Free Open Source Software Research Articles

Using Open-Source Data and Software to Analyse Land-Use Changes and Deforestation in Marqués de Comillas, Chiapa, Mexico (Work in Progress)

This project aimed to exploit existing open data and open-source software to allow visualising and finding spatial coincidences between three groups of indicators: 1) agricultural activity, 2) land use and forest cover changes, and 3) spatial distribution patterns of vegetation loss. This paper presents preliminary results of developing an interactive map using R, Leaflet, and QGIS to perform a simple overlay analysis of layers containing better policy and decision-making indicators. The map uses open data available through the Mexican government platforms, and all processing, storage and publication are done using free open-source software tools. The data used in this project was limited to the Marqués de Comillas municipality because of its importance in Mexico’s forest ecosystem. The maps are a work in progress and a continuation of research done for a geomatics graduate program in Centro de Investigación en Ciencias de Información Geoespacial.

PsiNorm: A fast, efficient and free open-source software for interpreting, reporting and archiving neuropsychological test results.

In many clinics, calculation and interpretation of neuropsychological test results, along with reporting, data organization and archiving of the data are done manually. In this era where most of the similar processes are automated, manual application may result in excessive time consumption, unnecessary use of qualified work-force, and is also open to error. A software that automates these processes for neuropsychological tests used for dementia assessment may overcome these issues. We aimed to develop a free, open source software not requiring specialized training, which would optimise the calculation, preparation of personal reports and archiving processes of neuropsychological tests, hence would easily be incorporated in to the daily work of psychologists. We've used Python 3.6 as the programming language, and JSON was used as the data interchange format to allow for personal alterations in the content. The tests were selected among those which are in common use for neuropsychological evaluation of adults in Turkey, with available norm values. (Funding: TUBITAK 214S048). PsiNorm was developed, comprising widely used standardized tests for cognitive evaluation of adults in Turkey. The software is lightweight, compatible with most common operating systems, and easy-to-use. We've shown that Psinorm significantly reduced the time required for calculation of percentiles and norms as well as for producing a draft report. The reports are prepared in .txt format and the databases are prepared in MS Excel ve CSV formats. PsiNorm is available freely at psinorm.org. PsiNorm is a free, open-source software which is available for researchers and clinicians who perform neuropsychological tests. PsiNorm provides significant time and labor-force benefits, is easy-touse and can be customized by the user.

PV Monitoring System for a Water Pumping Scheme with a Lithium-Ion Battery Using Free Open-Source Software and IoT Technologies

The development of photovoltaic (PV) technology is now a reality. The inclusion of lithium-ion batteries in grid-connected PV systems is growing, and the sharp drop in prices for these batteries will enable their use in applications such as PV water pumping schemes (PVWPS). A technical solution for the monitoring and tracking of PV systems is shown in this work, and a novel quasi-real-time monitoring system for a PVWPS with a Li-ion battery is proposed in which open-source Internet of Things (IoT) tools are used. The purpose of the monitoring system is to provide a useful tool for the operation, management, and development of these facilities. The experimental facility used to test the monitoring system includes a 2.4 kWpk photovoltaic field, a 3.6 kVA hybrid inverter, a 3.3 kWh/3 kW lithium-ion battery, a 2.2 kVA variable speed driver, and a 1.5 kW submersible pump. To address this study, data acquisition is performed using commercial hardware solutions that communicate using a Modbus-RTU protocol over an RS485 bus and open software. A Raspberry Pi is used in the data gateway stage, including a PM2 free open-source process manager to increase the robustness and reliability of the monitoring system. Data storage is performed in a server using InfluxDB for open-source database storage and Grafana as open-source data visualization software. Data processing is complemented with a configurable data exporter program that enables users to select and copy the data stored in InfluxDB. Excel or .csv files can be created that include the desired variables with a defined time interval and with the desired data granularity. Finally, the initial results of the monitoring system are presented, and the possible uses of the acquired data and potential users of the system are identified and described.

Skin cytokine profile in patients with mycosis fungoides

Aim of the study. To determine the concentration of cytokines in the skin of patients with mycosis fungoides and correlations between their concentration and the value of the modified scale for assessing the severity of skin lesions mSWAT.
 Methods. The concentration of cytokines was simultaneously determined using xMAP technology: IL-1, IL-4, IL-6, IL-10, IL-17A, IL-17F, IL-21, IL-22, IL-23, IL-25, IL -31, IL-33, IFN-, sCD40L, TNF- in skin biopsies of 21 patients with early (IAIIA) stages of mycosis fungoides and 4 healthy individuals. Analysis and visualization of the obtained data were carried out using R Statistical Software for MacOS (version 1.3.1056), a free open source software development environment for the R programming language.
 Results. An increase in the level of IL-4 and TNF- in the lesions in patients with mycosis fungoides compared with healthy individuals was shown (p = 0.025 and p = 0.012, respectively). Correlation analysis revealed the formation of cytokine networks in the skin of patients with mycosis fungoides that were not associated with the value of the modified scale for assessing the severity of skin lesions mSWAT. A tendency towards a negative relationship between the mSWAT and IFN scales was found (p = 0.056).
 Conclusion. None of the cytokines in lesions and visually unaffected skin from patients with mycosis fungoides were associated with mSWAT values.

Mining and Tailings Dam Detection in Satellite Imagery Using Deep Learning.

This work explores the combination of free cloud computing, free open-source software, and deep learning methods to analyze a real, large-scale problem: the automatic country-wide identification and classification of surface mines and mining tailings dams in Brazil. Locations of officially registered mines and dams were obtained from the Brazilian government open data resource. Multispectral Sentinel-2 satellite imagery, obtained and processed at the Google Earth Engine platform, was used to train and test deep neural networks using the TensorFlow 2 application programming interface (API) and Google Colaboratory (Colab) platform. Fully convolutional neural networks were used in an innovative way to search for unregistered ore mines and tailing dams in large areas of the Brazilian territory. The efficacy of the approach is demonstrated by the discovery of 263 mines that do not have an official mining concession. This exploratory work highlights the potential of a set of new technologies, freely available, for the construction of low cost data science tools that have high social impact. At the same time, it discusses and seeks to suggest practical solutions for the complex and serious problem of illegal mining and the proliferation of tailings dams, which pose high risks to the population and the environment, especially in developing countries.

Optimization of Prosthodontic Computer-Aided Designed Models: A Virtual Evaluation of Mesh Quality Reduction Using Open Source Software.

Mesh optimization reduces the texture quality of 3D models in order to reduce storage file size and computational load on a personal computer. This study aims to explore mesh optimization using open source (free) software in the context of prosthodontic application. An auricular prosthesis, a complete denture, and anterior and posterior crowns were constructed using conventional methods and laser scanned to create computerized 3D meshes. The meshes were optimized independently by four computer-aided design software (Meshmixer, Meshlab, Blender, and SculptGL) to 100%, 90%, 75%, 50%, and 25% levels of original file size. Upon optimization, the following parameters were virtually evaluated and compared; mesh vertices, file size, mesh surface area (SA), mesh volume (V), interpoint discrepancies (geometric similarity based on virtual point overlapping), and spatial similarity (volumetric similarity based on shape overlapping). The influence of software and optimization on surface area and volume of each prosthesis was evaluated independently using multiple linear regression. There were clear observable differences in vertices, file size, surface area, and volume. The choice of software significantly influenced the overall virtual parameters of auricular prosthesis [SA: F(4,15) = 12.93, R2 = 0.67, p < 0.001. V: F(4,15) = 9.33, R2 = 0.64, p < 0.001] and complete denture [SA: F(4,15) = 10.81, R2 = 0.67, p < 0.001. V: F(4,15) = 3.50, R2 = 0.34, p = 0.030] across optimization levels. Interpoint discrepancies were however limited to <0.1mm and volumetric similarity was >97%. Open-source mesh optimization of smaller dental prostheses in this study produced minimal loss of geometric and volumetric details. SculptGL models were most influenced by the amount of optimization performed.

Design and Printing of a Low-Cost 3D-Printed Nasal Osteotomy Training Model: Development and Feasibility Study.

BackgroundNasal osteotomy is a commonly performed procedure during rhinoplasty for both functional and cosmetic reasons. Teaching and learning this procedure proves difficult due to the reliance on nuanced tactile feedback. For surgical simulation, trainees are traditionally limited to cadaveric bones, which can be costly and difficult to obtain.ObjectiveThis study aimed to design and print a low-cost midface model for nasal osteotomy simulation.MethodsA 3D reconstruction of the midface was modified using the free open-source design software Meshmixer (Autodesk Inc). The pyriform aperture was smoothed, and support rods were added to hold the fragments generated from the simulation in place. Several models with various infill densities were printed using a desktop 3D printer to determine which model best mimicked human facial bone.ResultsA midface simulation set was designed using a desktop 3D printer, polylactic acid filament, and easily accessible tools. A nasal osteotomy procedure was successfully simulated using the model.Conclusions3D printing is a low-cost, accessible technology that can be used to create simulation models. With growing restrictions on trainee duty hours, the simulation set can be used by programs to augment surgical training.

Serac: an R package for ShortlivEd RAdionuclide chronology of recent sediment cores

Short-lived radionuclides are measured in surface sediment to provide a geochronology for the past century. Age-depth models are produced from 210Pbex activity-derived sedimentation rates and corroborated by known events, such as 137Cs and 241Am activities that are result of fallout from nuclear weapon tests and the Chernobyl accident. Different methods of age depth modelling using such data require expertise in lake sedimentation processes.Here, we present a package, serac, that allows the user to compute an age-depth model and generate a graph, the age-depth correspondence in a text file, and metadata, using the free open-source statistical software R. serac ensures the reproducibility of age-depth or age-mass depth models and allows testing of several 210Pbex models (CFCS, CIC, CRS, CRS piecewise) and sedimentation hypotheses (changes in sedimentation rates, presence of instantaneous deposits, varved sedimentation, etc.). Using several case studies, including lakes and lagoon in different environments, we demonstrate the use of the program in diverse situations that may be encountered.The rising number of sediment cores in recent palaeo studies and the need to correlate them require reproducible methods. serac is a user-friendly code that enables age model computation for the past century and encourages the standardisation of outputs.

Supercell-core software: A useful tool to generate an optimal supercell for vertically stacked nanomaterials

Vertically oriented materials, such as van der Waals heterostructures, which have novel hybrid properties, are crucial for fundamental scientific research and the design of new nano-devices. Currently, most available theoretical methods require applying a supercell approach with periodic boundary conditions to explore the electronic properties of such nanomaterials. Herein, we present supercell-core software, which provides a way to determine the supercell of non-commensurate lattices, in particular van der Waals heterostructures. Although this approach is very common, most of the reported work still uses supercells that are constructed “by hand” and on a temporary basis. The developed software is designed to facilitate finding and constructing optimized supercells (i.e., with small size and minimal strain accumulation in adjacent layers) of vertically stacked lattices. The developed software tool is accessible as open-source free software.

Vuln4Real: A Methodology for Counting Actually Vulnerable Dependencies

Vulnerable dependencies are a known problem in today&#x2019;s free open-source software ecosystems because FOSS libraries are highly interconnected, and developers do not always update their dependencies. Our paper proposes Vuln4Real, the methodology for counting actually vulnerable dependencies, that addresses the over-inflation problem of academic and industrial approaches for reporting vulnerable dependencies in FOSS software, and therefore, caters to the needs of industrial practice for correct allocation of development and audit resources. To understand the industrial impact of a more precise methodology, we considered the 500 most popular FOSS Java libraries used by SAP in its own software. Our analysis included 25767 distinct library instances in Maven. We found that the proposed methodology has visible impacts on both ecosystem view and the individual library developer view of the situation of software dependencies: Vuln4Real significantly reduces the number of false alerts for deployed code (dependencies wrongly flagged as vulnerable), provides meaningful insights on the exposure to third-parties (and hence vulnerabilities) of a library, and automatically predicts when dependency maintenance starts lagging, so it may not receive updates for arising issues.

MetIDfyR: An Open-Source R Package to Decipher Small-Molecule Drug Metabolism through High-Resolution Mass Spectrometry.

With recent advances in analytical chemistry, liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential tool for metabolite discovery and detection. Even if most of the common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, complicating metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited. In this article, we present MetIDfyR, an open-source and cross-platform R package for in silico drug phase I/II biotransformation prediction and mass-spectrometric data mining. MetIDfyR has proven its efficacy for advanced metabolite identification in semi-complex and complex mixtures in in vitro or in vivo drug studies and is freely available at github.com/agnesblch/MetIDfyR.

A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia

BackgroundMost repetitive transcranial magnetic stimulation (rTMS) studies aiming to reduce auditory verbal hallucinations (AVH) in schizophrenia target the left temporo-parietal junction (TPJ), but the efficacy of this approach remains controversial. The observed differences in efficacy could be attributed to inaccurate target localization. Here, to precisely quantify anatomical bias induced by localization method, we developed a free open-source software (GeodesicSlicer) that computes shortest curved path (i.e. geodesic) between rTMS targets. Here we compare a personalized target with accurate anatomical criteria with a standardized target based on the 10–20 EEG system (the middle between T3 and P3 electrodes: T3P3). MethodsWe compare in 69 patients with schizophrenia the geodesic distances of two approaches for rTMS target localization within the left TPJ. In addition, we characterize the personalized target according to the 10–20 EEG system. ResultsA differential of 3 cm in term of geodesic distance between rTMS localization approaches was observed. Moreover, this personalized target to treat AVH is located at 25% in the T3-P3 axis. ConclusionsThis software for rTMS localization comparison demonstrates the difference between standardized and personalized rTMS target. This difference has the potential to explain a part of the dissonant clinical results found in previous rTMS studies.

Abbattimento del particolato aerodisperso (PM10 e PM2.5) in tre aree protette e due ville storiche della città di Roma nei mesi di lockdown (marzo-aprile 2020)

Abstract: Airborne particulate matter (PM) has been widely demonstrated to play a role in the increase in mortality linked to cardio-respiratory diseases, in the reduction of immune system defense mechanisms, and in the transmission of pathogens. Equally accepted is the role that trees play in fine particulate matter absorption in urban areas. This study examined the capacity of particulate reduction in three protected areas in Rome within the park and nature reserve system managed by the regional organization “RomaNatura” (Riserva Naturale della Marcigliana, Riserva Naturale della Valle dell’Aniene and Parco Regionale Urbano di Aguzzano) and two historic Roman parks (Villa Ada and Villa Borghese). The study was held in March and April 2020 during the COVID 19 lockdown period. Due to the impossibility of physically gathering data and recording measurements in the field in order to define the biophysical characteristics of the areas under study, remote sensing techniques were utilized. Although such techniques may be influenced by a degree of uncertainty in the absence of calibration procedures based on in-field inspection and verification, they still constitute a preliminary phase for further investigation, especially for studying difficult-to-access areas or for project research with limited resources. The average quantities of fine and ultrafine particulate matter captured during the two-month period were 4.330.22 ± 1.429.54 Kg di PM10 and 373.33 ± 124.01 Kg di PM2.5. This data is not directly comparable to the results of similar studies conducted in much larger areas over longer periods of time. It nevertheless shows that remote sensing techniques based on free access databases and open source software can be employed by a community of motivated citizens with basic technical and scientific knowledge; it can also be a powerful means of awareness-building and involvement in the conservation of urban forests.

Numerical simulation of quantum anharmonic oscillator, embedded within an infinite square well potential, by matrix methods using Gnumeric spreadsheet

The quantum anharmonic oscillator has been solved numerically using matrix diagonalization technique. The interaction potential consisting of quadratic () and quartic (λx4) terms is embedded within an infinite square well potential of appropriate width, ‘a’ and its sine eigen functions are used as basis functions ‘N’ for the employed matrix method. The energy eigen values for the resultant Hamiltonian are solved in a free open source software (FOSS), Gnumeric, a simple worksheet environment. The numerical parameters ‘a’ and ‘N’ are optimized to converge to the expected energies for harmonic oscillator and those for anharmonic oscillator from perturbation theory for small values of physical parameter, ‘λ’. The pure quartic oscillator is studied for both small and large values of λ and validated with results obtained from other numerical techniques. The breakdown of perturbation approximation for large values of λ is also shown.

Computer-Aided Surgical Simulation for Correcting Complex Limb Deformities in Children

This work aims to present an in-house low-cost computer-aided simulation (CASS) process that was recently implemented in the preoperative planning of complex osteotomies for limb deformities in children. Five patients admitted to the Unit of Paediatric Orthopaedics and Traumatology from April 2018 to December 2019, for correcting congenital or post-traumatic limb deformities were included in the study. Three-dimensional (3D) digital models were generated from Computed Tomography (CT) scans, using free open-source software, and the surgery was planned and simulated starting from the 3D digital model. 3D printed sterilizable models were fabricated using a low-cost 3D printer, and animations of the operation were generated with the aim to accurately explain the operation to parents. All procedures were successfully planned using our CASS method and the 3D printed models were used during the operation, improving the understanding of the severely abnormal bony anatomy. The surgery was precisely reproduced according to CASS and the deformities were successfully corrected in four cases, while in one case, the intraoperative intentional undersizing of the bone osteotomy produced an incomplete correction of a congenital forearm deformity. Our study describes the application of a safe, effective, user-friendly, and low-cost CASS process in paediatric orthopaedics (PO) surgery. We are convinced that our study will stimulate the widespread adoption of this technological innovation in routine clinical practice for the treatment of rare congenital and post-traumatic limb deformities during childhood.

A novel open-source software-based high-precision workflow for target definition in cardiac radioablation.

Noninvasive ablative radiotherapy of cardiac arrhythmias (stereotactic ablative body radiation) has shown promising initial results. Precise targeting of the arrhythmogenic substrate is paramount to limit adverse effects to healthy myocardium, organs at risk, and cardiac implantable electronic devices. Using electroanatomic maps for treatment planning is technically challenging. Using the free open-source 3D Slicer software platform we established a workflow for high-precision target definition based on electroanatomic maps. An import plug-in for 3D Slicer has been designed that reads electroanatomic maps generated with three mapping systems in widespread clinical use. Using our proposed workflow in a real-world patient case we were able to align the map to the computed tomography (CT) with a mean distance of 3.1 mm. Thus, points defined on the map were translated into CT space with high accuracy and a radiotherapy treatment volume was defined in CT space based on these map-derived points. We describe a novel high-precision target definition method for stereotactic ablation of cardiac arrhythmias. Multimodal integration of the electroanatomic map with the planning CT allows for highly accurate localization of previously identified electrophysiological features in CT space. It remains to be shown whether this novel planning workflow leads to superior ablation outcomes when compared with other approaches.

Four-dimensional virtual reality cine cardiac models using free open-source software.

This is a proof-of-concept study to create a four-dimensional (4-D) cine model of the heart and visualize it in virtual reality by using freely available open-source software and inexpensive hardware. Four-dimensional cine models allow for real-time visualization of cardiac structures during processes such as complex congenital heart disease. Such models can be used for patient and trainee education, and potentially for surgical planning. Currently, 3-D printed models are more commonly used, but they are static, showing only one selected phase of the cardiac cycle. Second, they are limited by the selection of clipping planes before printing. Four-dimensional segmentation and virtual reality visualization overcome these limitations. Currently, most of the work in virtual/augmented reality models involves the segmentation of one cardiac phase or the use of expensive software for multiphase segmentation. In this study, we show an approach for multiphase cardiac segmentation as well as its display using free open-source software and relatively inexpensive hardware.

Imaging and printing in plastic and reconstructive surgery part 1: established techniques

Background: An increasing number of reconstructive surgeons are using modern imaging technologies for preoperative planning and intraoperative surgical guidance. Conventional imaging modalities such as CT and MRI are relatively affordable and widely accessible and offer powerful functionalities. In the first of a two-part series, we evaluate established three-dimensional (3D) imaging and printing techniques based on CT and MRI used in plastic and reconstructive surgery.&#x0D; Method: A review of the published English literature dating from 1950 to 2017 was taken using databases such as PubMed, MEDLINE®, Web of Science and EMBASE.&#x0D; Result: In plastic and reconstructive surgery, the most commonly used, free software platforms are 3D Slicer (Surgical Planning Laboratory, Boston, MA, USA) and OsiriX (Pixmeo, Geneva, Switzerland). Perforator mapping using 3D-reconstructed images from computed tomography angiography (CTA) and magnetic resonance angiography (MRA) is commonly used for preoperative planning. Three-dimensional volumetric analysis using current software techniques remains labour-intensive and reliant on operator experience. Three-dimensional printing has been investigated extensively since its introduction. As more free open-source software suites and affordable 3D printers become available, 3D printing is becoming more accessible for clinicians.&#x0D; Conclusion: Numerous studies have explored the application of 3D-rendered conventional imaging modalities for perforator mapping, volumetric analysis and printing. However, there is a lack of comprehensive review of all established 3D imaging and printing techniques in a language suitable for clinicians.

Simulation study of nuclear shell model using sine basis

Single-particle energy states for a neutron and a proton are obtained by solving the time-independent Schrödinger equation for the mean-field Woods–Saxon potential along with the spin-orbit term. The wavefunctions are expanded as a linear combination of simple sine-wave basis states, which are eigenfunctions of the infinite spherical-well potential. The requisite algorithm based on matrix diagonalization is implemented in Free Open Source Software (FOSS) Scilab. Initial values for the simulation were taken from model parameters given in the book on Nuclear Structure by Bohr and Mottelson, which were then optimized to obtain the best convergence with the available experimental energy values of various nuclei with magic proton and neutron numbers. The level scheme, as well as the energy values for doubly magic nuclei 82208Pb and 2040Ca, which are obtained using our simulation, is presented in this paper. Finally, energy level diagrams for neutrons and protons with respect to mass number A were arrived at, based on those obtained for various magic nuclei. The evaluation method, which is based on the sine-wave basis, is akin to Fourier analysis. When done with the aid of FOSS Scilab, this technique becomes easily accessible to students at the under-graduate (UG) level and may be studied through small projects.

Environmental factors and human activity as drivers of tree cover and density on the Island of Socotra, Yemen

Socotra Island, in the western Indian Ocean, harbors high biodiversity and endemism and makes up the largest part of the Socotra archipelago UNESCO World Heritage site. Its climatic, pedological, and geomorphological characteristics, together with the long geological isolation and inaccessibility, led to the flourishing of unique tree diversity, with great cultural and ecological value. Lately, trees on Socotra are facing new threats linked to the abandonment of traditional management practices, climate change impacts, and growing human pressure. This study assesses the relative influence of environmental factors and human activity as drivers of tree cover and density, which can be used to support land management policies for the conservation of this key local resource. Tree cover and density were assessed on a total of 3600 plots of 0.5 ha each, laid on a regular grid covering the entire area of the island through Collect Earth, a free open source software tool that allows an augmented visual interpretation of high-resolution satellite images. A total of 770,000 trees, with an average of 2.14 trees/ha, were estimated on the island. The collected data was validated by ground surveys in 26 plots. The relative influence of selected predictors (seven environmental, two anthropic) on tree cover and density was analyzed through logistic and survival regression. Tree cover and density were found to be impacted positively by steeper slopes, higher rainfall, and marked precipitation seasonality and negatively by relatively warmer temperatures and a higher sand content in the soil. Distance of each plot from the nearest road and settlement was calculated and neither of these anthropic predictors emerged as significant, indicating that the limited number of trees present are not currently as affected by anthropic pressure, but, instead, their presence is mostly limited by the harsh climatic and pedological factors. However, as human population and development increase, periods of drought rise, and extreme and random climatic events intensify, these additional stresses on the environment could negatively impact the availability of natural resources in the terrestrial environment. Lastly, potential recommendations to the existing conservation policies and Socotra Conservation Zoning Plan are discussed based on the results.