UnEDXpected Peaks

Over the past couple of days, I have been reviewing a series of Materials Science papers, all co-authored by the same group of researchers from the Universities of Lahore, Chakwal, and Sargodha in Pakistan. While reviewing them, one analytical technique kept standing out for unusual reasons.

Materials Science

Materials science studies the composition and structure of materials and how these determine their properties. It uses a range of different techniques, such as Scanning Electron Microscopy (SEM) or Transmission Electron Microscopy (TEM) to look at the compounds, X-ray Diffraction (XRD) to identify crystal structures, and calorimetry to study phase transitions. Many of these techniques sit at the intersection of physics and chemistry.

Coming from a molecular biology/microbiology background, I am not very familiar with these techniques or with what the expected results should look like. I am much more used to looking at photos of blots, gels, or tissues, so in my past searches for science integrity concerns, I have not really focused on materials science papers.

That changed thanks to the efforts of Reese Richardson and several other science sleuths, who created the Collection of Open Science Integrity Guides (COSIG). The collection currently contains dozens of guides explaining how to examine scientific papers for problems in general, but also on how to find problems in specific methods or fields, including those in materials science or statistics. As one of their slogans says: “Anyone can do forensic metascience“. These guides have helped me identify problems across a much broader range of analytical methods.

One technique covered in the COSIG guides is one that often appears in materials science papers: Energy-dispersive X-ray spectroscopy. And, as we will see below, some papers will claim to have produced some unbelievable results.

Energy-dispersive X-ray spectroscopy

Energy-dispersive X-ray spectroscopy (EDX or EDS) is a technique used to determine which elements are present in a material. When a sample is struck by an electron beam, it emits X-rays with energies characteristic of specific elements, enabling researchers to identify and quantify the material’s composition. The resulting spectrum shows peaks at energies corresponding to those elements.

Each element emits X-rays at specific, known energies, so the peaks that appear in an EDX spectrum occur at predictable positions. For example, carbon (C) will have a peak at 0.28 keV, nitrogen (N) at 0.39 keV, and oxygen (O) at 0.52 keV. Some elements might have multiple peaks, such as iron (Fe), with peaks around 0.7, 6.4, and 7.1 keV.

Below is an EDX spectrum of the mineral crust from a shrimp, taken from Wikimedia. We see the expected C peak around 0.3 keV, the O peak at 0.5 keV, and the Fe peaks at the expected positions. The Ka and Kb values behind the element labels indicate the electron shell (K, L, or M). The a/alpha denote the drop of an electron from the adjacent shell (e.g., L to K), while b/beta is an electron dropping two shells (e.g., M to K).

Elemental Energy dispersive X-Ray microanalyses of the mineral crust of Rimicaris exoculata. Source: Wikimedia. Taken from: Corbari L et al., Biogeosciences (2008), DOI: 10.5194/bg-5-1295-2008

Common concerns with EDX plots

Several issues in EDX papers in scientific papers might indicate data alteration or fabrication.

As explained in the COSIG guide on EDX, the easiest problem to spot is the presence of peaks at unexpected positions. There is a useful look-up table from the Lawrence Berkeley National Laboratory. Even just remembering that the O peak should be around 0.5 keV and that C, N, and O, should appear in that order, is enough to find many problems. Also, the elements hydrogen (H) and helium (He) do not produce peaks in an EDX spectrum, so if you see those peaks in a published paper, that is another sign that the data might be made up.

A problematic set of papers from Pakistani researchers

Following up on a lead provided by another sleuth, I found more than 30 problematic papers [spreadsheet] by collaborating materials scientists from the Universities of Lahore, Chakwal, and Sargodha, published from 2016 to 2025. The papers have one author in common, Asif Mahmood, who held several Assistant and Associate Professor positions at the Universities of Lahore, Chakwal, and Rasul.

Professor Mahmood is currently listed at a Chairperson and Associate Professor at the Department of Pharmacy at Rasul University. While his Google Scholar profile still works, his ORCID account [pdf] appears to have been deactivated, and his ResearchGate page leads to a dead link.

His frequent co-authors are Rai Muhammad Sarfraz from the University of Sargodha, Hira Ijaz at Riphah International University, Nadiah Zafar at the University of Lahore, and Umaira Rehman at the University of Sargodha.

At least four papers by Asif Mahmood have been retracted [PubPeer posts here, here, here, and here], mostly for overlapping images. One of these retractions was covered by Retraction Watch.

Most of Mahmood et al.’s papers follow the same structure: synthesizing hydrogel nanocomposites for the oral delivery of certain drugs, then testing their physical and chemical features. The concerns in these papers vary from SEM photos found in multiple papers representing different studies, repetitive noise patterns in XRD plots, bar plots with identical error bars, to unrealistic EDX plots.

UnEDXpected EDX plots

Several EDX plots in these papers contain peaks at unexpected positions.

Here is a figure from Zafar et al., Saudi Pharmaceutical Journal (2023), where the O peak deviates from the expected 0.52 keV position, or even shows two peaks!

Source: Zafar et al., Saudi Pharmaceutical Journal (2023), DOI: 10.1016/j.jsps.2023.06.004 [PubPeer]

In Mahmood et al., J. Drug Delivery Sci Techn (2016), the peaks do not follow the expected C-N-O order. While the O peak is at the expected 0.52 keV, the C peak jumps around from the correct position at 0.28 keV to an impossible 1.8 keV in the bottom plot. Hydrogen (H) does not produce an X-ray peak, so the H peaks indicated at 2.6 keV in panel A or at 0 keV in panels B or C are quite unexpected.

Source: Mahmood et al., J. Drug Del Sci Techn (2016), DOI: 10.1016/j.jddst.2016.09.005, [PubPeer]

This Hussain et al. paper published in Int J Biol Macromolecules (2022), has similar problems in its EDX plots, as shown below. The right plot shows C, N, and O peaks, but in the wrong order, the O peaks bounce around from 0.5 to 0.9 keV, and the peaks have a strange blocky appearance.

Source: Hussain et al., Int J Biol Macromol (2022), DOI: 10.1016/j.ijbiomac.2022.01.064, [PubPeer]

Six papers by Mahmood et al. describing various hydrogel materials for drug release unexpectedly contain very similar, wonky EDX plots. Note the incorrect order of C-N-O, overhanging peaks, and the same wavy lines on the right of the left and middle plots.

EDX plots from six different papers display unexpected similar features. DOI: Batool et al. (2022) DOI: 10.3390/gels8030190 [PubPeer]  – Batool et al. (2023), RETRACTED, DOI: 10.3390/gels9010060 [PubPeer] – Ayesha Mahmood et al., Polymer Bulletin (2023), DOI: 10.1007/s00289-022-04401-0 [PubPeer] – Saba Arshad et al., Polymer Bulletin (2024), DOI: 10.1007/s00289-024-05167-3 [PubPeer] – Kanza Shafiq et al., Pharmaceuticals 2022, DOI: 10.3390/ph15121527 [PubPeer] – Fatima Noor et al., Journal of Drug Delivery Science and Technology (2023), DOI: 10.1016/j.jddst.2023.104924 [PubPeer]

The EDX plots in this paper by Malatani et al., Gels (2023), DOI: 10.3390/gels9030187 have another disorderly set of C-N-O peaks, the O is found at the incorrect values, and peaks have strange serrated ‘shoulders’.

Source: Malatani et al., Gels (2023), DOI: 10.3390/gels9030187 [PubPeer]

Even stranger EDX plots in this set were from Shabir et al., Polymer Bulletin (2025), DOI: 10.1007/s00289-025-05917-x [PubPeer]. The peaks in these EDX spectra look unexpectedly wobbly and serrated, with some peaks appearing to fall to the left. Some elemental peaks are at unexpected positions. For example, several peaks appear to have <0 (negative) values, which is unexpected. For example, the element Ca has expected peaks at 0.34, 3.7, and 4 keV, but these plots show peaks at >6 keV. Perhaps related to the incorrect peak positions is the unclear labeling of the X-axis, where the numbers 2, 4, and 6 do not always appear to correspond to a tick.

Souce: Shabir et al., Polymer Bulletin (2025), DOI: 10.1007/s00289-025-05917-x [PubPeer]

Perhaps the wonkiest EDX plot was found in Farya Shabir et al., Pharmaceutics (2023), DOI: 10.3390/pharmaceutics15010062. Although the peaks appear to be at the correct positions, they look like they were hand drawn after a couple too many Gin and Tonics.

Source: Farya Shabir et al., Pharmaceutics (2023), DOI: 10.3390/pharmaceutics15010062. [PubPeer]

Other problems:

The troubled EDX plots were not the only problem in this set of papers. Several papers contained X-ray diffraction (XRD) plots with unexpected duplicated noise and peaks.

Source: Sana Hanif et al., Journal of Drug Delivery Science and Technology 71 (2022); DOI: 10.1016/j.jddst.2022.103271 [PubPeer]

Here are four papers by Mahmood et al. in which several histology images appear to have been reused, even though the hydrogels described in each paper differ.

Four papers with duplicated or overlapping histology panels. Sources: Umaira Rehman et al., Gels 8 (2022), DOI: 10.3390/gels8120775 [PubPeer] –
Nighat Batool et al., Gels 8 (2022), DOI: 10.3390/gels8030190 [PubPeer] –
Nighat Batool et al. RETRACTED: J Biomed Mater Res. 2022; DOI: 10.1002/jbm.b.35016 [PubPeer] –
Nighat Batool et al., RETRACTED: Gels (2023), DOI: 10.3390/gels9010060 [PubPeer]

There were many more problems in this set – currently standing at 38 papers. See the complete list here: [spreadsheet]

Peer Review Congress Chicago – Day 3

Good morning from Chicago! We will start Day 3 (last day) of the 10th International Congress on Peer Review and Scientific Publication. @peerreviewcongress.bsky.social / peerreviewcongress.org/peer-review-… #PRC10 <— This hashtag will give you all the posts! You can also click on this feed, created by @retropz.bsky.social: bsky.app/profile/did:…

[Day 1] and [Day 2].

Continue reading “Peer Review Congress Chicago – Day 3”

Peer Review Congress Chicago – Day 2

[Day 1] [Day 3]

Good morning from Chicago, where we are getting ready for Day 2 of the 10th International Congress on Peer Review and Scientific Publication. peerreviewcongress.org / @peerreviewcongress.bsky.social / #PRC10

Continue reading “Peer Review Congress Chicago – Day 2”

Peer Review Congress Chicago – Day 1

It’s Peer Review Week! A perfect time to post my notes from the 10th International Congress on Peer Review and Scientific Publication, which was held at the Swissôtel in Chicago, two weeks ago, September 3-5, 2025.

This was my first time attending this congress. I tried to live-post all the talks on BlueSky [except for one session where I sneaked out].

You can find most posts about this conference under the hashtag #PRC10 on BlueSky or X. Andrew Porter @retropz.bsky.social, Research Integrity and Training Adviser at the Cancer Research UK Manchester Institute, created a BlueSky feed as well.

This post will contain (lightly edited) notes from Day 1. Click here to see the posts from [Day 2] and [Day 3].

Continue reading “Peer Review Congress Chicago – Day 1”

Discontinuous ridiculous stools – a preprint full of tortured phrases and stolen data

Patients with provocative entrail illness unclassified gave to crisis division a 3-day history of sickness, retching, migraine and irregular stomach torment alongside discontinuous ridiculous stools as of late.

If you cannot wrap your brain around this sentence, don’t worry. Neither can I.

A photo of a very ridiculous stool: a poop-emoji cake, with big white googly eyes and twisted candles on top. Taken at uBiome headquarters, March 2017.
Continue reading “Discontinuous ridiculous stools – a preprint full of tortured phrases and stolen data”

Preprint claiming that COVID-19 mRNA vaccines cause transcriptomic dysregulation is deeply flawed

Today, 25 July 2025, a preprint was posted claiming that significant gene expression changes were found in individuals with new-onset cancer and other diseases after receiving mRNA COVID-19 vaccines, compared to healthy individuals.

A preprint is a non-peer reviewed manuscript – a study or hypothesis that has not yet been evaluated by other scientists. These articles should always be read with caution. Preprints can be brilliant, misguided, or completely bonkers – but they have not been peer-reviewed.

So let’s take a closer look at this preprint.

Update, 12 September 2025: The preprint was withdrawn for “unresolved ethical issues concerning ethical oversight, legitimacy of institutional boards, validity of the study design, and potential biases in study interpretation that compromise the overall trust in the research findings.

Continue reading “Preprint claiming that COVID-19 mRNA vaccines cause transcriptomic dysregulation is deeply flawed”

Science Integrity Digest Summer 2025

It is hard to find the time to post here. I’m getting lots of requests to help scanning papers for image problems, and am also traveling a lot to give talks and be in panels. So my ‘monthly’ digests have now turned into quarterly digests, hahaha.

These past months, I have traveled to Berlin to receive the Einstein Foundation Award, to Oxford for the FAIRS Meeting, participated in a workshop in Stockholm organized by the Royal Swedish Academy of Sciences about the Reformation of Science Publishing, a conference in London at the Royal Society about the Future of Science Publishing, and a gathering with other science detectives and journalists in Krakow, Poland. In between, I gave several talks at research institutions and medical schools. I am getting pretty good at packing suitcases!

Here is a round-up of some noteworthy articles about research integrity.

Continue reading “Science Integrity Digest Summer 2025”

ScienceGuardians, where disgruntled authors complain about PubPeer

On Twitter/X, @SciGuardians, associated with the website ScienceGuardians.com, is promising to ‘uncover’ some big conspiracy of fraudulent @pubpeer.com users.

But in reality, the account appears to be run by one or more disgruntled scientists with dozens of problematic papers. And there is no big reveal.

Continue reading “ScienceGuardians, where disgruntled authors complain about PubPeer”

Science Integrity Digest – catching up

Apologies for not posting for a while. Fall 2024 was a busy time for me, with travel to give talks in Australia and Singapore and some events in the US. Instead of trying to catch up with everything that has happened since September, here are some highlights.

Einstein Foundation Award

I’m thrilled to have won the 2024 Einstein Foundation Award for Promoting Quality in Research. The Einstein Foundation Berlin selects three winners each year. The 2024 winners are:

  • Early Career Award: Helena Jambor and Christopher Schmied at PixelQuality – Best practices for publishing images. ‘PixelQuality has established guidelines and checklists for publishing clear and reproducible images. It now aims to disseminate and refine them to handle AI-assisted image generation and analysis.’ ‘Research images are the proof of scientific findings, not just visuals. PixelQuality has set new standards for their reproducibility and transparency.
  • Institutional Award: PubPeer – ‘PubPeer has become an essential part of the research communication landscape, with over 300,000 comments logged so far. It is estimated that since 2012, 19 percent of all retractions of papers worldwide in all academic domains had a prior discussion on the site. Beyond identifying flaws and fraud, PubPeer functions as an important tool to jointly improve scientific publications through „liquid feedback“.
  • Individual Award: Elisabeth Bik – ‘Elisabeth Bik’s work in uncovering manipulated images, fraudulent research data and publications has created enormous impact all over the world. Her work has led to heightened awareness of questionable research practices and generated widespread attention to responsible conduct of research in the scientific community.

The award ceremony will take place in March 2025 in Berlin, Germany.

The Einstein Foundation Award trophy is a piece of chalk, created by Professor Axel Kufus at the Berlin University of the Arts to honor ‘a basic tool that has been used to bring knowledge into the world for as long as we can remember’. Source: https://award.einsteinfoundation.de/about

The Bik Fund

Instead of accepting the Einstein Foundation award money for myself, I’ve decided to put it into ‘The Elisabeth Bik Science Integrity Fund’ – where I hope to help other science sleuths with small grants for e.g., traveling to conferences, buying equipment or software, or training. Our type of work often does not fit into the hypothesis-driven model of government or charity funds, so I hope to help by filling this funding gap.

The Bik Fund will be part of The Center For Scientific Integrity, Retraction Watch’s parent 501(c)3 non-profit organization.

It is my hope that we can make this fund grow, so we can help more integrity warriors in the future – donations to the Bik fund are tax-deductible and very welcome.

Press coverage:

Doctored

Charles Piller’s new book ‘Doctored – Fraud, Arrogance, and Tragedy in the Quest to Cure Alzheimer’s’ came out earlier this month.

The book describes how Matthew Schrag, a neuroscientist at Vanderbilt University and a fellow image-sleuth, discovered possibly altered images in a highly-cited paper about amyloid plaques in Alzheimer’s patients and in other papers connected to the biotech company Cassava Sciences (see also below). It also gives a disturbing insight into the amount of fraud in neuroscience and the lack of action by journals, institutions, and government agencies.

Matthew Schrag and other ‘science sleuths’—Kevin Patrick, Mu Yang, and I—worked for two years checking thousands of papers in Alzheimer’s research and related fields for the book, uncovering a concerning number of potential problems in papers by Sylvain Lesné, Berislav Zlokovic, Eliezer Masliah, and others.

Press coverage of Piller’s book:

Podcasts with Charles Piller and/or Matthew Schrag (there are many more!)

Charles Piller (right) and I at a book signing event for ‘Doctored’ – February 2025 at the Commonwealth Club in San Francisco, CA

Cassava Sciences Phase 3 did not work

I have written in the past (here and here) about problematic images in papers by Dr. Hoau-Yan Wang and Cassava Sciences (NASDAQ: $SAVA), a biotech company testing a drug targeting Alzheimer’s disease. These concerns were first spotted by Matthew Schrag and published in a Citizen Petition, in an attempt to halt Cassava’s clinical trials. Despite the apparent problems, the FDA did not stop Cassava’s clinical trials of their Alzheimer’s drug, Simufilam. But Cassava’s stock dropped significantly, upsetting a lot of investors.

For three years, fans of the $SAVA stock harassed the Dr. Wang critics – including me – claiming that the drug would work fine; that all stockholders would be rich as long as they would HODL; and that all our concerns were FUD. They joined forces in a SAVAges Discord app, where they talked about how one day they would all buy Maseratis, Lamborghinis, and even a SAVA island — and how retarded and fraudulent the SAVA-critics were.

The authorities begged to differ, however. In March 2024, Science reported that FDA inspectors had found many problems in Dr. Wang’s lab, ranging from uncalibrated instruments, lack of control samples, and stored data files, to leaving out outliers based on subjective criteria. Another report by the City University of New York (CUNY) to the Office of Research Integrity (ORI), leaked to Science, described ‘egregious misconduct’ in Dr. Wang’s lab. In June last year the Department of Justice announced that Professor Wang had been charged with operating a ‘Multimillion-Dollar Grant Fraud Scheme’.

Meanwhile, lawsuits were filed back-and-forth. Cassava Sciences was suing the people who filed the FDA citizen petition and who set up the website CassavaFraud.com, while stockholders were suing Cassava in a class-action lawsuit for misrepresenting the quality of the experiments performed by Dr. Wang. The Securities and Exchange Commission (SEC) charged Cassava with misrepresenting clinical trials result, and later settled for $40M. And CUNY, instead of officially announcing their misconduct findings, was investigating who leaked their misconduct investigation report to Science.

Finally, last December the biotech company announced that the Phase 3 trial did not meet the anticipated endpoints. In other words, Simufilam did not halt or improve Alzheimer’s disease. The Cassava Sciences stock immediately dropped to $2-3 dollars, and the SAVAges Discord became a valley of despair. No more SAVA island.

$SAVA stock price, last 5 years. Source: https://www.nasdaq.com/market-activity/stocks/sava

Didier Raoult enters the Retraction Watch Leaderboard

As I’ve written previously, many papers from Professor Didier Raoult, the former director of the IHU Méditerranée Infection in Marseille, France, are problematic.

Some appear to contain manipulated images, while others describe research conducted without proper ethical permits. A number of Raoult’s studies were performed on vulnerable populations, such as homeless people, or on study participants in the Global South, which I [gasp!] dared to label neocolonial science.

As described in this paper by Fabrice Frank et al, the IHU-MI produced a set of 248 studies all with the same IRB approval number, 09–022. Despite sharing the same permit, the publications varied in terms of sample type, demographics, and countries. Other ‘multi-use’ IRB numbers were found too. Typically, an IRB approves one particular study, and researchers are not allowed to reuse this permit for other, unrelated, studies. Dr. Raoult appears to have cared little for such rules, however.

After raising our concerns on PubPeer and social media, and also writing to journal editors, several journals have started to issue Expressions of Concern and retractions.

Fabrice Frank has generated a list of all IHU-MI papers with concerns – there are over 800!

In fact, Raoult has now earned so many retractions (32 as of today) that he has entered the Retraction Watch Leaderboard. The most significant of them is the retraction of the paper that claimed that Hydroxychloroquine could treat COVID-19. I criticized this paper in my blog post in April 2020, days after its publication. It took more than four years to get it retracted.

With over 600 of his papers on PubPeer and 225 EoCs, it seems safe to assume that for Raoult’s position on the Retraction Watch Leaderboard list, the only way is up.

Artist: Sara Gironi Carnevale. Source: https://www.science.org/content/article/failure-every-level-how-science-sleuths-exposed-massive-ethics-violations-famed-french

Science Integrity Digest, September 2024

An overview of general news and articles about science integrity and some cases that I have worked on.

Science sleuths

Neuroscientist and top NIH official under scrutiny

Q-Collar under scrutiny

Nobel prize winner under scrutiny

Paper Mills

New ORI regulations

The US Office of Research Integrity updated its regulations on handling research misconduct allegations. Key updates include clarifying the inquiry process and adjusting how institutions should handle the allegations and record the process.

1 in 7 scientific articles might be fake

James Heathers published a preprint arguing that the old, often-cited number that 2% of papers are fake is outdated and a vast underestimate. In a new preprint, he argues it might be 1 in 7 papers, based on 12 studies that together analyze 75,000 scientific articles.

Francesca Gino lawsuit

Around the world

New Publication and Editorials

Retraction Watch’s Weekend Reads: