A novel method for assessing design fidelity in web-based behavioral interventions.

Abstract Fluorescence in situ hybridization (FISH) is a powerful single-cell technique that harnesses nucleic acid base pairing to detect the abundance and positioning of cellular RNA and DNA molecules in fixed samples. Recent technology development has paved the way to the construction of FISH probes entirely from synthetic oligonucleotides (oligos), allowing the optimization of thermodynamic properties together with the opportunity to design probes against any sequenced genome. However, comparatively little progress has been made in the development of computational tools to facilitate the oligos design, and even less has been done to extend their accessibility. OligoMiner is an open-source and modular pipeline written in Python that introduces a novel method of assessing probe specificity that employs supervised machine learning to predict probe binding specificity from genome-scale sequence alignment information. However, its use is restricted to only those people who are confident with command line interfaces because it lacks a Graphical User Interface (GUI), potentially cutting out many researchers from this technology. Here, we present OligoMinerApp (http://oligominerapp.org), a web-based application that aims to extend the OligoMiner framework through the implementation of a smart and easy-to-use GUI and the introduction of new functionalities specially designed to make effective probe mining available to everyone.

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Evaluation of Web Based Behavioral Interventions Using Spoken Tutorials

2012 IEEE Fourth International Conference on Technology for Education ◽

10.1109/t4e.2012.12 ◽

2012 ◽

Cited By ~ 8

Author(s):

Kiran L.N. Eranki ◽

Kannan M. Moudgalya

Keyword(s):

Behavioral Interventions ◽

Web Based

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Non-algorithmic approach to accessory pathway localization based on a mobile app

EP Europace ◽

10.1093/europace/euab116.024 ◽

2021 ◽

Vol 23 (Supplement_3) ◽

Author(s):

M Jastrzebski ◽

P Moskal

Keyword(s):

Accessory Pathway ◽

Mobile App ◽

Public Institution ◽

Atrial Pacing ◽

Maximum Probability ◽

Web Based ◽

Actual Distribution ◽

Accessory Pathways ◽

Novel Method ◽

Density Map

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): Polish Cardiac Society - Section of Non-invasive Electrocardiology and Telemonitoring (PTK SENIT) Background. Electrocardiographical localization of accessory pathways (AP) in WPW syndrome remains an elusive goal. Despite several, often very complex algorithms that were developed over the last three decades, none of them is very accurate - as demonstrated by several independent validation studies. Moreover, algorithms are difficult to remember, which further limits their usefulness. The accessory pathway regions are arbitrary and transitions between them are smooth, not binary. The same applies to ECG features such as QRS polarity – they are not binary. Moreover, even the most careful ECG lead placement cannot compensate for the variability in heart position within the chest. Therefore, it is unrealistic to expect that any ECG feature or feature set will precisely identify a particular location in a 0 vs. 1 fashion. Aim We intend to create a mobile app / web based localizing application, that would support a novel method for AP localization: a colour density map generator - based on actual distribution of a sizable number of accessory pathway with a particular QRS features. Methods A total of 881 consecutive AP ablation procedures were reviewed and patients with successful ablation of an overt accessory pathway were included. ECG with baseline and full preexcitation obtained during incremental atrial pacing were obtained. AP localization was based on stored fluoroscopic images in several projections and procedure description. Each AP localization, as well as QRS polarity in all 12 leads, separately for full and baseline preexcitation patterns, were coded and introduced into the application database. An application web-based, optimized for mobile devices was developed. This application enabled to graphically show changing localization of AP with regard to the introduced, at each step, QRS polarity in a particular ECG lead. User can choose his/her own steps or criteria; there is no need to adhere to the proposed steps. Results A total of 604 patients/ ECGs were available for density map generation. With each additional lead QRS information introduced into the application the user can appreciate more and more precise localization of the AP. This quickly enables to pinpoint the area of maximum probability, i.e. the most likely/frequent location, followed by the immediate adjacent locations. Representative screen shots of to typical inital steps for left- and right-sided APs are provided below (Figure 1 and Figure 2). Limited prospective assessment was very favourable. Conclusions A novel method, easy to use, not requiring to remember any algorithmic steps, and based on an analysis of by far the largest cohort of over accessory pathways (in comparison with published algorithms) was developed. Prospective validation of the localization application seems warranted. Abstract Figure.

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A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

Journal of The Royal Society Interface ◽

10.1098/rsif.2014.0937 ◽

2015 ◽

Vol 12 (102) ◽

pp. 20140937 ◽

Cited By ~ 10

Author(s):

Junwei Han ◽

Chunquan Li ◽

Haixiu Yang ◽

Yanjun Xu ◽

Chunlong Zhang ◽

...

Keyword(s):

Enrichment Analysis ◽

Distribution Functions ◽

Gene Set Enrichment Analysis ◽

Cumulative Distribution ◽

Global Network ◽

Web Based ◽

Novel Method ◽

Microarray Datasets ◽

Identification Analysis ◽

Global Influence

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools ( http://bioinfo.hrbmu.edu.cn/PAGI ).

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SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis

10.1101/2021.03.19.435534 ◽

2021 ◽

Author(s):

Marmar Moussa ◽

Ion Mandoiu

Keyword(s):

Data Analysis ◽

Single Cell ◽

Differential Expression Analysis ◽

Analysis Tool ◽

Rna Seq ◽

Web Based ◽

Inverse Document Frequency ◽

Sequencing Technologies ◽

Document Frequency ◽

Novel Method

Single cell RNA-Seq (scRNA-Seq) is critical for studying cellular function and phenotypic heterogeneity as well as the development of tissues and tumors. Here, we present SC1 a web-based highly interactive scRNA-Seq data analysis tool publicly accessible at https://sc1.engr.uconn.edu. The tool presents an integrated workflow for scRNA-Seq analysis, implements a novel method of selecting informative genes based on Term-Frequency Inverse-Document-Frequency (TF-IDF) scores, and provides a broad range of methods for clustering, differential expression analysis, gene enrichment, interactive visualization, and cell cycle analysis. The tool integrates other single cell omics data modalities like TCR-Seq and supports several single cell sequencing technologies. In just a few steps, researchers can generate a comprehensive analysis and gain powerful insights from their scRNA-Seq data.

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The Efficacy of Web-Based Cognitive Behavioral Interventions for Chronic Pain: A Systematic Review and Meta-Analysis

Journal of Pain ◽

10.1016/j.jpain.2010.06.005 ◽

2010 ◽

Vol 11 (10) ◽

pp. 917-929 ◽

Cited By ~ 161

Author(s):

Debora Duarte Macea ◽

Krzysztof Gajos ◽

Yasser Armynd Daglia Calil ◽

Felipe Fregni

Keyword(s):

Systematic Review ◽

Chronic Pain ◽

Behavioral Interventions ◽

Meta Analysis ◽

Cognitive Behavioral ◽

Web Based ◽

Cognitive Behavioral Interventions

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Student-athlete concussion disclosure and coach communication within collegiate athletics

Journal of Concussion ◽

10.1177/2059700219894104 ◽

2019 ◽

Vol 3 ◽

pp. 205970021989410

Author(s):

Jeffrey J Milroy ◽

David L Wyrick ◽

Lindsey Sanders ◽

Erin Refisteck ◽

Emily Beamon

Keyword(s):

Staff Member ◽

Sports Medicine ◽

Behavioral Interventions ◽

The United States ◽

Preliminary Evidence ◽

Athletic Trainer ◽

Student Athlete ◽

Web Based ◽

Biological Sex ◽

The Impact

Background Between 1.6 and 3.8 million sports- and recreation-related concussions occur in the United States annually. Reports indicate that a significant number of athletes who have experienced symptoms of a potential sport-related concussion did not disclose their symptoms. Aims The purpose of this study was to investigate the impact of coach communication about concussion disclosure on student-athlete intentions to disclose symptoms of a concussion and encourage another student-athlete to disclose their concussion symptoms. Methods A total of 2881 student-athletes completed a web-based survey during Fall of 2016. Multiple linear regression was conducted to primarily investigate the relationship between coach communication and intentions to disclose concussion symptoms. Secondarily, biological sex, year in school, athletic division, and sport category was also assessed. Results Coach communication predicted greater intentions to disclose symptoms to their coach, athletic trainer/sports medicine sports medicine staff member and encourage another athlete to disclose their symptoms of a concussion. Biological sex and sport category also predicted intentions to disclose concussion symptoms. Discussion Findings from this study provide support for the important role coaches play in an athlete’s regarding concussion safety and introduces preliminary evidence suggesting the impact of coach communication on athlete intentions to disclose concussion symptoms to a coach or athletic trainer/sports medicine staff member. Conclusion Future studies and behavioral interventions ought to consider the inclusion of coach communication or other coach-related variables when exploring concussion disclosure among athletes.

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