Current market rates for scholarly publishing services.

For decades, the supra-inflation increase of subscription prices for scholarly journals has concerned scholarly institutions. After years of fruitless efforts to solve this "serials crisis", open access has been proposed as the latest potential solution. However, the prices for open access publishing are also high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual costs of efficiently publishing a scholarly article using state-of-the-art technologies, such that informed decisions can be made as to appropriate price levels. Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large-scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative scholarly article today come to lie at around US$400. We discuss the additional non-publication items that make up the difference between publication costs and final price.

The orthopedic diseases of ancient Egypt.

BACKGROUND: CT scanning of ancient human remains has the potential to provide insights into health and diseases. While Egyptian mummies have undergone CT scans in prior studies, a systematic survey of the orthopedic conditions afflicting a group of these ancient individuals has never been carried out. METHODS: We performed whole body CT scanning on 52 ancient Egyptian mummies using technique comparable to that of medical imaging. All of the large joints and the spine were systematically examined and osteoarthritic (OA) changes were scored 0-4 using Kellgren and Lawrence classification. RESULTS: The cruciate ligaments and menisci could be identified frequently. There were much more frequent OA changes in the spine (25 mummies) than in the large joints (15 cases of acromioclavicular and/or glenohumeral joint OA changes, five involvement of the ankle, one in the elbow, four in the knee, and one in the hip). There were six cases of scoliosis. Individual mummies had the following conditions: juvenile aseptic necrosis of the hip (Perthes disease), stage 4 osteochondritis dissecans of the knee, vertebral compression fracture, lateral patella-femoral joint hyper-compression syndrome, severe rotator cuff arthropathy, rotator cuff impingement, hip pincer impingement, and combined fracture of the greater trochantor and vertebral bodies indicating obvious traumatic injury. This report includes the most ancient discovery of several of these syndromes. CONCLUSIONS: Ancient Egyptians often suffered painful orthopedic conditions. The high frequency of scoliosis merits further study. The pattern of degenerative changes in the spine and joints may offer insights into activity levels of these people.

Comparing sequences without using alignments: application to HIV/SIV subtyping.

BACKGROUND: In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. RESULTS: In this paper, HIV (Human Immunodeficiency Virus) and SIV (Simian Immunodeficiency Virus) sequence data are used to evaluate this method. The program produces tree topologies that are identical to those obtained by a combination of standard methods detailed in the HIV Sequence Compendium. Manual alignment editing is not necessary at any stage. Furthermore, only one user-specified parameter is needed for constructing trees. CONCLUSION: The extensive tests on HIV/SIV subtyping showed that the virus classifications produced by our method are in good agreement with our best taxonomic knowledge, even in non-coding LTR (Long Terminal Repeat) regions that are not tractable by regular alignment methods due to frequent duplications/insertions/deletions. Our method, however, is not limited to the HIV/SIV subtyping. It provides an alternative tree construction without a time-consuming aligning procedure.