What I learned as an Academic Editor for PLOS ONE

Open access week is just around the corner, and I thought I’d take the opportunity to share my experience as an Academic Editor for PLOS ONE.

I was invited to join the team following a conversation at Science Online 2010 with I think Steve Koch, who recommended me to PLOS ONE, and before I knew it I was receiving lots of emails asking me to handle a manuscript.

The nice thing about PLOS ONE is that I get to choose which articles I get to handle, and I am very picky. I think that my role is not just to’ handle’ the manuscript but also make sure that the review process is fair. To do this, I need to understand the manuscript myself. I read every article that I take on and write a ‘mini-review’ of it for myself. When I get the external peer reviews I go through every comment they make against the submitted version, compare the different reviews and revisit my first impression of the manuscript. I have learned a lot from the reviewers, they see things I have missed, and they miss things I have detected. It has been a great insight into the peer review process. And I love not having to pull my crystal ball out to determine whether the article is ‘important’ but just having to decide whether it is scientifically solid.

Image by Wiertz Sébastien on Flickr, licenced under CC-BY

If the science is fundamentally good the articles are sent back to the authors for either minor or major changes, and then it falls back into my inbox. I have found it really interesting to see how authors deal with the reviewer’s comments. The re-submission is also a lot of work. I need to compare the original and new version, make sure that the authors have done what they say they have done, make sure that all reviewer’s comments have been addressed. And then I decide if I send it back for re-review or not. One thing that I found interesting in this second phase is when authors respond to the reviewer’s comments in the letter but do not incorporate that into the article. It is almost as if the responses are for my and the reviewer’s benefit only. So back it goes asking them to incorporate that rationale into the actual manuscript. Oh well. That means another round. Luckily this does not happen that often.

And then it is time to ‘accept’ the paper – and so back to the manuscript where I go through commas, colons, paragraphs, spelling mistakes, in text citations, reference lists, formatting, image quality, figure legends, etc. This I normally send to the authors together with their acceptance letter but don’t ask for the article to be re-submitted.

The main challenge I find with the process is time management.

When I get the request to handle an article, I accept or nor based on how much time I have to process the article. That is all good. Except that I cannot predict when the reviews, resubmissions, etc will eventually happen – and many times these articles ‘ready for decision’ show up in my inbox at a time when I cannot give it the full attention it deserves.  Let alone being able to predict when the revised version will be submitted! I find it impossible to plan ahead for this, especially since I have very little control over a lot of my time commitments (like the days I need to lecture, submit exam questions, mark exams). So if an article arrives while I am somewhere at a conference with limited internet connection… How can I plan for this?

Finding reviewers is another challenge. Sometimes they are hard to find. Nothing as discouraging as finding the “reviewer declined…” emails in my inbox indicating that it is back to the system to do something that I thought was done and dusted. The other day someone asked what is a reasonable amount of reviewing one should do a year? My answer was that one should probably at minimum return the number of reviews provided for one’s articles. Say I publish 3 articles a year, each with 3 reviews, then I should not start complaining about reviewing until I have reviewed at least 9 articles. (of course, one can factor in rejection rate, number of authors, etc) but a tit for tat trade-off seems like a fair expectation. So then why is it so hard to find reviewers? Come on people – if it was your paper getting delayed you’d be sending letters to the journal asking how come the article shows as still sitting with the Editor!

And that is the other thing I learned. Editors don’t just sit on papers because they are lazy. There are many reasons why handling an article may take more or less time. In some cases, after receiving the reviews I feel that something has been raised that needs a specialist to look at a specific aspect of the paper. Sometimes I need a second opinion because there is too little agreement between reviewers. Sometimes the reviewers don’t submit in the agreed time. There are many reasons why an article can be delayed, and so what I learned is to be patient with the editors when I send my papers for publication.

But despite the headaches, the stress and the struggle of being an Academic Editor, it is also an extremely rewarding experience. I keep learning more about science because I see a range of articles before they take their final shape, because I get to look into the discussion of what is good and what is weak. And I get to be part of what makes science great: trying to put out the best we can produce.

It is unfortunate that this process is locked up. I think that there is a lot to learn from it. I think that students and early career scientists would really benefit from seeing the process in articles that are not their own, how variable the quality of the reviews are, what dealing well with reviewers comments and suggestions looks like. And the public too would benefit from seeing what this peer review is all about – what the strengths and weaknesses of the process are and what having been peer reviewed really means.

So, back to Open Access week. Access to the final product is really good. Access to the process of peer review can make understanding the literature even better, because it exposes a part of the process of science that is also worth sharing.


A First Post and the First Image of Brain Tissue under the Microscope

It is not easy to write a first post. So, as a first post I thought I’d share another first.

As far as I know, this image below is the first published image of ‘brain’ tissue under the microscope. (I hope Mo Costandi corrects me if I am wrong.) It is really picture of the nerve that connects the eye to the brain, still nervous tissue. The image was published in 1675 by Mr Antonie van Leeuwenhoek. [1]

Wellcome Library, London under Creative Commons by-nc 2.0 UK: England & Wales

What I find fascinating about this image is how it reminds me of how it all started. Most of what I do studying neuroscience involves using microscopes, and this image reminds me how far along we’ve come. I can’t but wonder what went through Leeuwenhoek’s mind when he saw this image – after all he did not know what we know now. In fact, even what light was at the time was not what we know now, so interpreting what that image of the optic nerve meant for visual neuroscience must have been quite an interesting challenge.

I can’t help but chuckle when I read in his manuscript this passage:

“I here thought to myself whether every one of these hollownesses might not have been a filament in the Nerve and besides, that twas needless, there should be a cavity in the Optic Nerve through which the Animal Spirits, representing the species or images in the Eye, might pass into the brain.”

I chuckle, because I am amused by his reference to ‘Animal Spirits’. But I can’t but try to imagine what that first observation might have looked like to someone who saw it for the first time, and without the experience that even the average biology student has. I often wish I could get one of those old microscopes and repeat his experiments and see what nervous tissue might have looked like at that time to understand why people thought of the brain the way they did. Microscopy was such a new thing that even a century after that image was produced a word of caution was expressed in Home’s Croonian lecture (1799) [2]

“It is scarcely necessary to mention that parts of an animal body are not fitted by being examined by glasses of a great magnifying power, and, whenever they are shewn one hundred times larger than their natural size, no dependence can be placed upon their appearance.”

It would take some time for microscopes and the methods to process tissues to get better so that we could make more sense of what we were looking at under the lens, and so it is not surprising that it was not until the end of the 19th century that the ‘cellular theory’ that was contemporary to Leeuwenhoek’s observation was accepted to be true for the brain as well.

After all, how much detail we know about anything in biology is only as good as the precision of the instruments we use to study them. I can’t help but wonder what Leewenhoek would think of the microscopic images of nerve tissue that we produce today. We have come a long way, and gained a lot of precision. And after all, that is the way that science moves on.

A few years back I came across this snippet by George Brecht at the Walker Art Center in Mineapolis, Minnesotta

Determine the limits of an object or event
Determine the limits more precisely
Until further precision is impossible”

I couldn’t help thinking how well this artist described the process of science. We keep hitting the limits of the precision we can measure stuff with, and have to wait until a new tool is developed to measure the same thing a little bit better. Sometimes, we confirm what we thought previously, on occasion we find something unexpected and are forced to change our minds about what we hold true. It is the hope of hitting that unexpected that gets me out of bed every morning to go to the lab.

[1] Mr. Leewenhoeck Microscopical Observations of Mr. Leewenhoeck, Concerning the Optic Nerve, Communicated to the Publisher in Dutch, and by Him Made English. Phil. Trans. January 1, 1675 10 378-380; doi:10.1098/rstl.1675.0032 (pdf)

[2] Everard Home The Croonian Lecture. Experiments and Observations upon the Structure of Nerves. By Everard Home, Esq. F. R. S.Phil. Trans. R. Soc. Lond. January 1, 1799 89 1-12; doi:10.1098/rstl.1799.0002 (pdf)

Preventing Veteran Suicide

The alarm clock, flashing 03:00 in green neon, signals to me that I should be fast asleep. I close my eyes and take deep breaths, trying to lull myself back into a peaceful slumber–the day ahead holds a daunting schedule with no room for yawns or fatigue.  Then it appears, pops right into the forefront of my mind, a solitary question that has needled its way through my dreams, forcing me to deal with its implications. “Did you miss something with Dave?”  Instantly I recognize this thought as residue from yesterday’s day at work, something that had been neglected amongst the whirlwind of patient visits, typing of progress notes, writing of prescriptions, answering of emails, voice mails and texts.

In the still darkness of my bedroom, I strain to recall the details of his clinic visit.  My patient Dave, a veteran, had been home from Iraq for two years, but the passage of time had not healed his psychological wounds. Through stifled tones he told me about his tormented nights and stunned days—horrifying memories, so difficult to erase, now dangerously directing his life. Tears had welled in his honey brown eyes that were dulled by the weight of war. Silence hung between us and I shifted uneasily in my chair, hesitating to reach for the Kleenex. Then, I asked the question I was duty bound to ask, “Have you had thoughts to kill yourself?” A pause, then, “No, Doc, No.”

I run through a mental checklist, to make sure I had done all that his clinical condition had required, I had: increased his Sertraline dosage (a medication to treat symptoms of posttraumatic stress); prescribed a short course of sleep medication to help ease the agony of his insomnia; recommended he see his therapist weekly instead of every other week; called his therapist and shared my concerns and asked him to return to my clinic in two weeks (the time it would take for the extra Sertraline to kick in) instead of the usual month.  As I had walked him to the door, I had made sure he had all the emergency numbers to call if things got worse.

It seemed, on paper at least, I had done all I was supposed to do — so then why am I tossing and turning at this ungodly hour?

My heart sinks as I realize what had been missing from my visit with Dave: the “click”.  The click is a feeling that is beyond rational comprehension, more intuition than fact, it can come and go in the blink of an eye and is hard to quantify or measure.  The presence of the click signals to me that my patient is telling me everything I need to know, we are on the same page and we share the same hope for their recovery. The click signals a mutual trust and respect and a healthy alliance in our relationship. Treating thousands of patients, over a decade of clinical practice, has taught me that the absence of the click invariably means trouble is brewing.

Now the green neon flashes 04:00. I sigh and get out of bed knowing full well that sleep will evade me. I wait for dawn and a reasonable time for when I can call Dave to make sure he is okay.

Available Research on Veterans and Suicide

30,000 to 32,000 Americans die from suicide per year and about 20% of these Americans are veterans. It is important to make the distinction between veterans i.e. persons who have served in the military, naval or air service and are now discharged from active duty personnel i.e. persons who are still serving in the military.  The distinction is important because in Army and Marine active duty personnel the statistics are different, for this population, suicide rates have nearly doubled between 2005 and 2009.  A recent and thoughtful analysis of this tragic situation can be found here.

I am a psychiatrist, working for Veterans Affairs (VA), so the subject of veteran suicide is never far from my mind. There are about 5 deaths from suicide, per day, among veterans who also receive care in VA hospitals like the one where I work.  More than 60% of these suicides occur among veterans who use VA services and are known to have a mental health condition.  The statistics are sobering and as troops return home from the conflicts in Iraq and Afghanistan the topic of veteran suicide will, no doubt, continue to vex and distress all concerned parties.

In high income countries, like the U.S., suicide usually occurs in the context of mental illness. Hence, the key to suicide prevention is providing high quality mental healthcare for the mental health disorder that ails the person seeking help. Whilst Posttraumatic Stress Disorder (PTSD) and Traumatic Brain Injury (the signature injury of the Iraq war) are always forefront in the minds of professionals treating veterans, our care would be reductionistic if we did not thoroughly evaluate for and treat other common mental health disorders such as clinical depression, alcohol or drug addiction, bipolar disorder and schizophrenia.  All of these mental health disorders are associated with an elevated suicide risk so getting the diagnosis correct is crucial. The diagnosis dictates what the treatment should be and the correct treatment increases the odds of recovery from the specific mental health disorder.  This is still our best strategy for preventing suicide.

In reality there are, however, many obstacles to this strategy.  For mental health treatment to be effective it often requires the steady delivery of treatment for several weeks (i.e. a certain dose of psychological treatments and psychotropic medication is often needed for a sustained recovery).  Yet, studies have shown that, amongst recent returnees from the conflicts in Iraq and Afghanistan who have PTSD, for instance, such treatment courses are less likely to be completed.

Specifically with regards to psychotropic medication: Guidelines addressing the treatment of veterans with PTSD strongly recommend a therapeutic trial (i.e. taking the medication for long enough and at enough dosage to see its full effect on symptoms) of medications called selective serotonin reuptake inhibitors (SSRIs) or serotonin-norepinephrine reuptake inhibitors (SNRIs).  Yet a recent study we published shows that, when compared to veterans from previous eras, recent returnees from the conflicts in Iraq and Afghanistan were less likely to complete such a therapeutic trial.  Moreover, if they were clinically depressed, in addition to having PTSD, their odds of getting a therapeutic trial were diminished even further.  This hints to, as yet, unexplained obstacles to engaging veterans from the recent conflicts in Iraq and Afghanistan, in mental health treatment—a disconcerting thought for clinicians who work with this population.

Another obstacle is that, despite the best efforts of an individual clinician, the reality is that conventional mental health services still fail to reach many individuals who are suicidal i.e. many of those who are suicidal are not even engaged in the healthcare system to begin with.  The health disparities literature is replete with evidence demonstrating how, in our society, those most in need of psychiatric and medical care are often the least likely to get it.  Social determinants such as where one lives, economic security, housing quality and employment opportunities all play a key role in the development of such inequities.  These limitations have been compounded by a historic lack of coordinated suicide prevention strategies by well-meaning organizations and agencies.  So this begs the question, what is the VA system doing to prevent veteran suicide?

In 2004, the VA started to focus on deficits in its mental healthcare services and developed a VA Comprehensive Mental Health Strategic Plan to address identified problems and focused suicide prevention efforts beginning in 2007.  Examples of outreach efforts are a 24/7 suicide prevention hotline where veterans, or those concerned about a veteran, can call 1-800-273-8255 and then press 1 to be connected to a VA mental health professional trained to deal with the immediate crisis. A written Chat Service at  http://veteranscrisisline.net/Default.aspx and a texting service, at 838255, both of which connect those in crisis directly to mental health professionals is also available.

In addition, screening and assessment processes have been set up through the system to assist in the identification of patients at risk for suicide.  The VA electronic medical record has a suicide risk flagging system that has been developed to assure continuity of care and enhance awareness among care-givers. Each VA medical center has a suicide prevention coordinator, whose job it is to ensure the Veteran, at risk, is connected to the right services and receives adequate followed up. Those identified as high risk receive an enhanced level of care, including missed appointment follow ups, safety planning and weekly follow up visits.

The relative recency of these efforts means their actual effectiveness in reducing suicide rates remains to be fully evaluated.  Speaking from the viewpoint of a physician, who has worked in a variety of hospital systems from public to private, it is hard not to be impressed by the comprehensive nature of VA’s current suicide prevention efforts. Furthermore, dedicated and well trained professionals continue to come up with thoughtful and innovative ways to tackle these tough problems head on.

Yet there has only been a slight decrease in suicide in VA treated veterans in recent years and this begs the question: Why does this goal of reducing suicide rates amongst Veterans (and, indeed, the general public also) remain so elusive?

Some of these reasons lie in the state of the science of suicide research.  We have a lack of knowledge regarding the fundamental biological markers that could help us predict who will commit suicide.  Risk of suicide is shared by biological, but not adoptive relatives, prompting the conclusion that familiality of suicide is due to genes rather than family environment or culture.  Yet, despite gargantuan efforts on the part of psychiatric researchers, there is currently no suicide gene or genetic test that would be useful in predicting risk of suicidal behavior in any particular individual.

From an epidemiological standpoint, we know several clinical factors that are associated with increasing the odds someone will commit suicide. These factors include: having a mental illness; endorsing suicidal ideation; a prior history of a suicide attempt; a recent interpersonal loss; recent discharge from a psychiatric hospital and family history of suicide.Yet, with an overall rate of 11.3 American suicide deaths per 100,000 people, it is very hard to predict who will actually commit suicide as there are many people who have these clinical risk factors (i.e. the risks are common) but relatively few of these people will actually commit suicide.  In short, the predictive validity of these clinical risk factors is poor.  Add to this the reality that human beings are infinitely complex (and not just a sum of their clinical risk factors) means identifying under what exact circumstances, and at what point in time, a high risk individual may actually attempt suicide is seemingly impossible.

To complicate matters further a clinician cannot simply rely on a patient’s denial of suicidal ideation when assessing suicide risk. The reality is a suicidal patient may not be inclined to admit their suicidality to a mental health professional for fear they will be forced into treatment or that this will result in their suicidal plans being challenged. This complicates the dynamic between caregiver and patient and regrettably means that even the most well meaning vigilant clinicians may not be able to identify a suicidal patient.

A Time Honored Tradition

Faced with the complexities and uncertainties surrounding the issues of veteran suicide, I find myself relying heavily on a time honored tradition of medicine—the power of a strong therapeutic alliance with my patient; the importance of creating an environment where they feel they can say whatever is on their mind and making it clear that, if things are not going well, I want to know about it.  Creating such an environment is no easy feat as 21st century medical practice offers no end of distraction to the practicing physician: back to back clinic schedules; an electronic medical record that dishes up a steady stream of alerts, notifications and orders that require your continued visual attention; instant messages, email, texts and phone calls that ask you to make, in real time, clinical decisions and judgments and, of course, mounds of paperwork.  In such an environment, I find listening—really listening– to my patient has become one of the most powerful things I can offer. Listening creates silent spaces that can be filled with a patient’s expressions of their worst fears and deepest secrets, untainted by fabrication or distortion.

The Click

In my office, I watch the clock ticking on the wall. The second it hits 8AM, I pick up the phone and call Dave’s cell phone number.  The phone rings and rings, my heart sinks as I fear it is heading for voice mail, then skips a beat as it is picked up,


“Hi Dave, its Dr. Jain from the Palo Alto VA”

“Oh hi Doc,

“I know yesterday was a bad day for you, so I thought I would just check in.”


“I am thinking you should come back to clinic in a week instead of next week; how does that sound?”


“Yes, I think that would be a good idea.”

There it is—in his voice, what had been missing from clinic, an inflection in his tone, a subtle change but somehow reassuring—the click. He is listening to me and, perhaps more importantly, he knows I am listening to him— we are a team working toward a mutually agreed upon goal. I know this does not guarantee that there will not be troubled times ahead but, for now, this is enough.

The views expressed are those of the author and do not necessarily reflect the official policy or position of the Department of Veterans Affairs or the United States Government.

In an effort to protect individual patient privacy the patient stories depicted here are composites of various real encounters brought together to illustrate the situation.