Author Archives: Marina

Navigating the Cochrane Library Content

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Cochrane library, a collection of databases containing high-quality evidence in healthcare, is produced by Cochrane collaboration.

Cochrane Library includes Cochrane Database of Systematic Reviews (CDSR), the Cochrane Central Register of Controlled Trials (CENTRAL), and Cochrane Clinical Answers.
Most heavily used databases are Database of Systematic Reviews and Central Register of Controlled Trials (CENTRAL) .

Finding Cochrane Reviews

Cochrane Systematic Reviews are produced by Cochrane Collaboration Review Group members who use explicit methodology “aimed at minimizing bias” and often viewed as the gold standard for conducting systematic reviews. This methodology is outlined in Cochrane Handbook. Researchers conducting systematic reviews outside of Cochrane collaboration can still use Cochrane methodology as a benchmark.

All current Cochrane Reviews can be found not just on the Cochrane Library itself, but via other databases as well, such as Pubmed and Embase. The biggest difference between searching within Cochrane Library compared to other databases, is that in Cochrane Library only the current or most recent review is retrieved in a search, whereas all versions can be located when searching PubMed or Embase (as seen in the example here). All Cochrane Reviews, including the superseded versions, can be found in Cochrane Library by browsing all issues of the CDSR.

Finding Central Register of Controlled Trials (CENTRAL) content

CENTRAL contains mostly RCTs (randomized controlled trials) which come from the outside sources, e.g. bibliographic databases such as Pubmed, Embase and CINAHL, unpublished sources, hand searching the literature, and web sources such as clinical trials.gov, World Health Organization.
Although trials ingested from Pubmed, Embase, CINAHL and select other sources can be found separately via those databases and websites, CENTRAL as a whole can be searched only via the Cochrane Library.

The advantage of finding controlled trials via bibliographic databases Pubmed, Embase or CINAHL separately lies in the use of the advanced functionality of those databases, all of which may not be available in the Cochrane Library original interface. Yet, since CENTRAL contains controlled trial records from other sources as well, it should be always searched by researchers conducting systematic reviews and meta-analyses, in addition to bibliographic databases.

Overcoming Resistance to Cancer Therapies, Nanomedicine and More

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Resistance to cancer therapy is one of the most challenging problems in oncology. Two recent papers report on new findings related to the phenomena of such resistance.

  • A UCSF team of researchers found that the presence of liver metastasis from any primary cancer causes resistance to immune checkpoint inhibitors therapy, specifically to anti–PD-1 immunotherapy. Using a mouse model, the scientists established a foundation for overcoming this resistance by combining anti-PD-1 with regulatory T cells targeting agents and thus restoring anti-PD-1 immunotherapy efficacy. The study was published in Science Immunology.
  • BRCA1/2 mutation-driven cancers, such as breast, ovarian, and prostate cancers, display high resistance to lifesaving therapies. Researchers from The University of Texas at Austin and Ajou University in South Korea identified a protein implicated in developing resistance to PARP inhibitors, a class of drugs that treat BRCA-deficient tumors. The study found that the low level of this protein, called PCAF, causes resistance to treatment with PARP inhibitors. The findings open the possibility of overcoming this resistance and increasing PARP inhibitors therapy’s effectiveness by combining them with a class of drugs called HDAC inhibitors, which boost PCAF. Research into PCAF protein, which has a role in chromatin modifications responsible for important DNA processes, contributes to the knowledge of cell replication and, therefore, to the understanding of disease pathophysiology. The study was published in Molecular Cell. 

In recent years, anti-cancer nanomedicine gained more and more ground. 

  • Researchers from two laboratories in Chicago conducted a recent study on nanotechnology that used charged nanoscale metal-organic frameworks (nMOFs) “for generating free radicals using X-rays within tumor tissue to kill cancer cells directly”. “Furthermore, the same frameworks can be used for delivering immune signaling molecules known as PAMPs to activate the immune response against tumor cells. By combining these two approaches into one easily administered “vaccine,” this new technology may provide the key to better local and systemic treatment of difficult-to-treat cancers”. This study was published in Science Advances. 
  • Yet another study on nanotechnology took a non-conventional approach to nanoparticle use. A research team from Singapore used a silica nanoparticle as a cancer drug, instead of a conventional drug carrier. The therapeutic nanoparticle caused cancer cells to self-destruct with the same efficiency as traditional cancer drug therapy in the lab mouse experiment. The researchers also “deceived” cancer cells, notoriously dependent on amino acids for their growth, by masking the therapeutic nanoparticle with an outer layer of amino acid L-phenylalanine. This research “may hold promise for the future design of nanotherapies” and “for cancer cells that have failed to respond to conventional treatment like chemotherapy.” The study was published in Small. 

More studies contributing to the knowledge of cancer biology were published recently.

  • Scientists from Rockefeller University in New York found that breast and lung tumor cancer cells can use blood vessels to gain access to a signaling pathway used by neurons. The tactics ultimately enable those cancers to metastasize. This research contributes to the knowledge of how cancers use or hijack normal cells and mechanisms to progress and establishes the foundation for new diagnostic and therapeutic approaches. The study was published in Nature. 

Browsing Search Results in PubMed

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When browsing your search results list in PubMed you have different options to help you navigate the list. They are related to the sort order of your search results, the format of records to view, and the ability to initially select references and put them aside to look at them closely later, as well as make changes to your selection(s). These options are explained below in more detail.

Changing Sort Order

You may change the default sort order of your search results depending on your search objective.

  1. If you need to find some most relevant articles quickly or your search topic is not time sensitive you may use Best Match sort order which is the PubMed default. Your most relevant search results (as determined by an internal algorithm) are found on the top of the results list and results may become less relevant as you go down the list. However, since there are no perfect algorithms, you may actually find the references you like most are not on the top but further down the results list.
  2. In other instances, you may want to see the most recent references at the top of your search results list, which is typical in most searches in the field of biomedicine. For that you will need to change the default. Click on the Display Option next to the Sort By in the right corner above the search results and change Best Match to Most Recent or Publication Date (with an arrow looking downward) from the drop down box.
  3. Sometimes you may prefer to see the oldest references first (when conducting a History of Medicine search, for example) and you may want to re-sort your results list in an ascending chronological order by clicking the Publication Date option with an upward arrow.

NOTE: Once you change the Sort By default, PubMed will remember your most recent selection and make it a default for you until you change it again. This may not work if you are on Virtual Desktop though.

Viewing Abstracts

You may also choose the format of references in your search results list.
If you want to browse the search results and read the abstracts at the same time you may do any of the following:

  1. Click on the articles’ titles to see the abstracts – one at a time
  2. Click on the Display Options and change the Format from Summary to Abstract to see the search results list in the abstract format

Displaying search results as a PMID list

New PubMed was enhanced with the new PubMed IDs display capabilities. You may display your search results as the list of PMIDs by clicking Display Options > Format > PMID. This will allow copying the PMID list to a document or e-mail and, when needed, restoring the references by pasting the PMIDs back in Pubmed search box and searching on them (see an older post on searching by PMIDs).

Sending to Clipboard

If you want to select references first and look at your selection in more detail later (such as if you are running multiple searches) use the Clipboard feature. Select (check mark) references when browsing the search results list; when done – click on Send To button above the search results and click Clipboard. You will be prompted to go to Clipboard immediately but you can do it any time before you shut down your computer – the moment you put something in Clipboard the Clipboard link appears under the PubMed search box.

In Clipboard, you may review your selected references again and make other choices, e.g. delete references from Clipboard. You also have the same options in Clipboard as in the search results list, e.g. you can send the references to your My NCBI account, or send to Citation Manager. Clipboard Details in Advanced Search (Clipboard is always the last line in the History and Search Details) are displayed as a PMID list.

NOTE: References will disappear from Clipboard after 8 hours of inactivity.