Vincent travels to the University of Pennsylvania and speaks with virologists Gary Cohen, Scott Hensley, Carolina Lopez, and Susan Weiss about their careers and their research.

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The scientists I know realize that they use jargon, both in their writing and in their seminars – but they can’t seem to stop. There is a very good reason to  stop using jargon – it has likely lead to a decrease in the readability of scientific texts for the past 100 years (link to article).

To determine if the readability of scientific writing has changed with time, over 700,000 abstracts were downloaded from PubMed, which indexes journal articles in the life sciences. These abstracts were published in 123 prominent journals (Nature, Science, PNAS, for example) in 12 selected fields of research (including microbiology, immunology, neuroscience, and more). The abstracts were subjected to two different measures of readability: the Flesch Reading Ease (FRE) and the New Dale-Chall Readability Formula (NDC).

An FRE score is calculated by considering the number of syllables in each word, and the number of words in a sentence. The NDC measures the number of words in a sentence and the percentage of difficult words – those not on a list of common words. Lower readbility is indicated by a low FRE score or a high NDC score.

When the 700,000+ abstracts were analyzed, the FRE and NDC scores showed a clear trend of decreasing readability in the biomedical science literature since 1890 (the graph shows the FRE score; image credit). To put these results in perspective, over 20% of the abstracts have a ‘readability considered beyond college graduate level English’, to quote the authors of the study.

Two sources for the trend of decreased science abstract readability were considered. An increase in the number of co-authors over time, the ‘too many cooks spoil the broth’ effect, was ruled out. But an increase in general scientific jargon correlated with the decreased readability (jargon in the abstracts was measured by using a table of 2,138 scientific jargon words, like ‘novel’, ‘robust’, ‘moreover’, ‘underlying’, and ‘therefore’.)

Why would scientists care about readability of their articles? Because lower readability impedes communicating science not only to the non-specialist, but even to people within the field!

The authors suggest several ways to reverse the trend of decreased readability, including having ‘lay summaries’ accompany articles (done by some journals). Another is to have scientists communicate via social media – I was happy that the authors believe that ‘this trend could be encouraged’.

Another suggestion is to make scientific communication part of undergraduate and graduate education. This suggestion often comes up when I speak to students about communicating science. As someone with a bit of experience in this area, I would be pleased to participate in such efforts.

Finally, I love the suggestion of determining a readability index (r-index) for scientists, analogous to the h-index for journal article citations.

By David Tuller, DrPH

In his welcome talk at last week’s annual conference of the CFS/ME Research Collaborative (CMRC), the chair, Professor Stephen Holgate, praised his colleague and second-in-command, Professor Esther Crawley, for her “stunning” and “amazing” work on the group’s main research initiative. There was just one problem: That initiative, the ME/CFS Epidemiology and Genomics Alliance (MEGA), had recently failed in its second high-profile bid for major funding.

Earlier this year, of course, MEGA announced that it had failed in its first big effort, a submission to the Wellcome Trust. This second unsuccessful bid was to the Medical Research Council (MRC). Professor Holgate tried to put a positive gloss on things by vowing that MEGA would learn from this defeat and press forward. Yet he undoubtedly knows that applicants who repeatedly get turned down for top grants can start to smell like losers. Funders prefer to shower money on those perceived as winners. Notwithstanding Professor Crawley’s stunning and amazing work, MEGA so far has proven itself more loser than winner.

Before sharing the unfortunate news about MEGA’s bid, Professor Holgate appeared to be trying to soften the blow and rationalize the rejection by praising proposals in this emerging research field that get “to the edge of being funded,” even if they ultimately fail.

“As we start to ramp up the quality of research, you won’t just see a switch and suddenly money pouring in,” Professor Holgate explained to those assembled for the two-day conference. “You see people almost getting there but not quite, reconfiguring their applications and then coming back in again and getting it right. So this is the right direction of travel and I think it’s absolutely wonderful that we’re seeing this happening now.”

As I interpret his remarks, Professor Holgate’s optimistic view is that MEGA, after two failed bids, is now traveling in the “right direction” on its “wonderful” journey. As he explained, the MEGA proposal survived the first round at the MRC and made it to the interview stage, along with several other candidates. Then the bid lost momentum, for reasons he did not share.

“We got down to the short list, which was great,” said Professor Holgate. “We were interviewed but at the interview we didn’t quite make the cut. That doesn’t mean this whole thing is just going to wither on the vine, it means we need to take the feedback from the Medical Research Council committee, sit down, get serious about what they said, and think about where we’re going next with this. But I can tell you this is not the end by any means, we are definitely going to move forward. We just have to make sure that when we do move forward we learn from the experience and then we look for opportunities for funding elsewhere.”

Whatever. Perhaps this is not the end for MEGA, and next year will be more productive. But apparently the reviewers for two major funders have not agreed with Professor Holgate’s assessment of Professor Crawley’s work. I presume she and her team put great effort into pulling together the proposal rejected by Wellcome. Putting on a brave front after that failure, MEGA appeared determined to regroup for the MRC bid. Now the MRC has also turned thumbs down on whatever it was that MEGA proposed. Hm. Professor Crawley must feel deeply disappointed and even embarrassed—an understandable reaction, of course, after such a humiliating public defeat.

It’s no secret that Professor Crawley and I are not the best of friends. I have accused her of problematic research practices, and she has accused me of writing “libellous blogs.” I have documented my charges and backed up every claim. Professor Crawley has failed to respond to my repeated requests for evidence that anything I’ve written about her work is inaccurate. I take her silence as acknowledgement that her libel claim is false.

I wrote several blog posts about this situation. I sent an open letter to the CMRC board, chastising Professor Holgate and the other members for failing to address their colleague’s unprofessional behavior. I complained to Bristol University, since Professor Crawley made her defamatory statement about my work at her inaugural lecture there this past spring. And I recently wrote about her curious failure to seek ethical review for a 2011 study of children, using the questionable claim that it was a “service evaluation” project and therefore exempt from such a review.

Have these and other developments begun to be noticed by the kinds of people who would serve on MRC and Wellcome review committees? Would these reviewers have heard by now of the mushrooming scandal around the conduct and findings of PACE, which Professor Crawley has declared to be a “great, great” trial? Would these reviewers know that large segments of the international scientific and public health communities, including the U.S. Centers for Disease Control, have rejected the GET/CBT ideological movement, for which Professor Crawley is an ardent advocate?

It is certainly possible that awareness of these developments is slowly spreading beyond the narrow confines of those actively engaged in the debate—that is, beyond the communities of patients, advocates and ME/CFS investigators. It is even possible that these developments are starting to impact Professor Crawley’s prospects for obtaining research funding. These two recent rejections suggest that could be the case. On the other hand, she has received support for her problematic FITNET-NHS trial, so perhaps the rejections had nothing to do with the debate around PACE/CBT/GET.

In any event, the issues are not going away. Given Professor Crawley’s apparent inability or unwillingness to provide satisfactory answers to legitimate concerns raised about some of her ethical and methodological choices, she is likely to face continued scrutiny.

As I have previously pointed out, Professor Holgate and the CMRC have enabled Professor Crawley’s bad behavior by endorsing her leadership despite her high-profile public campaign to discredit critics as vexatious and libelous. However, no matter what the CMRC does or does not do at this point, the CBT/GET approach to ME/CFS is collapsing under the weight of its own absurdity and the accumulating scientific evidence. In the face of this ongoing paradigm shift, Professor Holgate’s fulsome praise of Professor Crawley’s unsuccessful efforts to seek support for MEGA seemed like a desperate effort to forestall the inevitable reckoning.

On Saturday morning, I wrote to Professor Holgate and others on the CMRC leadership team, seeking comment about MEGA. I haven’t heard back—not that I expected to. Here’s what I wrote:

“I’m writing a post for Virology Blog about some of the news coming out of the conference. So I am wondering if you [i.e Professor Holgate]–or any other members of the CMRC executive committee–want to comment on the failure of MEGA at the interview stage in the MRC funding cycle. My blog will be posted on Monday or Tuesday, so please send me back any comments by Sunday evening, California time.

I have not included Professor Crawley on this e-mail; it is my understanding that she considers contact from me to be unwelcome. But I of course would include a statement from her about MEGA in my post. I am also still interested in a statement from her about her false accusation that I have written “libelous blogs,” since she has never bothered to clear up that issue or explain her charge. So please feel free to forward this e-mail to her!”

The TWiV team reviews the first FDA approved gene therapy, accidental exposure to poliovirus type 2 in a manufacturing plant, and production of a candidate poliovirus vaccine in plants.

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The US Food and Drug Administration recently approved the first gene therapy, Kymriah, to treat B-cell acute lymphoblastic leukemia. It uses a lentivirus to modify the patient’s T cells to kill tumor cells.

Acute lymphoblastic leukemia, or ALL, is caused by uncontrolled growth of B cells, which normally produce antibodies to fight off infections. It is the most common cancer in children. The uncontrolled production of these cells by the bone marrow causes a shortage of blood cell production, leading to fever, increased risk of infection, and anemia. These B cells have on their surfaces a protein called B19 – which is the key to understanding how Kymriah works.

The therapy begins with drawing blood from the patient, from which T cells are purified. These T cells are then infected with a lentivirus vector that encodes the gene for a chimeric antigen receptor (CAR) that recognizes the B19 protein. The CAR protein is synthetic – it doesn’t exist in any cell. The extracellular domain consists of a single-chain antibody directed against the B19 protein (pictured). The cytoplasmic domain of the protein contains sequences that stimulate the T cells to proliferate.

After the T cells are infected with the CAR-encoding lentivirus, they are infused back into the patient. Upon encountering a B cell producing B19, the T cells bind to the protein and kill the cells, thus eliminating the cancer.

Kymriah was licensed by the FDA after testing showed it was effective, leading to remission of cancers in the majority of children treated. But the price tag is steep – $475,000 for a treatment, and other similar drugs in the pipeline could be even more expensive. The drug makers justify the high price by arguing that it reflects the value to the patient – it saves their lives.

But vaccines also save lives, and they cost much less than Kymriah. The difference, of course, is that vaccines are given to millions of people. Kymriah, in contrast, would be given to thousands in the US.

In other words, the high cost of Kymriah reflects the need of drug companies to recoup their high investment in developing and testing the drug – not the value to the patient.  Rather than spinning a false story about the value of a drug to a patient, the drug companies should be honest about the pricing of their products. No wonder the public has a negative image of the industry.

By David Tuller, DrPH

My first recent freedom of information request to the National Institute for Health and Care Excellence (NICE) was for information about the experts consulted in the current process of reviewing CG53, the 2007 guidance for the illness the agency calls chronic fatigue syndrome/myalgic encephalomyelitis. In its response, the agency explained that seven topic experts had been consulted in the process of preparing the surveillance document, which recommended leaving the guidance as is.

(I have previously written about the NICE review process on CG53 here, here and here. My e-mail exchange with Sir Andrew Dillon, chief executive of the NICE guidance executive, is described here.)

NICE, of course, declined to reveal the names of the seven topic experts, although it reported that four of them were members of the original 2007 guidance development committee. NICE also told me, as it told the ME Association, that the panel included three psychiatrists, two neurologists, a pediatrician, and a patient. NICE did not explain why the panel included more psychiatrists than other specialists, but the selection of topic experts certainly provides insight into NICE’s perspective on the illness.

My next FOI request was for any reports prepared by these topic experts–properly anonymized, of course. I recently received them and have asked for them to be posted on Phoenix Rising. If this is the full extent of the input provided by the topic experts, it seems like NICE made a remarkably anemic effort to seek outside advice. And it sought that advice from a relatively narrow spectrum of professional opinion, especially given the enormous complexity of the disease.

In its e-mail to me, NICE explained that the topic experts provided “three types of contributions.” Each person was asked to fill out two questionnaires. The first questionnaire sought suggestions on new studies or research that could impact diagnostics, interventions and other aspects of the guidance. The second sought input about two specific studies and whether the surveillance report should contain in-depth commentaries on them. These questionnaire responses were due last December. The questionnaires were sent to me as separate documents.*

(The previous sentence has been corrected. The sentence originally read: “The questionnaires, which were often only partially filled out, were sent to me as separate documents.”)

In March of this year, NICE surveyed the same experts about three 2015 U.S. reports—from the Agency for Healthcare Research and Quality, the Institute of Medicine (now the National Academy of Medicine), and the CFS/ME Advisory Committee to the Department of Health and Human Services. NICE wanted to know about the possible impact of these reports on diagnostic criteria and other aspects of CG53. Not all of the topic experts answered. The responses were all sent to me as part of a single document.

Strangely, the first questionnaire sent to all seven topic experts included this sentence in the first paragraph: “As a member of the committee that developed this guideline we welcome your views on any areas that need updating.” That suggests that all seven topic experts consulted were, in fact, members of the committee that developed the 2007 guidance–even though NICE had already informed me that only four of the seven were on the 2007 committee.

I have no idea whether NICE misinformed me that only four of the seven were on the original committee, or whether the wrong form was sent three topic experts who were not actually on the 2007 guidance committee. Whatever. NICE obviously has glitches in its fact-checking department. I hope that problem gets worked out soon.

The documents I received include some interesting and irritating statements from the experts, but nothing particularly surprising. Two of the six medical experts (#4 and #7) expressed modest concerns that recent events had rendered the current guidance somewhat out-of-date. For example, #4 cited the “considerable on-going public and media interest in this disorder” and advised NICE to have “a current and up to date view on this controversial area.” The other four (#1, #2, #3, #6) found that the research supported the current recommendations.

The patient in the group (#5) expressed personal opinions about the difficulties patients face as well as concerns about case definition–but did not fill out the questionnaires provided by NICE and did not make recommendations related to the guidance. #5 attached two additional statements from other ME patients to his/her/their submission to NICE; together they included many references to the emerging science and to critiques of the PACE trial.*

(The previous sentence has been corrected–originally I wrote that NICE did not send me these two additional attachments as part of the FOI response, but it turned out I didn’t notice them in the set of documents.)

Expert #6, an apparent CBT/GET hardliner, had particularly firm opinions about what was what: “This guidance has stood the test of time well, and has been instrumental in shifting thinking about the common problem of CFS/ME and medically unexplained symptoms (functional) symptoms in general. I hope that a new guidance on management of functional disorders will extend this process further.”

In response to the CFSAC suggestion that it was important to focus on biomarkers and diagnostic tests, #6 wrote this: “In the UK I think we would see what the HHS CFSAC see as a failure to undertake rigorous research, more as a failure of the biological model to explain the condition adequately. However, I can understand that an alternative reaction to the failure of biological models to explain the condition is to try and define a subset of patients with the condition who appear to share a common biomarker. This approach has failed so far.”

Of the six medical professionals, #7 adopted the most moderate view, suggesting that “some aspects of practice have moved on considerably so this guideline needs at least partial review in relation to interventions, diagnostics and prognostics.”

Moreover, #7 made some key suggestions about the guideline development group that should undertake these critical revisions: “It is important that the chair is someone who has no previous connection to CFS/ME practice or research. That person should not be a mental health professional if the guideline is going to be accepted by NHS clinics and patient organizations. However, I think there should be a mental health professional on the guideline development group.”

#7 was also the only one to offer specific concerns about PACE. Here’s what he/she/they wrote in discussing the research since the guidance came out in 2007: “There are some larger and more definitive UK RCTs of treatments recommended for CFS/ME by NICE in 2007 but these are controversial and one in particular PACE in over 600 patients, published in the Lancet, has been subject to legal challenge on the grounds that after the study was started the primary outcome was changed.”

That comment isn’t exactly accurate and it does not indicate a full awareness of the facts or of the widespread rejection of the PACE trial by the larger scientific community. But it’s more skepticism and concern than shown by his/her/their colleagues, who mostly toed the standard line and responded as you’d predict.

In response to safety questions, #3 provided more evidence—if any were needed—that the Cochrane reviews of GET and CBT continue to be major obstacles. Here’s what #3 wrote: “Whilst the patient community remain concerned about safety, recent Cochrane reviews suggest exercise therapy is safe and patients are more likely to improve with treatment.”

So Cochrane says it’s safe, and that means the patients are wrong. And yet the reviews include the studies featuring the methodological flaws that patients—and the worldwide scientific community—are challenging in the first place. Reviews can’t provide good evidence if they’re based on bad studies, of course, but #3 did not point this out.

In the second questionnaire, the Dutch FITNET trial was one of two being considered as the subject of an in-depth commentary in the surveillance report. The questionnaire briefly described the study and asked for input. Here’s what NICE included in its description of FITNET in the questionnaire:

“CBT is already recommended by CG53 and this study shows it can be delivered via the internet, indicating an alternative mode of delivery for this treatment for this age group. Although the study was from the Netherlands, a UK trial is underway. There were some issues with the study (blinding was not possible due to nature of interventions, and usual care varied because the quality and quantity of CBT differed according to local availability and was often combined with other treatments such as GET). These issues would be discussed in full in the commentary.”

It must be pointed out that lack of blinding is not just some small problem with the Dutch FITNET study. The lack of blinding combined with the reliance on subjective outcomes renders FITNET, and the bulk of studies from the CBT/GET ideological brigades, incapable of providing reliable or valid evidence of treatment efficacy. Yet the topic experts generally agreed with NICE’s positive assessment of FITNET and largely failed to address the study’s serious flaws in their comments.

Among those problems was that the “usual care” group did very poorly. Unlike in PACE, usual care was not just a few meetings with a clinician. In FITNET, the usual care group mostly received CBT or GET, or both—in other words, the treatments already recommended for the illness in the Netherlands as well as in CG53. And yet apparently these treatments largely failed to work. That raises this critical question: If CBT and GET are performing so poorly, why are they the standard of care in the Netherlands, not to mention the U.K.?

In its comments about the study in the questionnaire, NICE fudged this enormous problem by suggesting that the usual care in the study “varied” in quality—suggesting that the treatments performed poorly because they were not optimally delivered. That’s a very convenient and self-serving explanation, when the obvious and simpler answer is that the therapies simply do not work as promised.

Citing this study, Professor Esther Crawley of Bristol University has received approval to inflict the FITNET approach on British children. But NICE, Professor Crawley, the topic experts and the Dutch investigators themselves have not actually considered one obvious reason why the patients assigned to the FITNET intervention might have reported better subjective outcomes. For sick patients, it would involve much less exertion to have online CBT at home than to run around town attending multiple in-person sessions. It seems logical that patients treated while in front of their laptops and not forced to travel weekly to clinic might do better than those in “usual care” for that reason alone.

In the document compiling the responses whether the 2015 U.S. reports should impact the diagnostic criteria used to define the illness in the NICE guidance, this comment from #1 jumped out as particularly uninformed: “I am unaware of any concerns about the inclusion criteria of trials in CFS.” Wow. Given the enormous international controversy over the range of case definitions that have been developed for the illness, it is hard to know how to respond to such a statement.

Not surprisingly, this person expressed satisfaction with the criteria outlined in CG53: “I do not see any need to change the diagnostic criteria at present. From a clinical perspective, CG53 are pragmatic and useful criteria. In my clinical experience in a CFS/ME clinic over the 10 years since the guidelines were published, no concerns have ever been expressed by patients attending the clinic about the diagnostic criteria used in CG53.”

And here’s what #6, the CBT/GET hardliner, had to say about the U.S.-based reports: “I am suspect [sic] that there is a tendency in the USA to push towards an entirely biological explanation for the condition, whereas in the UK there is an increasing acceptance amongst patients and clinicians alike of a model that includes CFS/ME in the umbrella of functional neurological disorders, i.e. that it is an emotionally driven disorder.”

Ok, then. The notion that CFS/ME is “an emotionally driven disorder” is certainly a popular concept in specific academic and medical circles in the U.K. But #6 does not cite any data to support the claim that there is an “increasing acceptance” of such an idea among British patients and clinicians. That this pet theoretical project of a powerful clique of psychiatrists (and some others) is now presented to NICE as having popular appeal and clinical legitimacy is distressing.

And that this set of comments is the best NICE could drum up in seeking external guidance for this critical review process is deeply worrying.

The TWiVians present an imported case of yellow fever in New York City, and explain how a dengue virus subgenomic RNA disrupts immunity in mosquito salivary glands to increase virus replication.

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Virologist Roger W. Hendrix died on 15 August 2017. I only met Roger once, at the 2011 ASM meeting in New Orleans where we recorded an episode of This Week in Virology. The video of that episode is below, starting at my conversation with Roger at 30:34. Harmit Malik and Rachel Katzenellenbogen were my other guests on TWiV 135.

Thirty-five years ago this month, in September 1982, I arrived at Columbia University College of Physicians & Surgeons to open my virology laboratory. I brought with me an infectious DNA copy of the poliovirus RNA genome, the first of its kind, and a lot of enthusiasm. Over the years we used this infectious DNA to study poliovirus neurovirulence, pathogenesis, and translation, among other topics; I wrote grant applications, published papers, and trained new scientists. In short, I was a typical academic scientist.

My career forked in 2000 with the publication by the American Society for Microbiology of the textbook Principles of Virology. Because this book was written by process, not by virus, each of the authors learned far more virology than ever before. As a consequence of writing this book, I became interested in disseminating virology to the public. Beginning with virology blog in 2004, I began to use social media to communicate science. This interest has lead to a collection of blogs, podcasts, lectures, and videos, in addition to four editions of Principles of Virology.

Recently virologist Islam Hussein, founder of Virolvlog and an avid science communicator, decided to summarize my modest scicomm career with an infographic. I’m grateful to Islam for this lovely chart, which was produced by Mohamed Gaawan. Here’s to the next 35 years.