PubSearch is an application for the iPhone designed to search Pubmed. It has a simple user interface and is pretty fast. Developers have already announced the enhanced version of this app, called PubSearchPlus which will offer more features.
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I started reading The Oxford Book of Modern Science Writing and so far I think it is great. This book is actually a collection of pieces by the very best scientists and science writers selected by Richard Dawkins. I recommend it to anyone who finds science interesting and if you don’t find science interesting, listen to what Richard himself has to say to you in this short video.
When you search PubMed the conventional way, via the Entrez system, two things happen. First your query is translated with identification of Medical Subject Headings (MeSH) terms and secondly this translated query is matched with words from all the abstracts. The second part is performed by term matching, which ultimately means that keyword synonyms are not used in the search. This way you can lose a lot of important articles. Finally, found abstracts are listed in the reverse chronological order. In most of the cases this is not what you want, and you are forced to manually go through all the abstracts to find those relevant to you.
GoPubMed can help you with the mentioned problems. When you submit the query, it retrieves the abstracts from PubMed but then does something extra. It categorizes them based on the relevance provided by the ontology terms used in MeSH and Gene Ontology (GO). Results are sorted in 4 categories: what, who, where and when. The what category is where abstracts are sorted according to the concept hierarchies of GO and MeSH enabling the combined search in molecular biology and medicine. This helps to systematically explore the results. The who category helps you identify leading scientists and centers in specific biomedical areas. The where category provides information about geographic localization of persons, centres, universities, together with journals in which found papers were published. Finally, the when category is all about distribution of publications through time.
To use GoPubMed simply enter the search query like you were using Entrez. After completing the search GoPubMed will inform you of the total number of articles found, and by default analyze the latest 1 000 abstracts. You can then go through these abstracts, choose to show statistics for these results or refine your search using the 4 categories (what, who, where and when). Choosing to show statistics will analyze results according to the 4 categories and present them in a clear manner. Especially interesting are graphs, depicting publications over time, and maps, indicating localizations of authors.
I like the design of the application, it feels very web 2.0. It takes some time to get used to it, but after a short learning period you start to enjoy it. This feeling is even more reinforced when you get good search results and ideas how to use it creatively start popping to your mind.
Here are some examples of the ways you can use GoPubMed, as proposed by the authors. I am sure you can come up with others to really boost your PubMed search.
Which diseases are associated with HIV?
Type “HIV”. Go to “What” and click on “more of Diseases”. Among others hepatitis and tuberculosis are mentioned. Clicking on tuberculosis retrieves the relevant articles including statements such as “Despite the synergy between the human immunodeficiency virus (HIV) and tuberculosis (TB) epidemics, the public health responses have largely been separate”.
Where are leading centers and who are scientists for liver transplantation in Germany?
Type “liver transplantation Germany[AD]”. At the top of the “Who” category the result shows the top author “Neuhaus P” and the city is “Berlin”. Prof. Peter Neuhaus works at the Charite Hospital in Berlin, Germany, is a leading specialist in the field.
Do you know in which topics Craig C. Mello and Andrew Z. Fire are working on?
Search for “Mello C[au] Fire A[au]”. Now inspect What, Where, Who and When categories!
Following the top categories the answer is automatically extracted:
Which disease is rhodopsin involved in?
Search for “rhodopsin ” and in just one mouse click on “Diseases ” your question is quickly found.
The group of more important diseases related to rhodopsin are shown under this ontological category.
Which biological processes are inhibited by aspirin?
Search for “aspirin inhibits ”.
By inspecting the most frequent term “biological processes ” you can very quickly understand that “cyclooxygenase pathway ” is the pathway related to this biological process. GoPubmed found more than 30% papers verifying that “cyclooxygenase pathway ” is inhibited by aspirin.
Professor Philip E. Bourne has been writing a series of “Ten Rules” editorials in PLoS Computational Biology for almost three years now. He is the Editor-in-Chief of the mentioned open-access scientific journal, who came up with this idea after giving a presentation on getting published to a group of students. Since then a total of 9 such articles were published, written by him alone or with a little help from his fellow colleagues. These articles are basically lists of ten simple rules, with some additional explanation, on various subjects mostly aimed at young researchers. Rules which professor Bourne and his coauthors propose are a product of rich personal experience and are written in a honest, concise and simple manner.
I am listing all the rules here, sorted by the publishing date. However, I strongly recommend that you visit and read the whole articles, as the short commentaries accompanying each rule are most valuable.
- Read many papers, and learn from both the good and the bad work of others
- The more objective you can be about your work, the better that work will ultimately become
- Good editors and reviewers will be objective about your work
- If you do not write well in the English language, take lessons early; it will be invaluable later
- Learn to live with rejection
- The ingredients of good science are obvious—novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion. The ingredients of good science reporting are obvious—good organization, the appropriate use of tables and figures, the right length, writing to the intended audience—do not ignore the obvious
- Start writing the paper the day you have the idea of what questions to pursue
- Become a reviewer early in your career
- Decide early on where to try to publish your paper
- Quality is everything
- Be Novel, but Not Too Novel
- Include the Appropriate Background and Preliminary Data as Required
- Find the Appropriate Funding Mechanism, Read the Associated Request for Applications Very Carefully, and Respond Specifically to the Request
- Follow the Guidelines for Submission Very Carefully and Comply
- Obey the Three Cs—Concise, Clear, and Complete
- Remember, Reviewers Are People, Too
- Timing and Internal Review Are Important
- Know Your Grant Administrator at the Institution Funding Your Grant
- Become a Grant Reviewer Early in Your Career
- Accept Rejection and Deal with It Appropriately
- Do Not Accept a Review Assignment unless You Can Accomplish the Task in the Requested Timeframe—Learn to Say No
- Avoid Conflict of Interest
- Write Reviews You Would Be Satisfied with as an Author
- As a Reviewer You Are Part of the Authoring Process
- Be Sure to Enjoy and to Learn from the Reviewing Process
- Develop a Method of Reviewing That Works for You
- Spend Your Precious Time on Papers Worthy of a Good Review
- Maintain the Anonymity of the Review Process if the Journal Requires It
- Write Clearly, Succinctly, and in a Neutral Tone, but Be Decisive
- Make Use of the “Comments to Editors”
- Select a Position that Excites You
- Select a Laboratory That Suits Your Work and Lifestyle
- Select a Laboratory and a Project That Develop New Skills
- Have a Backup Plan
- Choose a Project with Tangible Outcomes That Match Your Career Goals
- Negotiate First Authorship before You Start
- The Time in a Postdoctoral Fellowship Should Be Finite
- Evaluate the Growth Path
- Strive to Get Your Own Money
- Learn to Recognize Opportunities
- Do Not Be Lured into Just Any Collaboration
- Decide at the Beginning Who Will Work on What Tasks
- Stick to Your Tasks
- Be Open and Honest
- Feel Respect, Get Respect
- Communicate, Communicate, and Communicate
- Protect Yourself from a Collaboration That Turns Sour
- Always Acknowledge and Cite Your Collaborators
- Seek Advice from Experienced Scientists
- If Your Collaboration Satisfies You, Keep It Going
- Talk to the Audience
- Less is More
- Only Talk When You Have Something to Say
- Make the Take-Home Message Persistent
- Be Logical
- Treat the Floor as a Stage
- Practice and Time Your Presentation
- Use Visuals Sparingly but Effectively
- Review Audio and/or Video of Your Presentations
- Provide Appropriate Acknowledgments
- Define the Purpose
- Sell Your Work in Ten Seconds
- The Title Is Important
- Poster Acceptance Means Nothing
- Many of the Rules for Writing a Good Paper Apply to Posters, Too
- Good Posters Have Unique Features Not Pertinent to Papers
- Layout and Format Are Critical
- Content Is Important, but Keep It Concise
- Posters Should Have Your Personality
- The Impact of a Poster Happens Both During and After the Poster Session
- Drop Modesty
- Prepare Your Mind
- Age Is Important
- Brains Are Not Enough, You Also Need Courage
- Make the Best of Your Working Conditions
- Work Hard and Effectively
- Believe and Doubt Your Hypothesis at the Same Time
- Work on the Important Problems in Your Field
- Be Committed to Your Problem
- Leave Your Door Open
- Let Passion Be the Driving Force of Your Success
- Select the Right Mentor, Project, and Laboratory
- Independent Thinking Is a Mark of a True Scientist
- Remember, Life Is All about Balance
- Think Ahead and Develop Your Professional Career Early
- Remain Focused on Your Hypothesis While Avoiding Being Held Back
- Address Problems Earlier Rather Than Later
- Share Your Scientific Success with the World
- Build Confidence and a Thick Skin
- Help Select and Subsequently Engage Your Thesis Committee
In the latest issue of Pediatrics, official journal of the American Academy of Pediatrics, researchers from Nationwide Children’s Hospital in Columbus, Ohio have published a paper titled “Trial of Computerized Screening for Adolescent Behavioral Concerns“. This paper talks about the potential benefits of the Health eTouch systems to help pediatricians identify injury risks, depressive symptoms, and substance use among adolescent visiting urban clinics.
A total of 878 primary care patients 11 to 20 years of age where included in the study conducted in waiting rooms of 9 urban clinics. All of the patients where given wireless devices in clinic waiting rooms to answer questions about their health and behavior. The clinics were randomly assigned to have pediatricians receive these screening results either just before face-to-face encounters with patients (immediate-results condition) or 2 to 3 business days later (delayed-results condition).
What the study eventually found was that 59% of the respondents had positive results for 1 or more of the following behavioral concerns: injury risk behaviors, significant depressive symptoms, or substance use. Sixty-eight percent of youths in the immediate-results condition who screened positive were identified as having a problem by their pediatrician. This was significantly higher than the recognition rate of 52% for youths in the delayed-results condition.
Take a look at the video, including a short interview with one of the main researchers, to learn more.
Spam, or unsolicited e-mail, is everywhere and shows no signs of slowing down. In fact, it will never go away, at least not until people keep buying the stuff spammers offer. And oh boy aren’t there always some new suckers in the cyberspace. However, things get far less amusing when human health gets into play. Have you noticed that a high percentage of spam you receive today is health-related?
It is just this health-related spam that Peter Gernburd and Alejandro Jadad from the Centre for Global eHealth Innovation from Canada wanted to find out more about. In September 2007 issue of PLoS Medicine, an open-access, peer-reviewed medical journal, they published a very interesting paper on this subject titled “Will Spam Overwhelm Our Defenses? Evaluating Offerings for Drugs and Natural Health Products”.
In their research they used three e-mail accounts, unfiltered for spam, to gather all the spam they could get in the period of one month. Among all the received spam messages, they picked out the health-related ones, defined as those which included offers of interventions that could modify a physical, cognitive, behavioral, or emotional state in humans (e.g., medications, natural health products, devices, or professional services). All Web links included in such messages were further analyzed.
During the study period researchers received 4,153 spam messages, out of which 1,334 or 32% were health related. Majority of these messages (73%) were sent from the United States.
Scientists tried to order prescription drugs and natural health products from Web sites advertised in these messages. Eventually, they received 9 orders (5 prescription drugs and 4 natural health products). Some of the products they managed to buy where Clalis (for erectile dysfunction), Tramadol (for pain), Valium and Xanax (for anxiety and other disorders). There was no report of any evidence of credit card abuse by the spammers, except for one undelivered product.
What the study lacked, but authors promised to report on in the near future, was the analysis of the actual purchased pharmaceutical products to reveal whether they are genuine, fakes, and most importantly are they dangerous.
You can read the complete paper on PLoS Medicine Web site.