We have known for some time that vitamin D insufficiency is a risk factor for developing Multiple Sclerosis and we would like to know whether vitamin D levels influence the disease course of those who already have Multiple Slcerosis and what are the scientific articles dealing with the subject. This use case nis inspired by an article seen on ScienceDaily.

1. We first search for Low Vitamin D in novoseek. There are 8,916results in Pubmed and 3,714results in Free Full Text up to date.

2. We are interested in low Vitamin D Levels so we click on “Vitamin d” from the “Pharmacologicl Substances” category in sidebar to add it to the current search and make it more specific. We now have 4,584 results in Pubmed up to date.

3. Now, we need to look up for Multiple Sclerosis disease-related articles. In order to do so, we will check if it appears in the diseases category in the left sidebar. We need to click on the “more” link to see all the diseases related to the current search. Multiple Sclerosis diseases does not show up so we have to think of another search strategy.
4. The other way of searching for “multiple sclerosis”. It consists of typing in the search box: low vitamin d and “multiple sclerosis”. Typing the term “multiple sclerosis” between brackets will tell the system to look only for these two terms when they are mentioned together. We press search and we now have 61 results in Pubmed.

Note: in order to make the search even more specific and relevant, we can click on the “multiple sclerosis” filter that now appears at the top of the related concepts list in the Diseases category.
5. Last search term to be added to the current search consists of adding “children”. This will help us consult solely articles related to humans. You can either add and children in the search box or look in the sidebar where the category Organisms appears and add Homo Sapiens (showing up in 4th position) to the search. We now have 34 results in pubmed. 
   

Those articles found in a few steps in Pubmed are satisfactory and help start working on knowing if Low Vitamin D Levels Associated With Greater Risk of Relapse in Childhood Multiple Sclerosis.

There is one handy tool in novoseek that helps you create email alerts to keep updated and be notified of new papers in which may appear the query previously entered. Indeed, my novoseek users can easily create email alerts any of the searches they perform on novoseek biomedical search engine. These email alerts can be created after a search has been performed and they can be easily edited from your personal account on novoseek. There are a lot of possible uses: simple search for a biomedical concept (eg: a disease such as “asthma“), complex searches that require the use of filters and may require more time to achieve (eg: “Methacholine & Chronic obstructive pulmonary disease in Clinical Trial articles in Pubmed“), for a journal you are reading regularly (eg: “Journal of the American Geriatrics Society“) or for an author relevant in your field (eg: “Collins, Francis S.“).

1. First, save the search you have performed.

In order to create email alerts, you must first perform a search. When the search results are satisfying and you want to create an email alert accordingly, simply click the “save search and create alerts” button at top of results page. A box pops up and offers you to custom the name for this saved search and to save it.


If you haven’t signed up for a free account on my novoseek or aren’t yet connected, feel free to do so in a few clicks.
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2. After saving the search, novoseek offers you to create an email alert for this very search. Click the “create alert” button.

3. Adjust the sending parameters

You are taken to your personnal account on novoseek in the “alert details” category where you can fine tune the alert details.



The parameters allow you to receive email alerts as follows:

• Once a month, and specify on which day
• Once a week, and specify on which day
• Every Day
• The format: HTML or text
• The report format: Title, Short Fragment Text, Sentences or Abstract, depending on the amount of information you want to read in your inbox
• The number of items you want to read in every email alert
• Specify if you want to receive an email even if there is no new articles for your search query
• The corpus you want the articles to be searched in: Pubmed, Free Full Text or U.S. Grants





4. Create email alerts and managing them allow you to consult your existing alerts anytime and adjust their parameters from your personal account on novoseek.

Simply go to the My saved search and alerts panel on your account. From there, you can modify the names of your saved searches as well as adjusting parameters by clicking on the clock image .

Want more Tips to improve your searches in novoseek? Need more help? Just feel free to leave a comment below!

The Earth Day turns 40 this year. These idea and movement started over a diner, and they have now become a global action day which concern everybody. The Earth Day is a great opportunity to get involved in making the world better. This is as simple as planting a tree, riding a bus instead of your car, taking your kids to Disney’s last movie Oceans, install solar panel on your roof get a convection oven or tracking your energy usage online… I am sure that you will find what to do today on this special day. Beyond one’s involvement for Earth Day, there is all the scientific efforts that are made to improve life on Earth and face the new challenges on Earth. We thought it would be a good idea to share with you 10 Open Access (Free Full Text) articles interesting to read on the Earth Day 2010.

1. Air Pollution: Salt Mist Is the Right Seasoning for Ozone. by Portera Carol in Environmental Health Perspectives
   PMCID: 2453175
2. Room to Grow: Incentives Boost Energy-Efficient Homebuilding. by Schmidt, Charles W. on Environmental Health Perspectives
   PMCID: 2199292
3. Terra Cognita: Using Earth Observing Systems to Understand Our World. by Schmidt, Charles W. on Environmental Health Perspectives
   PMCID: 1277880
4. Cars, corporations, and commodities: Consequences for the social determinants of health by Woodcock, James and Alfred, Rachel in Emerging Themes in Epidemiology
   PMCID: 2289830, DOI: 10.1186/1742-7622-5-4
5. Perchlorate: Health Effects and Technologies for Its Removal from Water Resources. by Srinivasan, Asha and Viraraghavan, Thiruvenkatachari in International Journal of Environmental Research and Public Health
   PMCID: 2681191, DOI:10.3390/ijerph6041418
6. Indirect Potable Reuse: A Sustainable Water Supply Alternative. by Rodriguez, Clemencia; Van Buynder, Paul; Lugg, Richard; Blair, Palenque; Devine, Brian; Cook, Angus, and Weinstein, Philip; in International Journal of Environmental Research and Public Health
   PMCID: 2672392, DOI: 10.3390/ijerph6031174
7. Population policies, programmes and the environment. by Speidel, J. Joseph; Weiss, Deborah C.; Ethelston, Sally A., and Gilbert, Sarah M. in Philosophical Transactions of the Royal Society B: Biological Sciences
   PMCID: 2781834, DOI: 10.1098/rstb.2009.0162
8. The ecosystem-service chain and the biological spanersity crisis. by Mooney, Harold A. in Philosophical Transactions of the Royal Society B: Biological Sciences
   PMCID: 2842713, DOI: 10.1098/rstb.2009.0223e
9. Environmental Remediation and Conversion of Carbon Dioxide (CO2) into Useful Green Products by Accelerated Carbonation Technology. by Lim, Mihee; Han, Gi-Chun; Ahn, Ji-Whan, and You, Kwang-Suk in International Journal of Environmental Research and Public Health
   PMCID: 2819785, DOI: 10.3390/ijerph7010203
10. Is It Easy to Be Urban? Convergent Success in Urban Habitats among Lineages of a Widespread Native Ant. by Menke, Sean B.; Booth, Warren; Dunn, Robert R.; Schal, Coby; Vargo, Edward L., and Silverman, Jules 1 in PLoS ONE
    PMCID: 2820551, DOI: 10.1371/journal.pone.0009194
11. Development of a biomechanical energy harvester. by Li, Qingguo; Naing, Veronica; Donelan, J Maxwell; in Journal of NeuroEngineering and Rehabilitation
    PMCID: 2709631, DOI: 10.1186/1743-0003-6-22

These articles were found features of novoseek such as combinations of keywords, filters or advanced search. I also took good care to tag the articles in a “EarthDay” tag in my my novoseek account so I can retrieve them anytime as it is shown below.

Now tell us: What are your picks for 2010 Earth Day among novoseek’s Free Full Text articles? Share them with us!

Searching for relevant scientific articles in known to be a common task (more or less difficult depending on the searching knowledge and the tools used) for life sciences professionals. In fact, there are several web-based services, journals and/or paying (password-restricted) platforms to search from. It is often difficult to know the good search strategy (which platform, what keywords, what filters, etc) in the first place. You may find what you are looking for eventually, but you are desperate to fasten this process and make it easier and less resource-consuming. Even if most of us can ask a librarian (you will find valuable information and resources with these 10+1 medical librarians you should read) or have a Pubmed class, life science professionals need to improve their searches. Improving searches can be done through several ways: reading use cases, tips, using novoseek and, last but not least, knowing what kind of publication type you are looking for. Indeed, filtering a search in Pubmed database by one or several publication types will help you limit a large amount of search results and find what you need to read faster.

This list aims to help the life science professionals determine what the publication types correspond to and what they will allow them to find within the biomedical literature. We will put emphasis on the main and most common publication types you can find while searching for scientific articles in the biomedical literature. Each Publication Type is illustrated with an example on novoseek.

On top of that, we would like to present interesting facts as dealing with huge databases allow us to play around with figures and interpret them. For example, from the nearly 19 million articles available in Medline to date, nearly 97% are categorized as Journal Articles and more than 8% account for english abstracts. However, an article can be categorized in several publication types at the same time. The following image shows how the literature is categorized in publication types.

note:the publication types accounting for less of 2% are not shown in this graph and are gathered in the category “rest of publication types”.

• Clinical Trial


A Clinical Trial is a work that is the report of a pre-planned clinical study of the safety, efficacy, or optimum dosage schedule of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques in humans selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects.
Example: BRCA1 – Clinical Trial

• Comparative Study


A comparative study is a study in which a participant is randomly assigned to one of two or more different treatment groups for purposes of comparing the effects of the treatments.
Example: BRCA1 – Comparative Study

• Comment


A Comment is a work consisting of a critical or explanatory note written to discuss, support, or dispute an article or other presentation previously published. It may take the form of an article, letter, editorial, etc. It appears in publications under a variety of names: comment, commentary, editorial comment, viewpoint, etc.
Example: BRCA1 AND BRCA2 mutation – Comment

• Controlled Clinical Trial


A Controlled Clinical Trial is a work consisting of a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness.
Example: Sinusitis – Controlled Clinical Trial

• Consensus Development Conference


A Consensus Development Conference is a work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject.
Example: Asthma – Consensus Development Conference

• English Abstract


An English Abstract refers to publications that have been written in a language different from English and which abstracts and title have been translated to English for indexing reasons in NKM. When browsing results, you can notice the English Abstracts directly thanks to the bracket in the title.
Example: Asthma – English Abstract

• Evaluation Studies


An Evaluation Studies is a work consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
Example: Asthma – Evaluation Studies

• Guideline


A Guideline is a work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels.
Example: Asthma – Guideline

• Journal Article


Journal Articles are the predominant publication type for articles and other items indexed for NLM (National Library of Medicine) databases.
Example: BRCA1 – Journal Articles

• Meta-Analysis


Meta-Analysis are works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials.
Example: Asthma – Meta Analysis

• Multicenter Study


A Multicenter Study is a work consisting of a controlled study executed by several cooperating institutions.
Example: Asthma – Multicenter Study

• Practice Guideline


A Practice Guideline is a work consisting of a set of directions or principles to assist the health care practitioner with patient care decisions about appropriate diagnostic, therapeutic, or other clinical procedures for specific clinical circumstances. Practice guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels.
Example: Asthma – Practice Guideline

• Randomized Controlled Trial


A Randomized Controlled Trial (RCT) is a work consisting of a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.
Example: Asthma – Randomized Controlled Trial

For further information and benefits on RCT, I strongly recommend you to read the post “the best study for dummies” by Jacqueline Limpens.

• Research Support, NIH, Extramural


Research Support, NIH, Extramural, refers to publications of research resulting from extramural research funded by the National Institutes of Health.
Example: Asthma – Research Support, N.I.H., Extramural

• Review


A Review is an article or book published after examination of published material on a subject. It may be comprehensive to various degrees and the time range of material scrutinized may be broad or narrow, but the reviews most often desired are reviews of the current literature.
Example: Asthma – Review

• Validation Studies


A Validation Study is a work consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
Example: Asthma – Validation Studies

Regarding novoseek functionalities, it helps you filter by Publication Type easily as we explain in this TIP blogspot and you can refer to the following images to see where to filter by Publication Type when you are on the results page and where to identify the Publication Type when you are reading a publication on novoseek.

Resources: PubTypes, research, novoseek and insights from José Cristobal Buñuel .

This user case is inspired by a search tutorial for Pubmed (see page 61) brought to our knowledge by María, Medical Librarian from Torrevieja Hospital (Spain). We found it interesting to show how novoseek provides results as satisfactory as Pubmed in a simple and quick way.

1. We first search for « tamiflu » in novoseek.There are 840 results in pubmed and 144 in free full text to date.
   
2. Looking in the search details we notice that our search has been mapped to pharmacological substance « tamiflu ».
   Clicking on the the term tamiflu pops up a window with complementary information. This is handy to know the synonyms (alternative names) to Tamiflu : Oseltamivir phosphate , GS 4104 are some of them.

3. We need to look for influenza disease to keep building our search.Obviously, it should appear in the first relevant related concepts to the previous search. Indeed, it is the first related disease to the search Tamiflu. Clicking on it will add it directly to the current search (alternatively you can click on the « i » icon and click on « add filter » as shown on image). The search is now refined and we have gone from 840 results to 639 results in Pubmed.
   
   
   In this case, we are looking for Meta-Analysis publications. In science, “meta-analysis does more than just combine the effect sizes of a set of studies. It can test if the studies’ outcomes show more variation than the variation that is expected because of sampling different research participants” as explained in the Wikipedia. This should help us find publications showing the efficiency of Tamiflu to diminish the percentage of secondary complications.
4. We now need to select the publication type (or type or article).We click on the « bibliographics tab » and where publication type is, we click on the « more » button. Where « Meta Analysis » appears, we click on that term which is directly added to the current search. We now have gone from 639 results to 9 results in Pubmed.
   
   
5. The results are very satisfactory as they contain the same publications as in Pubmed. Should we need to look specifically for publication mentioning children, look for the filter “Homo Sapiens” in the related concepts tab on the left and add it to your search. We now have 5 results in Pubmed.
   • Check more User cases.
   • Check more Tips.


We can compare now these results to Pubmed’s and we notice that we have the 3 publications found in Pubmed in novoseek results. The advantage with novoseek is that we have performed a complex search in a simple way and in no time.