Dataset Information

MiRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico.

ABSTRACT: MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introduce microRNA sponge generator and tester (miRNAsong), a freely available web-based tool for generation and in silico testing of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation. URL: http://www.med.muni.cz/histology/miRNAsong/.

SUBMITTER: Barta T

PROVIDER: S-EPMC5114684 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico.

Barta Tomas T Peskova Lucie L Hampl Ales A

Scientific reports 20161118

MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly impor ...[more]

PMID: 27857164

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Project description:BACKGROUND:Several pain management guidelines recommend regular urine drug testing (UDT) in patients who are being treated with chronic opioid analgesic therapy (COAT) to monitor compliance and improve safety. Guidelines also recommend more frequent testing in patients who are at high risk of adverse events related to COAT; however, there is no consensus on how to identify high-risk patients or on the testing frequency that should be used. Using previously described clinical risk factors for UDT results that are inconsistent with the prescribed COAT, we developed a web-based tool to adjust drug testing frequency in patients treated with COAT. OBJECTIVE:The objective of this study was to evaluate a risk stratification tool, the UDT Randomizer, to adjust UDT frequency in patients treated with COAT. METHODS:Patients were stratified using an algorithm based on readily available clinical risk factors into categories of presumed low, moderate, high, and high+ risk of presenting with UDT results inconsistent with the prescribed COAT. The algorithm was integrated in a website to facilitate adoption across practice sites. To test the performance of this algorithm, we performed a retrospective analysis of patients treated with COAT between June 2016 and June 2017. The primary outcome was compliance with the prescribed COAT as defined by UDT results consistent with the prescribed COAT. RESULTS:979 drug tests (867 UDT, 88.6%; 112 oral fluid testing, 11.4%) were performed in 320 patients. An inconsistent drug test result was registered in 76/979 tests (7.8%). The incidences of inconsistent test results across the risk tool categories were 7/160 (4.4%) in the low risk category, 32/349 (9.2%) in the moderate risk category, 28/338 (8.3%) in the high risk category, and 9/132 (6.8%) in the high+ risk category. Generalized estimating equation analysis demonstrated that the moderate risk (odds ratio (OR) 2.1, 95% CI 0.9-5.0; P=.10), high risk (OR 2.0, 95% CI 0.8-5.0; P=.14), and high risk+ (OR 2.0, 95% CI 0.7-5.6; P=.20) categories were associated with a nonsignificantly increased risk of inconsistency vs the low risk category. CONCLUSIONS:The developed tool stratified patients during individual visits into risk categories of presenting with drug testing results inconsistent with the prescribed COAT; the higher risk categories showed nonsignificantly higher risk compared to the low risk category. Further development of the tool with additional risk factors in a larger cohort may further clarify and enhance its performance.

Project description:BackgroundChildhood obesity is a serious public health issue among minority youth in the United States. Technology-enhanced approaches can be effective for promoting healthy behavior change.ObjectiveThe purpose of this study was to test the usability of prototypes of a Web-based interactive tool promoting healthy dietary behaviors to reduce childhood obesity risk in urban minority youth. The Web-based tool comprised a manga-style comic with interactive features (eg, sound effects, clickable pop-ups), tailored messaging, and goal setting, and was optimized for use on tablet devices.MethodsLatino and black/African American children ages 9 to 13 years were recruited to participate in two rounds of usability testing. A modified think-aloud method was utilized. Self-reported surveys and field notes were collected. Audio recordings and field notes from usability testing sessions were systematically reviewed by extracting and coding user feedback as either positive comments or usability or negative issues. The quantitative data from self-reported questionnaires were analyzed using descriptive statistics.ResultsTwelve children (four female; eight black/African American) with a mean age of 10.92 (SD 1.16) years participated. Testing highlighted overall positive experiences with the Web-based interactive tool, especially related to storyline, sound effects, and color schemes. Specific usability issues were classified into six themes: appearance, content, special effects, storyline, terminology, and navigation. Changes to the Web-based tool after round 1 included adding a navigation guide, making clickable icons more visible, improving graphic designs, and fixing programming errors. In round 2 of testing (after modifications to the Web-based tool were incorporated), many of the usability issues that were identified in round 1 did not emerge.ConclusionsResults of testing will inform further development and finalization of the tool, which will be tested using a two-group pilot randomized study, with the goal of reducing childhood obesity risk in minority, low-income youth.

Dataset Information

MiRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico.

Publications

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico.

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