scholarly journals J une : open-source individual-based epidemiology simulation

2021 ◽  
Vol 8 (7) ◽  
pp. 210506
Author(s):  
Joseph Aylett-Bullock ◽  
Carolina Cuesta-Lazaro ◽  
Arnau Quera-Bofarull ◽  
Miguel Icaza-Lizaola ◽  
Aidan Sedgewick ◽  
...  
Keyword(s):  
Social Interactions ◽  
Open Source ◽  
Census Data ◽  
Initial Model ◽  
Mortality Statistics ◽  
Virtual Population ◽  
Social Mixing ◽  
Open Source Framework ◽  
Detailed Simulation

We introduce J une , an open-source framework for the detailed simulation of epidemics on the basis of social interactions in a virtual population constructed from geographically granular census data, reflecting age, sex, ethnicity and socio-economic indicators. Interactions between individuals are modelled in groups of various sizes and properties, such as households, schools and workplaces, and other social activities using social mixing matrices. J une provides a suite of flexible parametrizations that describe infectious diseases, how they are transmitted and affect contaminated individuals. In this paper, we apply J une to the specific case of modelling the spread of COVID-19 in England. We discuss the quality of initial model outputs which reproduce reported hospital admission and mortality statistics at national and regional levels as well as by age strata.

scholarly journals JUNE: open-source individual-based epidemiology simulation

2020 ◽  
Author(s):  
Frank Krauss ◽  
Joseph Bullock ◽  
Carolina Cuesta-Lazaro ◽  
Arnau Quera-Bofarull ◽  
Miguel Icaza-Lizaola ◽  
...  
Keyword(s):  
Social Interactions ◽  
Open Source ◽  
Census Data ◽  
Initial Model ◽  
Mortality Statistics ◽  
Virtual Population ◽  
Social Mixing ◽  
Open Source Framework ◽  
Detailed Simulation

We introduce JUNE, an open-source framework for the detailed simulation of epidemics on the basis of social interactions in a virtual population constructed from geographically granular census data, reflecting age, sex, ethnicity, and socio-economic indicators. Interactions between individuals are modelled in groups of various sizes and properties, such as households, schools and workplaces, and other social activities using social mixing matrices. JUNE provides a suite of flexible parameterisations that describe infectious diseases, how they are transmitted and affect contaminated individuals. In this paper we apply JUNE to the specific case of modelling the spread of COVID-19 in England. We discuss the quality of initial model outputs which reproduce reported hospital admission and mortality statistics at national and regional levels as well as by age strata.

scholarly journals A standardized framework for testing the performance of sleep-tracking technology: step-by-step guidelines and open-source code

SLEEP ◽  
2020 ◽  
Author(s):  
Luca Menghini ◽  
Nicola Cellini ◽  
Aimee Goldstone ◽  
Fiona C Baker ◽  
Massimiliano de Zambotti
Keyword(s):  
Open Source ◽  
Validation Studies ◽  
Large Scale ◽  
Analytical Framework ◽  
Clinical Settings ◽  
Large Scale Data ◽  
Fast Pace ◽  
Epoch Analysis ◽  
Tracking Devices

Abstract Sleep-tracking devices, particularly within the consumer sleep technology (CST) space, are increasingly used in both research and clinical settings, providing new opportunities for large-scale data collection in highly ecological conditions. Due to the fast pace of the CST industry combined with the lack of a standardized framework to evaluate the performance of sleep trackers, their accuracy and reliability in measuring sleep remains largely unknown. Here, we provide a step-by-step analytical framework for evaluating the performance of sleep trackers (including standard actigraphy), as compared with gold-standard polysomnography (PSG) or other reference methods. The analytical guidelines are based on recent recommendations for evaluating and using CST from our group and others (de Zambotti and colleagues; Depner and colleagues), and include raw data organization as well as critical analytical procedures, including discrepancy analysis, Bland–Altman plots, and epoch-by-epoch analysis. Analytical steps are accompanied by open-source R functions (depicted at https://sri-human-sleep.github.io/sleep-trackers-performance/AnalyticalPipeline_v1.0.0.html). In addition, an empirical sample dataset is used to describe and discuss the main outcomes of the proposed pipeline. The guidelines and the accompanying functions are aimed at standardizing the testing of CSTs performance, to not only increase the replicability of validation studies, but also to provide ready-to-use tools to researchers and clinicians. All in all, this work can help to increase the efficiency, interpretation, and quality of validation studies, and to improve the informed adoption of CST in research and clinical settings.

scholarly journals Three Strategies for Describing Social Interactions of Adolescents in a Multicultural Environment—Indicators for the Quality of Life Research

2021 ◽  
Vol 18 (15) ◽  
pp. 8166
Author(s):  
Alicja Szerląg ◽  
Arkadiusz Urbanek ◽  
Kamila Gandecka
Keyword(s):  
Quality Of Life ◽  
Social Interactions ◽  
Social Relationships ◽  
Social Relations ◽  
Living Environment ◽  
Life Assessment ◽  
Multicultural Environment ◽  
Multicultural Community ◽  
The Social

Background: The analysis has involved social interactions in a multicultural environment. The social context has been defined by the Vilnius region (Lithuania), where national, religious, and cultural differences exist across generations (multicultural community). The space of “social relationships”, as one of the modules of the WHO quality of life assessment, has been studied. An innovation of the research has been related to the analysis of the phenomenon of community of nationalities and cultures as a predictor of quality of life (QoL). The social motive of the research has been the historical continuity (for centuries) of the construction of the Vilnius cultural borderland. Here, the local community evolves from a group of many cultures to an intercultural community. Interpreting the data, therefore, requires a long perspective (a few generations) to understand the quality of relationships. We see social interactions and strategies for building them as a potential for social QoL in multicultural environments. Methods: The research has been conducted on a sample of 374 respondents, including Poles (172), Lithuanians (133), and Russians (69). A diagnostic poll has been used. The respondents were adolescents (15–16 years). The research answers the question: What variables form the interaction strategies of adolescents in a multicultural environment? The findings relate to interpreting the social interactions of adolescents within the boundaries of their living environment. The description of the social relations of adolescents provides an opportunity to implement the findings for further research on QoL. Results: An innovative outcome of the research is the analysis of 3 interaction strategies (attachment to national identification, intercultural dialogue, and multicultural community building) as a background for interpreting QoL in a multicultural environment. Their understanding is a useful knowledge for QoL researchers. The data analysis has taken into account cultural and generational (historical) sensitivities. Therefore, the team studying the data has consisted of researchers and residents of the Vilnius region. We used the interaction strategies of adolescents to describe the category of “social relationships” in nationally and culturally diverse settings.

scholarly journals PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mohammadreza Yaghoobi ◽  
Krzysztof S. Stopka ◽  
Aaditya Lakshmanan ◽  
Veera Sundararaghavan ◽  
John E. Allison ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Metals And Alloys ◽  
Analysis Tool ◽  
Computational Framework ◽  
Crystal Plasticity Finite Element ◽  
Polycrystalline Metals ◽  
Simulation Based ◽  
Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

scholarly journals Population-based rapid assessment of avoidable blindness survey in Sohag governorate in Egypt

BMJ Open ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. e036337
Author(s):  
Heba AlSawahli ◽  
Ian McCormick ◽  
Caleb D Mpyet ◽  
Gamal Ezzelarab ◽  
Mohammad Shalaby
Keyword(s):  
Cataract Surgery ◽  
Census Data ◽  
Rapid Assessment ◽  
Population Based ◽  
Vision Impairment ◽  
Health System Strengthening ◽  
Secondary Outcome ◽  
Institutional Setting ◽  
Financial Barriers

ObjectivesTo determine the prevalence and causes of blindness and vision impairment, and the coverage and quality of cataract surgical services, among population aged 50 years and older in Sohag governorate in Egypt.DesignA population-based cross-sectional survey using two-stage cluster random sampling following the rapid assessment of avoidable blindness methodology.SettingA community-based survey conducted by six teams of ophthalmologists, assistants and local guides. Enrolment and examination were door-to-door in selected clusters.ParticipantsUsing 2016 census data, 68 population units were randomly selected as clusters (of 60 people) with probability proportionate to population size. Anyone aged 50 years and older, residing in a non-institutional setting in a cluster for at least 6 months, was eligible to participate.Primary and secondary outcome measuresThe prevalence and causes of blindness and vision impairment. Secondary outcomes were CSC and effectiveness and participant-reported barriers to cataract surgery.ResultsOf 4078 participants enrolled, 4033 (98.9%) were examined. The age-adjusted and sex-adjusted prevalence of blindness, severe vision impairment and moderate vision impairment were 5.9% (95% CI 4.8% to 6.9%), 4.7% (95% CI 3.8% to 5.7%) and 18.9% (95% CI 16.8% to 21.0%), respectively. Cataract caused most of blindness (41.6%), followed by non-trachomatous corneal opacity (15.7%) and posterior segment diseases (14.5%). Cataract surgical coverage (CSC) for persons for visual acuity <3/60 was 86.8%, the proportion of cataract surgeries with poor visual outcome was 29.5% and effective CSC (eCSC) was 44.9%. eCSC was lower in women than men. The most frequently reported barrier to surgery was cost (51.5%).ConclusionsThe prevalence of blindness in Sohag governorate is higher than districts in other middle-income countries in the region. CSC was high; however, women suffer worse quality-corrected CSC than men. The quality of cataract surgery needs to be addressed, while health system strengthening across government and private settings could alleviate financial barriers.

scholarly journals Recognizing Affiliation: Using Behavioural Traces to Predict the Quality of Social Interactions in Online Games

2020 ◽  
Author(s):  
Julian Frommel ◽  
Valentin Sagl ◽  
Ansgar E. Depping ◽  
Colby Johanson ◽  
Matthew K. Miller ◽  
...  
Keyword(s):  
Social Interactions ◽  
Online Games

scholarly journals PoreAnalyzer—An Open-Source Framework for the Analysis and Classification of Defects in Additive Manufacturing

2021 ◽  
Vol 11 (13) ◽  
pp. 6086
Author(s):  
Nils Ellendt ◽  
Fabian Fabricius ◽  
Anastasiya Toenjes
Keyword(s):  
Additive Manufacturing ◽  
Open Source ◽  
Total Porosity ◽  
Shape Accuracy ◽  
Process Maps ◽  
Defect Type ◽  
Open Source Framework ◽  
New Material ◽  
High Cooling Rates

Additive manufacturing processes offer high geometric flexibility and allow the use of new alloy concepts due to high cooling rates. For each new material, parameter studies have to be performed to find process parameters that minimize microstructural defects such as pores or cracks. In this paper, we present a system developed in Python for accelerated image analysis of optical microscopy images. Batch processing can be used to quickly analyze large image sets with respect to pore size distribution, defect type, contribution of defect type to total porosity, and shape accuracy of printed samples. The open-source software is independent of the microscope used and is freely available for use. This framework allows us to perform such an analysis on a circular area with a diameter of 5 mm within 10 s, allowing detailed process maps to be obtained for new materials within minutes after preparation.

scholarly journals Internal Quality Evolution of Open-Source Software Systems

2021 ◽  
Vol 11 (12) ◽  
pp. 5690
Author(s):  
Mamdouh Alenezi
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Evolution ◽  
Quality Metrics ◽  
Internal Quality ◽  
Software Systems ◽  
Software Metric ◽  
Significant Difference ◽  
The Relationship

The evolution of software is necessary for the success of software systems. Studying the evolution of software and understanding it is a vocal topic of study in software engineering. One of the primary concepts of software evolution is that the internal quality of a software system declines when it evolves. In this paper, the method of evolution of the internal quality of object-oriented open-source software systems has been examined by applying a software metric approach. More specifically, we analyze how software systems evolve over versions regarding size and the relationship between size and different internal quality metrics. The results and observations of this research include: (i) there is a significant difference between different systems concerning the LOC variable (ii) there is a significant correlation between all pairwise comparisons of internal quality metrics, and (iii) the effect of complexity and inheritance on the LOC was positive and significant, while the effect of Coupling and Cohesion was not significant.

scholarly journals COMANDO: A Next-Generation Open-Source Framework for Energy Systems Optimization

2021 ◽  
pp. 107366
Author(s):  
Marco Langiu ◽  
David Yang Shu ◽  
Florian Joseph Baader ◽  
Dominik Hering ◽  
Uwe Bau ◽  
...  
Keyword(s):  
Open Source ◽  
Energy Systems ◽  
Next Generation ◽  
Open Source Framework
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