Weekend reads: Rector in Spain faces more scrutiny; Wiley to shut down 19 more journals; chemistry journal folds after outcry

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The week at Retraction Watch featured:

Our list of retracted or withdrawn COVID-19 papers is up past 400. There are more than 48,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 250 titles. And have you seen our leaderboard of authors with the most retractions lately — or our list of top 10 most highly cited retracted papers? What about The Retraction Watch Mass Resignations List — or our list of nearly 100 papers with evidence they were written by ChatGPT?

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly updatefollow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

Visualize This (2nd ed.): Finding the Best Visualization Tools

There are a lot of tools to visualize data. Some are visualization-specific. Some are tools that let you make charts but are focused on other data things. New apps come out with new features that promise new things. This can make it tricky to find the best visualization tool.

Also, the “best” depends on what you want to visualize and how you want to do it. A data dashboard on a projected screen carries different requirements than an exploratory tool on a laptop, which carries different requirements than a data story that scrolls on your phone. Look for the tools that are best for you.

For me, I started using charts as an analysis and exploration tool. I needed to see data quickly, answer data questions, and move on to the next thing. The aesthetics didn’t matter. The more barebones the better, really.

However, my needs shifted when I had to develop interactive and animated visualizations so that others could analyze their own data. Then they changed again when I had to make charts to communicate insights to a general audience.

I use the tools that I know until they no longer let me do everything I want. Then I find a new tool to supplement. Over time, the toolbox gets bigger and I use different things for different tasks. I’ve converged to a combination of R, Python, and JavaScript/HTML/CSS, along with a mix a smaller, task-specific apps.

But what’s best for me is likely not the best for you. To figure that out, you have to know what’s available and try new things.

Visualize This helps you kick the tires on point-and-click software and popular programming languages. Download real datasets, files, and code explained step-by-step. Try new methods with your own data. You’ll see how various tools fit together so you can start from raw data and design to a finished graphic that’s meaningful, useful, and nice to look at.

The outlined process in this second edition is based on my experiences working with data, but the goal is to help you draw your own and find what works best for you. Maybe have fun with data while you’re at it.

You can order Visualize This now. It lands on doorsteps and bookshelves on March 29.

Order on Amazon

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HiFi WGS As A (Nearly) Unified Tool For Rare Genetic Disease Diagnosis

What is now way back in February, Alexander Hoischen presented a talk at AGBT which described early results from an effort to apply PacBio HiFi sequencing at scale for solving rare disease cases.  Hoischen passionately made the case for how providing a diagnosis can change affected families.  It's also worth noting how important rare disease genetics has been to the history of biology, illuminating new processes and entire pathways.  Something I hadn't appreciated until his presentation is how many technologies are currently thrown at a case in current workflows because each technology can cover a few types of mutations but miss others.  So this is good snapshot of the current state of human genomics technology with hints of where it might be going.  And Hoischen made a strong case that many other technologies  - but not all of them - can be retired if PacBio HiFi sequencing is the lead approach.  A longer, similar talk is also available as a PacBio-sponsored webinar given by Lissenka Vissers from the same institution and some of the data is in a preprint linked below.Read more »

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How the Karolinska protected Paolo Macchiarini — and whistleblowers paid the price

Carl Elliott

Retraction Watch readers may recall the story of Paolo Macchiarini, about whom we first wrote in 2012 before he became the subject of international scrutiny — and who has now been sentenced to prison. We are pleased to present an excerpt about the Macchiarini case from The Occasional Human Sacrifice: Medical Experimentation and the Price of Saying No by Carl Elliott published by W. W. Norton, May 2024.

One incident illustrates just how determined the leaders of the Karolinska Institute were to protect Paolo Macchiarini. In November of 2014, a leaked copy of the whistleblowers’ report came into the hands of the New York Times, which published an article titled “Leading Surgeon Is Accused of Misconduct in Experimental Transplant Operations.” The article detailed several of the most serious allegations against Macchiarini: that he had never obtained ethical permission to conduct his experiments, that his 2011 study in The Lancet had misrepresented the outcome of Beyene’s implant, and that of the three patients at the Karolinska Institute that Macchiarini had given synthetic implants, only Beyene had signed a consent form— and the form was dated two weeks after his surgery. The publicity generated by the article all but forced the Karolinska Institute to act. Anders Hamsten, the vice-chancellor, said he would ask for an external inquiry. 

Retaliation against the whistleblowers came quickly. According to Simonson, the whistleblowers were told that they had violated patient privacy and would be fired immediately. That didn’t happen, but in December the Karolinska Institute informed the whistleblowers that the head of the cardiothoracic clinic would deliver a formal warning, the last step before an employee is terminated.

The Karolinska Institute also reported the whistleblowers to the police. “I was called down to the police and put in a room with no windows, with a tape recorder and a lawyer and a policeman in front of me, and interrogated. That was pretty scary,” Matthias Corbascio, a cardiothoracic surgeons says. “It was exactly what it’s like on television. And you know, it’s hard to be a tough guy in that room.” 

The accusations were baseless; the whistleblowers had anonymized all the identities in their report, and Corbascio had applied in advance for ethical permission to access patient records. “I wrote that ethics application because I knew that they were going to try to fire us,” he says. 

In the spring of 2015, the external inquiry Hamsten had promised was completed. Dr. Bengt Gerdin, an emeritus professor at Uppsala University Hospital, concluded that Macchiarini was guilty of scientific misconduct. The inquiry didn’t address any potential abuses of human subjects, but the result of the inquiry was clear. Macchiarini had falsified his research. 

But even an external corroboration of misconduct didn’t deter the Karolinska Institute leaders. It took months for them to respond, and when they finally came to a conclusion, they called a press conference. “We asked if we could attend the press conference, and they said no,” Simonson says. “They then called our boss at the time and said that they were hiring guards to stop us from attending.” 

Accompanied by members of the Nobel Committee, Hamsten disavowed Gerdin’s external inquiry and proclaimed his confidence in Macchiarini. The whistleblowers were stunned. Macchiarini responded with gratitude. “To have been falsely accused of such serious misconduct is every researcher’s nightmare,” he said. The Lancet applauded the decision with an editorial titled “Paolo Macchiarini Is Not Guilty of Scientific Misconduct.”

Grinnemo remembers this entire period as a very dark time. The stress was overwhelming. “I mean, I couldn’t sleep. I was always thinking of this next strategic move,” he says. People he considered friends stopped returning his calls and emails. He could not concentrate on his research. He found it hard to give his children the attention they needed. “It was also hard doing surgery, to be standing there focusing on the operation,” he says. 

The thought that he might have sacrificed his career for a futile cause sent him into a panic. Corbascio felt the same way. The hostility at work was palpable. He says, “I think that Kalle and I were like the two most hated people at Karolinska, and I’ve no doubt about that.”

Carl Elliott teaches medical ethics at the University of Minnesota and the author of The Occasional Human Sacrifice: Medical Experimentation and the Price of Saying No, from which this post is excerpted.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly updatefollow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

Shifting to batteries for electricity

To capture solar energy for use in the evening, batteries have grown in popularity over the last few years, especially in California. For the New York Times, Brad Plumer and Nadja Popovich show the shift with a pair of stacked area charts.

Five years ago, these pair of charts would have been a single animated one.

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Lack of permits, ‘selective’ data halt research at Swedish prosthetics research center

In the late afternoon at a conference in Cartagena last year, a team of Swedish researchers presented their work on a technique that uses machine learning to translate the body’s own electric signals used to move a limb. They had tested it on a minor recovering from a stroke. 

Documents from an internal investigation shared by Chalmers University have now revealed, however, that this case study was part of a series of regulatory lapses and suspicious research practices at the Centre for Bionics and Pain Research (CBPR) where the clinical research was conducted. The researchers seem to have conducted the study before Max Ortiz-Catalán, the center’s founder and former manager, had secured regulatory approval from the relevant Swedish agency. 

Chalmers, the Centre’s home, has now suspended it after also suspecting that its data and research participants seemed “systematically selected” so that treatments appeared effective, and excluded data when treatments caused health problems. The investigation also uncovered the center had no person responsible for compliance, which is a requirement under Swedish law, and that personal data had been handled poorly. 

This isn’t the first time CBPR has come under scrutiny for questionable research practices. Two years ago, a divided committee absolved several of its researchers from charges of misconduct after a local newspaper pointed out serious omissions in a published paper. 

In September 2022, Forskning & Framsteg reported that researchers affiliated with CBPR, again including Ortiz-Catalán, had excluded the life-threatening complications — such as sepsis and infection — experienced by a patient who had received a prosthetic arm. The paper, ‘Self-Contained Neuromusculoskeletal Arm Prostheses’ published in the New England Journal of Medicine, had generated buzz for its advances in ‘mind-controlled’ prosthetic limbs. 

CBPR had conducted the research in collaboration with Swedish prosthetics company, Integrum. When the deficiencies in the paper were first reported, Integrum CEO Rickard Brånemark said the omissions were “regrettable” and that the authors’ intention was not to hide information, since the complications had been reported at conferences. A month later, in October 2022, the authors published a lengthy correction explaining the patient’s adverse events. 

But when the correction was published, an investigation into alleged falsification was still underway. Chalmers University had submitted a case to Sweden’s national board for research misconduct one day after the newspaper’s report, followed by the University of Gothenburg submitting the same suspicions to the board a month later. 

The authors argued that the patient who experienced the life-threatening complications had received a different kind of prosthetic arm, and that they had intended to publish the medical complications in a subsequent paper, according to the board’s decision published in June 2023. The authors also claim the Journal’s editor wanted the patient to be included, despite the team’s initial plan to exclude them from the paper because of issues with follow-up. 

The board found the authors not guilty of research misconduct, though three members dissented, writing: 

When the article was ready for publication, the authors knew about the complications that affected Patient 4. However, the reasons why Patient 4, who is mentioned in several places in the article, was excluded are not made clear and the context in which complications arose is not knowable either…

We consider it was gross negligence not to report the complications that arose in one of the few research participants included in the study described in the article.

Ortiz-Catalán left CBPR while an internal investigation was being carried out due to “issues in his leadership,” media relations manager Henrik Dahlberg wrote in an email to Retraction Watch. “I won’t go into any detail here,” he added. Ortiz-Catalán has since moved to Australia, where he works at the Bionics Institute in Melbourne.  He has not responded to several requests for comment. 

New information about operational issues at CBPR came from a staff tip-off in March 2024, prompting the latest internal investigation at Chalmers that has resulted in the center’s suspension. “The ethics committee decided that they needed to investigate, since what had been revealed indicated irregularities in the research that had been carried out at CBPR,” Dahlberg wrote. 

The investigators examined 50 publications that were published between 2020 and 2024 which include Ortiz-Catalán as an author. They found a large number of ethical permits, but only one regulatory permit since the CBPR was formed — dated several weeks after researchers had presented their clinical case study at the conference in Colombia. 

The report also noted a lack of legal agreement between Integrum, the company that collaborated in the 2020 study, and Chalmers University. 

“It is our assessment that the activities at CBPR violate the law regarding regulatory permits.” the investigators wrote, noting that this carries a maximum imprisonment of two years according to Swedish law. “In addition, there is a suspicion that they do not comply with the European regulations for medical devices and do not live up to the Declaration of Helsinki,” the report continues. The investigators also found issues with security in the management of personal data. 

While the investigation focused on whether permits were in place for the work, the report suggests that data was selected to appear favorable to the treatments. Chalmers and the other collaborating institutions — the University of Gothenburg and Sahlgrenska University Hospital — agreed to suspend CBPR’s operations and have asked Swedish research authorities to review work from the group dating back to 2020. 

In response to questions about whether this affects research produced collaboratively between Integrum and CBPR, Integrum CEO Rickard Brånemark wrote: 

The NEJM article you refer to has already been thoroughly re-examined, after which a correction was published on November 1, 2022. Moreover, an academic research evaluation confirmed that no misconduct had been committed. I feel confident that everything in that paper is correct and balanced. To my current knowledge, there are no reasons to correct or retract any of the other articles I have co-authored with researchers at CBPR. Should the evaluation following the closure of CBPR find any inconsistencies in any publication, we will of course make sure to correct these.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly updatefollow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

✚ Does the data make sense?

When you analyze data, there are times when a trend, pattern, or outlier jumps out and smacks you in the face. Or, you might calculate results that seem surprising. Maybe they’re real, but maybe not. Make sure know which before you go shouting your insights from the rooftop.

Become a member for access to this — plus tutorials, courses, and guides.

Spring Cleaning! Let’s Talk Single ID

Photo credit: JESHOOTS via unsplash

As previously reported, and as you may have noticed if you served on a panel within the past year, you may have been asked to update your NSF ID. Well, for those of you who have not done that, you will have to update your reviewer profile when we send you an ad hoc request! You see, a lot of people had old, incorrect, or superfluous profiles in our system, and this is part of a multi-year process to clean up redundant IDs.

This process also includes merging researcher and reviewer profiles into a single, self-managed profile/ID to make your lives easier, too. It also means you will no longer require a PIN provided by program staff to access assigned proposals and will instead be able to use a single sign-on from Research.gov to access FastLane Proposal Review functions. Hooray!

You can update your profile now or wait to be prompted by a request from NSF. Either way, the instructions are below for those among us who do not enjoy the thrill and adventure of procrastination.  

Here’s how you do it:

  1. Register for an NSF account in Research.gov if you don’t have one.
  2. Sign in to Research.gov. If you are prompted to verify your information (email and phone number), you must complete this step before proceeding to step 3.
  3. Click the Provide Reviewer Profile Information link under “Reviews & Meetings”. If you do not see the Provide Reviewer Profile Information link, contact your program officer.
  4. Enter the email address where you received this ad hoc request to initiate the one-time process to link your NSF investigator and reviewer profiles.
  5. You will be invited to update your demographic profile.

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Simulation for Probability of Success

Imagine that you try to do something and there’s a 20% chance of success. If you try to do the thing six times, what is the probability that you succeed at least once?

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