scholarly journals Analysis of patchclamp recordings: model-free multiscale methods and software

2021 ◽  
Vol 50 (2) ◽  
pp. 187-209 ◽  
Author(s):  
Florian Pein ◽  
Benjamin Eltzner ◽  
Axel Munk
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Hidden Markov ◽  
R Package ◽  
Multiscale Methods ◽  
Advantages And Disadvantages ◽  
Model Free ◽  
Practical Guidance ◽  
The Right ◽  
Selection Of

AbstractAnalysis of patchclamp recordings is often a challenging issue. We give practical guidance how such recordings can be analyzed using the model-free multiscale idealization methodology JSMURF, JULES, and HILDE. We provide an operational manual how to use the accompanying software available as an R-package and as a graphical user interface. This includes selection of the right approach and tuning of parameters. We also discuss advantages and disadvantages of model-free approaches in comparison to hidden Markov model approaches and explain how they complement each other.

scholarly journals LexOPS: An R package and user interface for the controlled generation of word stimuli

2020 ◽  
Vol 52 (6) ◽  
pp. 2372-2382
Author(s):  
Jack E. Taylor ◽  
Alistair Beith ◽  
Sara C. Sereno
Keyword(s):  
User Interface ◽  
Factorial Design ◽  
Graphical User Interface ◽  
R Package ◽  
Psycholinguistic Research ◽  
Link Type ◽  
Control Current ◽  
Word Lists ◽  
And Control ◽  
Manipulation And Control

AbstractLexOPS is an R package and user interface designed to facilitate the generation of word stimuli for use in research. Notably, the tool permits the generation of suitably controlled word lists for any user-specified factorial design and can be adapted for use with any language. It features an intuitive graphical user interface, including the visualization of both the distributions within and relationships among variables of interest. An inbuilt database of English words is also provided, including a range of lexical variables commonly used in psycholinguistic research. This article introduces LexOPS, outlining the features of the package and detailing the sources of the inbuilt dataset. We also report a validation analysis, showing that, in comparison to stimuli of existing studies, stimuli optimized with LexOPS generally demonstrate greater constraint and consistency in variable manipulation and control. Current instructions for installing and using LexOPS are available at https://JackEdTaylor.github.io/LexOPSdocs/.

scholarly journals ntbox : An r package with graphical user interface for modelling and evaluating multidimensional ecological niches

2020 ◽  
Vol 11 (10) ◽  
pp. 1199-1206 ◽  
Author(s):  
Luis Osorio‐Olvera ◽  
Andrés Lira‐Noriega ◽  
Jorge Soberón ◽  
Andrew Townsend Peterson ◽  
Manuel Falconi ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
R Package ◽  
Ecological Niches

scholarly journals genBaRcode: a comprehensive R-package for genetic barcode analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2189-2194 ◽  
Author(s):  
Lars Thielecke ◽  
Kerstin Cornils ◽  
Ingmar Glauche
Keyword(s):  
User Interface ◽  
Next Generation Sequencing ◽  
Error Correction ◽  
Graphical User Interface ◽  
R Package ◽  
Next Generation ◽  
Analysis Strategies ◽  
Genetic Sequences ◽  
Reproducible Analysis ◽  
Generation Sequencing

Abstract Motivation Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance. Results We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies. Availability and implementation The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

scholarly journals Migration of Inferior Vena Caval filter to the Right Atrium: Is any model free of this complication?

2016 ◽  
Vol 9 (3) ◽  
Author(s):  
Haider Zaman ◽  
Anjum Jalal ◽  
Zulfiqar Haider
Keyword(s):  
Inferior Vena ◽  
Inferior Vena Caval ◽  
Model Free ◽  
Inferior Vena Caval Filter ◽  
Ivc Filters ◽  
Life Threatening ◽  
And Migration ◽  
The Right ◽  
Vena Caval Filter ◽  
Selection Of

The use of inferior vena caval (IVC) filters has been an accepted method for preventing pulmonary embolism, especially in cases where there are contraindications to anticoagulation. However, these filters have numerous potential complications some of which could be life threatening like, thrombosis and migration of the filter. The "Antheor" filter was designed to prevent this complication. Unfortunately, we encountered one patient where it has been unsuccessful in this regard. We therefore, believe that there is no ideal filter and the selection of a filter requires thorough knowledge of the limitations of individual brand.

Blade Tip Measurement Advanced Visualization Using a Three Dimensional Representation

2011 ◽  
Author(s):  
Michae¨l A. Hafner ◽  
Thomas A. Holst ◽  
Scott A. Billington
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Gas Turbines ◽  
Three Dimensional ◽  
Tip Clearance ◽  
Shape Fitting ◽  
Multiple Sensors ◽  
Three Dimensional Representation ◽  
The Right ◽  
3D Graphical User Interface

A microwave tip clearance sensor capable of measuring the hottest stages of industrial and aero gas turbines has been developed. This new microwave sensor has been integrated into a commercial package for online real-time monitoring of machine data. However, data analysis of large numbers of tip clearance probes makes standard industry graphic techniques cluttered. A method has been developed to reduce this data and visualize it in order to provide intuitive representations of the data from which a user can quickly draw the right conclusions about machine behavior. The main motivation for the development of a 3D graphical user interface is the density of information that can be shown to the user at one time. Tip clearance measurement is very data-rich, as every individual blade for each sensor mounted around the engine case is available. The result is that it may be difficult to find slight changes within hundreds of clearance trends. Only specialists with long experience in tip clearance measurement can synthesize all the data quickly enough using standard 2D plots. The 3D graphical user interface brings all of this data together to calculate the aggregated blade pattern, rotor positioning, and estimated case shape. All of these measurements are available to the user in a single visualization. Colors indicating alarm or clearance scale quickly draw attention to the most important data such as the minimum clearance point around the engine case where a rub may be likely to occur. This method is based about a case shape fitting algorithm that combines data from multiple sensors to make a case shape estimate based on fitting of a non-uniform rational B-spline (NURB). The scaling is also distorted in order to accentuate the graphics in a way that provides an intuitive understanding of the machine state. The method of applying this data accentuation is important so as to not be misleading. This innovative navigation interface presented in this paper capitalizes on modern advances in computer graphics to aid engineers and operators in understanding, access, monitoring, and analysis of tip clearance and air-gap measurements.

scholarly journals digeR: a graphical user interface R package for analyzing 2D-DIGE data

2009 ◽  
Vol 25 (22) ◽  
pp. 3033-3034 ◽  
Author(s):  
Yue Fan ◽  
T. Brendan Murphy ◽  
R. William G. Watson
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
R Package ◽  
2D Dige
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