RIP OAPL: An Academic Publisher Vanishes

By Neuroskeptic | October 15, 2018 2:08 pm

A dubious predatory academic publisher called Open Access Publishing London (OAPL) seems to have died. Their website has gone down, taking some 1,500 scientific papers with it. What can we learn from this?

rip_oapl

Long-time readers will remember my series of posts on OAPL back from when I first investigated it in 2013. As far as I can tell, it was a one-man operation. The man turned out to be a Dr. Waseem Jerjes. Jerjes is a dental surgeon with many legitimate research papers to his name, and he was formerly editor of a journal for well-known publishers BioMed Central (BMC).

OAPL published dozens of journals on their now-defunct website, from OA Anaesthetics to OA Women’s Health. These journals claimed to be peer-reviewed and some boasted well-known researchers on their editorial boards.

Eventually, the OAPL story went cold. By early 2015, the OAPL site was no longer being updated. Some researchers who’d had papers accepted by OAPL journals in the final few months were left in the lurch by this, their manuscripts lost in limbo. At that point, however, papers that had been published were still accessible.

Now, the OAPL website hosts nothing more than a ‘domain name expired’ message and a series of links to things like “Bass Fishing Trips Near Me”. All those papers – over 1,500 if I recall correctly – have just been un-published. Vanished. The journals that published these papers no longer exist.

Fortunately, many of the lost papers are still available elsewhere online, e.g. on the author’s own webpage, or on mirroring services such as SemanticScholar.org. However, some papers seem to have fallen through the cracks and, with no mirrors, they really have vanished. For example, a Google Scholar citation is all that remains of this one:

deadpaper

It would be wrong to think that none of this matters because OAPL were never a serious publisher. Although OAPL did publish some dreadful papers, most of their output seemed to be serious work from legitimate researchers. These innocent researchers are the victims here. They paid money for OAPL to publish their work, and now it’s gone.

This case also raises interesting questions about the nature of academic publication. Can the former OAPL papers still be considered “published work”, if they are nowhere to found in any publication? Will anyone really miss the lost papers – or have they already become ‘too old’ to bother reading in today’s fast-paced science world? Does anyone read papers, anyway?

As for OAPL, I’m sure they’re not the first publisher to vanish and they surely won’t be the last, but it doesn’t seem right to allow papers, trusted into your care by the authors, to just disappear. Then again, what do I know? I’m no expert on ethics – unlike, say, Waseem Jerjes, who recently edited a book about “Research Integrity and Publication Ethics.”

CATEGORIZED UNDER: ethics, law, PIE, select, Top Posts

The Fidgeting Brain

By Neuroskeptic | October 14, 2018 7:52 am

A new review paper in The Neuroscientist highlights the problem of body movements for neuroscience, from blinks to fidgeting.

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“Can I Have My Amygdala Removed?”

By Neuroskeptic | October 7, 2018 6:45 am

Brain surgery is not usually something that people actively seek out. However, there may be an exception: the idea of the removal of the amygdala seems to hold a fascination for many people.

Questions about the desirability of an amygdala-free life can be found in many places online. On Quora, there have been many queries about what amygdala removal would entail, and at least one brave user outright asked Can I have my amygdala removed? I came across the question on two other sites within the past week.

amygdala21

So what’s going on? Those curious about amygdala removal seem to see it as the embodiment of fear, anxiety and stress. Would its removal really render you fearless? What would the side effects be?

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“Rick and Morty” Sting Predatory Journals

By Neuroskeptic | September 29, 2018 7:48 am

Last year I wrote and published a fake ‘scientific paper’ to highlight the problem of predatory scientific journals. My article, following in the tradition of earlier fake journal ‘stings’, was complete nonsense, full of Star Wars references and quotes, but it was published by a number of dodgy journals.

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CATEGORIZED UNDER: FixingScience, funny, papers, select, Top Posts

A Chink in the Brain Armor: the NFL, Concussion and Omega-3s

By Neuroskeptic | September 17, 2018 5:03 pm

On Twitter, I was pointed to the strange story of Brain Armor®, a nutritional supplement which is supposed to promote brain health.

While there are many supplements that are sold for the same purpose, Brain Armor has a unique claim to fame: it is the official brain health supplement of Pro Football Legends (PFL), the “commercial marketing arm of the NFL Alumni.”

brain_armor

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CATEGORIZED UNDER: ethics, law, papers, select, Top Posts

The Evolution of Neuroimaging

By Neuroskeptic | September 15, 2018 8:28 am

A fun new paper looks at the changing landscape of neuroimaging research through an analysis of the journals Neuroimage and PNAS. The article comes from UPenn researchers Jordan D. Dworkin, Russell T. Shinohara and Danielle S. Bassett.

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CATEGORIZED UNDER: EEG, fMRI, papers, select, Top Posts

Bad Mobs of Good People: The Paradox of Viral Outrage

By Neuroskeptic | September 2, 2018 2:45 pm

People become less approving of social media outrage the more people join in with it. One person rebuking another is fine, but ten people doing it looks like a mob.

This is the key finding of an interesting new paper called The Paradox of Viral Outrage, from Takuya Sawaoka and Benoît Monin of Stanford. Read More

White Matter Worries: A Problem for DTI?

By Neuroskeptic | September 1, 2018 12:43 pm

A new preprint called “A systematic bias in DTI findings” could prove worrying for many neuroscientists. In the article, authors Farshid Sepehrband and colleagues of the University of Southern California argue that commonly-used measures of the brain’s white matter integrity may be flawed.

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CATEGORIZED UNDER: methods, papers, select, Top Posts

“Non-Western Magic in the European Brain” – Return of Voodoo fMRI?

By Neuroskeptic | August 26, 2018 7:34 am

A preprint recently posted on bioRxiv has garnered a lot of attention – mainly because of its title. The article, from Jan Willem Koten Jr et al., is called Occurrence of non-western magic in the European brain, an intriguing although not very informative title for a scientific paper.

The intrigue deepens once we read the paper and find references to the famous ‘voodoo correlations’ and also a new species of neuro-monster: ‘zombie oscillations’, which the authors claim to have discovered and which, they say, may “reflect brain activity that is not under the voluntary control of the individual.”

But spooky terminology aside, what’s really going on?

As far as I can see, this preprint is not about magic or even voodoo correlations. Rather, it is about a signal processing technique called Savitzky Golay (SG) filter, widely used in chemistry and elsewhere. The authors propose that using SG filters instead of conventional filters could help improve fMRI data processing. To this end, they coded a MATLAB toolbox for SG-izing fMRI data and used it on data from a simple working memory fMRI experiment.

The trick, however, is that an SG filter is defined by two parameters: window length and polynomial order. Koten et al. didn’t know the optimal parameters so they tried, well, almost all of them – which is a lot:

For the detrending [high-pass filtering] optimization procedure, the whole window space from 3 to 487 TR’s was investigated in steps of 2. For each window size, the whole polynomial order space from one to window size -1 was investigated.

By their own description, this was a “brute force” approach to statistics. They did the whole thing again to find the optimal SG filter for low-pass filtering. This must have taken a while to run.

Having found the optimal filters, Koten et al. go on to show that they are more effective than existing approaches (unfiltered data or classical SPM filters) with a dizzying set of comparisons:
koten_magic

The bottom line is that the SG filters performed better, in terms of increasing the test-restest reliability of the task-related signal (there were two fMRI sessions, on the same day). SG filters also produced higher connectivity between brain regions compared to SPM (slightly):

A true connectivity of r = 0.22 was detected in raw and denoised timecourses… application of the HRF and Gaussian filters as available in the SPM packages leads to true average connectivities of r = 0.37 and r = 0.34. While application of quasi-optimal and optimal SG filters lead to true average connectivities of r = 0.37 and r = 0.43.

I’m not sure if we can really describe these as ‘true’ connectivities because we don’t know the ground truth (as the authors acknowledge), though.

So what about those ‘zombie oscillations’? These do seem to be a mystery. Koten et al. say that only SG filters, but not SPM, removes these oscillations:

Our analyses suggest that SG filters detect oscillations not related to task, which are substantially faster than oscillations removed through classic SPM high pass filters. We can exclude the possibility that zombies are related to scanner drift, physiological noise as captured by our regressors or head motions…

We can only speculate about the biological meaning of zombie oscillations. Zombie oscillations may contain physiological noise that was not removed by the standard denoising method. Furthermore, Figure S5 shows that SG filters suppress oscillations that originate from the “resting state frequency band”. Hence, one might speculate that resting state signals contaminate working state signals… zombie oscillations may reflect brain activity that is not under the voluntary control of the individual.

Here is, as far as I can tell, the only known picture of a zombie oscillation in the wild (from Fig 10) – the zombies are in red and pink:

koten_zombie

I’m not sure what to make of this: these seem to be oscillations slightly faster than the ones picked up by the SPM detrend, but I’m sure SPM would pick them up if the parameters were changed. Whether they have any zombie-like properties remains to be seen.

Overall, this preprint has a brilliant title while the topic described is highly technical and quite preliminary. Savitzky Golay filters may be useful for fMRI, but the specific optimal filters identified by Koten et al. are unlikely to be optimal under other conditions. As they put it, “We are left with the platitude that one study is no study… It is very unlikely that our pipeline generalizes to other fMRI experiments.”

CATEGORIZED UNDER: fMRI, methods, papers, select, Top Posts, voodoo

Science’s Bullying Problem

By Neuroskeptic | August 19, 2018 10:45 am

Over the past few weeks, the stories of three high-profile scientists accused of bullying have emerged: geneticist Nazneen Rahman, psychologist Tania Singer and astrophysicist Guinevere Kauffmann.

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CATEGORIZED UNDER: ethics, science, select, Top Posts
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