Author Archives: Marina

Automated MeSH Indexing in PubMed

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This year the National Library of Medicine (NLM) is transitioning the process of MeSH indexing in PubMed from manual to automated.

MeSH (Medical Subject Headings) are assigned to MEDLINE citations for the purposes of enriching the metadata and increasing discoverability.

Until 2022 MeSH indexing was done by human indexers at the National Library of Medicine. Starting 2022 human indexers will only oversee and troubleshoot MeSH indexing.

One of the major benefits of automating the process of MeSH indexing is almost instant appearance of MeSH in MEDLINE citations in PubMed. With manual indexing this was delayed for a few months on average. Citations awaiting MeSH indexing were called In Process citations which could be found by keyword searches only.

The downside of automated MeSH indexing, at least in the beginning, could be, potentially, increase in indexing errors. The NLM will be engaged in the ongoing improvement of MeSH indexing algorithm.

Read more about the transition.

Tissue Regeneration Helping Cancer Spread, Viruses and Bacteria Working Together in Cancer Development and More

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  • Researchers at the Francis Crick Institute (U.K.) discovered that a process involved in regenerating tissue damaged by radiation could promote the spread of cancer. An animal experiment demonstrated that this was happening due to the signaling of immune cells called neutrophils which help repair tissue damage. The study was published in Nature Cancer.
  • It is well known that patients who develop cervical cancer are often infected not only with the human papillomavirus (HPV) but also simultaneously with the bacteria Chlamydia trachomatis. Researchers from Germany and the U.S. have proven that the two pathogens work together in a concerted effort to “reprogram” the infected cells so that they multiply uncontrollably. The study was published in Nature Communications.
  • The researchers at the University of Virginia and MD Anderson Cancer Center investigated the role of EP300 gene mutations in the development of small cell lung cancer (SLLC) and discovered, in preclinical experiments, that this gene makes a protein that acts as a tumor promoter and inhibitor. By stopping this protein from working as a tumor promoter, it is possible to prevent the formation and spread of SLCC. As EP300 mutations are frequently found in a wide range of cancers, targeting the EP300 has potential for treatments of more than one cancer type. The study was published in Science Advances.
  • Researchers from Germany, the United States, and the Netherlands explored in-depth programmed cell death, or apoptosis, processes. They found that the NOXA protein (a key proapoptotic factor) is being suppressed in aggressive forms of pancreatic cancer. The researchers aimed at identifying drug candidates that may promote NOXA’s cancer-fighting properties. By systematically testing substances in genetically altered cell lines, they identified one effective substance. The findings pave the way to new options in treating pancreatic cancer. The study was published in PNAS.
  • In a somewhat similar approach, researchers from Wellcome Sanger Institute (U.K.) and collaborators used systematic testing of combinations of already clinically relevant drugs along with analysis of genetic information and multi-omics techniques on cell lines. As a result, they created a new resource to predict effective cancer treatment combinations. The study was published in Nature.
  • Researchers from Australia established that two molecular pathways (Hippo/YAP and PI3K/mTOR) work together in cancer cells to promote fat metabolism that drives tumor growth. These findings may lead to new cancer therapeutics. The study was published in Developmental Cell.

Citation Number Limits in PubMed

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When handling search results in PubMed a user may encounter a situation when some operations are limited to a certain number of citations. While some users may think that, in practice, they will never need to deal with a very large number of citations, such situations do occur.

Below are instances when PubMed users will encounter a limit to the number of citations (and Pubmed messages alerting to that):

  • When browsing a lengthy list of search results or jumping to a page towards the end of a search results list (This site can display up to 10,000 results. Please see the User Guide for more information on navigating your search results.)
  • When saving citations to file (Only the first 10,000 citations will be saved in your file.)
  • When e-mailing your citations (Only the first 1,000 citations will be sent in your email. You will receive citations in multiple emails.)
  • When adding citations to a Collection in My NCBI account: (Only the first 1,000 citations will be added to collection.)
  • When sending citations to Clipboard (Only the first 500 items will be sent to clipboard.)

These problems can be addressed with the following options:

Other databases, such as Embase, CINAHL, Scopus, Web of Science, have similar, but not exactly the same maximums of the number of citations allowed for certain operations.