last updated by Pluto on 2024-07-26 08:15:47 UTC on behalf of the NeuroFedora SIG.
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in Science News on 2024-07-25 23:52:14 UTC.
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The FENS is the biggest neuroscientific conference in Europe. It is 5 days long and is attended by 5’000-10’000 participants. This year, the conference took place in Austria’s capital, Vienna, roughly 600 km from my current workplace in Zürich. Of course, there are regular and cheap flight between the two cities; however, there are good reasons why to use other means of transportation instead (check out Anne Urai‘s work): busses, regular trains, and night trains. In this blog post, I will share my impression what it is like to take a night train in Europe and why it is a great option for some (but not for everybody).
What’s special about night trains?
Night trains (also called sleeper cars) typically cover longer distances than regular trains. Traditionally, they tried to offer more comfort for an over-night stay, like comfortable beds, additional cars with proper restaurants and bars, or at least a breakfast served at your seat. Especially in times when trains were slower and airplanes not available, night trains were one of the more comfortable options to make a long trip enjoyable. I was surprised to find out that some of the earliest night trains were actually operated in the USA! However, the probably most famous examples of night trains traverse the Eurasian continent. For example, the Transiberian Railway, which extends from the Western to the Eastern Border of Russia; or the Orient Express, which passes through a large part of Europe from Paris to Istanbul.
Seating carriages, sleeper’s carriages and things between
In most night trains that I know, there are three different carriages. First, the cheaper carriages where you stay on a seat over night. Sometimes, these seats can be pulled out and converted into an improvised bed. Second, the couchette, which offers bunk beds, usually with 4 or 6 beds within one compartment, with 2 or 3 stories on the left and the right. And finally, a more spacious and more private sleeper compartment, with typically 1 to 3 beds. It is also possible, for an additional fee, to reserve a sleeper compartment for oneself, for a couple or a family. The prices are moderate when booked much in advance; for example, I paid <150 Euros for the round trip from Zürich to Vienna. However, one must also state that (and wonder why) a cheap flight is not much more expensive than that.
The current state of night trains in Europe
Unfortunately, night trains have been on the decline for several decades in Western Europe. With more and more cheap flights or good high-speed train connections between many European cities, the operation of the slower night trains became less interesting for railway companies, and investments stalled. Around 2020, some governments in central Europe tried to countersteer this decline by pushing for a stronger network of night trains. But it will still take several years until these efforts will show some effect, and the success is not a given.
The re-growing interest for night trains didn’t come out of nowhere. With the public opinion looking more skeptically at short-distance intracontinental airplane flights, night trains in Europe became increasingly popular, in particular after the pandemic, as a CO2-friendly option for long distance-traveling. However, the infrastructure could not really hold up to the increasing interest. Most importantly, the fleet of trains was both too old and too small for the rising demand. The companies responded by using their trains at maximum capacity; therefore, if a carriage broke down (which was not unlikely due to their old age and the scarcity of spare parts), often there was no replacement carriage, and the passengers who were supposed to calmly sleep in a reserved bed were regrouped into an overcrowded seating carriage. Addtionally, the infrastructure inside of the carriages, like toilets, bed lights, etc. is often rather old and not always in a good state – far from the luxury atmosphere associated with, e.g., the Orient Express! Moreover, night trains are often delayed by one or several hours, especially on high-demand routes such as Zürich-Amsterdam.
In summary, one needs to face the fact that night trains are currently not as reliable and not as comfortable as they should be in order to make this mode of traveling attractive for a broader audience. It is likely that the situation will improve during the next years, with more modern cars being produced, replacing and supporting the existing fleets, and making night trains in Europe again more reliable and also luxurious. I have the impression that the companies have already taken some good first steps towards such an improved scenario, because when I took the night train to Vienna, the train was purposefully underbooked, most likely to prevent major problems in case a carriage would break down. But let’s see what the next years and decades will bring.
My own experience has so far been limited to night trains operated by the German-speaking railway companies, with the Austrian railway company ÖBB being at the heart of it. However, there are other night trains as well. For example, it’s possible to go from Milano in Northern Italy to Sicily within a long night, passing not only the largest part of Italy, but also the Mediterranean Sea with a train ferry (!). So if you’re planning your next series of Summer conferences to attend across Europe, maybe you can connect the conferences with an adventurous night train trip?
Traveling from Zürich to Vienna with the night train
The conference in Vienna started on Tuesday, June 25th, with a workshop on closed-loop neuroscience that I wanted to attend (and I was particularly impressed by the cool work from Valerie Ego-Stengel’s lab). I worked normally in Zurich on Monday and went directly from work to the main train station, where the night train departed at 8.40 pm. With me, the luggage for a Summer’s week and a big poster roll.
My train was, to be fair, quite old. I had booked a sleeper’s bunk bed in a 6-person compartment but the middle beds on each side were not used, as you can see below. You can also guess from the first picture and see from the second picture that there was not a lot of space between my bunk bed and the ceiling. It was enough to sit on the bed and work, but barely.
When I entered the compartment, I realized that I would share it with an elderly Indian couple, who were, while the train was still waiting in the station, accompanied by several family members. The couple was from Vienna and had attended a wedding in Switzerland. As most people in night trains, they had little experience with the night train experience. What are the rules? What bed should you take? When will the lights be turned off? Where are the electric plugs? Is there wifi? (Usually, there is none.) Will I be woken up in the morning? I could see the anxiety and the adventure in their eyes, and they were grateful that I could help out with some of their simplest questions.
We had a pleasant discussion about their lifes in Vienna, but after a short time, we decided to go to bed. I went up to my bed and spent an hour or two going through the scientific abstracts of the conference to figure out the best trajectory for the next days. Around midnight, I went to sleep. It turned out that this particular car and this particular bed was not perfect for me – the bed measured almost exactly 180 cm, which is a few cm too short for my height. I noticed that the lower beds were slightly longer, from which I benefitted gladly when I took the train back a few days later.
Usually, I can sleep pretty well in night trains. I like the rhythmic rattling of the train wheels, it even helps me fall asleep (to the extent that I find it difficult to sleep when the train is not rolling but standing still in the middle of the night for an hour!). It’s a pleasant feeling to know that the goal is coming closer by itself while I do nothing but sleep.
This time, however, I was a bit unlucky. My two cabin mates were very friendly when awake, but rather annoying during sleep. The woman was snoring in an irregular way that I found difficult to deal with, while her husband was occasionally speaking or shouting in his sleep with an agitated voice. Not my best night train night so far! I heard later that a colleague of mine who also took the night train to FENS was much luckier, sharing the cabin with other attendants of the FENS conference and having a good time during the evening and night.
In any case, the train arrived at 6.34 am in Vienna, perfectly on time. The breakfast in the train had not been exceptional (which is unfortunately the rule rather than the exception according to my experience). Therefore, I benefitted from the great Viennese baking culture and got a very decent breakfast at a price that seemed so much more affordable as I was directly coming from Switzerland…
After the 5-day conference, which was a pleasant mix of meeting old friends and meeting people for the first time I knew from Twitter, from collaborations or from eMail exchanges, interspersed with some interesting pieces of neuroscience, I spent another day with a good old friend of mine who happens to live in Vienna, before I took the train back to Zürich. My plan was to take the night train on Sunday just after 11 pm, to arrive on Monday morning in Zürich and go directly to work. Maybe an ambitious plan, but it worked out well. During the last hour before my train departed, I waited at the train station in Vienna, with the vibrant atmosphere of Summer still around me. Due to the European soccer championship, one of the games was publicly displayed on a huge screen just in front of the station, and a Spanish crowd cheered every time their team scored a goal.
Back on the train, I entered the compartment that was already occupied by one woman, sleeping in one of the beds, hidden below the blanket. I tried to do my best not to wake her up and took over the bed on the left.
I wrote a few notes on my laptop to record the recently passed very eventful and inspiring days, and then fell asleep.
I woke up in the early morning around 6.30 am. With joy, I noticed that we were passing by Lake Walenstadt, a beautiful lake in the East of Switzerland, and already quite close to Zürich. Through their diffuse reflection, the grey and white clouds created a beautiful metallic shimmer in the water, and I sat there, looking out of the window, being happy.
Soon after, we passed by Lake Zürich, and when I arrived at Zürich main station, I had my breakfast with delicious Viennese pastries before I went to work. A very efficient way of traveling!
Why you should (not) take the night train
It should have become clear now that night trains in their current state are not for everybody. The comfort is too low and the prices are a bit too high, and delays too frequent. But still … I would recommend this experience to anybody who is not afraid of it and can manage to sleep in such a context. It’s not only about avoiding airplanes, but also about embracing the adventure that is much more palpable for the night train experience compared to airplane flights. The sense of adventure not only makes the travel special but also bonds the travellers within one compartment to each other more easily. A great opportunity to meet with people from outside your social circles!
The probably most famous night train, the Orient Express, has long been associated with an atmosphere of both luxury and adventure. And both aspects are reflected by its prominent occurrence in works of fiction, ranging from Agatha Christie’s famous novel The murder on the Orient Express to the most recent Mission Impossible movie. Nowadays, it is mostly the atmosphere of adventure which still remains part of the night train experience. Almost 20 years ago, I was deeply fascinated by the novel Night Train to Lisbon. In this book, the daily life of a high school teacher transitions to a philosophical and linguistic adventure within a single night: in the night train from Bern to Lisbon. I still believe that this is the essence that is the most attractive aspect of night trains: the vague promise of adventure, a memorable night and a new world that opens up to the awakening senses on the morning of the next day.
in Peter Rupprecht on 2024-07-25 16:47:00 UTC.
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In June, a scientist researching sarcopenia came across a relevant paper about treatment for elderly patients with complications from the disease as well as type 2 diabetes. The paper was “very bad,” he told us. “It looked like someone just copied two or three times the same text.”
The scientist, who asked to remain anonymous, became even more concerned when he realized the paper, which had the word “elderly” in its title, had been published in a pediatric journal.
“I started reading other issues of the same journal and noticed that this is a widespread problem: Chinese papers about older adults being published in pediatric journals!” he said.
He suspected the problems were the work of a “careless editor.”
“I hope that no one is getting money to publish this,” he said.
The volume of the journal with the sarcopenia paper, Minerva Pediatrics, included 29 articles, of which at least eight letters to the editor described experiments and clinical trials with adult participants, according to our analysis. Two contained the word “elderly” in their titles, including the article on sarcopenia. Others concerned knee osteoarthritis, lumbar spine fractures and other conditions most often seen in geriatric, rather than pediatric, patients.
All of the authors of the out-of-scope papers were from China, most with email addresses not associated with an institution and containing seemingly random sequences of letters and numbers, which some have suggested is a sign of paper mill activity. We attempted to email several of these addresses, but our queries went unanswered.
Aside from the issue with the sarcopenia paper, we found two letters about “elderly” patients in the June 2023 edition of the journal and one in the February 2024 edition. We’ve compiled a list of out-of-scope papers included in Minerva Pediatrics.
Dorothy Bishop, a sleuth and emeritus professor of developmental neuropsychology at the University of Oxford, England, who reviewed the articles for us, noted that in many journals, letters to the editor are not peer reviewed, and are generally “not a suitable format for papers reporting results of clinical trials, which several of these articles claim to be.”
The journal, which calls itself the “most ancient international peer-reviewed journal in the field,” purports to publish “articles related to Pediatrics and all its various sub-disciplines.” The papers which fall outside of this scope “all look pretty terrible in terms of quality and I think would not survive peer review in a respectable journal,” Bishop said.
Minerva Pediatrics’ “publishing options” page says for open access, “authors will be asked to pay” an article processing charge (APC) of €1500, or €1200 for letters to the editor. Publishing for subscription access only is free.
Three other journals from the publisher, Minerva Medica, were denied impact factors by Clarivate this year due to suspicion of citation manipulation.
Cecilia Belletti, a representative from the publisher, thanked us for our email but did not respond to our questions about why research on elderly patients was included in the pediatric journal or whether her company would remove the suspect papers.
“A proper editor would be horrified to find this material in their journal and would take steps to sack the editor who let this material through,” Bishop said. “Any other reaction would be suspect.”
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in Retraction watch on 2024-07-25 12:00:00 UTC.
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A political scientist in Canada copied his postdoc’s work without credit in a paper, according to the retraction notice and a university inquiry report.
The paper by Charles Conteh, a professor at Brock University in St. Catharines, Ontario, appeared in Sage’s Outlook on Agriculture in October 2023. It has one citation, according to Clarivate’s Web of Science.
An inquiry by Brock identified plagiarism and uncredited authorship in the article, according to the report finalized this March and seen by Retraction Watch. Failure to give post-doctoral fellows the “opportunity to publish in peer-reviewed journals negatively impacts [them] both reputationally and financially,” the report states.
Amy Lemay, now a science analyst and founder at VISTA Science & Technology Inc., was Conteh’s postdoctoral fellow from August 2020 to January 2023.
In emails seen by Retraction Watch, Conteh asked Lemay and another faculty member for feedback in March 2023, on a draft of the article they were writing. After reviewing their feedback, Conteh said he could no longer proceed with the project, citing “serious reservations” about Lemay’s suggestions to publish separate papers based on policy reports they had produced for Niagara’s Community Observatory platform.
“We can (and most likely will) cite them in future papers, but I object to the idea of us reproducing and republishing them in their current forms,” Conteh wrote in an email seen by Retraction Watch. “I plan to revisit this project at a future date, but at this point, after some reflection, what I can candidly say is that I am not clear about a collaborative way forward.”
Months later, Lemay discovered the published paper online by accident. The article used text from the policy briefs she had worked on, without citing those sources.
“When it finally sunk in, I was angry (outraged, really) and felt betrayed,” Lemay told Retraction Watch. “I took a couple of days to calm down and think through my options for responding. I knew what Dr. Conteh had done was wrong. I felt that I was in a unique position to call it out.”
Lemay asked Conteh to add her as a co-author to the paper. In October, Conteh asked a journal editor if the authorship could be updated to include Lemay and another co-author’s name.
Conteh replied he was “glad that you’ve suddenly taken an interest in being a co-author in the manuscript now that it has been published. I am adding your name not because I think you deserve it or are entitled to it, but because it is the noble thing to do.”
In November, Jillian Lenne, an editor at Outlook on Agriculture, said it was too late to update the authorship as the paper was already accepted. Lemay then requested Sage retract the paper for misrepresented authorship and copying previous publications without citation.
In response to Lemay’s request for retraction, Conteh wrote in the email she “has no basis for claiming co-authorship or requesting retraction of a paper she did not write.” Conteh said Lemay’s acknowledgment in the manuscript as a postdoc should have been sufficient. “By the logic of Amy’s claim to authorship, all research assistants I’ve hired to help me on a project should claim co-authorship whenever I publish an article that draws from a data source they helped me collect or analyze,” he wrote.
Lemay said she finds Conteh’s views on authorship troublesome and that she was responsible for the majority of the research. “This view about what constitutes co-authorship contradicts one of the most fundamental and canonical academic principles,” she said. “That it is an attitude that may be held by other faculty is a serious concern that needs to be addressed to protect graduate students and postdoctoral fellows.”
The article was retracted in May, with the following notice:
Due to the unattributed text which calls into question the author contributions in this article, the Journal Editor has retracted this article.
Conteh, who disagreed with the retraction, told Retraction Watch he has no further comment beyond reiterating he was the principal investigator of the project and the retracted article came from that project.
Lemay said the citations listed in the retraction are incorrect because they credit Conteh as the lead author when it should be her. A spokesperson for Sage said they are working to correct the citations.
Though she recently finished a postdoc, Lemay worked in academia for 25 years before pursuing her PhD. At this point in her career, she said, she is not intimidated by the “power imbalance” in academia, as some younger students who are still forging a career path may be.
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Predictive processing is one of the most influential ideas from computational neuroscience for the experimental neurosciences. However, definitions of predictive processing vary broadly, to the extent that “predictive coding” is used sometimes in a very narrow sense (there are specific cell types for negative or positive expectation errors) or in a very broad sense (anything related to error signals or expectation mismatch is predictive processing).
Jerome Lecoq now started the great initiative to write a review about error signals for predictive processing, but in a very collaborative manner. He invited anybody interested to join the writing of the review.
I think that this way of writing a collaborative and open review is a great idea, even though it might be difficult to reconcile all the different opinions! This link will lead you to the Google document with the main text and with the instructions on how to contribute. And if you don’t feel like you want to contribute, it is at least a useful opportunity to learn about the current opinions in the field and how people agree or disagree about the interpretation of predictive coding, error signals and the literature that covers both. Take a look!
in Peter Rupprecht on 2024-07-23 16:39:34 UTC.
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Elsevier is investigating the journal Geoscience Frontiers after a PubPeer thread flagged an editorial advisor whose articles in the journal were edited by his frequent co-authors.
The editorial advisor, M. Santosh, is a professor at the University of Adelaide in Australia and a “Highly Cited Researcher” with more than 1,500 published articles, according to Clarivate’s Web of Science.
The PubPeer commenter, “Desmococcus antarctica,” noted that two associate editors of the journal, Vinod O. Samuel of Yonsei University in Seoul and Erath Shaji of the University of Kerala in Thiruvananthapuram, India, are often listed as “Handling Editors” of Santosh’s articles published in Geoscience Frontiers — despite each frequently publishing other work with him.
A representative from Elsevier told us the publisher was looking into the matter, adding that “we expect our publishing partners to uphold our publishing policies, including the proper conduct of peer-review.” Elsevier publishes Geoscience Frontiers on behalf of China University of Geosciences (Beijing) and Peking University.
None of the researchers have responded to our request for comment, nor has Xuanxue Mo, editor-in-chief of the journal and professor at China University of Geosciences (Beijing).
Samuel edited at least 20 of Santosh’s papers in Geoscience Frontiers from 2017 to 2024, according to the PubPeer post. “Due to the massiveness of the scale on which this happened,” the Pub Peer comment stops at 20 instances, Desmococcus states.
Samuel and Santosh have co-authored at least 15 papers together in multiple journals, according to Clarivate’s Web of Science.
Similarly, Shaji edited at least 10 of Santosh’s articles in Geoscience Frontiers from 2017 to 2024. The two were co-authors on at least 29 papers from 2016 to 2023 in different journals, according to Web of Science.
Desmococcus has flagged many other papers by Santosh in Geoscience Frontiers on PubPeer.
Beyond Geoscience Frontiers, Desmococcus has chronicled similar instances of Santosh’s frequent co-authors editing his papers at other journals, as reported by For Better Science.
In one incident, a report from the 5GH Foundation, a China-based “non-profit organization for promoting science and technology,” alleged Santosh had initially been listed as the handling editor of his own paper at Geoscience Frontiers. The paper now lists Chakravadhanula Manikyamba, a researcher at the National Geophysical Research Institute, as handling editor (although her name is misspelled as “Manikyabma”).
Manikyamba is another frequent editor of Santosh’s articles in Geoscience Frontiers, as Desmococcus points out on PubPeer. She edited at least four of his papers and has co-authored three papers with him since 2022, according to Web of Science.
Santosh’s record also includes a retraction. In 2020, his paper “Hydrocarbon reserves of the south China sea: Implications for regional energy security” was removed “because it inadvertently included unlawful content.” The editor-in-chief of the journal where it appeared, Energy Geoscience, did not respond to our request for clarity on what constitutes “unlawful content,” but an Elsevier spokesperson told us that the authors requested the removal “because they had inadvertently breached legal regulations.”
Elsevier’s website states it will remove an article only in “extremely limited number of cases,” in which the article is “defamatory, or infringes others’ legal rights, and retraction is not a sufficient remedy.” An article will also be removed if Elsevier “has good reason to expect it will be” the subject of a court order, or if it would pose a “serious health risk” if acted upon.
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in Retraction watch on 2024-07-23 11:38:05 UTC.
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In an episode reminiscent of the AI-generated graphic of a rat with a giant penis, another paper with an anatomically incorrect image has been retracted after it attracted attention on social media. The authors admit using ChatGPT to make the diagram.
According to the retraction notice published July 12, the article, by researchers at Guangdong Provincial Hydroelectric Hospital in Guangzhou, China, was retracted after “concerns were raised over the integrity of the data and an inaccurate figure.”
The paper, published in Lippincott’s Medicine, purported to describe a randomized controlled trial that found alkaline water could reduce pain and alleviate symptoms of chronic gouty arthritis.
Morgan Pfiffner, a researcher for Examine.com, an online database for nutrition and supplement research, first noticed the study while on vacation and posted on X about the erroneous diagram in the article.
“I planned to inform the journal when I got back, but that graphic was just too absurd not to share on social media once I saw it,” Pfiffner told Retraction Watch. Another X user found the paper’s introduction to be 100% AI-generated.
Commenters including Elisabeth Bik and Thomas Kesteman chimed in on PubPeer, echoing Pfiffner’s concerns. Bik pointed out that Figure 4 had the wrong number of bones in the lower leg and arm and had nonsensical labels such as “chlsinkestead atlvs no ctivktty greuedis” and “Aliainine jerve sreiter.” She also noted inconsistencies in the data and seemingly unrealistic methods.
Kesteman highlighted additional issues: Some of the references in the article do not appear in PubMed or Google Scholar, and the authors’ email addresses were not institutional – which, we note, is considered a red flag but not always a sign of problems. Further, the results of some statistical analyses were “virtually impossible,” Kesteman said, and data on pain scores in a table “present patterns that are impossible to find in real life.”
Yong Wu, the corresponding author of the study, told Retraction Watch English is not the team’s first language, and the cost for translation was prohibitively expensive.
“Therefore, our research team has resorted to using AI for text translation and refinement. Similarly, the expense of scientific illustration is beyond our means, which led us to use ChatGPT for generating research diagrams,” Wu said. “We apologize for any controversy this may have caused.”
A spokesperson for Medicine said the journal is continually improving its editorial review process. “We are working on a number of initiatives to help shape the future of medical research reviews based on collaboration with other leading publishers, dedication to peer reviews and leveraging new technologies,” they said.
“It seems to me that AI graphic itself was just the tip of the iceberg of research misconduct permeating that study,” Pfiffner said. “I’m glad it has been swiftly retracted.”
Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.
in Retraction watch on 2024-07-22 12:00:00 UTC.
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BMC Ecology and Evolution – Diuqin lechiguanae gen. et sp. nov., a new unenlagiine (Theropoda: Paraves) from the Bajo de la Carpa Formation (Neuquén Group, Upper Cretaceous) of Neuquén Province, Patagonia, Argentina
Unenlagiine theropods are a group of dinosaurs that are key to understanding how living birds evolved. However, fossils of these dinosaurs are rare, especially from the Late Cretaceous period. Therefore, it has been rather challenging to piece together their evolutionary history and understand the modifications that occurred within the Unenlagiinaen lineage over time.
A recent paper published in BMC Ecology and Evolution describes the discovery of Diuqin lechiguanae gen. et sp. nov., a new unenlagiine theropod dinosaur from the Upper Cretaceous (Santonian) Bajo de la Carpa Formation in Neuquén Province, Argentina. This new taxon, described from an incomplete postcranial skeleton, exhibits unique morphological features, particularly in the humerus, which appears intermediate between older and younger unenlagiines. Phylogenetic analysis places Diuqin within Paraves, with a strong affinity to Unenlagiinae. Interestingly, the humerus bears tooth marks, likely from a crocodyliform, mammal, or another theropod, which offers additional insights into the paleoecology of these theropods and their interactions with other animal species of their time. This finding marks a significant advancement in the field of paleontology, bridging a 15-million-year gap in the unenlagiine fossil record.
BMC Medical Genomics – Exploring the potential of genetic analysis in historical blood spots for patients with iodine-deficient goiter and thyroid carcinomas in Switzerland and Germany (1929–1989)
Iodine is crucial for producing thyroid hormones and maintaining thyroid gland health, with deficiencies leading to goiter and severe developmental issues, including growth and mental impairments. Historically, Switzerland faced significant iodine deficiency, causing high rates of goiter and cretinism until iodine fortification of salt began in the early 20th century. Despite the success of these programs in reducing goiter prevalence, some cases remain, emphasizing the need to explore additional factors, including genetic predispositions.
To examine the genetic factors contributing to goiter development, despite adequate iodine supplementation, a recent study published in BMC Medical Genomics assessed the feasibility of extracting and analyzing DNA from historical blood spots found in medical records of patients with iodine deficiency-induced goiter and thyroid cancer between 1929 and 1989 in Switzerland. The researchers found that DNA yields varied significantly between samples, with many showing substantial degradation and mixtures of DNA from different contributors. The study concludes that each sample must be individually evaluated for genetic analysis, and larger or entire blood ablations should be collected to mitigate insufficient DNA quantities.
The impact of this advance is significant for historical epidemiology and genetic research, as it allows for the exploration of genetic predispositions in populations from past decades, potentially leading to a better understanding of disease causes and the development of targeted interventions.
BMC Environmental Science – Is “green” ammonia a misnomer? Unpacking the green label from a food-water-energy nexus perspective in water-scarce regions
The production of conventional fertilizers, such as ammonium nitrate, significantly contributes to greenhouse gas emissions and environmental degradation due to energy-intensive processes and the release of nitrous oxide. In contrast, green ammonia production, which uses renewable energy sources for hydrogen generation, tries to reduce carbon footprints and environmental impact, thereby offering a more sustainable alternative to traditional methods.
A recent Comment article published in BMC Environmental Science, takes a close look at the term “green ammonia,” especially in areas with limited water resources. The authors point out that while green ammonia is produced using green hydrogen (which comes from water split using renewable energy) and does cut down on carbon emissions, it still has other serious environmental effects. These include a high demand for fresh water and potential ecological harm from desalination.
The authors argue that the fertiliser industry should use a wider perspective on environmental impact, focusing not only on carbon emissions but also on reducing the flow of reactive nitrogen and phosphorus. They suggest that recycling human waste and other organic materials could be a better and more sustainable option than green ammonia. This approach could greatly cut down on carbon emissions and nutrient pollution.
BMC Genomics – Transcriptomic responses in the nervous system and correlated behavioural changes of a cephalopod exposed to ocean acidification
Ocean acidification, caused by increased CO2 levels, which leads to higher concentrations of carbonic acid in seawater, significant effects the marine ecosystem. As we are facing increasingly adverse climatic parameters, understanding how animals respond to future environmental conditions is crucial for predicting their adaptability and survival.
In a recent study published in BMC Genomics, Thomas et al. investigated the neurobiological effects of ocean acidification (OA) on the two-toned pygmy squid (Idiosepius pygmaeus). By using a de novo transcriptome assembly approach, the authors assessed transcriptomic alterations in the squid’s central nervous system (CNS) and eyes under elevated CO2 conditions and correlated molecular changes with varying CO2 levels and behavioral modifications.
Their findings indicate that OA triggers transcriptomic responses related to neurotransmission, neuroplasticity, immune function, and oxidative stress. These molecular changes were also associated with changes in behavior (e.g. increased activity levels and changes in visually guided interactions), suggesting a mechanistic link between environmental changes and behavioral responses.
BMC Digital Health – Potential for use of tetris in the neonatal unit – a scoping review
Post-traumatic stress symptoms (PTSS) significantly affect the daily lives and relationships of those affected, especially preterm parents in the stressful environment of Neonatal Units (NNUs). Tetris, a popular computer game, may offer a novel method for reducing PTSS by minimizing intrusive memories associated with trauma. This review aims to evaluate the potential of Tetris as an intervention for preterm parents, exploring its feasibility and effectiveness in mitigating PTSS within this vulnerable population.
A study published in BMC Digital Health investigated the potential application of the computer game “Tetris” as an initial intervention to alleviate post-traumatic stress symptoms (PTSS) in parents of preterm infants within Neonatal Units (NNUs). In their scoping review of 13 relevant articles, Craig et al. identified four recurring themes: memory consolidation, the impact of Tetris on intrusive memories (IMs), its neurological effects, and its feasibility in clinical trials.
The review shows that playing Tetris can interfere with the consolidation of traumatic memories, thereby reducing the frequency and intensity of disturbing memories. Additionally, the game is deemed both acceptable and feasible for clinical implementation, suggesting it could serve as a beneficial tool for preterm parents in mitigating PTSS.
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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 49,000 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):
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A 14-year-old paper has earned an expression of concern after an anonymous whistleblower found evidence of image duplication in the work.
The authors have had images from several more papers flagged on PubPeer. The corresponding author, Kelly McMasters, is chair of the Hiram C. Polk, Jr., MD Department of Surgery at the University of Louisville School of Medicine in Kentucky.
The 2010 paper, “Adenovirus-mediated expression of truncated E2F-1 suppresses tumor growth in vitro and in vivo,” appeared in Cancer. It has been cited 12 times, according to Clarivate’s Web of Science.
The expression of concern highlights “suspected duplication of elements between figures 2b and 2c.”
The author [sic] admitted mistakes were made during preparation of the figures; however, since the paper was published in 2010, they were unable to provide the original raw data for figure 2c. Although the conclusions are not believed to be affected, the journal is issuing this expression of concern to alert readers that blots in figure 2c were inappropriately modified without disclosing the processing in the figure caption.
McMasters did not respond to our request for comment.
Carissa Gilman, director of editorial operations for Cancer, told Retraction Watch an “anonymous whistleblower” raised concerns about the paper by email. The person “said they had been aided by ImageTwin, an image integrity analytical tool,” Gilman told us.
Despite the inappropriate image modification, Gilman told us the editors did “not believe we have enough evidence that the paper should be retracted.”
The journal uses expressions of concern “if there are issues we believe cannot be resolved,” the representative continued. “In this case, since the original blot cannot be found, we cannot satisfactorily resolve this issue.”
A January 2024 comment in PubPeer from “Actinopolyspora biskrensis” on the 2010 paper points out possible duplications of signals and gel slices in the figures mentioned in the notice, as well as possible differential splicing between gel lanes.
The lead author, Jorge Gomez-Gutierrez, an associate professor at the University of Missouri School of Medicine in Columbia, Missouri, was unable to find the original blots “given the age of the paper,” according to Gilman.
Gomez-Gutierrez “agreed that the bands corresponding to actin were inadvertently duplicated during the figure preparation,” but stands by the paper “since they have been able to reproduce the same results in the intervening years multiple times using different cell lines,” according to Gilman. He did not respond to our request for comment.
McMasters has several other papers with PubPeer comments, including a second 2010 paper, “Developing adenoviral vectors encoding therapeutic genes toxic to host cells: Comparing binary and single-inducible vectors expressing truncated E2F-1.” Actinopolyspora pointed out image overlap in figure 3C of the paper.
Gomez-Gutierrez responded on PubPeer with original images. However, a second commenter, “Nerita vitiensis,” created an animation which “only confirms that Actinopolyspora biskrensis was correct – the images do indeed overlap.”
A second paper in Virology has comments on PubPeer pointing out image issues. Actinopolyspora noted in January that “[t]wo images in Figure 6D seem to overlap, but are described differently.”
A spokesperson from Elsevier, the publisher of Virology, has confirmed that the papers in Virology with PubPeer comments are currently “under investigation.”
In April, the MDPI journal Cancers issued a correction for “Temozolomide Enhances Triple-Negative Breast Cancer Virotherapy In Vitro,” a 2018 paper for which Gomez-Gutierrez and McMasters are corresponding authors.
The correction concerns an “error” in figure 1A of the paper, again following a PubPeer comment from Actinopolyspora. According to the correction, “the image of a crystal violet plate of MDA-MB-231 cells was inadvertently duplicated from a previous manuscript,” but a “new set of experiments was performed to replace the duplicated crystal violet plate and generate a new quantification graph.”
Another Cancers article by McMasters and Gomez-Gutierrez has PubPeer comments regarding potential image manipulation. MDPI didn’t respond to our request for comment about any plans to investigate further.
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in Retraction watch on 2024-07-19 14:27:24 UTC.
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A Frontiers journal has taken down the abstract of a “provisionally accepted” article about harms from an herbal supplement after the company that sells the products sued the first author for defamation.
The author of the paper, Cyriac Abby Philips, a hepatologist at Rajagiri Hospital in Kerala, India, has over 266,000 followers on his X account “TheLiverDoc.” In 2020, another of Philips’ papers about harm from supplements was retracted and removed after the large supplement company Herbalife, whose products the paper impugned, put legal pressure on Elsevier.
Himalaya Wellness, an herbal supplement company which says its products are based on Ayurvedic practices, last year sued Philips for defamation based on his posts on X about the company’s products.
X suspended his account following a court order that also barred Philips from speaking about Himalaya or its products. After Philips appealed the order and said he would hide the X posts at issue, a higher court ordered the social media platform to restore his account, but the gag order remains in effect.
Before Himalaya filed its lawsuit, Philips had submitted a paper to Frontiers in Pharmacology describing cases of liver damage linked to one of Himalaya’s products, Liv.52. The journal accepted the article in January and posted it online.
Soon after, Philips received an email from a research integrity staffer at Frontiers, who wrote:
It has come to our attention that there are ongoing court proceedings involving you and the Himalaya Wellness Company. Alongside this, we have received information suggesting a potential undisclosed financial relationship. As stated in COPE’s guidelines, it is required to highlight any perceived conflicts of interest in a statement. For more information, please see our guidelines here: https://www.frontiersin.org/guidelines/policies-and-publication-ethics#conflicts-of-interest
In order to comply with COPE guidelines, we kindly request your input regarding the potential financial conflict of interest. Additionally, considering the ongoing legal matters, we would like to ask whether it would be preferable for you to halt publication until court proceedings are over?
Philips responded that he had an advisory position with the pharmaceutical company Cipla Limited that lapsed in 2020, and had no other conflicts of interest to report.
Regarding the legal proceedings, Philips wrote they were “irrelevant” to the publication:
There is no active legal order from a Court of Law currently in place that precludes Frontiers Journal or the authors from publishing this scientifically accepted peer-reviewed manuscript since the currently ongoing legal proceedings are independent of this publication and the submission, peer-review and final acceptance of the manuscript is independent of current Court proceedings.
In June, the Frontiers staffer replied the publisher had decided to “place the publication of the article on hold until the legal proceedings in India have been resolved.” The email continued:
To explain, based on the information that we have received, we have been advised that publication of the article could already be covered by the current court order, or that the claimant will most likely take measures to this effect. Therefore, until the legal proceedings have been resolved, we will proceed to withdraw your article temporarily from the publication process.
Once the legal proceedings have been concluded, we would of course be happy to reexamine the position. Please kindly keep us informed once the situation has been resolved.
Philips and his co-authors subsequently received an automated notification from the Frontiers in Pharmacology editorial office that their manuscript had been “withdrawn” and “is no longer under consideration for publication in this journal.” The publisher refunded the authors’ payment, and removed the abstract from its website.
A spokesperson for Frontiers confirmed that the journal had “temporarily withdrawn the article from the publication process pending the outcome of the legal proceedings currently taking place in India.”
The spokesperson continued:
We have explained this in writing to Dr Philips, who agreed with our decision. We have also informed Dr Philips that we are happy to reexamine this position once the legal proceedings are concluded.
A representative from Himalaya told us “the matter is sub judice,” meaning under consideration in court and not supposed to be discussed publicly. “Based on a Court’s direction the paper was withdrawn.”
Philips was not available for comment. Arif Hussain Theruvath, a researcher at Rajagiri Hospital and an author on the paper, said Philips “is currently prohibited by Karnataka Civil Court’s injunction orders from speaking on Himalaya Wellness company or their products, especially Liv.52.”
Theruvath, who provided documentation of Frontiers’ correspondence with the authors, told us:
There was no reason for Frontiers to hold publication or halt further proceedings on a scientifically accepted publication on [in response to] a “soft threat” based on misleading civil suit from the Ayurveda product manufacturer who had no right to extend the gag order towards scientific publications, rather than only Dr. Philips’ social media posts. …
This has been a disappointing decision from a scientific integrity and moral context for science, and medical scientists – that law and legal can be twisted in any manner to silence important scientific findings that have great impact on public health.
Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.
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As Retraction Watch recently reported, three of the top 10 philosophy journals in the highly influential Scopus database turned out to be fakes: Not only did these dubious journals manage to infiltrate the list, but they also rose to its top by trading citations. This news is embarrassing in itself, but it is hardly shocking. Our rankings-obsessed academic culture has proven time and again that it is prone to data manipulation. Rankings for both publications and institutions are routinely hacked by scholars, editors, and administrators who are ready to tweak or even falsify numbers as needed.
The problems with the Scopus journal rankings, however, run much deeper. The issue is not that inflated citation numbers have occasionally propelled impostor journals to the top of the list. Rather, at least in my own field of literary studies, the ranking makes no sense whatsoever: the list is full of journals that have no business being there at all because they belong to entirely different areas of scholarly enquiry, and even when the ranking gets the field right, it systematically places marginal publications close to the top. In what follows, I briefly break down the major ways the Scopus Literature and Literary Theory Ranking is not just skewed but downright nonsensical.
Scopus ranks journals based on SJR (SCImago Journal Rank), which it defines as a “measure of journal’s impact, influence or prestige.” The ranking includes a little over 1,000 titles, but for the purposes of this analysis I have focused mostly on the top 100. My main finding: the majority of journals in the upper part of the list quite simply do not belong to the fields of literature and literary theory.
The top 10 are particularly telling. Within that group is exactly one (!) journal – an annual publication dedicated to the work of the Spanish Golden Age dramatist Lope de Vega – that specializes in literature. Another two are wide-ranging humanities journals in which literary scholars do publish, although these also are highly idiosyncratic. The first is South Atlantic Quarterly, a long-standing journal dedicated to “urgent political, cultural, and social questions,” whose editorial board consists primarily of literary theorists, and the second is Journal of Cultural Analytics, a relatively new open-access publication “dedicated to the computational study of culture.”
The rest of the top 10 belong to translation studies (two), criminology (one), and writing studies (two); one is an interdisciplinary journal with a primary focus on sociology and gender studies, and one (Poetics) has been founded as a literary journal in the 1970s and continues to address issues related to literature (among other topics), but it does so from a distinctly sociological perspective. The editors are sociologists, who also make up the bulk of the contributors.
In short, Scopus’ list of top 10 literature journals includes one journal specializing in literature, two general humanities journals with some footing in literary studies, one journal that used to specialize in literature but no longer does, and six journals with absolutely no relation to literary studies.
RANK | JOURNAL TITLE | ACTUAL FIELD |
1 | Translation Spaces | Translation Studies |
2 | Criminology and Public Policy | Criminology |
3 | Anuario Lope de Vega | Literature |
4 | Journal of Writing Research | Writing studies |
5 | Men and Masculinities | Sociology |
6 | Perspectives: Studies in Translation Theory and Practice | Translation Studies |
7 | Poetics | Sociology of Culture |
8 | Writing Communication | Writing Studies |
9 | South Atlantic Quarterly | Interdisciplinary Humanities |
10 | Journal of Cultural Analytics | Digital Humanities |
Table 1. Top 10 journals in the Scopus Literature and Literary Theory Ranking
The situation becomes only slightly better when we analyze the top 100. In that cohort the number of journals belonging to the fields of literature and literary theory rises to somewhere between 35 and 45, depending on how one counts. However, even with that improvement, well over half of the titles on the list do not belong there. They belong to a range of different fields, including primarily language and linguistics, but also education, library science, anthropology, history, theology, and so on.
What accounts for this failure of most basic classification? One might assume that the creators of the list have simply lumped literature and some adjacent fields together: Although it is deeply frustrating to scholars who share little in terms of publication venues, research methodologies, and departmental affiliations, the use of joint categories that encompass fields like literature, linguistics, and writing is not unprecedented.
But Scopus seems to be doing something different. The database has a separate category for Language and Linguistics, and although some journals may publish in both fields (none of the remotely good ones do), many of those included in the Literature category are in fact pure linguistics journals, full stop. Besides, even if overlapping classifications can account for some of these intruders, one cannot justify the presence of journals like Performance Measurement and Metrics or Men and Masculinities on the list. No methodological choice, however dubious, can explain this ranking. One has to assume that those who created it simply couldn’t be bothered to properly attend to the task at hand.
To make things worse, even when we remove the noise created by the inclusion of journals from other fields and focus only on actual literature journals, the ranking’s ability to identify quality publications does not seem to improve. A look at the top 100 journals reveals that publications with no discernable international footprint systematically outrank highly selective world-leading venues. To use just one startling example, Malaysian pay-to-play publication 3L: Language, Linguistics, Literature (40th overall) far outranks almost every major literature journal published in the US and Europe, including such cutting-edge publications as PMLA (59th), English Literary History (110th), and Diacritics (415th).
Many other interesting quirks would require further scrutiny, such as the curious overrepresentation of journals published in Slovenian, a language with barely 2 million speakers, as well as the equally curious overrepresentation of journals focusing on the Spanish Golden Age, an important period in early modern literary history, but surely not one that could plausibly attract more high-quality scholarship than the entire fields of German and French literary studies, Comparative Literature, and Medieval Studies, all of which are completely absent from the top 100. And yet, here we are.
The Scopus ranking under the rubric of “Literature and Literary Theory” is many things but a meaningful ranking of journals in the field of literary studies, it is not. It contains scores of journals that have absolutely nothing to do with that particular field, and it routinely awards very high rankings to publications with no international relevance whatsoever. On what criteria, it is impossible to say. Unsurprisingly, most of the publications that are ranked highly in Scopus are not good enough to be included in Clarivate’s much more selective Arts & Humanities Citation Index. Some have made it into the less selective Emerging Sources Citation Index, but most are not picked up by Web of Science at all.
I wish I could offer some more constructive criticism, but such criticism would imply that the Scopus ranking, such as it is, has some redeeming features, which it does not. How do you improve a list that ranks Criminology and Public Policy as one of the top literature journals? That would be like taking seriously a list that treats Shakespeare Quarterly as a top journal in the field of chemical engineering. It would probably be easier to just start from scratch.
Of course, the biggest problem with Scopus is that, despite its profound unseriousness (at least in my field), it is generally taken seriously and produces real-world consequences. A tenure case at a major US research university is unlikely to hinge on a journal’s standing in Scopus, but in many parts of the world, especially in developing countries, administrators routinely rely on Scopus rankings as a proxy measure of research quality. And yet, in its existing form the ranking is not only an utterly inadequate tool for achieving that goal but may well be counterproductive given the sheer number of marginal journals on which it confers the veneer of respectability.
I don’t know what the situation in the sciences is, but in the humanities, Scopus must get its act together. Until then, its rankings will not be a serious indicator of journal quality.
Aleksandar Stević is assistant professor of English at Lingnan University in Hong Kong.
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