How does scientific publishing work?

So we talk a lot about the studies we do, and we’ve had a lot of summaries on here of the published papers detailing the results of the research studies.  What might be a bit of a mystery though is how the process between those two points works…  So here’s an overview.

Once we’ve gone through all the hard slog of acquiring research data and analysing the results, we write up a report, that we generally call a manuscript.  This is normally something around 3,000 words long, and contains:

– An introduction to the area of study, why we decided to do the research, and what we expected to find (our hypothesis).

– The ‘methods’ section, which is a detailed description of what we did and how (what equipment we used, how long we measured things for, where we identified participants from, in what order our measurements were made, etc.).

– Results:  this is where we put all the numbers, in the form of tables and graphs and some explanatory text.

– The discussion, which is where we talk about what we think the results mean.  It might be that we found what we expected (i.e. supported our hypothesis), or that we got completely different results to what we hypothesised.  Either way, we discuss aspects of the study that we think were particularly strong, highlight any weaknesses, and then refer to our results within the context of other research in the same (and related) fields.  This section often contains suggestions of what future studies could do to build on the results we’re presenting.

So once we’ve written the manuscript and all authors are happy with it (everyone who has contributed significantly to the research is listed as an author, with the first person in the list being the person who did the majority of the work, and the last person being the senior academic responsible for overseeing the project), we decide on a journal to send it to.  This decision is based on the type of research study we’ve done (there are some journals more suited to studies with a pure physiology focus, and some better for more clinically-orientated work) and how significant we think the work is.  A larger study, or one with more exciting findings (perhaps that would really change the way people think about that area of study), would be sent to a more prestigious journal.

Once the journal receives the manuscript via their online submission system, it is evaluated by a member of the journal’s editorial team.  They judge whether the manuscript is the sort of thing they’re looking for, and at that point either reject it straight away (disappointing) or decide to send it out to review.  If the latter, the manuscript will be sent to usually two or three expert researchers who work in the same field to ask them to give their opinion.  These reviewers will write a report of the manuscript and suggest how suitable they think the manuscript is for publication in the journal.  The editors of the journal will take into account the opinions of all the reviewers (and these opinions won’t always agree…) and make their decision.   They will send us an email informing us of the outcome, which will be one of three things:  that the manuscript has been rejected, that it will be reconsidered after some changes are made, or that it is accepted as it stands (a relatively unusual outcome, but one that we would celebrate with some vigour!).

If the manuscript is rejected, we will look carefully at the reviewers’ comments and make any appropriate changes to the manuscript before choosing a new journal to send it to (and the process starts again).

If changes are requested, these could be relatively simple (such as adding in some more details about the participants, including some different graphs to represent the data more clearly, or referring to some other research within the discussion section), or could be complex (for example requiring some major data reanalysis or lengthy explanations of why a certain approach was chosen).  We would work on these changes and send back a revised manuscript with a detailed letter describing what changes we have (or sometimes haven’t) made and why.  These documents then are sent back to the reviewers and they write another report.  Based on this, the editors decide whether we’ve done a good enough job for the manuscript to be accepted.  Sometimes the changes and corrections process is repeated once (or more), but generally the manuscript will be accepted in response to the first or second set of changes.

Once the manuscript has been accepted by a journal (whether that’s the first, second or fifth journal to which it was sent), the journal’s editorial assistants prepare the written document in their own specific format and send ‘proofs’ to the authors to approve (making sure that everything looks correct, there are no spelling errors, and that the layout for the journal hasn’t led any data to be presented in a misleading manner).  The paper (no longer just a manuscript) is then first published online, and a few months later appears in print (though actually very few people read journals in paper form any longer).  And importantly, we add it to our CVs!

Lung function in dolphins!

Dan came across a research paper the other day that was all about measuring respiratory function in dolphins – and it turns out that dolphins have pretty fascinating respiratory systems so we thought it worth sharing.  Obviously measuring lung function in any animal is tricky, but when they live in water…  We’re pretty impressed with the data these researchers managed to get, given that we often struggle with adult humans.  One good thing is that dolphins are so smart that the research team were actually able to train them to perform specific respiratory manoeuvres (“chuffs”) so that they could compare normal dolphin breathing to these effortful breaths.  The researchers also emphasised that the dolphins were free to swim away or resist the measurements if they wished, so actually they ‘gave consent’ for the study in their own way (tricky to sign a consent form when you’ve only got flippers).

Dolphins’ lungs get exposed to a much wider range of pressures than animals who live on the ground, as they have to be able to breathe at the surface but also cope with the increasing pressure as they dive.  It has been thought for some time that diving mammals probably have much floppier small airways and alveoli in order to allow these parts of the lungs to collapse when under pressure during dives, and then re-expand easily when they re-surface.  In this study, the researchers passed small tubes with pressure sensors down into the dolphins’ stomachs so that they could measure the pressure being generated by the dolphins’ respiratory muscles.  This is the same as we do in our studies – though probably a bit harder to do…  This showed that dolphins’ lungs are about four times ‘stretchier’ than human lungs, in line with the researchers’ hypothesis.

F1.largeThe researchers also used a very large flow sensor over the dolphins’ blowholes to measure how much and how fast they were breathing, along with the concentrations of oxygen and carbon dioxide in the air.  Dolphins only breathe about 3 or 4 times per minute (compared to 12-15 breaths per minute in an adult human), but when they do take a breath they have to exchange a huge amount of air very quickly (their total time to breathe in and out is only about 0.7 seconds).  This study showed that even during a normal breath, air moves out of the blowhole at a rate of over 2,600 litres per minute, which is almost four times higher than the fastest human cough we’ve ever measured in our lab!  During a “chuff”, the highest flow recorded in this study was 8,400 litres per minute – that would be 84 bathtubs full of air over a minute!  During a normal breath the dolphins tended to take breaths of about 5-6 litres (which is about the total lung size in adult humans), but this went up as high as 18 litres during chuffs.  They also absorb more oxygen than humans do from the air they breathe – air contains 21% oxygen.  Exhaled breath from a human is normally about 17% oxygen, but dolphins get quite a lot more from it and breathe out gas at only 12.3% oxygen.  They also breathe out a bit more carbon dioxide than us (7% compared to 5% for humans).

So, in summary…  Dolphins:  big lungs, fast lungs, effective lungs.  We are in awe of the research team for what looks like an exceptionally challenging study, with fascinating results!

The value of working together

Research is tough at times – much of the time in fact.  Progress is slower than in many other jobs, and getting turned down is a frequent aspect of the work (funding applications and submissions to research journals are very rarely successful on the first attempt).  There are also a lot of things you need to know.  This can range from complex stuff like specific scientific techniques to something as simple as knowing who to contact to get a replacement lightbulb in the office.  Also, difficult things happen in researchers’ personal lives too, and such things can make the research work much harder.  The thing that makes this all manageable is that we work together as a team and help one another.

This might seem like a simple thing, and an obvious one.  It would however be possible to let everyone figure out their difficulties on their own – it would take longer, but you can learn techniques by going on courses or reading about them in books and papers, and despite the fact that the King’s College London website can be a bit of a challenge, you’ll find the email address for the facilities helpdesk eventually.  Doing it that way would be stupid, and we’d all probably be really grumpy too.  So instead, we use each others’ experience and knowledge to complement one another and get things done quicker and better.  Some examples:

Alan has spent a lot of time learning new and (sometimes) complicated statistical methods.  We use statistics to demonstrate that the findings of our studies haven’t just occurred by chance, so stats are in many ways the crux of our work.  We have generally used relatively simple statistical methods in our lab, but Alan’s willingness to explore new techniques (and do all the really hard reading and learning for the rest of us) means that we can explore our research data in ways we hadn’t thought possible, and robustly demonstrate findings that we felt were there but couldn’t quite show.

Caroline is the only doctor in the lab at the moment, so can help others with questions about things like the prognosis for a certain disease, or how particular medications work.  The training for physiotherapists, nurses, physiologists and the like doesn’t cover these things in as much depth.

Ged has more experience in, and greater knowledge of, human physiology than any of the other lab members.  It’s always surprising how detailed an explanation of the physiology underlying a particular process Ged can give!  This is invaluable in allowing us to understand why things that we see in our studies might happen, and how different body systems interact.  Ged’s knowledge of how the body controls breathing is particularly impressive (as that’s what his PhD concentrated on).

Manuel is a super-clever signal processing engineer, and so understands the data we acquire in a completely different way to any of the rest of us.  He can explain why it might be that we get a strange wibbly line in the middle of a study – and more importantly can often get rid of it, which means we can use a recording that otherwise we would have had to ignore.

Dan has a lot of experience as an ICU nurse, caring for patients at the bedside as well as doing research.  We do quite a lot of studies in intensive care and Dan’s insight into the minute-to-minute reality of an intensive care unit patient’s stay is hugely beneficial in allowing us to plan studies around patients’ needs, and make sure what we do is sensible and feasible.

Alongside all these skills, the silly little things that people pick up along the way are incredibly helpful too – how to change a setting to format your Word document correctly, what time to go to the canteen to avoid the big queue (and get the best chips), which screwdriver fits that bit of equipment the best, what forms you need to complete to submit your PhD thesis, what type of tape when securing the tubes we put up people’s noses to measure their diaphragm function…  The list goes on.

Most important though is the fact that we’re all friends.  If things are a bit tough, we offer words of encouragement, cups of tea, a help with something tricky, sympathy (and a bit of a whinge) if you’ve just had a grant or paper rejected, and perhaps even a quick trip to the pub (we are all over 18, and we do do it out of working hours).  Knowing that someone will help you out if needed is absolutely priceless.

Max Thomas’ journey to clinical physiology

Max Thomas was a student on the MSc course in Human and Applied Physiology in 2012-13, some of which is taught by Ged, Vicky, Alan and Caroline.  He is now a trainee Clinical Scientist in Birmingham and recently contacted us for some advice about respiratory muscle testing.  Here he tells us about his career path to date.

 

What made you decide to study physiology at King’s?

Prior to arriving at King’s, I studied Biology. Science had always been the only subject that could keep my focus and attention. I knew my passion was within the field of biological science, but was clueless as to where. My first year reflected this lack of uncertainty with the modules I selected ranging from microbiology and comparative physiology, to forensic biology and pharmacology.

As the years progressed I found myself more drawn to subjects involving health, disease and physiological function. My final year research project looking at age-related muscle decline was what sold me on the MSc in Human and Applied Physiology. My project supervisor was Dr Jamie McPhee, an enthusiastic and knowledgeable physiologist, who suggested the course as one of the best in the country.

I’ll be perfectly honest, at that point I had no career goal at the end of the MSc; I studied because I was truly passionate about the science and knew that interest would take me forward. That fact is something I am more proud of myself for every time I reflect on it.

 

What did you think of the course?

What would you think of a course that teaches about the physiology in health, disease, extreme temperatures, space, the deep sea and fighter pilots? Also throw in some lectures about the astronaut selection process given by astronauts, a lecture on blast injuries, and the chance to contribute to some really interesting research. It was awesome. Although, it was equally as challenging as it was fun.

Its broad content suited my uncertainty about the aspect of the science I most enjoyed. We were exposed to everything physiological science can offer from micro, such as staining muscle biopsies for microscopy, to full body physiology in health, disease and extreme environments – with some excellent in-house experiments and research project field trips. Being exposed to so much allowed me to really determine what I was interested in and where I wanted to focus.

 

Tell us your one favourite thing about the MSc.

On top of the course programme, the guest lectures we had throughout the year were fantastic. However, the field trips were hands down the best part about the course. My particular favourite was the trip to an RAF station in Henlow where we helped out with a research project there using the hypobaric chambers. The team there were looking at the efficacy of two breath-actuated breathing devices used by Chinook helicopter crews who can be exposed to altitudes of 10,000 feet. We were able to participate in and operate the experiment for a week, and it is still one of the coolest things I’ve done to date.

…and one thing you really didn’t like.

Douglas bags

 

What have you been up to since you left King’s?

I spent a year getting as much exposure to clinical science as I could (mostly observational experience in cardiac and respiratory physiology) whilst applying to graduate schemes.

I’m currently in year 2 of a highly competitive graduate scheme called the NHS Scientist Training Programme (STP). The STP is a 3 year clinical scientist training scheme where you work in a hospital and develop competence in performing diagnostic tests and clinical assessment whilst undertaking an MSc in your relevant field – mine is Respiratory and Sleep Science.

The MSc in at King’s is definitely the reason why I was a cut above the rest when applying. There were 7 positions for Respiratory and Sleep Science when I applied, and this graduate scheme has thousands of applicants.

 

Can you tell us what your job involves now?

I spent the last year rotating around cardiology, vascular sciences, pathology and radiology learning incredible amounts and getting to see some really interesting procedures and surgeries. Now I am back in my Respiratory and Sleep department I perform lung function tests on patients (including respiratory muscle function which Dr MacBean must be super proud of me for), and help with sleep studies, consultations and issuing treatment for sleep apnoea. We work with a range of patients and diseases i.e. COPD, neuromuscular disorders (like Duchenne muscular dystrophy), lung cancer, etc.

Next year I will move on to performing cardiopulmonary exercise tests (CPET) in a clinical setting, and blood gas analysis for the issuing of oxygen therapy.

Whilst working, I am also able to perform clinical research and I am currently in the midst of a project looking at two different forms of occupational asthma.

 

Do you have one favourite geeky physiological fact?

Aren’t they all inherently geeky? My favourite fact comes from someone asking me if the human body is seven years old, or if that is a fabricated pub-fact. My research lead me to the answer: there are tissues in the brain that never regenerate and are as old as us. However, the interesting part of this story is not that Dave at the pub was blowing hot air, but how we’re certain of this fact. This all relies on the nuclear bomb.

Testing of nuclear bombs in the late ‘50s and early ‘60s vastly increased atmospheric concentrations of an isotope of carbon, carbon-14 (C14). C14 is used along with other forms of carbon by plant matter during photosynthesis, the plant matter is eaten by animals, and humans eat either the animals or plants, or both. The C14 is incorporated into the tissues formed and the concentrations in the tissues are remarkably accurate of atmospheric concentrations around that date.

Max Thomas, Trainee Clinical Scientist, Birmingham Heartlands Hospital

A bit more from Vicky’s grandfather

Here is Dr Joules’ personal copy (maybe even the script he used) of a talk he gave at the 1,144th meeting of the Reading Pathological Society on 18th December 1952.  The science would be well known to any doctors working in the field these days, and obviously advances have been made in many areas, but the language used is very elegant.  We particularly like the opening sentence:  “I do not suggest that this is a learned paper”.  People in medical science are not always as humble nowadays! Manuscript P1  Manuscript P2Manuscript P3Manuscript p4Manuscript P5Manuscript P6Manuscript P7Manuscript P8Manuscript P9Manuscript P10Manuscript P11Manuscript P12Manuscript P13

A bit of medical history

It’s rare to get an insight into medical practice from sixty years ago – but today you can.  Vicky’s grandfather was a doctor and, after he finished his war service as a medic in the RAF, was the Superintendent Physician at the Milford Chest Hospital in Surrey.  The hospital has quite an interesting history, including being credited as ‘the birthplace of the British sitcom’.  You can read about the hospital here – and there is mention of Vicky’s grandfather, Dr Joules.  Below is his contract of employment, commencing in 1954 and offering a salary of £2225 per year.  Dr Joules and his family lived in a house (Allison House, named after the first Superintendent) on the hospital site, for which he paid £120 a year (including heating and bills!).  Amazing to see how times have changed…

Joules contract 2 Joules contract 1 Joules contract 4 Joules contract 5Joules contract 3