last updated by Pluto on 2025-03-26 08:22:21 UTC on behalf of the NeuroFedora SIG.
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in For Better Science on 2025-03-26 06:00:00 UTC.
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in The Transmitter on 2025-03-26 04:00:47 UTC.
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Clicklike noises made by a small species of shark represent the first instance of a shark actively producing sound
in Scientific American on 2025-03-25 23:00:00 UTC.
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The bankruptcy of 23andMe highlights a lack of protections for genetic privacy in the U.S.
in Scientific American on 2025-03-25 20:10:00 UTC.
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in Women in Neuroscience UK on 2025-03-25 19:42:06 UTC.
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in The Transmitter on 2025-03-25 19:05:33 UTC.
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Supersymmetry, long considered the golden child of theoretical physics, has officially lost its luster at the world’s reigning particle accelerator
in Scientific American on 2025-03-25 16:00:00 UTC.
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MRI scans show that the brains of infants and toddlers can encode memories, even if we don’t remember them as adults
in Scientific American on 2025-03-25 15:30:00 UTC.
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Over the course of 18 months, we are working on an ambitious new project to Redefine Publishing. Working with stakeholders from across scholarly communications, we aim to go beyond the traditional research article to address two systemic barriers to open science: a lack of recognition for all research outputs, and the economic costs that prevent broader participation.
The first of four stakeholder convenings brought together institutional leadership, early career researchers, and open science organizations to discuss open science and academic incentives, and took place last month in Washington D.C. We heard from different perspectives on the need for better recognition of all contributions to science which aren’t captured when research articles remain the central measure of academic merit – for research funding, and researcher career advancement. What emerged from our talks was consensus around the following three points:
1. We need to change how science is evaluated.
Participants shared concerns over the use of “false metrics”, such as journal prestige and publication counts, which constrain how scientists actually do their work.
2. Researchers should be recognized for all research outputs and results.
Traditional incentives, they explained, overlook many vital contributions to research, from datasets, code, and protocols to preregistrations.
3. Contributions that are not research outputs also deserve recognition.
Participants also pointed to the value of non-research outputs, such as engaging with society, and mentorship.ll
So where do we start?
To understand how we can design new solutions for open science, we have to consider the incentive systems which drive current ways of working. Recognition for diverse contributions to science is critical to driving systemic change in how research is funded, assessed, and rewarded.
It isn’t enough to create technology solutions or implement policies to improve open science behaviors, as we’ve seen in our continued monitoring of open science practices. To accelerate the uptake of open science, researchers must be appropriately rewarded.
Attendees emphasized that credit must begin before an article is published and continue well beyond it. This approach could reward risk-taking, failures, mentorship, and peer review, as well as promote the re-use of scientific outputs.
Moving from the article to a full “knowledge stack”
The inspiration for our work is to shift beyond research articles to a new model for publishing. We invited participants to explore our initial concept for a “knowledge stack”. Under this model, we aim to publish, showcase, and credit all the key elements of research, incentivizing openness at every step and fostering a culture where sharing is not just encouraged but recognized and rewarded.
As a publisher, we can’t drive change on our own. But we can deliver a piece of the solution, and we’re committed to doing exactly that. To help validate what we have heard so far, we will continue to engage with funders, institutions, researchers, librarians, and infrastructure providers, in the coming months to refine and test the knowledge stack design. We want to hear from every part of the community, in every region that PLOS serves to understand your challenges, motivations, and aspirations. Your feedback can help shape our thinking and deliver something that truly works.
Contact us to take part in user panel research, get involved in stakeholder feedback, or stay up to date on our progress.
The post Why we need to go ‘beyond the article’ to transform research appeared first on The Official PLOS Blog.
in The Official PLOS Blog on 2025-03-25 14:54:47 UTC.
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Have you seen something inexplicable in the sky? Jon Kosloski, director of the U.S. Department of Defense’s All-Domain Anomaly Resolution Office, wants to hear from you
in Scientific American on 2025-03-25 13:30:00 UTC.
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Too few people get diagnosed and treated for postpartum depression. But a blood test could change that
in Scientific American on 2025-03-25 13:00:00 UTC.
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On this week's Journal Club session, Shamim Ibne Shahid will talk about his review paper "Detecting Anxiety via Machine Learning Algorithms: A Literature Review".
Recent machine learning (ML) advances have opened up new possibilities for addressing various challenges. Given their ability to tackle complex problems, the use of ML algorithms in diagnosing mental health disorders has seen substantial growth in both the number and scope of studies. Anxiety, a major health concern in today's world, affects a significant portion of the population. Individuals with anxiety often exhibit distinct characteristics compared to those without the disorder. These differences can be observed in their outward appearance—such as voice, facial expressions, gestures, and movements—and in less visible factors like heart rate, blood test results, and brain imaging data. In this context, numerous studies have utilized ML algorithms to extract a diverse range of features from individuals with anxiety, aiming to build predictive models capable of accurately identifying those affected by the disorder. This paper performs a comprehensive literature review on the state-of-the-art studies that employ machine learning algorithms to identify anxiety. This paper aims to cover a wide range of studies and categorize them based on their methodologies and data types used.
Papers:
Date: 2025/03/28
Time: 14:00
Location: SP3011 & online
in UH Biocomputation group on 2025-03-25 12:28:32 UTC.
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in Science News: Health & Medicine on 2025-03-25 12:00:00 UTC.
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in OIST Japan on 2025-03-25 12:00:00 UTC.
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Measles is not a disease to take lightly—but it is also very preventable with vaccines
in Scientific American on 2025-03-25 12:00:00 UTC.
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Uncorrected errors in science and the unconscionable reluctance to correct them erodes trust in science, throws away taxpayer money, harms the public’s health and can kill innocent people
in Scientific American on 2025-03-25 11:30:00 UTC.
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Researchers have found an environmentally safer way to extract the lithium 6 needed to create fuel for nuclear fusion reactors. The new approach doesn’t require toxic mercury, as conventional methods do
in Scientific American on 2025-03-25 11:00:00 UTC.
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A riotous photography collection from a recent underwater mission off the coast of Chile shows new and fascinating deep-sea creatures—including a “mystery mollusk,” a bioluminescent jellyfish and a “sea pig”
in Scientific American on 2025-03-25 10:30:00 UTC.
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in The Transmitter on 2025-03-25 04:00:40 UTC.
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The detection of bird flu in a sheep is another sign that the H5N1 virus is adapting to hop to new hosts
in Scientific American on 2025-03-24 21:30:00 UTC.
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The Journal of Trauma and Acute Care Surgery has retracted a letter it published about a purportedly novel injury observed during the two deadly waves of pager explosions in Lebanon and Syria in 2024, reportedly linked to Israeli intelligence services.
The original letter, “‘Pager’s trauma’ as a new and destructive type of blast injuries,” published Dec. 26, 2024, had not been indexed by Clarivate’s Web of Science. It focused on the September 2024 attacks in Lebanon and Syria, which led to dozens of deaths and thousands of injuries among Hezbollah fighters and some civilians. The attacks were carried out by boobytrapping walkie-talkies and pagers with explosives and are widely believed to have been carried at the direction of Israeli authorities.
The new letter argued such injuries are novel, dubbing them “Pager’s trauma.”
The letter read:
It is necessary for international organizations to deal seriously with individuals, groups, and governments responsible for these terrible terrorist acts.
It added:
Iran can play a central role in the field of prevention, treatment, and rehabilitation of victims of such attacks in the region and even the world.
According to the retraction notice, issued by the journal’s editors and publisher February 10, a review conducted by senior editorial board members of the journal identified “significant issues” leading the journal to conclude that the findings are unreliable and not supported by scientific data.
Study coauthor Fathollah Ahmadpour, who works at the Trauma Research Center at the Baqiyatallah University of Medical Sciences in Tehran, did not respond to our request for comment. We also received no response from the journal’s editor-in-chief, Raul Coimbra, surgeon-in-chief of the Riverside University Health System Medical Center in California.
Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on X or Bluesky, like us on Facebook, follow us on LinkedIn, 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 2025-03-24 20:10:33 UTC.
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From job interviews to dating, we subconsciously judge one another based on sound quality when we interact digitally
in Scientific American on 2025-03-24 19:00:00 UTC.
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A previously undisclosed FEMA review could block disaster assistance to millions of undocumented people and deter legal immigrants from seeking help in extreme weather
in Scientific American on 2025-03-24 17:30:00 UTC.
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in Science News: Science & Society on 2025-03-24 17:00:00 UTC.
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Calcium imaging is used to record the activity of neurons in living animals. Often, these activity patterns are analyzed after the experiments to investigate how the brain works. Alternatively, it is also possible to extract the activity patterns in real time, decode them and control a device or computer with them. Such brain-computer-interface (BCI) or closed-loop paradigms have one important limiting factor: the delay between the neuronal activity and the control that this activity exerts over the device or computer.
For calcium imaging, this delay comprises the time to record the calcium images from the brain, but it is also limited by the slowness of calcium indicators. How are calcium indicators limiting such an online processing step in practice? And how is this limitation potentially mitigated by the family of GCaMP8 indicators, which have been shown to exhibit faster rise times than previous genetically indicators (<10 ms)?
We addressed this question using a supervised algorithm for spike inference (CASCADE), which extracts spiking information from calcium transients. We slightly redesigned the algorithm such that it only has access to a small fraction of the time after the time point of interest:
This modification of the algorithm was very simple since it is a simple 1D convolutional network, and we simply shifted the receptive field in time very slightly. The time defined in the scheme, which we call “integration time”, determines the delay for closed-loop application like BCI paradigms for calcium imaging. To achieve a very good performence in inferring the spiking activity from calcium signals, an integration time of 30-40 ms was required for GCaMP8 and 50-150 ms for GCaMP6.
The CASCADE models trained for online spike inference are available online on our GitHub repository. The model names are starting with an “Online”, are listed as usual in this text file, and can be used as any other CASCADE models. For example, you can perform spike inference with your normal CASCADE model, and then perform the same spike inference with an “online” model, which will give you an impression how well the model performs. The only difference is that the “online” model takes only a few time points from the future, while the regular CASCADE model uses typically 32 time points from the future.
What does “a few time points” mean? Let’s look at a model’s name to break this down, for example the model Online_model_30Hz_integration_100ms_smoothing_25ms_GCaMP8
. This model is trained for calcium imaging data acquired at 30 Hz with the calcium indicators GCaMP8 (the ground truth consisted of all GCaMP8 variants), with a smoothing of 25 ms. The crucial parameter is the integration
time, here indicated as 100ms. This means that the model uses 100 ms from the future, which is 3 frames for the 30 Hz model.
If you are not sure which model to select for your application, or if you need another pretrained model for online spike inference, just drop me an email or open an issue for the GitHub repository.
For more details about the analysis and how the best choice of integration time for online spike inference depends on the noise levels of the calcium imaging recordings or potentially also other conditions such as calcium indicator induction methods or temperature, check out our recent preprint, where we also analyzed several other aspects of spike inference with a specific focus on GCaMP8: Spike inference from calcium imaging data acquired with GCaMP8 indicators.
in Peter Rupprecht on 2025-03-24 15:12:18 UTC.
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in Science News: Health & Medicine on 2025-03-24 15:00:00 UTC.
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Programming devices with parental controls may seem daunting, but they can help parents ensure what their kids find on TV and the Internet is age-appropriate
in Scientific American on 2025-03-24 11:00:00 UTC.
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A test for abnormal fetal chromosomes can also detect maternal cancers—and physicians are struggling to incorporate that knowledge into routine care
in Scientific American on 2025-03-24 10:45:00 UTC.
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In this week’s news roundup, two NASA astronauts finally return to Earth after nine unexpected months in space, gray seals hold their breath for more than an hour, and penguin poop panics krill.
in Scientific American on 2025-03-24 10:00:00 UTC.
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in The Transmitter on 2025-03-24 04:00:23 UTC.
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Dear RW readers, can you spare $25?
The week at Retraction Watch featured:
Our list of retracted or withdrawn COVID-19 papers is up past 500. There are more than 57,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 300 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, follow us on X or Bluesky, like us on Facebook, follow us on LinkedIn, 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 2025-03-22 10:00:00 UTC.
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A calving iceberg exposed a region that never before had been seen by human eyes, revealing a vibrant, thriving ecosystem
in Scientific American on 2025-03-21 20:00:00 UTC.
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Two former professors and a former graduate student at Osaka Dental University in Japan reused images between three published articles, according to the findings of an institutional investigation.
The school released the findings of its investigation in January, with a full report in Japanese. The university has not responded to our request for comment.
According to a machine translation of the report, the university found former graduate student Helin Xing, former assistant professor Isao Yamawaki, and former associate professor Yoichiro Taguchi were involved in misconduct. A recent paper of Taguchi’s lists his affiliation as Matsumoto Dental University in Nagano, Japan. He and Xing have not responded to our requests for comment. We were not able to find a current affiliation or email address for Yamawaki.
The university said it could not confirm misconduct for the first paper, which appeared in Dove Press’ International Journal of Nanomedicine in 2014. The university’s regulations at the time did not require retaining experimental records, and they were not preserved, according to the report. Because images in the other two articles were identical to images in the 2014 paper, the university determined the data in the later papers were fabricated.
In 2021, the journal retracted the article, citing “alleged image duplication observed in several figures.” Anonymous users on PubPeer had posted about the alleged duplications earlier that year. The authors did not respond to the journal’s queries about the images, according to the notice. Xing was first author on the paper, on which Taguchi was a coauthor. The paper has been cited 55 times, according to Clarivate’s Web of Science.
The second paper in the university’s investigation appeared in 2015 in the Journal of Periodontology, a title of the American Academy of Periodontology. In August 2021, an anonymous user left a comment on PubPeer highlighting areas of similarity in two figures. The investigation report does not address these alleged duplications, only the images found to be identical to images from the 2014 paper, without specifying which figures. Xing was the first and corresponding author of the paper and conducted the experiment, according to the investigators. Because Taguchi supervised the research and could have verified the experimental results, the university found he was responsible for the paper’s content.
Osaka Dental University has asked for the journal to retract the paper, according to the report, but it remains unmarked. Effie Ioannidou, the editor in chief of the title, has not responded to our request for comment. The paper has been cited four times.
Yamawaki was the first author of the third paper investigators examined, which appeared in the Journal of Periodontal Research in 2017. The article has been cited 19 times.
Taguchi was the second and corresponding author, and requested its retraction, according to the report. The retraction notice, published in August 2024, cites the authors’ request and an investigation by the university “which determined that this article contains data that the first two authors had fabricated/falsified in Figures 1 and 5, respectively.” The publisher’s own investigation “confirmed duplication of previously published images,” the notice stated.
The university report attributed the misconduct to sloppy data management, a lack of awareness of research ethics, and inappropriate guidance from supervisors.
Yamawaki and Taguchi resigned voluntarily, according to the report.
Xing and Yamawaki received degrees in 2014 and 2017, respectively, and the titles of their dissertations are identical to those of the retracted articles on which they were the first authors.
Hat tip: lemonstoism, world fluctuation watch.
Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on X or Bluesky, like us on Facebook, follow us on LinkedIn, 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 2025-03-21 19:02:14 UTC.
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The Defense secretary aims to purge climate work from the Pentagon. But critics say his carve-out for weather resiliency misses the point
in Scientific American on 2025-03-21 16:15:00 UTC.
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About 20 people die every day in the U.S. after being hit by a car. To make walking safer, we need a big cultural shift in how we view pedestrian safety
in Scientific American on 2025-03-21 16:00:00 UTC.
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Experiments suggest an unusual magnetic material could help harness energy from Earth’s rotation. But not everyone is convinced
in Scientific American on 2025-03-21 15:45:00 UTC.
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in Science News: Psychology on 2025-03-21 14:30:00 UTC.
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in Science News: Health & Medicine on 2025-03-21 13:00:00 UTC.
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Most movies follow one of six emotional arcs. Which one sells the most tickets?
in Scientific American on 2025-03-21 13:00:00 UTC.
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There are two mutually exclusive holy grails of calcium imaging: First, recording from the highest number of neurons simultaneously. Second, detecting spike patterns with single-spike precision. This blog post focuses on the latter.
Many studies have claimed to demonstrate single-spike detection, but often only under specific conditions or for a subset of neurons. At the same time, nearly as many other studies have demonstrated that such single-spike detection is not possible under their respective conditions.
In our recent preprint, we’ve added systematic analyses based on ground truth recordings as our contributions to this debate. Specifically, we analyzed how single-spike detection depends on calcium indicators (GCaMP8s, GCaMP8m, GCaMP8f; GCaMP6f, GCaMP6m; XCaMP-Gf) and on the noise levels of the recordings.
What I particularly like about our approach is that it does not rely on arbitrary thresholds for false-positive vs. false-negative detections of action potentials. Instead, we trained a deep network (CASCADE) to predict spiking activity in general – optimizing for mean squared error loss when compared to ground truth spike rates.We then applied this network to individual single spike-related calcium transients, allowing us to quantify single-spike detection across calcium indicators and noise levels.
Without giving away all the details, I’ll say that I was pleasantly surprised by the performance of GCaMP8s and GCaMP8m! For the full analyses and more context, check out our preprint: Spike inference from calcium imaging data acquired with GCaMP8 indicators.
in Peter Rupprecht on 2025-03-21 12:55:13 UTC.
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President Donald Trump is threatening steep tariffs on virtually all imports. Here’s what that means and what economics research suggests would be the impact
in Scientific American on 2025-03-21 12:00:00 UTC.
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Defining the word “moon” is harder than you might think
in Scientific American on 2025-03-21 10:45:00 UTC.
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A neurosurgeon who has acted as a consultant for Severance explains the science behind the show’s brain-altering procedure—and whether it could ever become reality.
in Scientific American on 2025-03-21 10:00:00 UTC.
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in For Better Science on 2025-03-21 06:00:00 UTC.
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in The Transmitter on 2025-03-21 04:00:31 UTC.