Ultrasound speckle tracking to detect vascular distensibility changes from angioplasty and branch ligation in a radio-cephalic fistula: Use of novel open source software

2020 ◽  
pp. 112972982095991
Author(s):  
William F Weitzel ◽  
Nirmala Rajaram ◽  
Yihao Zheng ◽  
Brian J Thelen ◽  
Venkataramu N Krishnamurthy ◽  
...  
Keyword(s):  
High Resolution ◽  
Open Source ◽  
Open Source Software ◽  
Vessel Wall ◽  
Speckle Tracking ◽  
Wall Motion ◽  
Wide Range ◽  
Before And After ◽  
Conventional Ultrasound ◽  
Duplex Doppler

We used novel open source software, based on an ultrasound speckle tracking algorithm, to examine the distensibility of the vessel wall of the inflow artery, anastomosis, and outflow vein before and after two procedures. An 83-year-old white man with a poorly maturing radio-cephalic fistula received an angioplasty at the anastomosis followed by branch ligation 28 days later. Duplex Doppler measurements corroborated the blood flow related changes anticipated from the interventions. The experimental distensibility results showed that it is technically feasible to measure subtle vessel wall motion changes with high resolution (sub-millimeter) using standard Digital Imaging and Communications in Medicine (DICOM) ultrasound data, which are readily available on conventional ultrasound scanners. While this methodology was originally developed using high resolution radiofrequency from ultrasound data, the goal of this study was to use DICOM data, which makes this technology accessible to a wide range of users.

scholarly journals P342 Left atrial contraction longitudinal strain is a volume-independet parameter

2020 ◽  
Vol 21 (Supplement_1) ◽  
Author(s):  
S Unlu ◽  
B Sezenoz ◽  
A Sahinarslan ◽  
T Arinsoy ◽  
A Cengel
Keyword(s):  
Speckle Tracking ◽  
Longitudinal Strain ◽  
Heart Diseases ◽  
Left Ventricular ◽  
Reference Points ◽  
Volume Index ◽  
Valvular Heart Diseases ◽  
Wide Range ◽  
Before And After ◽  
2D Speckle Tracking

Abstract Background The left atrium (LA) is the main contributor of left ventricular (LV) filling. LA volume and volume index are routinely evaluated during echocardiographic assessment as having prognostic value in a wide range of cardiovascular pathologies. Yet, LA volume is easily affected by volume status. Thus, a non-invasive novel parameter such as indices of LA longitudinal strain (LS) have been proposed as alternative measurements. LA strain was shown to be associated with LV filling pressures and it has been suggested to provide prognostic information in patients with heart failure, atrial fibrillation, ischemic and valvular heart diseases. Nevertheless the acute effect of hemodynamic changes on LA LS indices is not well-established due to lack of evidence in healthy subjects and patient populations. The aim of this study is to evaluate the LA mechanics and change in echocardiographic methods used for assessment of LA by examining the end stage kidney patients before and after the hemodialysis (HD). Methods Patients between 18 and 85 years of age, receiving HD for at least 6 months were included. The echocardiographic images were obtained before and after HD. 2D speckle tracking strain analysis was performed for LA in 45 patients. Reference points for analysis are set on the "P" waves. LA reservoir, conduit and contraction phase LS were calculated. The changes in echocardiographic methods before and after hemodialysis were examined. Correlation between volume depletion and change in echocardiographic parameters were calculated. Results 45 patients (47.7 ± 14.7 years of age, 19 women) were included in study. The mean volume of ultrafiltration was 2755.12 ± 845.5 ml . The chamber sizes of LA are decreased after hemodialysis (LA diameter; 4.9 ± 0.8 cm vs. 4.4 ± 0.5 cm p < 0.001, LA area; 27.8 ± 4.0 cm2 vs. 19.6 ± 3.8 cm2 p < 0.001). LA reservoir phase LS measurements (% 44.6 ± 10.8 vs. % 38.15 ± 8.11 p < 0.001) showed significant changes after HD. In contrast LA contraction LS measurements (% -16.6 ± 7.0 vs. % -16.4 ± 7.1 p:0.893) did not differ after HD. The relative change in LA reservoir phase LS (r = 0.74, p:0.001) showed correlation with the ultrafiltrated volume. Conclusion LA contraction LS is a volume independent measurement obtained by 2D speckle tracking. Assessment of LA mechanics with echocardiography would be an easy and repeatable assessment which can guide to describe the cardiac pathophysiology and hemodynamics better. Moreover defining novel volume independent parameters for evaluation of LA would contribute to clinical perspectives of the patients.

scholarly journals Short communication: A semi-automated method for rapid fault slip analysis from topographic scarp profiles

2019 ◽  
Author(s):  
Franklin D. Wolfe ◽  
Timothy A. Stahl ◽  
Pilar Villamor ◽  
Biljana Lukovic
Keyword(s):  
Monte Carlo ◽  
High Resolution ◽  
Open Source ◽  
Hanging Wall ◽  
Temporal Analysis ◽  
Fault Scarp ◽  
Fault Slip ◽  
Source Characterization ◽  
Automated Method ◽  
Wide Range

Abstract. Here, we introduce an open source, semi-automated, Python-based graphical user interface (GUI) called the Monte Carlo Slip Statistics Toolkit (MCSST) for estimating dip slip on individual or bulk fault datasets. Using this toolkit, profiles are defined across fault scarps in high-resolution digital elevation models (DEMs) and then relevant fault scarp components are interactively identified (e.g., footwall, hanging wall, and scarp). Displacement statistics are calculated automatically using Monte Carlo simulation and can be conveniently visualized in Geographic Information Systems (GIS) for spatial analysis. Fault slip rates can also be calculated when ages of footwall and hanging wall surfaces are known, allowing for temporal analysis. This method allows for rapid analysis of tens to hundreds of faults in rapid succession within GIS and a Python coding environment. Application of this method may contribute to a wide range of regional and local earthquake geology studies with adequate high-resolution DEM coverage, both regional fault source characterization for seismic hazard and/or estimating geologic slip and strain rates, including creating long-term deformation maps. ArcGIS versions of these functions are available, as well ones that utilize free, open source Quantum GIS (QGIS) and Jupyter Notebook Python software.

scholarly journals Mapping of land cover with open‐source software and ultra‐high‐resolution imagery acquired with unmanned aerial vehicles

2020 ◽  
Vol 6 (4) ◽  
pp. 487-497 ◽  
Author(s):  
Ned Horning ◽  
Erica Fleishman ◽  
Peter J. Ersts ◽  
Frank A. Fogarty ◽  
Martha Wohlfeil Zillig
Keyword(s):  
High Resolution ◽  
Land Cover ◽  
Unmanned Aerial Vehicles ◽  
Open Source ◽  
Open Source Software ◽  
Aerial Vehicles ◽  
High Resolution Imagery

scholarly journals Monitoring Cropping Systems: From Data Collection to Cloud Database Storage Using Open Source Software

Proceedings ◽  
2020 ◽  
Vol 30 (1) ◽  
pp. 79
Author(s):  
Ioanna Panagea ◽  
Dangol Anuja ◽  
Marc Olijslagers ◽  
Jan Diels ◽  
Guido Wyseure
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Web Application ◽  
Cropping Systems ◽  
Cropping System ◽  
Query Languages ◽  
Climatic Conditions ◽  
Raw Data ◽  
Wide Range ◽  
Study Sites

Agricultural cropping systems and experiments include complex interactions of processes and various management practices and/or treatments under a wide range of environmental and climatic conditions. The use of standardized formats to monitor and document these systems and experiments can help researchers and stakeholders to efficiently exchange data, promote interdisciplinary collaborations, and simplify modelling and analysis procedures. In the scope of the SoilCare Horizon 2020 project monitoring and assessment work package, an integrated scheme to collect, validate, store, and access cropping system information and experimental data from 16 study sites, was created. The aim of the scheme is to make the data readily available in a way that the information is useful, easy to access and download, and safe, relying only on open source software. The database design considers data and metadata required to properly and easily monitor, process, and analyse cropping systems and/or agricultural experiments. The scheme allows for the storage of data and metadata regarding the experimental set-up, associated people and institutions, information about field management operations and experimental procedures which are clearly separated for making analysis procedures faster, links between system components, and information about the environmental and climatic conditions. Raw data are entered by the users into a structured spreadsheet. The quality is checked before storing the data into the database. Providing raw data allows processing and analysing as each other user needs. A desktop import application has been created to upload the information from spreadsheet to database, which includes automated error checks of relationship tables, data types, data constraints, etc. The final component of the scheme is the database web application interface, which enables users to access and query the database across the study sites without the knowledge of query languages and to download the required data. For this system design, PostgreSQL is used for storing the data, pgAdmin 4 for database management administration, MongoDB for user management and authentication, Python for the development of the import application, Angular and Node.js/Express for the web application and spreadsheets compatible with LibreOffice Calc. The system is currently tested with data provided by the SoilCare study sites. Preliminary testing indicated that extended quality control of the spreadsheets was required from the system’s administrator to meet the standards and restrictions of the import application. Initial comments from the users indicate that the database scheme, even if it initially seems complicated, includes all the variables and details required for a complete monitoring and modelling of an agricultural cropping system.

scholarly journals Free and Open Source Software for Computational Chemistry Education

2021 ◽  
Author(s):  
Susi Lehtola ◽  
Antti Karttunen
Keyword(s):  
Computational Chemistry ◽  
Open Source ◽  
Open Source Software ◽  
Density Functional ◽  
Chemistry Education ◽  
Tight Binding ◽  
Industrial Applications ◽  
Bring Your Own Device ◽  
Wide Range ◽  
The Masses

Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on various free and open source software (FOSS) quantum chemistry packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. Combined with the remarkable increase in the computing power of personal devices, which now rivals that of the fastest supercomputers in the world of the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS computational chemistry packages, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device (BYOD) scheme. FOSS software can be made trivially simple to install and keep up to date, eliminating the need for departmental support, and also enables comprehensive teaching strategies, as various algorithms' actual implementations can be used in teaching. We exemplify what kinds of calculations are feasible with four FOSS electronic structure programs, assuming only extremely modest computational resources, to illustrate how FOSS packages enable decentralized approaches to computational chemistry education within the BYOD scheme. FOSS also has further benefits: the open access to the source code of FOSS packages democratizes the science of computational chemistry, and FOSS packages can be used without limitation also beyond education, in academic and industrial applications, for example. For these reasons, we believe FOSS will become ever more pervasive in computational chemistry.

scholarly journals RADAR-Base: Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices

10.2196/11734 ◽  
2019 ◽  
Vol 7 (8) ◽  
pp. e11734 ◽  
Author(s):  
Yatharth Ranjan ◽  
Zulqarnain Rashid ◽  
Callum Stewart ◽  
Pauline Conde ◽  
Mark Begale ◽  
...  
Keyword(s):  
High Resolution ◽  
Data Collection ◽  
Open Source ◽  
Mobile Health ◽  
Large Scale ◽  
Streaming Data ◽  
Security And Privacy ◽  
The European Union ◽  
Wide Range ◽  
Remote Assessment

Background With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field. Objective Wide-bandwidth networks, smartphone penetrance, and wearable sensors offer new possibilities for collecting near-real-time high-resolution datasets from large numbers of participants. The aim of this study was to build a platform that would cater for large-scale data collection for remote monitoring initiatives. Key criteria are around scalability, extensibility, security, and privacy. Methods RADAR-base is developed as a modular application; the backend is built on a backbone of the highly successful Confluent/Apache Kafka framework for streaming data. To facilitate scaling and ease of deployment, we use Docker containers to package the components of the platform. RADAR-base provides 2 main mobile apps for data collection, a Passive App and an Active App. Other third-Party Apps and sensors are easily integrated into the platform. Management user interfaces to support data collection and enrolment are also provided. Results General principles of the platform components and design of RADAR-base are presented here, with examples of the types of data currently being collected from devices used in RADAR-CNS projects: Multiple Sclerosis, Epilepsy, and Depression cohorts. Conclusions RADAR-base is a fully functional, remote data collection platform built around Confluent/Apache Kafka and provides off-the-shelf components for projects interested in collecting mHealth datasets at scale.

FRAME-Sim: A Free-Software, Multibody-Based, Pilot in the Loop Rotorcraft Flight Simulator

2018 ◽  
Author(s):  
Andrea Zanoni ◽  
Luca Conti ◽  
Pierangelo Masarati
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Development Process ◽  
Free Software ◽  
Design Stage ◽  
Careful Planning ◽  
Modern Approach ◽  
Handling Qualities ◽  
Wide Range ◽  
Representative Model

In the context of a modern approach to the design of rotocraft, handling qualities should be the result of careful planning, rather than the output of a multitude of other choices, made primarily focusing on more immediate constraints. For a wide range of flight conditions and mission task elements, the test pilot feedback is the essential measure upon which the design choices are made. Thus, it is becoming of fundamental importance to be able to simulate a representative model of the vehicle in a pilot-in-the-loop environment as early as possible in the design stage. This work is intended to document the development process of one such system currently being realized at the facilities belonging to the Aerospace Science and Technology Department of Politecnico di Milano. Particular attention is given to the software architecture, based on the free and open-source multibody solver MBDyn. The development of a module specifically designed to exploit the environment visualization capabilities of FlightGear, also a free and open-source software, is presented.

A Longitudinal Study of Fan-In and Fan-Out Coupling in Open-Source Systems

2011 ◽  
Vol 2 (4) ◽  
pp. 1-26 ◽  
Author(s):  
Asma Mubarak ◽  
Steve Counsell ◽  
Robert M. Hierons
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Classes ◽  
Future Problem ◽  
Wide Range ◽  
Type Classes ◽  
Low Levels ◽  
The Relationship ◽  
Open Source Systems ◽  
Maintenance Problem

Excessive coupling between object-oriented classes is widely acknowledged as a maintenance problem that can result in a higher propensity for faults in systems and a ‘stored up’ future problem. This paper explores the relationship between ‘fan-in’ and ‘fan-out’ coupling metrics over multiple versions of open-source software. More specifically, the relationship between the two metrics is explored to determine patterns of growth in each over the course of time. The JHawk tool was used to extract the two metrics from five open-source systems. Results show a wide range of traits in the classes to explain both high and low levels of fan-in and fan-out. Evidence was also found of certain ‘key’ classes (with both high fan-in and fan-out) and ‘client’ and ‘server’-type classes with high fan-out and fan-in, respectively. This paper provides an explanation of the composition and existence of such classes as well as for disproportionate increases in each of the two metrics over time. Finally, it was found that high fan-in class values tended to be associated with small classes; classes with high fan-out on the other hand tended to be relatively large classes.

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