Prediction of MicroRNA Precursors Using Parsimonious Feature Sets

MicroRNAs (miRNAs) are a class of short noncoding RNAs that regulate gene expression through base pairing with messenger RNAs. Due to the interest in studying miRNA dysregulation in disease and limits of validated miRNA references, identification of novel miRNAs is a critical task. The performance of different models to predict novel miRNAs varies with the features chosen as predictors. However, no study has systematically compared published feature sets. We constructed a comprehensive feature set using the minimum free energy of the secondary structure of precursor miRNAs, a set of nucleotide-structure triplets, and additional extracted sequence and structure characteristics. We then compared the predictive value of our comprehensive feature set to those from three previously published studies, using logistic regression and random forest classifiers. We found that classifiers containing as few as seven highly predictive features are able to predict novel precursor miRNAs as well as classifiers that use larger feature sets. In a real data set, our method correctly identified the holdout miRNAs relevant to renal cancer.

International retrospective study of the pipeline embolization device: a multicenter aneurysm treatment study

BACKGROUND AND PURPOSE

Flow diverters are increasingly used in the endovascular treatment of intracranial aneurysms. Our aim was to determine neurologic complication rates following Pipeline Embolization Device placement for intracranial aneurysm treatment in a real-world setting.

MATERIALS AND METHODS

We retrospectively evaluated all patients with intracranial aneurysms treated with the Pipeline Embolization Device between July 2008 and February 2013 in 17 centers worldwide. We defined 4 subgroups: internal carotid artery aneurysms of ≥10 mm, ICA aneurysms of <10 mm, other anterior circulation aneurysms, and posterior circulation aneurysms. Neurologic complications included spontaneous rupture, intracranial hemorrhage, ischemic stroke, permanent cranial neuropathy, and mortality. Comparisons were made with t tests or ANOVAs for continuous variables and the Pearson χ(2) or Fisher exact test for categoric variables.

RESULTS

In total, 793 patients with 906 aneurysms were included. The neurologic morbidity and mortality rate was 8.4% (67/793), highest in the posterior circulation group (16.4%, 9/55) and lowest in the ICA <10-mm group (4.8%, 14/294) (P = .01). The spontaneous rupture rate was 0.6% (5/793). The intracranial hemorrhage rate was 2.4% (19/793). Ischemic stroke rates were 4.7% (37/793), highest in patients with posterior circulation aneurysms (7.3%, 4/55) and lowest in the ICA <10-mm group (2.7%, 8/294) (P = .16). Neurologic mortality was 3.8% (30/793), highest in the posterior circulation group (10.9%, 6/55) and lowest in the anterior circulation ICA <10-mm group (1.4%, 4/294) (P < .01).

CONCLUSIONS

Aneurysm treatment with the Pipeline Embolization Device is associated with the lowest complication rates when used to treat small ICA aneurysms. Procedure-related morbidity and mortality are higher in the treatment of posterior circulation and giant aneurysms.

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure

Summary: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. MAGI’s salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication.

Availability and implementation: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu.

Contact:j5kim@ucsd.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

EPODE - A Model for Reducing the Incidence of Obesity and Weight-related Comorbidities

Obesity is a global epidemic: it is estimated that the majority of the world's adults will be overweight or obese by 2030. It is therefore important to reverse trends towards increasing childhood obesity by interventions at the community level. Ensemble Prévenons l'obésité Des Enfants (EPODE, Together Let's Prevent Childhood Obesity) is a large-scale, coordinated, capacity-building approach for communities to implement effective and sustainable strategies to address this challenge. EPODE comprises four critical components: political commitment, public and private partnerships, community-based actions, and evaluation. The multi-stakeholder approach promoted through the EPODE methodology has already shown encouraging results in preventing childhood obesity in France and Belgium and has reduced the socioeconomic gap in obesity prevalence in France. The EPODE methodology has now been implemented in a number of countries worldwide, and provides a valuable model that may be applicable to other lifestyle-related diseases.

EPODE—A Model for Reducing the Incidence of Obesity and Weight-related Comorbidities

Obesity is a global epidemic: it is estimated that the majority of the world’s adults will be overweight or obese by 2030. It is therefore important to reverse trends toward increasing childhood obesity by interventions at the community level. Ensemble Prévenons l’Obésité Des Enfants (EPODE, Together Let’s Prevent Childhood Obesity) is a large-scale, coordinated, capacity-building approach for communities to implement effective and sustainable strategies to address this challenge. EPODE comprises four critical components: political commitment, public and private partnerships, community-based actions, and evaluation. The multistakeholder approach promoted through the EPODE methodology has already shown encouraging results in preventing childhood obesity in France and Belgium and has reduced the socioeconomic gap in obesity prevalence in France. The EPODE methodology has now been implemented in a number of countries worldwide, and provides a valuable model that may be applicable to other lifestyle-related diseases.