Rapid detection of microbial DNA ... [Biochem Biophys Res Commun. 2012] - PubMed - NCBI

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Rapid detection of microbial DNA ... [Biochem Biophys Res Commun. 2012] - PubMed - NCBI

Biochem Biophys Res Commun. 2012 Apr 20;420(4):738-42. Epub 2012 Mar 17.

Rapid detection of microbial DNA by a novel isothermal genome exponential amplification reaction (GEAR) assay.

Prithiviraj J, Hill V, Jothikumar N.

Source

Georgia Tech, Institute of Bioengineering and Biosciences, 315 Ferst Drive, Atlanta, GA 30332, USA.

Abstract

In this study we report the development of a simple target-specific isothermal nucleic acid amplification technique, termed genome exponential amplification reaction (GEAR). Escherichia coli was selected as the microbial target to demonstrate the GEAR technique as a proof of concept. The GEAR technique uses a set of four primers; in the present study these primers targeted 5 regions on the 16S rRNA gene of E. coli. The outer forward and reverse Tab primer sequences are complementary to each other at their 5' end, whereas their 3' end sequences are complementary to their respective target nucleic acid sequences. The GEAR assay was performed at a constant temperature 60°C and monitored continuously in a real-time PCR instrument in the presence of an intercalating dye (SYTO 9). The GEAR assay enabled amplification of as few as one colony forming units of E. coli per reaction within 30min. We also evaluated the GEAR assay for rapid identification of bacterial colonies cultured on agar media directly in the reaction without DNA extraction. Cells from E. coli colonies were picked and added directly to GEAR assay mastermix without prior DNA extraction. DNA in the cells could be amplified, yielding positive results within 15min.
Published by Elsevier Inc.

PMID:

22450319

[PubMed - in process]

May 9, 2012, NIAID Funding Newsletter

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May 9, 2012, NIAID Funding Newsletter

May 9, 2012

Feature Articles

• Take Time to Size Up Potential Study Sections

Opportunities and Resources

• Help Enhance and Evaluate Human Subjects Protections

In The News

• File for a Change of Institution Electronically
• News Briefs
  • FCOI Checklist for Institutions
  • NIAID Clarifies Areas of Interest for an R21/R33 RFA
  • NCATS Creates Web Sites for Its Rare Diseases Programs

Advice Corner

• Don't Be Conflicted About Financial Conflicts of Interest
• Reader Questions
  • In my progress report, do I need to justify an increase in my level of effort?
  • I'm a sixth-year postdoc. Should I apply for an NRSA Postdoctoral Fellowship (F32) when I move to another lab?

New Funding Opportunities

• See the list

Take Time to Size Up Potential Study Sections

Proposing high-quality science is key to a successful application, but if that's your sole focus you're missing out on a big piece of the equation: getting the right peer reviewers.
Even the most elegant science is not likely to impress reviewers who don't have your scientific perspective. You’ll need your reviewers’ enthusiasm to carry your application to a fundable score.
So when you’re still picking a project, it’s helpful to know who shares your perspective and would best appreciate your work.  Then when you write your application, you can keep those people in mind too.
But because you can't control who reviews your application, you do need to write an application that appeals to a broad audience: your primary and secondary reviewers, including those you did not expect, and the others on the review panel.
If some of those statements seem contradictory, they are. There are no simple answers, but keep reading to get our best advice.
Research Your Reviewers
Grant applications are no exception to the saying: beauty is in the eye of the beholder. Some reviewers are bound to deem your work boring, while others will find it exciting.
Though it takes some intelligence-gathering, one strategy for success is to look for a study section that has reviewers in the latter category from the outset when choosing a topic.

• Explore the perspectives and expertise of different standing study sections in light of the research you are planning.
• Peruse the Roster Index for Regular Standing Study Sections and Continuing SEPs linked below to find a study section whose members seem to share your scientific perspective and whose work is most relevant to your field.
• Read the descriptions, skim the rosters, and scan the lists of topics assigned to the various study sections.

After you find some good options, look at study section members in more depth, for example, by visiting their Web sites and reviewing their publications. You can use RePORTER to see what projects they have underway.
Once you've looked at your reviewers, identify the three or so whose backgrounds and scientific records align best with your research area. While you can't know for certain who your reviewers will be, those closest to your field are most likely to be assigned as primary or secondary reviewers or readers, assuming you get your requested study section.
Ask yourself how enthusiastic they and possibly the others may be about topics you are considering. Would they view a project as high impact? In their own publications, have they identified gaps your research would fill or areas of exploration that your work would pursue?
 Then choose a topic and write an application that meets their expectations so they’ll sit up and take notice.
No Good Fit? Rethink It
What happens if you don't find a good study section for the work you're contemplating?
You could hunt down a "second best" study section, but first rethink your research. Consider modifying your project, changing your scope, or asking a different scientific question.
Center for Scientific Review (CSR) has 184 standing study sections covering almost all areas of science, and that doesn't include special emphasis panels and institute-specific review groups. Your best bet is to carefully select a project that a study section can fully appreciate. 
For those who propose multidisciplinary and highly innovative work, read our advice on these types of projects:

• Getting a Grant for Innovative Research
• Team Science

Also consider contacting a program officer in your area of science for advice. If you don't know who that is at this point, take a step back and figure out where your project belongs. Read more at Pick a Research Project, linked below.
Cover Yourself
Once you've found the right reviewers for your application, aim to get your application in their hands: request your chosen study section in your cover letter.
While that request can put the odds in your favor, there’s no guarantee CSR will assign your application to your top pick. As a fallback, also list the necessary expertise to review your application, in case CSR wants to assign it to a different panel.
Get more advice in Create a Cover Letter, linked below.
There are myriad reasons CSR can assign your application to a study section other than the one you request, for example, due to a reviewer conflict of interest or a scientific review officer who disagrees with your assessment of the science.
Within 10 days after applying, log into the eRA Commons to check that your application is assigned to a study section with appropriate expertise. Ideally this will be the study section you requested, but CSR may have more than one study section that fits the bill and it sometimes creates ad hoc groups to fill in gaps.
Later, once the actual roster appears in the Commons about 30 days before the review meeting, check that members have a track record or interest in your research. Rosters change from one review to the next as reviewers rotate on and off or miss a meeting.
At any time, contact your scientific review officer to discuss your options if you're concerned with the study section assignment, expertise of study section members, or a reviewer who you feel cannot give your application an impartial review. For more information and advice, go to Ensure You Get the Right Assignments, linked below.
Related Links
CSR

• Integrated Review Groups
• Roster Index for Regular Standing Study Sections and Continuing SEPs

Strategy for NIH Funding

• Part 2
  • Pick a Research Project
• Part 3
  • Investigate Committees and Members
  • Know Your Audience
• Part 4
  • Create a Cover Letter 
• Part 5
  • Ensure You Get the Right Assignments

NLM Databases and Electronic Resources—find publications
NIH RePORTER—find funded projects, experts in your field, their publications and grants, and study sections that reviewed their applications

Help Enhance and Evaluate Human Subjects Protections

Help us help HHS with its plans to potentially revise the Common Rule (45 CFR 46, subpart A).
Through a new funding opportunity announcement (FOA), you can contribute to enhancing the effectiveness of human subjects research protections while facilitating research and reducing the burden for investigators.
Before you jump in, take note.
This isn't a "come one, come all" FOA. That is, it limits competition by seeking only revision (aka, competing supplement) applications from grantees whose parent awards are active cooperative agreements when they apply.
Consider responding if your research can contribute to either or both of these areas:

• The effectiveness of current protections in regulations, rules, and policies governing research with human subjects.
  
• The use of broad, prospective consent for acquiring biospecimens in clinical settings.
  

Read the April 20, 2012, Guide notice for more details.
If you have questions, contact your program officer or NIH's Valery Gordon. Get answers as soon as possible since applications are due by May 25, 2012.
For information on the proposal to improve the Common Rule, go to HHS's ANPRM for Revision to Common Rule.

File for a Change of Institution Electronically

If you’re considering a move to another organization, some news for you: on April 20, NIH launched a new pilot that allows electronic requests for a change of institution.
You and the signing officials from both institutions can use the new pilot workflow in the Commons. Learn more in the Change of Institutions FAQs and get more details in the Commons Change of Institution user guide.
The new process should be easier than the traditional method of filling out the PHS 3734 form and routing it manually through your institution to NIAID.  
As always, the eRA Help Desk welcomes your questions.

News Briefs

Here's news from around NIH.
FCOI Checklist for Institutions. NIH released a Checklist for Financial Conflict of Interest Policy Development to help institutions construct and maintain comprehensive policies regarding financial conflicts of interest. Read the April 18, 2012, Guide notice for more information.
NIAID Clarifies Areas of Interest for an R21/R33 RFA. New text in the Partnerships for Interventions to Treat Chronic, Persistent and Latent Infections (R21/R33) makes clear that applicants can propose approaches that seek to completely and permanently suppress an agent’s pathogenic processes without ongoing interventions. Get details in the May 1, 2012, Guide notice.
NCATS Creates Web Sites for Its Rare Diseases Programs. The National Center for Advancing Translational Science published Web pages for two programs: Therapeutics for Rare and Neglected Diseases and Office of Rare Diseases Research.

Don't Be Conflicted About Financial Conflicts of Interest

With the release of NIH's Checklist for Financial Conflict of Interest Policy Development, we'd like to take the opportunity to mention again how important it is to disclose conflicts of financial interest—even potential ones—to your business office.
Your institution has to manage, reduce, or eliminate all conflicts for you and your collaborators, and also ensure your subawardees comply with the NIH policy. Help it by knowing the rules and checking with your institutional official to see what you need to do.
And be forewarned: we may suspend your research funding if your institution doesn't comply with NIH's conflict of interest policy.
Read our Financial Conflicts of Interest for Awardees SOP for instructions, and visit NIH's Financial Conflict of Interest page for more information.

Feel free to send us a question at deaweb@niaid.nih.gov. After responding to you, we may include your question in the newsletter, incorporate it into the NIAID Research Funding site, or both.
"In my progress report, do I need to justify an increase in my level of effort"—Charles A. Paxton, University of Washington
No. As long as the increase would not result in a change of scope, you do not need to justify it.
If you're significantly increasing your effort, you may want to contact your program officer for advice on NIH rules you might need to follow, as well as other ways you may be able to support your research, e.g., by requesting an administrative supplement.
"I'm a sixth-year postdoc. Should I apply for an NRSA Postdoctoral Fellowship (F32) when I move to another lab?"—anonymous reader
While you can apply for an NRSA Postdoctoral Fellowship (F32) award in any year of your postdoctoral period, you would have to provide a very strong justification as to why you would still need mentored support at this point in your career.
Instead, you may want to apply for an R01 grant and take advantage of new investigator benefits, such as a higher payline and lower expectations for preliminary data and publications. Read our New Investigator Guide to NIH Funding for advice and take a look at our R01 Investigator Resources.

• PAR-12-182, Native American Research Centers for Health (NARCH)

See these and older announcements at NIAID Funding Opportunities List.

AHRQ Innovations Exchange | Pediatric Asthma Care

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AHRQ Innovations Exchange | Pediatric Asthma Care



Pediatric Asthma Care
Pediatric asthma affects nearly 6 million children in the United States, reducing quality of life and often leading to costly emergency department visits and inpatient admissions. Low-income, urban children experience higher asthma-related morbidity due to environmental factors and poor access to appropriate care. Managing pediatric asthma according to existing guidelines can help minimize the potential for negative outcomes.

The featured Innovations describe one program that provided services to urban preschool children in an effort to improve asthma-related outcomes, and two programs that improved pediatric asthma care by increasing adherence to well-established care guidelines.

The featured QualityTools provide parents and health care practitioners with resources to help manage pediatric asthma and improve quality of life. Featured Innovations: •  Mobile Clinic and In-Home Educator Generate Small, Short-Term Increases in Symptom-Free Days in Inner-City Preschool Children With Asthma But No Improvements in Other Key Outcomes •  National Academy and Affiliated State Chapters Support Pediatricians in Improving Asthma Care, Leading to Better Guideline Adherence and Disease Control, Fewer Acute Episodes •  Real-Time, Color-Coded Alerts Improve Adherence to Pediatric Asthma Guidelines in Primary Care Practices Featured QualityTools: • Child Asthma Risk Assessment Tool^© (CARAT)
Developed by National Cooperative Inner-City Asthma Study • Parents Helping Parents Fight Asthma
Developed by Aurora-Sinai Hospital; Children's Hospital of Wisconsin; Children's Medical Center Dallas; Medical College of Wisconsin; University of Texas Southwestern Medical Center; Wheaton Franciscan - St. Joseph • Pediatric Asthma Initiative: Environmental History Form
Developed by National Environmental Education Foundation
Also in This Issue:
Innovations > • Disease Management Programs Improve Adherence to Evidence-Based Processes and Outcomes by Targeting Sickest Patients and Working Closely With Physicians • Immediate Post-Event Debriefing Improves Multiple Aspects of Response to Codes and Increases Staff Satisfaction • Public-Private Partnership Supports Medical Homes in Managing Medicaid Enrollees via Disease/Case Management and Other Initiatives, Leading to Higher Quality and Significant Cost Savings QualityTools > • AHRQ Quality Indicators™ Toolkit for Hospitals
Developed by RAND Corporation; University HealthSystem Consortium • Always Events® Toolbox
Developed by Picker Institute, Inc. • Playnormous Health Games
Developed by Baylor College of Medicine; National Institutes of Health; Playnormous, LLC; University of Texas Health Science Center

AHRQ Innovations Exchange | Expert Commentary: National Academy and Affiliated State Chapters Support Pediatricians in Improving Asthma Care, Leading to Better Guideline Adherence and Disease Control, Fewer Acute Episodes

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AHRQ Innovations Exchange | Expert Commentary: National Academy and Affiliated State Chapters Support Pediatricians in Improving Asthma Care, Leading to Better Guideline Adherence and Disease Control, Fewer Acute Episodes



Innovation Profile:

National Academy and Affiliated State Chapters Support Pediatricians in Improving Asthma Care, Leading to Better Guideline Adherence and Disease Control, Fewer Acute Episodes

 

Pediatric Asthma Is a Worthy Quality Improvement Target

By Paul V. Williams, MD
Northwest Asthma & Allergy Center

Efforts to improve pediatric asthma care are important, given the prevalence of the condition and its potential for causing adverse health outcomes. As a pediatric allergist, I’ve been involved in quality improvement in my own practice, though not specifically focused on adherence to asthma treatment guidelines. We can gain some insights into the challenges of quality improvement related to asthma care by considering two innovation profiles featured on the AHRQ Health Care Innovations Exchange. One profile—National Academy and Affiliated State Chapters Support Pediatricians in Improving Asthma Care, Leading to Better Guideline Adherence and Disease Control, Fewer Acute Episodes—describes a 1-year quality improvement project by the American Academy of Pediatrics (AAP) that helped 49 pediatric practices in 4 states to better adhere to established asthma care guidelines. The other profile—Mobile Clinic And In-Home Educator Generate Small, Short-Term Increases in Symptom-Free Days in Inner-City Preschool Children With Asthma But No Improvements in Other Key Outcomes—describes an attempt to use a mobile pediatric asthma clinic to improve asthma management among children enrolled in the Head Start program in Baltimore.

The pediatricians who organized the AAP initiative succeeded in what they tried to do, based on the impressive improvements in physician performance reported among the participating practices, with the percentage of patients receiving “optimal” care rising from 35 percent at baseline to 85 percent a year later. It appears that the practices—located in Alabama, Maine, Ohio, and Oregon—represent a reasonable cross-section of pediatric practices in the United States. It’s somewhat surprising that only 58 percent of the patients were considered to have well-controlled asthma at baseline, because you might expect that primary care pediatricians would tend to care for patients with relatively well-controlled, intermittent asthma. However, the practices may have tended to focus their quality improvement efforts on patients with a history of having less-than-optimal disease control.

After the intervention, 72 percent of the patients were classified as having well-controlled asthma, an outcome similar to results in other studies aimed at improving pediatric asthma care. As with other quality improvement studies, the key question is, what will happen to these patients over the long term? If the practices achieved lasting improvement in the asthma care process, the measured gains in physician performance could lead to long-term improvements in asthma control. In any case, if pediatricians in other settings can achieve even a fraction of the reported performance improvements, and demonstrate that the gains are sustainable, there’s a real potential for success. That’s why the AAP is continuing to support quality improvement initiatives that focus on asthma care.

Assuming that proper assessment of asthma severity and control has been accomplished, inadequate adherence to prescribed treatment is generally the main barrier to successful asthma management. We know that many patients who say that they are taking their medications actually haven’t filled or refilled their prescriptions, but their physicians often lack a good way to assess adherence. Even in practices like my own that use an electronic health record system, the infrastructure often is not yet in place to enable electronic communication with pharmacies.

The mobile pediatric asthma clinic that was used in the Baltimore program was introduced in 1995 in Los Angeles. The original Breathmobile program achieved some great successes by taking care to the patients. Back in the 1990s, though, it was probably easier to make a big difference in asthma care. After all, it was only in 1991 that the National Asthma Education and Prevention Program had distributed its initial guidelines on diagnosis and management of asthma, in response to the lack of standardization in asthma care. By 2005, when Baltimore’s Breathmobile program began serving children enrolled in Head Start, the level of asthma care may have been fairly good already. And given the low rates of family participation, we shouldn’t be surprised that the program had such a limited impact on patient outcomes.

Asthma diagnosis is difficult in preschool children, because young children have great variability in disease expression and are not developmentally able to undergo spirometry assessments. Also, we have relatively few data on treatment efficacy in preschool children and their symptoms often improve spontaneously. Although these factors can make it difficult to assess the value of early intervention, efforts to identify and treat high-risk populations are worth pursuing as we seek to address unmet needs for effective care among children with asthma.
About the Author:

Paul V. Williams, MD, is an allergy and asthma specialist at the Mount Vernon, WA, office of the Northwest Asthma & Allergy Center. He is a member of the Board of Directors of the Joint Council on Allergy, Asthma and Immunology, and represents the American Medical Association on the National Asthma Education and Prevention Panel.

Disclosure Statement: Dr. Williams has been involved in a variety of leadership roles with the American Academy of Pediatrics, which developed the asthma care quality improvement project described in the innovation profile about the AAP initiative. 

Original publication: May 09, 2012.
Original publication indicates the date the profile was first posted to the Innovations Exchange.Last updated: May 09, 2012.
Last updated indicates the date the most recent changes to the profile were posted to the Innovations Exchange.

National Guideline Clearinghouse | ACR Appropriateness Criteria® ductal carcinoma in situ.

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National Guideline Clearinghouse | ACR Appropriateness Criteria® ductal carcinoma in situ.



Guideline Title ACR Appropriateness Criteria® ductal carcinoma in situ.   Bibliographic Source(s)

Moran MS, Bai HX, Haffty BG, Harris EER, Arthur DW, Bailey L, Bellon JR, Carey L, Goyal S, Halyard MY, Horst KC, MacDonald SM, Expert Panel on Radiation Oncology-Breast. ACR Appropriateness Criteria® ductal carcinoma in situ. [online publication]. Reston (VA): American College of Radiology (ACR); 2011. 14 p. [52 references]

  Guideline Status This is the current release of the guideline.
This guideline updates a previous version: Rabinovitch R, Solin LJ, Shank BM, Green S, Haffty BG, Halberg FE, Mitchell SE, Strom EA, Taylor ME, White JR, Cobleigh MA, Edge SB, Mauch PM, Expert Panel on Radiation Oncology-Breast Work Group. Ductal carcinoma in situ. [online publication]. Reston (VA): American College of Radiology (ACR); 2006. 15 p.
The appropriateness criteria are reviewed biennially and updated by the panels as needed, depending on introduction of new and highly significant scientific evidence.

National Guideline Clearinghouse | ACR Appropriateness Criteria® external beam radiation therapy treatment planning for clinically localized prostate cancer.

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National Guideline Clearinghouse | ACR Appropriateness Criteria® external beam radiation therapy treatment planning for clinically localized prostate cancer.


Guideline Title ACR Appropriateness Criteria® external beam radiation therapy treatment planning for clinically localized prostate cancer.   Bibliographic Source(s)

Abdel-Wahab M, Mahmoud O, Merrick G, Hsu IC, Arterbery VE, Ciezki JP, Frank SJ, Mohler JL, Moran BJ, Rosenthal SA, Rossi CJ II, Yamada Y, Expert Panel on Radiation Oncology-Prostate. ACR Appropriateness Criteria® external beam radiation therapy treatment planning for clinically localized prostate cancer. [online publication]. Reston (VA): American College of Radiology (ACR); 2011. 13 p. [133 references]

  Guideline Status This is the current release of the guideline.
This guideline updates a previous version: Michalski JM, Roach M III, Merrick G, Anscher MS, Beyer DC, Lawton CA, Lee WR, Pollack A, Rosenthal SA, Vijayakumar S, Carroll PR, Expert Panel on Radiation Oncology-Prostate. External beam radiation therapy treatment planning for clinically localized prostate cancer. [online publication]. Reston (VA): American College of Radiology (ACR); 2006. 12 p.
The appropriateness criteria are reviewed biennially and updated by the panels as needed, depending on introduction of new and highly significant scientific evidence.

National Guideline Clearinghouse | ACR Appropriateness Criteria® recurrent rectal cancer.

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National Guideline Clearinghouse | ACR Appropriateness Criteria® recurrent rectal cancer.



Guideline Title ACR Appropriateness Criteria® recurrent rectal cancer.   Bibliographic Source(s)

Konski AA, Suh WW, Blackstock AW, Herman JM, Hong TS, Poggi MM, Rodriguez-Bigas M, Small W Jr, Thomas CR Jr, Zook J, Expert Panel on Radiation Oncology-Rectal/Anal Cancer. ACR Appropriateness Criteria® recurrent rectal cancer. [online publication]. Reston (VA): American College of Radiology (ACR); 2011. 9 p. [43 references]

  Guideline Status This is the current release of the guideline.
This guideline updates a previous version: Konski AA, Herman J, Suh WW, Blackstock AW, Mohiuddin M, Poggi MM, Regine WF, Rich TA, Cosman BC, Saltz L, Expert Panel on Radiation Oncology-Rectal/Anal Cancer. ACR Appropriateness Criteria® recurrent rectal cancer. [online publication]. Reston (VA): American College of Radiology (ACR); 2008. 7 p.
The appropriateness criteria are reviewed biennially and updated by the panels as needed, depending on introduction of new and highly significant scientific evidence.