Worth a Thousand Words: Mummy Dearest

Figure 1. Image of one of the corridors of the Catacombs.

Figure 1. Image of one of the corridors of the Catacombs.

Have humans always suffered from the same kinds of health issues? When we age, do we experience the same aches and pains as our ancestors? Did our joints become stiff and painful back in the 1700s, just like they still do today? Researchers in Germany and Italy posed this question and attempted to answer it by scanning the hip bones of Sicilian friars from the 18th and 19th centuries. They looked for markers of osteoarthritis in the mummified remains of these former clergymen, and have now concluded that a specific type of bone marker, herniation pits on the femoral neck, should be considered when scientists examine remains for signs of that ailment. The results are published in this paper, “Herniation Pits in Human Mummies: A CT Investigation in the Capuchin Catacombs of Palermo, Sicily.” You can see a larger version of the image here.


Herniation pits (HPs) of the femoral neck were first described in a radiological publication in 1982 as round to oval radiolucencies in the proximal superior quadrant of the femoral neck on anteroposterior radiographs of adults. In following early clinical publications, HPs were generally recognized as an incidental finding. In contrast, in current clinical literature they are mentioned in the context of femoroacetabular impingement (FAI) of the hip joint, which is known to cause osteoarthritis (OA). The significance of HPs in chronic skeletal disorders such as OA is still unclear, but they are discussed as a possible radiological indicator for FAI in a large part of clinical studies.

In this paleoradiological study we examined a sample of mummies from the Capuchin Catacombs of Palermo, Sicily, by a mobile computed tomography (CT) scanner. Evaluation of the CT examinations revealed HPs in six out of 16 (37.5%) adult male mummies.

The first aim of this study was to compare the characteristics of HPs shown in our mummy collection to the findings described in clinical literature. Thereby CT evaluation revealed that their osseous imaging characteristics are in accordance, consisting of round to oval subcortical lesions at the anterior femoral neck, clearly demarcated by a sclerotic margin.

The second aim was to introduce HPs to the paleoradiological and paleopathological methodology as an entity that underwent a renaissance from an incidental finding to a possible radiological indicator of FAI in the clinical situation. As FAI plays an important role in the development of OA of the hip, which is a very common finding in human skeletal remains, HPs should always be considered in paleoradiological evaluation of hip joint diseases.

Citation: Panzer S, Piombino-Mascali D, Zink AR (2012) Herniation Pits in Human Mummies: A CT Investigation in the Capuchin Catacombs of Palermo, Sicily. PLoS ONE 7(5): e36537. doi:10.1371/journal.pone.0036537

Ask everyONE: Why does my corrected article show up twice in PubMed?

After my paper was published, I discovered an error and contacted PLoS ONE to have it fixed. Now my paper shows up twice in PubMed. Is this a mistake?

If your paper had a formal correction, then this is not a mistake: your paper will be listed on PubMed twice.


In short: it’s because the formal correction counts as a different publication. On the PLoS ONE journal site, the correction of the error will be integrated into the original article and this correction will be announced via text in a red box at the top of the article page; however, in PubMed, the original article and the corrected are listed separately.

In more detail: if a published paper contains a major error, we issue a formal correction to fix that error, and the formal correction has its own DOI, or Date of Original Issue, from PLoS ONE.  The formal correction then receives its own, separate entry in PubMed in order to link to the original document. The corrected entry will contain the word “correction” in its title, while the original will not. PubMed mandates that the original and the correction must both be entered in its database, as you can see here.

Please note that your corrected paper will show up only once in PMC (PubMed central), because the correction will be embedded in the PMC entry.

If you discover an error after publication and you feel that it’s important that your paper be listed only once in PubMed, you have two options. First, you can request that PLoS issue a minor correction, which will appear only on the manuscript page and not on PubMed; alternatively, you can request a republication, although this option is only available to you if you catch the error 48 hours or less after the date of publication in PLoS ONE. An important proviso: it’s ultimately up to the PLoS Publication department to decide what type of correction to issue, so please understand that while we will do our best to accommodate your requests, we’ll also need to keep journal policies and procedures in mind.

As you can see, the corrections process is a little on the complex side, even if you have a PhD like many members of the PLoS community do! Since PLoS ONE doesn’t have an author proofing step, let me put in a plug here to remind you to double-, triple-, and quadruple-check your paper before you approve it for publication.

Submitting your Manuscript: Artwork Quality Failure

I’m trying to submit my manuscript, but when I follow the prompt to check my Artwork Quality results after I build my PDF, I see a “Fail” message. What happened?

First of all, don’t panic! We know you spent a long time putting your manuscript file together. Don’t worry, you won’t lose any of that time.

Next, check to make sure you’ve followed the Figure & Table Guidelines. In short, your figures should be in .TIF or .EPS format, and should be under 10MB each.

If your figures are in the correct format and are less than 10MB each in size, and the figures are visible, clear, and readable in your merged PDF, you can override the error message. For the editorial (pre-publication) process, the most important thing is that the Academic Editor and reviewers can see your figures. Once accepted, our Production team will be able to assist you with making any minor but changes to your figures.

However, please be advised that PLoS ONE does not have an author proofing step: you won’t be able to view the pre-publication formatted proof of the paper after it’s accepted but before it is published, so your paper should be as close to publishable as possible in every other respect.

Worth a thousand words: ¡Felices Fiestas! from Mexico’s deepest lake

Image showing Lake Alchichica's Stromatolites

Happy holidays from Lake Alchichica!

In addition to holding the title for deepest natural lake in Mexico, Lake Alchichica can also claim some other unique titles. It’s the largest of the lakes in Mexico’s crater-made Oriental Basin , for example, and also boasts the extremely high pH of 8.7-10.0.

The lake also has a remarkable amount of stromatolites, which are kind of stalagmites except they are made by microorganisms and they look like they are from another planet.

The authors of “Prokaryotic and Eukaryotic Community Structure in Field and Cultured Microbialites from the Alkaline Lake Alchichica (Mexico) ” investigated these stromatolites, looking specifically at why they tend to crop up in highly alkaline environments.

Also, please permit me a moment of holiday spirit here: doesn’t the schematic sort of look like half of an outer-space Christmas tree?

Here is what they found:


The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0–14 m depth) and long-term-maintained laboratory aquaria. Using small subunit (SSU) rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms.

Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia.

Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota), Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than in field samples, possibly due to more stable and favorable laboratory conditions. The maintenance of highly diverse natural microbialites in laboratory aquaria holds promise to study the role of different metabolisms in the formation of these structures under controlled conditions.

Worth a Thousand Words: Ancient soybeans from Japan

This image comes from the paper Archaeological Soybean (Glycine max) in East Asia: Does Size Matter?—which also includes a few other interesting photos of fossilized soybeans. The authors explain that their paper “critically reviews archaeological soybean size and its usefulness to understanding the relationship between people and soybean in East Asia.”

In addition to being interesting in and of itself, I think this paper demonstrates PLoS ONE’s breadth of scope. As the authors mention, tracking the domestication of what has come to be one of the world’s most important crops is an interdisciplinary endeavor, requiring input from physical and cultural anthropologists, evolutionary biologists, and taxonimists, among others. At PLoS ONE, they can all publish under one roof.

From the Abstract:

The recently acquired archaeological record for soybean from Japan, China and Korea is shedding light on the context in which this important economic plant became associated with people and was domesticated. This paper examines archaeological (charred) soybean seed size variation to determine what insight can be gained from a comprehensive comparison of 949 specimens from 22 sites. Seed length alone appears to represent seed size change through time, although the length×width×thickness product has the potential to provide better size change resolution. A widespread early association of small seeded soybean is as old as 9000–8600 cal BP in northern China and 7000 cal BP in Japan. Direct AMS radiocarbon dates on charred soybean seeds indicate selection resulted in large seed sizes in Japan by 5000 cal BP (Middle Jomon) and in Korea by 3000 cal BP (Early Mumun). Soybean seeds recovered in China from the Shang through Han periods are similar in length to the large Korean and Japanese specimens, but the overall size of the large Middle and Late Jomon, Early Mumun through Three Kingdom seeds is significantly larger than any of the Chinese specimens. The archaeological record appears to disconfirm the hypothesis of a single domestication of soybean and supports the view informed by recent phyologenetic research that soybean was domesticated in several locations in East Asia.

Citation: Lee G-A, Crawford GW, Liu L, Sasaki Y, Chen X (2011) Archaeological Soybean (Glycine max) in East Asia: Does Size Matter? PLoS ONE 6(11): e26720. doi:10.1371/journal.pone.0026720