The Role of P53 in Radiosensitivity, Cancer in Whales, and More

  • The advent of mining large datasets for cancer data made it possible to discern patterns shared by different cancer types. Therefore, providing an opportunity for applying the approaches proved to be successful in one type of cancer to another type based on the shared characteristics. The method is often used in predicting anti-cancer drug response. Researchers from the University of Michigan Rogel Cancer Center developed a visualization method aimed at improving anti-cancer drug response predictions “by teasing apart and allowing for simultaneous examination of differences across multiple cancer types as well as within individual types”. The method supports an evidence-based approach in making treatment decisions by considering both cancer type and individual variation within that cancer type. This research was published in PLOS Computation Biology.
  • An international team of scientists studied a novel approach to drug discovery, different from the traditional small molecule approach that target only some percentage of proteins active in causing the disease. The new method, aimed at battling the cancer cell drug resistance, “uses a family of human enzymes called ubiquitin ligases that exist in human cells”, which, potentially, can be guided to degrade and kill the disease-causing protein. The study was published in Nature.
  • As cancer radiation therapy efficiency depends on multiple factors, the scientists continue their efforts to understand the biology of tissues sensitivity to radiotherapy. The scientists from the Blavatnik Institute at Harvard Medical School, Massachusetts General Hospital and the Novartis Institutes for BioMedical Research focused their research on the role of a well-known tumor suppressor protein p53. It is long established that p53 is linked to the degree of a tissue’s sensitivity to radiation, but the exact nature of this connection was unknown. This new research found that post radiation exposure, tissues sensitive to radiation show persistent p53 signaling while more resistant tissues show just brief p53 activation. The researchers concluded that it is the dynamics of p53 signaling after radiation that is a factor in the tissues’ radiosensitivity. and not the excess of p53 protein in a tissue. The study was published in Nature Communications.
  • Cancer research is conducted not only in humans but in other species. Cancer research in animals may have potential implications for treating human cancers. In the new study, the international team of scientists focused on whales and the reasons for their low cancer rates. The scientists “used DNA sequencing to create a genetic map of whales’ tumor suppressor genes and those of 15 other mammal species”. This study that contributed to the knowledge of genetic mechanisms of tumor suppression in whales was published in Proceedings of the Royal Society.

Pubmed Prompts on Errors in your Searches

When conducting searches in Pubmed, a searcher may make errors, either by omission or by mistyping. In many cases (but not all) Pubmed alerts you to the error and helps you identify it.

When are you alerted to an error?

Sometimes, it happens that a searcher omits one of a pair of parentheses or double quotes, which may result in the search done not as you’ve intended and producing different results. If you made such an error, the “first line of defense” that Pubmed offers would be a message that appears right above the search results.

For example, your intended search strategy was: “lung carcinogenesis” AND (cell* OR molecular)
Instead, you typed “lung carcinogenesis AND cell* OR molecular). In that case you will see, right above the search results: The following terms were ignored: “, )

The “second line of defense” could be found in Advanced Search. Details next to your Query in Advanced Search always display how your Query, or the exact search strategy you entered in the search box, was “translated” by Pubmed, i.e. what was actually processed and searched upon. So, when trying to get more details about the error and the exact place in the search where the error has occurred (especially in the case of complex and lengthy search strategies) you can go to Advanced Search and look at the Details for the search Query in question. A red Warnings icon with an Exclamation Mark would alert you to the problems and by clicking the caret symbol next to it you will see the unmatched quotes and parentheses in red in the search you entered.

Another example: you are searching with the keyword “breast” in the title or abstract fields of the Pubmed record but instead of breast[tiab], where [tiab] is a combined title/abstract field, you mistyped it as breast[taib]. You will see the following message above the search results Unknown field was ignored: [taib] and in the Advanced Search>Details you will see more details related to how Pubmed “translated” your search strategy, as shown below:

In some cases, when you enclose a phrase in double quotes intending to find references that include exactly same phrase, Pubmed actually does not find such references despite the fact that some of them do exist. That’s because Pubmed does not index all phrases and in this it differs from other databases, such as Embase, Scopus, etc. For example, if you type “chemoradiotherapy side effect*” you will be alerted by Pubmed that Quoted phrase not found: “chemoradiotherapy side effect*”. In fact, such references may be present in Pubmed but the search for this exact phrase will be “translated” by Pubmed as a broader query. Pubmed would parse the phrase and search on its components combining them with a Boolean Operator “AND”, behind the scenes. The details of how it was done can be found in Advanced Search>Details.

When are you not alerted to an error?

There are some instances where your error by omission or mistyping may go undetected. If your search includes the Boolean operator “OR” and you omitted it in error, Pubmed will not alert you to it. That’s because a space (in place of the “OR” that you’ve omitted) is treated by Pubmed as a Boolean Operator “AND”. So, your search will produce totally different results, but the error will go unnoticed.

Also, if you mistyped but the term you entered in error is still a legitimate term Pubmed would not detect anything as incorrect. In the first example, if you omit an asterisk in the keyword cell*, where the asterisk was used for truncation, allowing retrieval of references with words with different endings (e.g. cell, cells, cellular), Pubmed will process the search without noticing your error as the noun cell is a legitimate term.

Of course, if you made an error not by omission or mistyping but because of the lack of expertise, e.g. you incorrectly used an “AND” operator or a space instead of an “OR” between the terms in the same category or synonyms, Pubmed will not detect this error either. The takeaway for minimizing the chance of making such an error is taking a Library Pubmed class or, if you feel that the search results are not what you expected, consulting a Research Informationist at the Memorial Sloan Kettering Cancer Center Library.

Changes Coming to Pubmed’s My NCBI Account Sign In

Experienced Pubmed users are enjoying the convenience of saving their search strategies and search results to their personal My NCBI accounts. We have promoted the use of these accounts and explained their features in previous blog posts.

In June 2021 the change will come to how the users log in to their personal My NCBI account. The National Library of Medicine stated its concern for user privacy as the reason for the coming change. The users will no longer be able to log in their My NCBI account with their “NCBI-managed credentials”, i.e. username and password they created specifically for MY NCBI account access.

The detailed instruction on how to change the way you log in to My NCBI using your linked accounts such as Google (your gmail credentials) and their credentials (called “federated account credentials”) can be found in the National Library of Medicine publication called NLM Technical Bulletin.

Once you have linked your account you can then log in to My NCBI using the linked account credentials. Click on Log In button in the right upper corner on the Pubmed page

and you will be prompted with a screen similar to the one below (depending on what account you would choose to link):

Enjoy using My NCBI!