Name: comparing bibliometric analysis using pubmed, scopus, and web of science databases
Uploaded: 2019-10-24T12:30:00
Description: Watch this Scientific Journal Video about Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases at JoVE.com

The authors would like to thank the Deanship of Scientific Research for its fund to support the video production for this study. The authors would also like to thank Dr. Aseel Zabin, Department of English Language and Literature, The University of Jordan for English language review of this study.

NOTE: The following are search methods and an example search for each method is provided. Note that the part related specifically to bibliometric analysis is also supplied.
1. PubMed
<ol>
	<li>Choose Advanced Search from PubMed homepage (www.ncbi.nlm.nih.gov/pubmed).</li>
	<li>Enter the desired search term in the search field. Choose the search terms from the medical subject heading (MeSH) database. The following example details how to assess research in &#34;cancer&#34;.
	<ol>
		<li>Open th...

<ol>
	<li>McGowan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PRESS+peer+review+of+electronic+search+strategies:+2015+guideline+statement.">PRESS peer review of electronic search strategies: 2015 guideline statement.</a> Journal of Clinical Epidemiology. 75, 40-46 (2016).</li><li>Hood, W., Wilson, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+literature+of+bibliometrics,+scientometrics,+and+informetrics.">The literature of bibliometrics, scientometrics, and informetrics.</a> Scientometrics. 52 (2), 291-314 (2001).</li><li>Bar-Ilan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Citations+to+the+Introduction+to+infometrics+indexed+by+WOS,+Scopus+and+Google+Scholar.">Citations to the Introduction to infometrics indexed by WOS, Scopus and Google Scholar.</a> Scientometrics. 82 (3), 495-506 (2010).</li><li>Boudry, C., Baudouin, C., Mouriaux, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=International+publication+trends+in+dry+eye+disease+research:+A+bibliometric+analysis.">International publication trends in dry eye disease research: A bibliometric analysis.</a> The Ocular Surface. 16 (1), 173-179 (2018).</li><li>Kulkarni, A. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparisons+of+citations+in+Web+of+Science,+Scopus,+and+Google+Scholar+for+articles+published+in+general+medical+journals.">Comparisons of citations in Web of Science, Scopus, and Google Scholar for articles published in general medical journals.</a> Journal of the American Medical Association. 302 (10), 1092-1096 (2009).</li><li>AlRyalat, S. A., Malkawi, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=International+Collaboration+and+Openness+in+Jordanian+Research+Output:+A+10-year+Publications+Feedback.">International Collaboration and Openness in Jordanian Research Output: A 10-year Publications Feedback.</a> Publishing Research Quarterly. 34 (2), 265-274 (2018).</li><li>Falagas, M. E., Karavasiou, A. I., Bliziotis, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estimates+of+global+research+productivity+in+virology.">Estimates of global research productivity in virology.</a> Journal of Medical Virology. 76 (2), 223-229 (2005).</li><li>Young, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The ALA glossary of library and information science. , (1983).</li><li>Broadus, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+a+definition+of+bibliometrics.">Toward a definition of bibliometrics.</a> Scientometrics. 12 (5-6), 373-379 (1987).</li><li>Falagas, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+PubMed,+Scopus,+web+of+science,+and+Google+scholar:+strengths+and+weaknesses.">Comparison of PubMed, Scopus, web of science, and Google scholar: strengths and weaknesses.</a> The FASEB Journal. 22 (2), 338-342 (2008).</li><li>Guz, A. N., Rushchitsky, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scopus:+A+system+for+the+evaluation+of+scientific+journals.">Scopus: A system for the evaluation of scientific journals.</a> International Applied Mechanics. 45 (4), 351 (2009).</li><li>Jacso, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=As+we+may+search-comparison+of+major+features+of+the+Web+of+Science,+Scopus,+and+Google+Scholar+citation-based+and+citation-enhanced+databases.">As we may search-comparison of major features of the Web of Science, Scopus, and Google Scholar citation-based and citation-enhanced databases.</a> CurrentScience. 89 (9), 1537-1547 (2005).</li><li>Li, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Citation+analysis:+Comparison+of+Web+of+Science,+Scopus,+Scifinder,+And+Google+Scholar.">Citation analysis: Comparison of Web of Science, Scopus, Scifinder, And Google Scholar.</a> Journal of Electronic Resources in Medical Libraries. 7 (3), 196-217 (2010).</li><li>Levine-Clark, M., Kraus, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Finding+chemistry+information+using+Google+Scholar:+a+comparison+with+Chemical+Abstracts+Service.">Finding chemistry information using Google Scholar: a comparison with Chemical Abstracts Service.</a> Science &amp; Technology Libraries. 27 (4), 3-17 (2007).</li><li>Gavel, Y., Iselid, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Web+of+Science+and+Scopus:+a+journal+title+overlap+study.">Web of Science and Scopus: a journal title overlap study.</a> Online Information Review. 32 (1), 8-21 (2008).</li><li>Harzing, A. W., Alakangas, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Google+Scholar,+Scopus+and+the+Web+of+Science:+a+longitudinal+and+cross-disciplinary+comparison.">Google Scholar, Scopus and the Web of Science: a longitudinal and cross-disciplinary comparison.</a> Scientometrics. 106 (2), 787-804 (2016).</li><li>Aghaei Chadegani, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> A comparison between two main academic literature collections: Web of Science and Scopus databases. , (2013).</li><li>Testa, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Thomson+Reuters+journal+selection+process.">The Thomson Reuters journal selection process.</a> Transnational Corporations Review. 1 (4), 59-66 (2009).</li><li>Burnham, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Scopus database: a review. 3 (1), 1 (2006).</li><li>Small, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualizing+science+by+citation+mapping.">Visualizing science by citation mapping.</a> Journal of the American society for Information Science and Technology. 50 (9), 799-813 (1999).</li><li>Cobo, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Science+mapping+software+tools:+Review,+analysis,+and+cooperative+study+among+tools.">Science mapping software tools: Review, analysis, and cooperative study among tools.</a> Journal of the American Society for Information Science and Technology. 62 (7), 1382-1402 (2011).</li><li>. Statistical Yearbook – 60th issue Available from: <a target="_blank" href="https://unstats.un.org/unsd/publications/statistical-yearbook/">https://unstats.un.org/unsd/publications/statistical-yearbook/</a> (2018)</li><li>Mongeon, P., Paul-Hus, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+journal+coverage+of+Web+of+Science+and+Scopus:+a+comparative+analysis.">The journal coverage of Web of Science and Scopus: a comparative analysis.</a> Scientometrics. 106 (1), 213-228 (2016).</li></ol>

In this study, the steps through which PubMed, Scopus, and Web of Science databases are used to perform a bibliometric analysis were provided. It was indicated that the friendliest and the easiest tool to use for bibliometric analysis services is Web of Science; however, its drawback is that its services are not available for free. PubMed is devoted for biomedical sciences and is affiliated with several other National Library of Medicine (NLM) tools that can help to optimize analysis of biomedical subjects. Medical Subje...

Classically, researchers have used literature databases to perform literature review for their studies1. Another use of these literature databases arose at the end of the 19th century, where researchers analyzed the body of literature, a use that has slowly grown since2. In the last few decades, digitizing literature and the formation of online literature databases provided an opportunity to researchers to analyze the body of literature and research performance easily and efficiently. An example would be analyzing the research performance for a document3, a subject4, a discipline5, a country6, or even a region in the world7. This type of analysis is known as bibliometric analysis. Heartsill Young defined bibliometric analysis as the use of statistical methods to analyze a body of literature to reveal historical development8. In other words, bibliometrics is the quantitative study of published units on the basis of citation and text analysis9.
Different databases are used to do bibliometric analysis and each database has different characteristics and can provide different services10. Currently, the most commonly used literature databases are the Web of Science and Scopus for almost all disciplines, both only available on a subscription basis11, and PubMed for biomedical and life sciences, a freely available database10. There is also Google Scholar, which might be an easy tool to handle, but it should not be used as a bibliometric analysis tool currently due to some deficiencies such as its unclear scope and coverage, its lack of citation analysis tools, and its inclusion of non-peer reviewed non-scientific contents12,13. Moreover, Google Scholar lacks the tools for performing advanced search and keyword optimization14.
Several previous studies have compared the features of the previously mentioned literature databases for literature review purposes3,5,10,12,13,15,16,17. However, in this study, the means by which PubMed, Scopus, and Web of Science databases are used to perform a bibliometric analysis will be provided, and the pros and cons for each of them will be compared. Bibliometric analysis can be used to analyze the research output in almost any discipline, so the target audience would be any researcher who intends to analyze publication trends. An example of analyzing a publication trend in Jordan as a country will be presented using each database. Jordan was chosen because doing a bibliometric analysis for a country (in contrast to a subject) is not very straightforward. In addition, Jordan, specifically, is poorly studied in a bibliometric way as it can be both an author name and a country name. We explain how to overcome such a challenge in the search.

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			<td style="width:123px;">clarivate</td>
			<td style="width:344px;">N/A</td>
			<td style="width:584px;">Web of Science provider, where the access was provided by the subscription made by the University of Jordan.</td>
		</tr>
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			<td height="40" style="height:40px;"></td>
			<td>Elsevier</td>
			<td>N/A</td>
			<td>Scopus provider, where the access was provided by the subscription made by the University of Jordan.</td>
		</tr>
	</tbody>
</table>

comparing bibliometric analysis using pubmed, scopus, and web of science databases

Literature databases (i.e., PubMed, Scopus, and Web of Science) differ in terms of their coverage, focus, and the tool they provide. PubMed focuses mainly on life sciences and biomedical disciplines, whereas Scopus and Web of Science are multidisciplinary. The protocol described in the current study was used to search for publications from Jordanian authors in the years 2013-2017. In this protocol, how to use each database to conduct this type of search is explained in detail. A Scopus search resulted in the highest number of documents (11,444 documents), followed by a Web of Science search (10,943 documents). PubMed resulted in a smaller number of documents due to its narrower scope and coverage (4,363 documents). The results also show a yearly trend in: (1) the number of publications, (2) the disciplines that have the most publications, (3) the countries of collaboration, and (4) the number of open access publications. In contrast, PubMed has a sophisticated keyword optimization service (i.e., Medical Subject Heading, or MeSH), while both Scopus and Web of Science provide search analysis tools that can produce representative figures. Finally, the features of each database are explained in detail and several indices that can be extracted using the search results are provided. This study provides a base for using literature databases for bibliometric analysis.

Results from PubMed search
A total of 4,363 documents were retrieved based on the search conducted in this study. Free full text was available for 1,767 documents (40.5%). In 2013, a total of 532 documents were published, 663 documents in 2014, 811 documents in 2015, 952 documents in 2016, and 1,405 documents in 2017.
The results reveal that 1,008 (23....

Watch this Scientific Journal Video about Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases at JoVE.com

Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases

Literature databases are commonly used to assess publications in a certain subject, discipline, country, or region of the world, a practice known as bibliometric analysis. The current protocol details how to use PubMed, Scopus, and Web of Science databases to do bibliometric analysis.

Literature databases (i.e., PubMed, Scopus, and Web of Science) differ in terms of their coverage, focus, and the tool they provide. PubMed focuses mainly ...

This method can help answer key questions in the bibliometric analysis field about the available search databases and how to choose the most appropriate one. The main advantage of this protocol is that it provides a step-by-step approach to using different databases so that any researcher can perform a bibliometric analysis successfully. To analyze Jordanian research output during a five-year period between January 1st, 2013, and December 31st, 2017, using PubMed, open the Advanced Search form and enter Jordan as the search term, specifying Affiliation as the search field.To exclude all documents authored by a researcher named Jordan from an affiliated country that is not Jordan, type Jordan in another field and select the field type Author. Select the NOT operator as the connector between the two fields, and click Search. Specify the publication dates from between January 1st, 2013, to December 31st, 2017, in the results window, and select Journal Article and Review from article types.To analyze the Jordanian research output during a five-year period between January 1st, 2013, and December 31st, 2017, using Scopus, open the Scopus website and enter the appropriate Elsevier login information. Next, enter Jordan as the search term, and specify Affiliation country as the search field. Limit the search duration from 2013 to 2017.Note that from 2013 means from January 1st, 2013, and to 2017 means to December 31st, 2017. Then, limit the document type to Article or Review, and click Search. To analyze the Jordanian research output during a five-year period between January 1st, 2013, and December 31st, 2017, using Web of Science, open the Web of Science website and log in with the appropriate Web of Science account information.Enter Jordan in the search field, and specify Address. Identify the duration of the search as between 2013 and 2017, and click Search. Restrict the search using the Article and Review filters, and select to analyze the results saved in the search history now or later.Then, indicate whether the results should be displayed in a table, a visual tree map, or bars. Here, the yearly trends in Jordanian publication during the five-year 2013 to 2017 interval according to the Scopus search and the Web of Science search are shown. According to the country of collaboration in the Scopus search, the United States of America is the most common country with which Jordanian researchers collaborate, followed by Saudi Arabia and the United Kingdom.According to the Web of Science search, the United States is the most common country with which Jordanians collaborate, followed by France and Austria. Of the 10 most common disciplines within which Jordanians have published, medicine is the most common, followed by engineering and the social sciences according to the Scopus search. According to the Web of Science search, of the 10 most common disciplines within which Jordanians have published, engineering, mathematics, and computer sciences are the top three.While attempting this protocol, it's important to remember to select the appropriate database before starting your analysis. For example, PubMed is devoted to biomedical sciences only. Following this protocol and after downloading the results in CSV format, additional analysis methods like a bibliometric mapping can be performed for spatial representation of the results.After its development, this protocol paved the way for researchers in all fields to explore the research trends in their disciplines easily and efficiently.

comparing-bibliometric-analysis-using-pubmed-scopus-web-science

Research

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Medicine

Quantitative Analysis of Cancer Metastasis using an Avian Embryo Model

During metastasis cancer cells disseminate from the primary tumor, invade into surrounding tissues, and spread to distant organs. Metastasis is a complex process that can involve many tissue types, span variable time periods, and often occur deep within organs, making it difficult to investigate and quantify. In addition, the efficacy of the metastatic process is influenced by multiple steps in the metastatic cascade making it difficult to evaluate the contribution of a single aspect of tumor cell behavior. As a consequence, metastasis assays are frequently performed in experimental animals to provide a necessarily realistic context in which to study metastasis. Unfortunately, these models are further complicated by their complex physiology. The chick embryo is a unique in vivo model that overcomes many limitations to studying metastasis, due to the accessibility of the chorioallantoic membrane (CAM), a well-vascularized extra-embryonic tissue located underneath the eggshell that is receptive to the xenografting of tumor cells (figure 1). Moreover, since the chick embryo is naturally immunodeficient, the CAM readily supports the engraftment of both normal and tumor tissues. Most importantly, the avian CAM successfully supports most cancer cell characteristics including growth, invasion, angiogenesis, and remodeling of the microenvironment. This makes the model exceptionally useful for the investigation of the pathways that lead to cancer metastasis and to predict the response of metastatic cancer to new potential therapeutics. The detection of disseminated cells by species-specific Alu PCR makes it possible to quantitatively assess metastasis in organs that are colonized by as few as 25 cells. Using the Human Epidermoid Carcinoma cell line (HEp3) we use this model to analyze spontaneous metastasis of cancer cells to distant organs, including the chick liver and lung. Furthermore, using the Alu-PCR protocol we demonstrate the sensitivity and reproducibility of the assay as a tool to analyze and quantitate intravasation, arrest, extravasation, and colonization as individual elements of metastasis.

Using quantitative PCR, we demonstrate how the well-established chick CAM model can be used to quantitatively analyze the metastasis of human tumor cells to distant organs.

During metastasis cancer cells disseminate from the primary tumor, invade into surrounding tissues, and spread to distant organs. Metastasis is a complex ...

Clinicopathological Analysis of miRNA Expression in Breast Cancer Tissues by Using miRNA In Situ Hybridization

In this article, we describe a detailed protocol for miRNA detection in breast cancer tissue using in situ hybridization with a digoxigenin-labelled LNA (Locked Nucleic Acid) probe. The probe was recognized by anti-DIG alkaline phosphatase antibodies and later developed using alkaline phosphatase substrate producing fluorescence signals. Here we utilized miRNA in situ hybridization (MISH) technique to analyze expression of miR-489 in tissues from breast cancer patients. This technique can detect the localization of miRNA of interest in individual tissue samples. This technique can be used to compare the expression of desired miRNA in tumor tissue with that in adjacent normal tissue and to identify the specific structures responsible for expressing this miRNA. This technique can be very useful in answering certain clinical questions, such as role of specific miRNA in the development of cancer. Our results indicate that mammary epithelial cells express significantly higher levels of miR-489 than adjacent tumor cells.

Clinicopathological Analysis of miRNA Expression in Breast Cancer Tissues by Using miRNA In Situ Hybridization

Here we present a protocol to detect miRNA expression in breast cancer patient samples using miRNA in situ hybridization.

In this article, we describe a detailed protocol for miRNA detection in breast cancer tissue using in situ hybridization with a digoxigenin-labelled LNA ...

Strategic Endothelial Cell Tube Formation Assay: Comparing Extracellular Matrix and Growth Factor Reduced Extracellular Matrix

Malignant tumors require a blood supply in order to survive and spread. These tumors obtain their needed blood from the patient's blood stream by hijacking the process of angiogenesis, in which new blood vessels are formed from existing blood vessels. The CXCR2 (chemokine (C-X-C motif) receptor 2) receptor is a transmembrane G-protein-linked molecule found in many cells that is closely associated with angiogenesis1. Specific blockade of the CXCR2 receptor inhibits angiogenesis, as measured by several assays such as the endothelial tube formation assay. The tube formation assay is useful for studying angiogenesis because it is an excellent method of studying the effects that any given compound or environmental condition may have on angiogenesis. It is a simple and quick in vitro assay that generates quantifiable data and requires relatively few components. Unlike in vivo assays, it does not require animals and can be carried out in less than two days. This protocol describes a variation of the extracellular matrix supporting endothelial tube formation assay, which tests the CXCR2 receptor.

This manuscript describes a tube formation assay to quantify the effects of a given compound or condition on angiogenesis by using endothelial cell tube formation in a controlled environment.

Malignant tumors require a blood supply in order to survive and spread. These tumors obtain their needed blood from the patient's blood stream by ...

Video Movement Analysis Using Smartphones (ViMAS): A Pilot Study

The use of smartphones in clinical practice is steadily increasing with the availability of low cost/freely available &#34;apps&#34; that could be used to assess human gait. The primary aim of this manuscript is to test the concurrent validity of kinematic measures recorded by a smartphone application in comparison to a 3D motion capture system in the sagittal plane. The secondary aim was to develop a protocol for clinicians on the set up of the smartphone camera for video movement analysis.
The sagittal plane knee angle was measured during heel strike and toe off events using the smart phone app and a 3D motion-capture system in 32 healthy subjects. Three trials were performed at near (2-m) and far (4-m) smartphone camera distances. The order of the distances was randomized. Regression analysis was performed to estimate the height of the camera based on either the subject&#39;s height or leg length.
Absolute measurement errors were least during toe off (3.12 &#177; 5.44 degrees) compared to heel strike (5.81 &#177; 5.26 degrees). There were significant (p &#60; 0.05) but moderate agreements between the application and 3D motion capture measures of knee angles. There were also no significant (p &#62; 0.05) differences between the absolute measurement errors between the two camera positions. The measurement errors averaged between 3 - 5 degrees during toe off and heel strike events of the gait cycle.
The use of smartphone apps can be a useful tool in the clinic for performing gait or human movement analysis. Further studies are needed to establish the accuracy in measuring movements of the upper extremity and trunk.

Video Movement Analysis Using Smartphones ViMAS: A Pilot Study

This manuscript describes the method to test the concurrent validity of kinematic measures recorded by the smartphone application in comparison to a 3D motion capture system in the sagittal plane. This protocol will enable clinicians to set up smartphones for video capture of human movement.

The use of smartphones in clinical practice is steadily increasing with the availability of low cost/freely available &#34;apps&#34; that could be used to ...

Comparing the Effects of Electronic Cigarette Vapor and Cigarette Smoke in a Novel In Vivo Exposure System

Electronic cigarettes (E-cigarettes) are being widely used, and growing in popularity. It is estimated that more than 9 million adults use them regularly. The potential adverse health effects of electronic cigarette vapor (E-vapor) exposure are poorly defined. While several animal models of E-vapor exposure have been developed, few models expose rodents to clinically relevant quantities of nicotine and make direct comparisons to cigarette smoke within the same exposure system. Here, we present a method for constructing and operating an E-vapor chamber and cigarette smoke chamber. The chambers are constructed by outfitting anesthesia chambers with a computer controlled pumping system that delivers consistent amounts of E-vapor or cigarette smoke to rodents. Nicotine exposure is measured indirectly by quantifying pre and post-exposure serum cotinine levels. This exposure system can be modified to accommodate various types of E-cigarettes&#160;and tobacco cigarettes, and can be used to compare the effects of E-vapor&#160;and cigarette smoke in vivo.

Comparing the Effects of Electronic Cigarette Vapor and Cigarette Smoke in a Novel In Vivo Exposure System

This protocol describes a method for exposing rodents to electronic cigarette vapor (E-vapor) and cigarette smoke. Exposure chambers are constructed by modifying anesthesia chambers with an automated pumping system that delivers E-vapor or cigarette smoke to rodents. This system can easily be modified to accommodate many experimental endpoints.

Electronic cigarettes (E-cigarettes) are being widely used, and growing in popularity. It is estimated that more than 9 million adults use them regularly. ...

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping&#160;(ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist.
The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist.
NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases.
One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form.

Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases

This study compares relational and non-relational (NoSQL) standardized medical information systems. The computational complexity of the response times of querying such database management systems (DBMS) is computed using doubling-sized databases. These results help the discussion of the appropriateness of each database approach to different scenarios and problems.

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query ...

'Boden Food Plate': Novel Interactive Web-based Method for the Assessment of Dietary Intake

Different methods can be used in research to assess dietary intake, many of which are still paper-based. Written estimated food diaries are often utilized in clinical trials, despite being a burden for both study participants and researchers. This method requires participant literacy, it is time consuming, labor intensive, and can easily lead to under-reporting. With advancements in technology, there is a growing interest in electronic diaries that automate the dietary assessment process. These are focused on improving accuracy, reducing both time and cost and providing users with a visual and more enjoyable experience. The methodology presented here aimed to validate the &#39;Boden Food Plate&#39;, a novel web-based platform for self-recording of food and drink items, compared to a traditional estimated food diary. The application was also rated on a satisfaction scale by study participants using a paper-based questionnaire. Sixty-seven participants completed the dietary measures on both the three-day electronic and paper food diaries. For the analysis, only dietary data completed at both study time points (baseline and week six) was utilized. Despite small mean differences between dietary data collection methods, Bland Altman analysis showed fairly wide 95% limits of agreement between the electronic platform and the written estimated food diary and there were few cases which did not fall within the 95% confidence intervals. Overall, participants found the electronic food diary to be more fun than the paper method and as easy to use as hard copy diaries. The new platform has potential as a self-recording tool for the collection of dietary data, particularly when utilized in clinical trial settings. However, further validation studies are needed to improve the validity of this novel electronic dietary data collection tool.

&#039;Boden Food Plate&#039;: Novel Interactive Web-based Method for the Assessment of Dietary Intake

The &#39;Boden Food Plate&#39; is an electronic food diary designed to be an interactive and fun method to collect dietary intake using visual depictions. The purpose of this study was to validate the web-based application against a traditional three-day estimated food diary method.

Different methods can be used in research to assess dietary intake, many of which are still paper-based. Written estimated food diaries are often utilized ...

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

Optical mapping is an established technique for high spatio-temporal resolution study of cardiac electrophysiology in multi-cellular preparations. Here we present, in a step-by-step guide, the use of ElectroMap for analysis, quantification, and mapping of high-resolution voltage and calcium datasets acquired by optical mapping. ElectroMap analysis options cover a wide variety of key electrophysiological parameters, and the graphical user interface allows straightforward modification of pre-processing and parameter definitions, making ElectroMap applicable to a wide range of experimental models. We show how built-in pacing frequency detection and signal segmentation allows high-throughput analysis of entire experimental recordings, acute responses, and single beat-to-beat variability. Additionally, ElectroMap incorporates automated multi-beat averaging to improve signal quality of noisy datasets, and here we demonstrate how this feature can help elucidate electrophysiological changes that might otherwise go undetected when using single beat analysis. Custom modules are included within the software for detailed investigation of conduction, single file analysis, and alternans, as demonstrated here. This software platform can be used to enable and accelerate the processing, analysis, and mapping of complex cardiac electrophysiology.

This protocol describes the setup and use of ElectroMap, a MATLAB-based open-source software platform for analysis of cardiac optical mapping data. ElectroMap provides a versatile high-throughput tool for analysis of optical mapping voltage and calcium datasets across a wide range of cardiac experimental models.

Optical mapping is an established technique for high spatio-temporal resolution study of cardiac electrophysiology in multi-cellular preparations. Here we ...

A Non-Invasive Method for Generating the Cyclic Loading-Induced Intra-Articular Cartilage Lesion Model of the Rat Knee

The pathophysiology of primary osteoarthritis (OA) remains unclear. However, a specific subclassification of OA in relatively younger age groups is likely correlated with a history of articular cartilage damage and ligament avulsion. Surgical animal models of OA of the knee play an important role in understanding the onset and progression of post-traumatic OA and aid in the development of novel therapies for this disease. However, non-surgical models have been recently considered to avoid traumatic inflammation that could affect the evaluation of the intervention. 
In this study, an intra-articular cartilage lesion rat model induced by in vivo cyclic compressive loading was developed, which allowed researchers to (1) determine the optimal magnitude, speed, and duration of load that could cause focal cartilage damage; (2) assess post-traumatic spatiotemporal pathological changes in chondrocyte vitality; and (3) evaluate the histological expression of destructive or protective molecules that are involved in the adaptation and repair mechanisms against joint compressive loads. This report describes the experimental protocol for this novel cartilage lesion in a rat model.

Here, we present the cyclic loading-induced intra-articular cartilage lesion model of the rat knee, generated by 60 cyclic compressions over 20 N, resulting in damage to the femoral condylar cartilage in rats.

The pathophysiology of primary osteoarthritis (OA) remains unclear. However, a specific subclassification of OA in relatively younger age groups is likely ...

Enhancing Radiotherapy with Web-Based Radiation Planning Assistant

Radiation Planning Assistant - A Web-based Tool to Support High-quality Radiotherapy in Clinics with Limited Resources

Access to radiotherapy worldwide is limited. The Radiation Planning Assistant (RPA) is a fully automated, web-based tool that is being developed to offer fully automated radiotherapy treatment planning tools to clinics with limited resources. The goal is to help clinical teams scale their efforts, thus reaching more patients with cancer. The user connects to the RPA via a webpage, completes a Service Request (prescription and information about the radiotherapy targets), and uploads the patient&#39;s CT image set. The RPA offers two approaches to automated planning. In one-step planning, the system uses the Service Request and CT scan to automatically generate the necessary contours and treatment plan. In two-step planning, the user reviews and edits the automatically generated contours before the RPA continues to generate a volume-modulated arc therapy plan. The final plan is downloaded from the RPA website and imported into the user&#39;s local treatment planning system, where the dose is recalculated for the locally commissioned linac; if necessary, the plan is edited prior to approval for clinical use.

Author Spotlight: Improving Radiation Therapy Access with Radiation Planning Assistant

This protocol describes a series of automated tools designed for high-quality radiotherapy autocontouring and autoplanning that are being packaged into a web-based service to maximize robustness and scalability while minimizing operational costs.

Access to radiotherapy worldwide is limited. The Radiation Planning Assistant (RPA) is a fully automated, web-based tool that is being developed to offer ...