Open-source Hybrid Research Articles

Validation of an open-source hybrid testing framework for RC structures by a large-scale shaking table test

In recent decades, hybrid testing (HT) technology, which combines numerical simulation with large-scale structural experiments to simulate the nonlinear response of seismic structures more economically, has been developed as an alternative to the shaking table test (STT). However, research focused on validating HT results through large-scale structural dynamic tests is limited. This study aims to investigate the reliability of HT results by comparing them with those of the STT for a large-scale RC structure. The prototype structure considered in the HT is a half-scale seven-story RC building that was previously tested on a (8 m × 8 m) shaking table to investigate the dynamic response of RC structures during extreme ground motions. An open-source HT framework, involving the finite-element software OpenSees and control middleware OpenFresco, is employed as the HT tool. The hybrid model used in the HT consists of a two-column physical substructure and a nonlinear numerical substructure with plastic hinges, which was validated by numerical simulation before the test. A comparison between the results of the HT and STT reveals that the HT effectively reproduces the STT results for the 7-story RC structure, including inter-story drifts, inter-story shear forces, and floor accelerations under different ground motion intensities. This validates the reliability of the HT and demonstrates its advantages in conducting large-scale RC structure experiments.

Cardiac Substructure Dose and Survival in Stereotactic Radiotherapy for Lung Cancer: Results of the Multi-Centre SSBROC Trial

Background and PurposeStereotactic ablative body radiotherapy (SABR) is increasingly used for early-stage lung cancer, however the impact of dose to the heart and cardiac substructures remains largely unknown. The study investigated doses received by cardiac substructures in SABR patients and impact on survival. Materials and MethodsSSBROC is an Australian multi-centre phase II prospective study of SABR for stage I non-small cell lung cancer. Patients were treated between 2013 and 2019 across 9 centres. In this secondary analysis of the dataset, a previously published and locally developed open-source hybrid deep learning cardiac substructure automatic segmentation tool was deployed on the planning CTs of 117 trial patients. Physical doses to 18 cardiac structures and EQD2 converted doses (α/β = 3) were calculated. Endpoints evaluated include pericardial effusion and overall survival. Associations between cardiac doses and survival were analysed with the Kaplan–Meier method and Cox proportional hazards models. ResultsCardiac structures that received the highest physical mean doses were superior vena cava (22.5 Gy) and sinoatrial node (18.3 Gy). The highest physical maximum dose was received by the heart (51.7 Gy) and right atrium (45.3 Gy). Three patients developed grade 2, and one grade 3 pericardial effusion. The cohort receiving higher than median mean heart dose (MHD) had poorer survival compared to those who received below median MHD (p = 0.00004). On multivariable Cox analysis, male gender and maximum dose to ascending aorta were significant for worse survival. ConclusionsPatients treated with lung SABR may receive high doses to cardiac substructures. Dichotomising the patients according to median mean heart dose showed a clear difference in survival. On multivariable analyses gender and dose to ascending aorta were significant for survival, however cardiac substructure dosimetry and outcomes should be further explored in larger studies.

Qibolab: an open-source hybrid quantum operating system

We present Qibolab, an open-source software library for quantum hardware control integrated with the Qibo quantum computing middleware framework. Qibolab provides the software layer required to automatically execute circuit-based algorithms on custom self-hosted quantum hardware platforms. We introduce a set of objects designed to provide programmatic access to quantum control through pulses-oriented drivers for instruments, transpilers and optimization algorithms. Qibolab enables experimentalists and developers to delegate all complex aspects of hardware implementation to the library so they can standardize the deployment of quantum computing algorithms in a extensible hardware-agnostic way, using superconducting qubits as the first officially supported quantum technology. We first describe the status of all components of the library, then we show examples of control setup for superconducting qubits platforms. Finally, we present successful application results related to circuit-based algorithms.

HD-sEMG-CORE: An Open-Source Hybrid Network Algorithm for Efficient Compression and Accurate Restoration of High-Density Surface Electromyography Signals

HD-sEMG-CORE: An Open-Source Hybrid Network Algorithm for Efficient Compression and Accurate Restoration of High-Density Surface Electromyography Signals

A novel integrated framework for reproducible formability predictions using virtual materials testing

Background: Formed aluminium alloy sheet materials are increasingly adopted in production processes such as vehicle manufacturing, due to the potential for weight-saving and improved recyclability when compared to more traditional steel alloys. To maximise these benefits whilst maintaining sufficient mechanical properties, the link between formability and microstructure must be better understood. Virtual materials testing is a cost-effective strategy for generating microstructure-informed formability predictions. Methods: We developed an open-source hybrid framework, combining experimental and computational tasks, for generating reproducible formability predictions. Starting with experimental texture measurements and stress-strain curves, we calibrated crystal plasticity (CP) model parameters. The framework used these parameters to perform a large set of multiaxial full-field CP simulations, from which various anisotropic yield functions were fitted. With these anisotropy parameters, we then employed a Marciniak-Kuczyński finite-element model to predict forming limit curves, which we compared with those from experimental Nakazima tests. Results: We executed the workflow with the aluminium alloy Surfalex HF (AA6016A) as a case study material. The 18-parameter Barlat yield function provided the best fit, compared to six-parameter functions. Predicted forming limits depended strongly on the chosen hardening law, and good agreement with the experimental forming limit curve was found. All of the generated data have been uploaded to the Zenodo repository. A set of Jupyter notebooks to allow interactive inspection of our methods and data are also available. Conclusions: We demonstrated a robust methodology for replicable virtual materials testing, which enables cheaper and faster formability analyses. This complete workflow is encoded within a simple yet highly customisable computational pipeline that can be applied to any material. To maximise reproducibility, our approach takes care to ensure our methods and data — and the ways in which that data is processed — are unambiguously defined during all steps of the workflow.

HS-FRAG: An open source hybrid segmentation tool to delineate agricultural fields in fragmented landscapes

Fragmented croplands with small and irregular fields pose formidable challenges to represent agricultural field boundaries. Existing freeware do not consider novel segmentation algorithms, thus restrict their application to relatively homogeneous, large landholdings. We developed an open source QGIS plug-in ‘HS-FRAG’ to delineate agricultural fields of a fragmented landscape from a multi-spectral imagery using an object-based, hybrid segmentation algorithm. ‘HS-FRAG’ uses Sobel operator to extract the edges from individual spectral bands, followed by watershed algorithm to close the polygons. Three metrics, namely geometric evaluation (GE), quantitative completeness (QC), and spatial correctness (SC) were considered to evaluate segmentation performance. Robustness of the tool was demonstrated on a highly fragmented, heterogeneous cropland in south India using Sentinel-2 (10 m spatial) and Cartosat-2 (1.6 m spatial) imagery. Both Sentinel-2 and Cartosat-2 have resulted in over-segmentation (OS) with a generalization of 1.30, 1.37 and an overall accuracy (OA) of 38.06 %, 75.61 % respectively. Segmentation with Cartosat-2 has outperformed in representing the geometry, number, and extent of the reference polygons. A user guide with working examples is provided for quick acquaintance of ‘HS-FRAG’ tool and its application to other fragmented regions.

Waste Plastic Direct Extrusion Hangprinter

As the additive manufacturing industry grows, it is compounding the global plastic waste problem. Distributed recycling and additive manufacturing (DRAM) offers an economic solution to this challenge, but it has been relegated to either small-volume 3D printers (limiting waste recycling throughput) or expensive industrial machines (limiting accessibility and lateral scaling). To overcome these challenges, this paper provides proof-of-concept for a novel, open-source hybrid 3D printer that combines a low-cost hanging printer design with a compression-screw-based end-effector that allows for the direct extrusion of recycled plastic waste in large expandable printing volumes. Mechanical testing of the resultant prints from 100% waste plastic, however, showed that combining the challenges of non-uniform feedstocks and a heavy printhead for a hangprinter reduced the strength of the parts compared to fused filament fabrication. The preliminary results are technologically promising, however, and provide opportunities to improve on the open-source design to help process the volumes of waste plastic needed for DRAM to address the negative environmental impacts of global plastic use.

Navigating Diabetes Online Communities in Clinical Practice.

This purpose of this study was to conduct a rapid review and environmental scan of diabetes online communities (DOCs) to highlight the clinical impact of DOC engagement and provide guidance to health care providers for navigating and prescribing DOCs. This two-phase review included a rapid review of clinical outcomes and an assessment of DOC content. We conducted a literature search for studies evaluating DOC use and glucometric (glycated hemoglobin [A1C], time-in-range, hypoglycemia), behavioral, and psychosocial outcomes. The environmental scan of current DOC sites established key features, including available platforms, target population, content areas, and reach. Twelve papers were included-eight reported DOC use within a context of do-it-yourself (DIY) noncommercial, opensource hybrid closed loop systems community and four were non-DYI related. In latter, all studies were cross-sectional, describing patient-reported outcomes. Two studies reported A1C lowering with DOC use, two DOC use was associated with high self-efficacy, one showed association with higher self-care levels, and one showed higher quality of life scores when compared with population norms. All DIY studies showed improvement in glucometrics after initiation of sensor augmented pump technology with DOC support. Of 54 DOC sites reviewed in the environmental scan, 29 were included. Diabetes online community sites were heterogenous in social media platform and type of diabetes targeted. Diabetes online communities have the potential to improve clinical, behavioral, and psychosocial outcomes. Randomized control trials and/or longitudinal prospective studies evaluating outcomes are needed to further examine the potential benefits of DOC use. Diabetes online communities are diverse and span a variety of social media platforms, providing clinicians opportunities to individualize recommendations for DOC use.

Open-source hybrid 3D-bioprinter for simultaneous printing of thermoplastics and hydrogels

3D-bioprinting is a promising technology applicable in areas such as regenerative medicine or in vitro organ model development. Various 3D-bioprinting technologies and systems have been developed and are partly commercially available. Here, we present the construction and characterization of an open-source low-cost 3D-bioprinter that allows the alternated microextrusion of hydrogel and fused deposition modeling (FDM) of thermoplastic filaments.The presented 3D-bioprinter is based on a conventional Prusa i3 MK3 printer and features two independent printheads: the original FDM-head and a syringe-based microextrusion printhead for soft materials. Modifications were designed modularly to fit various syringe formats or heating elements to the device. The bioprinter is the first hybrid DIY 3D-bioprinter that allows switching between materials as often as required during a print run to produce complex multi-material constructs with arbitrary patterns in each layer.For validation of the printer, two designs suitable for relevant bioprinting applications were realized. First, a porous plastic construct filled with hydrogel was printed, serving as a mechanically stable bone replacement tissue model. Second, a plastic chamber, which might be used in organ-on-a-chip applications, was printed with an extruded silicone sealing that enables the liquid-tight attachment of glass slides to the top and bottom of the chamber.

VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology

Petri nets are a common method for modeling and simulation of systems biology application cases. Usually different Petri net concepts (e.g. discrete, hybrid, functional) are demanded depending on the purpose of the application cases. Modeling complex application cases requires a unification of those concepts, e.g. hybrid functional Petri nets (HFPN) and extended hybrid Petri nets (xHPN). Existing tools have certain limitations which motivated the extension of VANESA, an existing open-source editor for biological networks. The extension can be used to model, simulate, and visualize Petri nets based on the xHPN formalism. Moreover, it comprises additional functionality to support and help the user. Complex (kinetic) functions are syntactically analyzed and mathematically rendered. Based on syntax and given physical unit information, modeling errors are revealed. The numerical simulation is seamlessly integrated and executed in the background by the open-source simulation environment OpenModelica utilizing the Modelica library PNlib. Visualization of simulation results for places, transitions, and arcs are useful to investigate and understand the model and its dynamic behavior. The impact of single parameters can be revealed by comparing multiple simulation results. Simulation results, charts, and entire specification of the Petri net model as Latex file can be exported. All these features are shown in the demonstration case. The utilized Petri net formalism xHPN is fully specified and implemented in PNlib. This assures transparency, reliability, and comprehensible simulation results. Thus, the combination of VANESA and OpenModelica shape a unique open-source Petri net environment focusing on systems biology application cases. VANESA is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

Modelica-based simulation of electromagnetic transients using Dynaωo: Current status and perspectives

This paper presents the current status, the open challenges, and perspectives for Modelica-based simulation of Electromagnetic Transient (EMT) using Dynaωo environment. The simulation efficiency in native Modelica environments requires improvements for larger-scale systems, as they have been primarily developed and used for complex but small problems. This paper investigates the use of Dynaωo, an open-source hybrid C++/Modelica tool originally developed for large-scale electromechanical transient studies, for electromagnetic transient simulations. It demonstrates that its approach manages to bring improvements in terms of performances while keeping the flexibility, accuracy, and robustness of full Modelica tools, but that there is still room for further improvements.

Implementing Participatory Site Stewardship through Citizen Science and Mobile Apps

ABSTRACTHistoric archaeological resources in the American West are increasingly at risk of loss because of prolonged droughts, wildfires, earthquakes, general deterioration, and the negative impact of increasing visitation. Casual visitors regularly remove objects from their original contexts in the landscape, either taking them home as souvenirs or bringing them to local staff because they are concerned about the items disappearing. As a result, many sites of cultural significance are losing the ability to convey the information required for scholarly interpretation and for drafting community and life histories of their past residents. We argue that citizen science and mobile apps specifically designed for site stewardship are viable tools for alleviating negative human impacts on cultural landscapes and enhancing our capacity to record and monitor sites of cultural heritage. We contend that our approach uses an innovative interface, the Citizen Preservationist app, an open-source hybrid mobile/desktop software we developed to foster both current use and protection of archaeological sites and historic parks. We demonstrated the viability of our app by conducting a user study at Bodie, California (ca. 1859–1942), that assessed how this software promotes a sense of stewardship and appreciation for the archaeological heritage of this beloved California State Historic Park.

Gnowee: A Hybrid Metaheuristic Optimization Algorithm for Constrained, Black Box, Combinatorial Mixed-Integer Design

This paper introduces Gnowee, a modular, Python-based, open-source hybrid metaheuristic optimization algorithm (available from https://github.com/SlaybaughLab/Gnowee). Gnowee is designed for rapid convergence to nearly globally optimum solutions for complex, constrained nuclear engineering problems with mixed-integer (MI) and combinatorial design vectors and high-cost, noisy, discontinuous, black box objective function evaluations. Gnowee’s hybrid metaheuristic framework is a new combination of a set of diverse, robust heuristics that appropriately balance diversification and intensification strategies across a wide range of optimization problems. There are many potential applications for this novel algorithm both within the nuclear community and beyond. Given that a set of well-known and studied nuclear benchmarks does not exist for the purpose of testing optimization algorithms, comparisons between Gnowee and several well-established metaheuristic algorithms are made for a set of 18 established continuous, MI, and combinatorial benchmarks representing a wide range of types of engineering problems and solution space behaviors. These results demonstrate Gnoweee to have superior flexibility and convergence characteristics over this diverse set of design spaces. We anticipate this wide range of applicability will make this algorithm desirable for many complex engineering applications.

Hybrid IP/SDN Networking: Open Implementation and Experiment Management Tools

The introduction of SDN in large-scale IP provider networks is still an open issue and different solutions have been suggested so far. In this paper we propose a hybrid approach that allows the coexistence of traditional IP routing with SDN based forwarding within the same provider domain. The solution is called OSHI - Open Source Hybrid IP/SDN networking as we have fully implemented it combining and extending Open Source software. We discuss the OSHI system architecture and the design and implementation of advanced services like Pseudo Wires and Virtual Switches. In addition, we describe a set of Open Source management tools for the emulation of the proposed solution using either the Mininet emulator or distributed physical testbeds. We refer to this suite of tools as Mantoo (Management tools). Mantoo includes an extensible web-based graphical topology designer, which provides different layered network "views" (e.g. from physical links to service relationships among nodes). The suite can validate an input topology, automatically deploy it over a Mininet emulator or a distributed SDN testbed and allows access to emulated nodes by opening consoles in the web GUI. Mantoo provides also tools to evaluate the performance of the deployed nodes.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5–50 kbp) at such high error rates (between ∼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.