Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a ...multitude of parameters. However, there are currently no tools for guiding study design nor are there applications that could predict the performance of somatic structural variant detection. To address this gap, we developed Shiny-SoSV, a user-friendly web-based calculator for determining the impact of common variables on the sensitivity, precision and F1 score of somatic structural variant detection, including choice of variant detection tool, sequencing depth of coverage, variant allele fraction, and variant breakpoint resolution. Using simulation studies, we determined singular and combinatoric effects of these variables, modelled the results using a generalised additive model, allowing structural variant detection performance to be predicted for any combination of predictors. Shiny-SoSV provides an interactive and visual platform for users to easily compare individual and combined impact of different parameters. It predicts the performance of a proposed study design, on somatic structural variant detection, prior to the commencement of benchwork. Shiny-SoSV is freely available at guide and example use-cases.
CohViz is a feedback system that provides students with concept maps as feedback on the cohesion of their writing. Although previous studies demonstrated the effectiveness of CohViz, the accuracy of ...CohViz remains unclear. Thus, we conducted two comprehensive validation studies to assess the accuracy of CohViz in terms of its reliability and validity. In a reliability study, we compared the concept maps generated by CohViz with concept maps generated by four human expert raters based on a text corpus comprising students' explanatory texts (N = 100). Regarding the depiction of cohesion gaps, we obtained high accordance between the CohViz concept maps and the concept maps generated by the human expert raters. However, CohViz tended to overestimate the number of relations within the concept maps. In a validity study, we examined the validity of CohViz and compared central features of the CohViz concept maps with convergent linguistic features and divergent linguistic features based on a Wikipedia text corpus (N = 1020). We found medium to high agreement with the convergent cohesion features and low agreement with the divergent features. Together, these findings suggest that CohViz can be regarded as an accurate feedback system to provide feedback on the cohesion of students' writing.
The paper evaluates the usability of remote satellite-based and proximal ground-based agrometeorological data sources for precision agriculture and crop production in Croatia. The compared ...agrometeorological datasets stem from the open-access data sources Copernicus CDS and the Agri4Cast portal, and commercial in situ agrometeorological stations (PinovaMeteo) which monitor environmental parameters relevant to the physiological state of crops. The study compares relevant parameters for 10 different locations in Croatia for three consecutive years (2019, 2020, and 2021) to investigate whether model-based data from ERA5-Land and Agri4Cast are well-correlated with ground measurements from independent in situ stations (PinovaMeteo) for specific agrometeorological parameters (air and soil temperature, and precipitation). Our results indicate the following: both the ERA5-Land and Agri4Cast datasets show mostly strong positive correlations with ground observations for air temperature, modest correlations for soil temperature, but modest or even low correlations for precipitation. Analysis of the residuals indicates higher overall residual values, especially in areas with complex topography and near large bodies of water or the sea, and deviations of residuals that may limit the usability of satellite- and model-based data for decision-making in agriculture.
The problem of the rapid creation of effective web-applications of one class with using formal means are considered. The conceptual approach to its solution is offered on the basis f analysis of the ...peculiarities of web-applications construction. The approach is based on defining the standard web application architecture and selecting its components using formal methods in accordance with user requirements. A formal logical system is used, which uses the design of web-applications as a process of outputting the formula specified according to the needs of the user, which defines the schemes of execution of the modules of the system. An important feature of the approach is the ability to 3D-visualize the process of designing the system, which creates conditions for effective interaction between developers and machine development tools. Ref. 4, pic. 2
Multi-state models are used in complex disease pathways to describe a process where an individual moves from one state to the next, taking into account competing states during each transition. In a ...multi-state setting, there are various measures to be estimated that are of great epidemiological importance. However, increased complexity of the multi-state setting and predictions over time for individuals with different covariate patterns may lead to increased difficulty in communicating the estimated measures. The need for easy and meaningful communication of the analysis results motivated the development of a web tool to address these issues.
MSMplus is a publicly available web tool, developed via the Shiny R package, with the aim of enhancing the understanding of multi-state model analyses results. The results from any multi-state model analysis are uploaded to the application in a pre-specified format. Through a variety of user-tailored interactive graphs, the application contributes to an improvement in communication, reporting and interpretation of multi-state analysis results as well as comparison between different approaches. The predicted measures that can be supported by MSMplus include, among others, the transition probabilities, the transition intensity rates, the length of stay in each state, the probability of ever visiting a state and user defined measures. Representation of differences, ratios and confidence intervals of the aforementioned measures are also supported. MSMplus is a useful tool that enhances communication and understanding of multi-state model analyses results.
Further use and development of web tools should be encouraged in the future as a means to communicate scientific research.
The remote delivery and monitoring of individually-tailored exercise programs using voice-controlled intelligent personal assistants (VIPAs) that support conversation-based interactions may be an ...acceptable alternative model of digital health delivery for older adults. The aim of this study was to evaluate the enablers and barriers for older adults participating in a home-based exercise program delivered and monitored by VIPAs.
This qualitative study used videoconferencing to conduct semi-structured interviews following a 12-week, prospective single-arm pilot study in 15 adults aged 60 to 89 years living alone in the community. All participants were prescribed an individualized, brief (10 min, 2-4 times per day), home-based muscle strengthening and balance exercise program delivered and monitored using an Amazon Echo Show 5 device (Alexa). Qualitative interview data were analysed using inductive thematic analysis.
All 15 participants (aged 70.3 ± 4.3 years, mean ± SD) attended the semi-structured interview. Themes including enjoyability and ease of use, social engagement and motivation were enablers for participation in the exercise program. Errors in voice recognition, lack of feedback, and preference for other existing digital health modes of exercise delivery were barriers associated with the Alexa technology.
This qualitative study identified enablers and barriers associated with using an Alexa device to deliver and monitor an individualized, home-based exercise program in older adults living alone. Future interventions using VIPAs should focus on reducing technical errors, providing regular exercise feedback, and comparing participants' experiences of exercise programs delivered by VIPAs to programs delivered via other digital health tools.
Electron is one of the most popular JavaScript frameworks for building cross-platform desktop applications. This project-based guide will help you explore the components of the Electron framework and ...its integration with other JS libraries to build real-world desktop apps with an increasing level of complexity.
Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells' karyotype. The nomenclature identifies locations on ...chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype.
Our tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments.
CytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/ . Supplemental Material detailing the underlying algorithms is available.
PDF
