working on your notes, numbering them according to the lectures, slides and further reading material available. It will save loads of time and won’t add fatigue to your shoulders during revision.

If you spend your last term writing up, then it’s worth starting preparing your introduction early by making notes on papers you’ve read or creating an online library using EndNote. Your methods will also be in your lab book quite early, so make sure you transfer them to your word document. It’s all about making a start really!

Source: http://www.boro.gr/

2. Make a realistic schedule

Start by setting the basic parameters of your revision, described by the following questions: “what module I am studying for each day?” and possibly (if you can) “what amount of the curriculum will I have finished each 3-4 of days?”. If you organise it strictly by day, something will go wrong and you’ll be depressed from the first week of revision.

Same with your dissertation; start early and set deadlines for your introduction. You’ll soon realise you needed more allocated time for this part and maybe less than what you had expected for methods and results. Plan realistically and leave some margin for procrastination and bad mood.

Source: https://www.pexels.com

3. Follow the schedule and reward yourself

At the end of each day, whether it’s early or late, go back to your precious schedule and compare where you should be and where you are. If you’re close enough, you might consider continuing for another half an hour to reach your target. Otherwise, you might give up.

In any case, remember to buy some treats for yourself for each target you reach. Hopefully, it will increase your motivation! Oh and… ask your flatmate or friend to keep them, it’s always a better idea!

4. Change the environment

Sitting on the same chair, looking at the same view and studying at the same place for a month won’t offer you something important you need during this period of time: visual memory.

I have always combined spaces with information. Something I did, the way I was sitting, the person or the wall in front of me were different while I was studying about this rare genetic syndrome. That’s how I now remember it’s symptoms. Don’t you believe me? Well, try it! Replace your desk at home, with the library, then a quiet cluster and then a different library. You’ll see it happening automatically, especially for information you don’t really care about.

Source: https://www.pexels.com

5. Keep the 10-minute break precise

One of the biggest rules of exams is a ten-minute break for every hour of study. This has been predicted from the average time our concentration lasts. Therefore, even if you don’t organise this break, you’ll have it in the form of not paying attention to what you study.

Keep your break short enough so that you don’t get totally out of the flow. Also, make sure it’s a proper relaxing break, so avoid stimulating activities such as playing video games.

Stay away from social media, as well. It can take hours to find the courage to close the “window”/app.

Source: https://quotesgram.com

6. Prepare your biological clock

Different students choose different times of the day to study. I was one of those students who would start in the morning and would finish in the evening. Night was not my best as I always felt sleepy. It was important that I organise my lunch and dinner at reasonable hours to keep my brain up and running. I would wake up early and go to bed quite early.

If your daily routine differs, you would have to consider keeping it stable for the whole revision or writing-up period, as any changes would disturb your brain function and would take days for your body to adapt. For this reason, make sure you keep in mind your biological clock, without leaving behind your examination hours. Imagine staying up the whole night and struggling to wake up at 9am for your exam at 10am. NOT pleasant at all and probably impossible!

Source: https://www.cartoonstock.com

7. Fruits and chocolate vs salty snacks

Leave your favourite crisps in the cupboard and avoid hamburgers from McDonalds. Choose healthier options for your breaks. Fruits will help your body stay hydrated, without overloading your stomach and making you feel hungry all the time. A significant quantity, combined with yogurt, cereals and/ or chocolate will feel in the gap much better. Vitamins and minerals will help you stay focused, taking good care of yourself will increase your confidence and chocolate will definitely provide enough glucose for our brain.

8. Repeat before sleep

This only applies to ‘revisioners’. A final tip I always follow is: keep a note of the most difficult things, the ones you’ve failed to remember the whole day, then give it a read just before you turn off your lights (and brain) in bed. While asleep, you will subconsciously repeat it, you might even dream of it and in the morning it will be somewhere in your mind when you need it.

These might sound too much or impossible to implement. They are not! Certainly, there are few of them you definitely follow already. Your experience will show you the best way to study and that will be according to your results. So, think about these small details that make great changes and adapt them to your own study needs. Good luck with this and your exams and try the best for yourself.

By Emma Kampouraki

By Emma Kampouraki

After surviving St Valentine’s Day one more year, I was back in the office next morning with a weird feeling that I’ve forgotten something. While opening my inbox, I found an e-mail from Nature Alert about the contents of the next issue. This is when I found myself reading an article titled “Train PhD students to be thinkers not just specialists”. And I thought… this is a good way of starting this week’s blog.

PhD life is long and difficult for each and every student. This is the best reason why we should look into ways of making it better and far more interesting than any other period of our lives. One way could be to pretend we are not doing a PhD, don’t be bothered too much and run in hell during the final year or never finish. Another way is to try and sort out your everyday workload asap and then relieve your depression with alcohol and sleep. We could do better than that, right?

Source: http://www.allbusinessideas.net/becoming-a-successful-accountant-main-skills-to-develop/

 

The abovementioned article in Nature explains how changing the curricula of PhD studies can broaden the horizon of doctorate students, based on the view that “researchers who are educated more broadly will do science more thoughtfully”. Now, this is definitely what new generation of scientists is aiming for and they are absolutely right. Nevertheless, with less than 15% of doctorate graduates ending up in academia, we need to consider other skills that PhD students must acquire on the way to their last degree.

First could be team work and collaboration. During your PhD you might be asked to learn various techniques and join other research groups for training and/or data collection. You might even be required to perform experiments in a hospital or collaborate with other groups during field work. When that happens, grab the opportunity to check your team work and be prepared and willing to share your knowledge, experience and passion for science with them. Don’t forget to make friends and keep contacts.

The next skill would be problem solving. It might relate to your own work and assays or even to an assay of a new PhD or other student you are helping. It is a skill that few people acquire these days, doe to the massive help technology and technicians offer in our labs nowadays. In addition, it teaches you how to start thinking out of the box, be creative and of course how to deal with stress, which is always there accompanying every moment when things go wrong. Once you manage to solve a problem once, your confidence can reach the sky.

Speaking of students, ask your supervisor to give you the chance to supervise an undergraduate or master’s student. This is where you will find your leadership skills being developed. Being a proper leader requires much more than you’ve ever thought. But you will never know until you actually experience it first-hand.

Project management is one of those skills your employer will look for desperately when they are recruiting for managing positions, like a team leader. I know what you’re thinking; project management is your whole PhD. What about any other projects you might be managing simultaneously? What have this project taught you about time management and balance between different workload? Exactly…

Finally, communication is crucial in every job. Make sure you attend conferences, scientific meetings and other opportunities like this. Also, make sure you speak about your science in a lay audience as well. This is not only because you will have to do this at some point (during an interview for example), but because it can be quite fun as well. Science communication can be interesting for you, so can be science writing. So, next time you will be offered the chance to write for a student newspaper or magazine, grab it! Who knows how many job opportunities it could offer you in the future.

After all these, what had I forgotten to do in the first instance? I don’t know either. Is it still that important? I doubt it…

Train PhD students to be thinkers not just specialists, Bosch G. Nature 554, 277 (2018)

By Emma Kampouraki

In our days, there is no such thing as dong a PhD without at some point finding yourself in need of something used, produced or ordered by the previous doctorate student before you even arrive. We’ve all been there, and if you haven’t you will get there at some point. My own experience has showed that those “somethings” are much more than I could ever imagine, so it is now a good time to define the 5 golden rules of how to complete your PhD without leaving a mess behind.

1. Keep an organised lab book

A Latin proverb says “Verba volant, scripta manent”. It is so true that spoken words fly away, while written words remain. Especially so for protocols optimised or developed during your PhD, but haven’t been published yet.

2. Share your secrets

It is always kind and wise of you to make good notes of what worked and what didn’t in your experiments. Random observations that can really make a difference, experiments to test different factors that might have an influence on the technique and all those little things you learned or changed during working in this particular lab. Make a list or have a quick meeting with the newbie that’s about to start working where you used to and make sure you pass on this information. The way you have organised the drawers, or the place where you’ve stored those important chemicals will save loads of time and effort. Think about how you felt when you were searching for something and three months later, when you finally located it, it was nowhere near where you would expect it to be. Grrr…

3. Leave your bench tidy

No matter what time of the year you are leaving, you should always remember to throw all the things you stuck on walls or hung above your bench and which are totally useless for the next poor guy that will have to spend 3 years at least in this bench. Organise the stuff you used to throw in your drawers, dispose of any chemicals that have expired but you kept them in the fridge “just in case” and in general, make every effort to return the bench better than how you found it. It is a gesture of respect to the next generations.

4. Share your thesis with your colleagues

Another cute gesture that everyone who completes a PhD should consider would be to send an electronic copy of the thesis to the guys you leave behind. This simple thing will save them hours of searching for a paper you have talked to them about in the past, or for a paper with more clearly defined methods as in your lab book, or for results that they may be asked to replicate, or even a good template when they decide to start writing their own thesis. Not to mention that your thesis will be certainly referenced in theirs.

5. Keep in touch

I’ve always hated those people that never reply to my e-mails. Even worse when at some point I asked a previous PhD student about where some samples were stored and never bothered to get back to me. I spent days looking for them and when I found them and had one more question, my supervisor dropped them a line and they replied the same day!!! For this reason, the 5^th golden rule will have to be: “Keep in touch with your lab group and always reply back when someone contacts you about samples you have worked with before, no matter who it is that’s asking”.

Photo credit: http://circleccowboychurch.org/