When PubMed searching yields few good results – 28 biomedical literature search tools evaluated

Image via Wikipedia

Have you ever searched PubMed and have been disappointed with the results?
Or have been frustrated with the search interface?

Read on for other ways to search the biomedical literature.

From the Krafty Librarian posting, 28 April 2011

“PubMed and beyond: a survey of web tools for searching biomedical literature” (free full text) from Database (2011) Vol. 2011, doi: 10.093/database/baq036

The article looks at and reviews 28 web tools for searching the biomedical literature and compares them to PubMed and each other and has a website dedicated to tracking existing tools and future advances in the area of biomedical literature search tools.

Abstract:

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.

Not only does the article look at these 28 interfaces but it also looks at the recent changes to PubMed that were often influenced by these and other outside interfaces.

There is no way any library or librarian can teach or support every one of these interfaces, but this paper is free and is a nice resource to whip out when somebody asks about one of them.

 

 

Related Resources and Articles

• Biomedical Literature Search Tools – Links to PubMed alternatives as well as a tool selection filter (natural language, similar results, semantic search with biological concepts)

* indicates the 28 systems surveyed in Lu, Database 2011 (PubMed and Beyond)

# indicates other systems added to the list after the above publication through request or regular update (last update: April 2011)

• How many Medline platforms on the Web? ( slide presentation, highlighting a few PubMed alternatives, Science Intelligence and InfoPros)

• Third Party PubMed Tools (slide presentation, highlighting a few PubMed alternatives, Alison Aldrich, National Network of Libraries of Medicine)
• PubMed Alternatives: Research Guide
  Margaret Henderson, Virginia Commonwealth University Tompkins-McCaw Library
• PubMed® Online and App Resources (NLM) includes links to PubMed alternatives (including individual search engines/interfaces)

 

• PubMed Mobile Beta (jflahiff.wordpress.com)
• PubMed Toxicology Subset Streamlines Biomedical Searches in the Professional Literature (jflahiff.wordpress.com)
• My NCBI Redesign (jflahiff.wordpress.com)
• PubMed Health Provides Disease and Treatment Information for Consumers (jflahiff.wordpress.com)
• PubMed’s Sudden Death Averted… For Now. (laikaspoetnik.wordpress.com)
• Related Services: Outside Tool and Document Delivery Service – LinkOut Help – NCBI Bookshelf (ncbi.nlm.nih.gov)
• Searching PubMed for Articles on Health Literacy (aa47.wordpress.com)
• PubMed Search Help Items (jflahiff.wordpress.com)

Frequently hospitalized patients may benefit from new medical specialty focused on their needs

From the 29 April 2011 Eureka News Alert

Declining rates of hospitalization have discouraged primary care doctors from seeing their patients in the hospital and encouraged the growing use of “hospitalists,” a new physician specialty focused on the care of hospitalized patients. Further developments in the field mean that frequently hospitalized patients also may need a specialist focused on their care, according to an expert on hospital care at the University of Chicago.

The model defining the role of hospitalists, who practice only in hospitals, was first identified in a 1996 article in the New England Journal of Medicine, said David O. Meltzer, an associate professor of medicine and director of the University of Chicago’s Center for Health and the Social Sciences.

“Since that time, hospitalists have become the fastest-growing medical specialty in the United States, providing more than one-third of all general medical care in the United States,” Meltzer wrote in the paper, “Coordination, Switching Costs and the Division of Labor in General Medicine: An Economic Explanation for the Emergence of Hospitalists in the United States,” [full text link ]published by the National Bureau of Economic Research.

Meltzer discussed the growth of the field as well as the potential need for a new specialty — the comprehensive care physician, who would specialize in care of the seriously ill Friday at a conference organized by the Milton Friedman Institute at the University of Chicago. The conference, “Individuals and Institutions in the Health Care Sector,” also will look at issues such as technology and insurance.

The hospitalist specialty developed in response to the growing needs of severely ill patients, combined with reduced hospitalization of patients by general care or ambulatory physicians, Meltzer argues. As their number of hospitalized patients declined, general care physicians saw their travel costs loom large compared to the small number of hospitalized patients, Meltzer points out.

The use of hospitalists also has grown as hospitals have changed how they are reimbursed for their services, Meltzer contends. “Though the evidence that hospitalists produce savings is not consistent, it is clear that the growth of hospitalists accelerated as evidence to support cost-savings began to appear in the mid-1990s,” he said.

The use of hospitalists has the potential of creating communication problems, however, as these specialists do not always know the full medical histories of their patients as well as those patients’ general care physicians. The establishment of a specialty called the comprehensive care physician, or comprehensivist, could overcome that problem, Meltzer contends. The comprehensivist would work both in a hospital and an attached clinic and attend to those at greatest risk of hospitalization.

“Congestive heart failure, end-stage renal disease or liver disease, sickle cell disease or chronic-obstructive pulmonary disease might all be reasonable models for such care, especially if cases could be collected into centers of excellence with sufficient volume to support such degrees of specialization,” he said.

Although the comprehensivist model has yet to be introduced in the United States, it is similar to other approaches in Canada, the United Kingdom, Australia and New Zealand, he said.

Related Articles

• Specialty hospitalists joining forces with the generalist hospitalists (kevinmd.com)
• Should a hospitalist be given more information on hospital costs? (kevinmd.com)
• Hospitalist medicine is moving in the wrong direction (doctorrw.blogspot.com)
• What has the hospital medicine movement wrought? (medrants.com)

Our own status affects the way our brains respond to others

[http://wwwapps.nimh.nih.gov/science-news/2004/depression-traced-to-overactive-brain-circuit.shtml]

From the 28 April 2011 Eureka News Alert

Our own social status influences the way our brains respond to others of higher or lower rank, according to a new study reported online on April 28 in Current Biology, a Cell Press publication.

[A copy of the abstract of this article may be found here, for suggestions on how to get this article for free or at low cost, click here ]

These differences register in a key component of the brain’s value system, a region known as the ventral striatum.

People of higher subjective socioeconomic status show greater brain activity in response to other high-ranked individuals, while those with lower status have a greater response to other low-status individuals…

… socioeconomic status isn’t based solely on money but can also include factors such as accomplishments and habits. Socioeconomic status is also just one hierarchical system among many that humans belong to and that can influence our everyday interactions.

And of course, our socioeconomic status isn’t fixed; it shifts over time, for better or for worse. Exactly how the brain will respond to such changes is an intriguing question for future study.

“As humans, we have the capacity to assess our surroundings and context to determine appropriate feelings and behavior,” Zink said. “We, and our brain’s activity, are not static and can adjust depending on the circumstances. As one’s status changes, I would expect that the value we place on status-related information from others and corresponding brain activity in the ventral striatum would also change.”

NIH researchers create comprehensive collection of approved drugs to identify new therapies

                                                                                                   http://www.ncgc.nih.gov/

From the 27 April 2011 Eureka News Alert

Researchers have begun screening the first definitive collection of thousands of approved drugs for clinical use against rare and neglected diseases. They are hunting for additional uses of the drugs hoping to find off-label therapies, for some of the 6,000 rare diseases that afflict 25 million Americans. The effort is coordinated by the National Institutes of Health’s Chemical Genomics Center (NCGC).

“This is a critical step to explore the full potential of these drugs for new applications,” said NIH Director Francis S. Collins, M.D., Ph.D. “The hope is that this process may identify some potential new treatments for rare and neglected diseases.”

The researchers assembled the collection of approved drugs for screening based on information from the NCGC Pharmaceutical Collection browser at http://tripod.nih.gov/npc. This publicly available, Web-based application described in a paper appearing in the April 27 issue of Science Translational Medicine, provides complete information on the nearly 27,000 active pharmaceutical ingredients including 2,750 small molecule drugs that have been approved by regulatory agencies from the United States, Canada, Europe and Japan, as well as all compounds that have been registered for human clinical trials……

Related Rare Diseases Resources

• National Organization for Rare Disorders
• Genetic and Rare Diseases Information Center(Office of Rare Diseases, National Human Genome Research Institute)
• Office of Rare Diseases
• Rare Diseases Clinical Research Network(Office of Rare Diseases, National Center for Research Resources)
• Rare Diseases (MedlinePlus)

Related Articles

• Push to spur more drugs for deadly rare diseases (seattletimes.nwsource.com)
• U.S. Rolls the Dice on Pharmaceutical Drug Innovation (livescience.com)
• Guidelines on rare diseases: Methods on handling evidence neither identified nor required

  Manuals and methods papers provide only isolated references; different requirements than those for more common diseases do not seem meaningful

New Hospital Survey on Patient Safety Culture: 2011 User Comparative Database Report Is Available

Image via Wikipedia

From the AHRQ (Agency for Healthcare Research and Quality) press release

Based on data from 1,032 U.S. hospitals, the Hospital Survey on Patient Safety Culture: 2011 User Comparative Database Report provides initial results that hospitals can use to compare their patient safety culture to other U.S. hospitals.  In addition, the 2011 report presents results showing change over time for 512 hospitals that submitted data more than once.  The report consists of a narrative description of the findings and four appendixes, presenting data by hospital characteristics and respondent characteristics for the database hospitals overall and separately for the 512 trending hospitals.

Select to download print version (Part 1, PDF File, 1.7 MB; Parts 2 and 3, PDF File, 1.6 MB). PDF Help.

Excerpts from the Executive Summary

Survey Content

The hospital survey, released in November 2004, was designed to assess hospital staff opinions about patient safety issues, medical errors, and event reporting. The survey includes 42 items that measure 12 areas, or composites, of patient safety culture:

1. Communication openness.
2. Feedback and communication about error.
3. Frequency of events reported.
4. Handoffs and transitions.
5. Management support for patient safety.
6. Nonpunitive response to error.
7. Organizational learning—continuous improvement.
8. Overall perceptions of patient safety.
9. Staffing.
10. Supervisor/manager expectations and actions promoting safety.
11. Teamwork across units.
12. Teamwork within units.

Areas of Strength for Most Hospitals

Three areas of strength emerged. Results are expressed in terms of percent positive response. Percent positive is the percentage of positive responses (e.g., Agree, Strongly agree) to positively worded items (e.g., “People support one another in this unit”) or negative responses (e.g., Disagree) to negatively worded items (e.g., “We have safety problems in this unit”).

Teamwork Within Units (average 80 percent positive response)—This composite is defined as the extent to which staff support each other, treat each other with respect, and work together as a team. This composite had the highest average percent positive response.

Supervisor/Manager Expectations & Actions Promoting Patient Safety (average 75 percent positive response)—This composite is defined as the extent to which supervisors/managers consider staff suggestions for improving patient safety, praise staff for following patient safety procedures, and do not overlook patient safety problems. This composite had the second highest average percent positive response.

Patient Safety Grade—On average, most respondents within hospitals (75 percent) gave their work area or unit a grade of either “A-Excellent” (29 percent) or “B-Very Good” (46 percent) on patient safety.

Areas With Potential for Improvement for Most Hospitals

Three areas showed potential for improvement.

Nonpunitive Response to Error (average 44 percent positive response)—This composite is defined as the extent to which staff feel that their mistakes and event reports are not held against them and that mistakes are not kept in their personnel file. This composite had the lowest average percent positive response.

Handoffs and Transitions (average 45 percent positive response)—This composite is defined as the extent to which important patient care information is transferred across hospital units and during shift changes. This composite had the second lowest average percent positive response.

Number of Events Reported—On average, most respondents within hospitals (54 percent) reported no events in their hospital over the past 12 months. It is likely that events were underreported. This is an area for improvement for most hospitals because underreporting of events means potential patient safety problems may not be recognized or identified and therefore may not be addressed.

Related Articles

• HSS, Obama Team On Partnership For Patients’ Healthcare Safety (medicalnewstoday.com)
• “Patient Safety Awareness Week” may be over, but we should continue to focus on safety (medicineandtechnology.com)
• Gov’t List Ranks Hospitals by Patient Safety (healthcaremarcom.wordpress.com)
• Hospital Safety Varies Widely Nationwide (nlm.nih.gov)
• 1 in 3 patients harmed during hospital stay (kboreilly.com)
• Report: Hospital Errors May Be Far More Common Than Suspected (nlm.nih.gov)
• HHS: New Patient Safety Initiative Will Save Lives, Reduce Health Care Costs (kaiserhealthnews.org)
• Sustaining vulnerable lives (scienceblog.com)