Free Open Source Research Articles

Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico.

Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico.

Automated PD-L1 Scoring for Non-Small Cell Lung Carcinoma Using Open-Source Software

PD-L1 expression in non-small cell lung cancer (NSCLC) is predictive of response to immunotherapy, but scoring of PD-L1 immunohistochemistry shows considerable interobserver variability. Automated methods may allow more consistent and expedient PD-L1 scoring. We aimed to assess the technical concordance of PD-L1 scores produced using free open source QuPath software with the manual scores of three pathologists. A classifier for PD-L1 scoring was trained using 30 NSCLC image patches. A separate test set of 207 image patches from 69 NSCLC resection cases was used for comparison of automated and manual scores. Automated and average manual scores showed excellent correlation (concordance correlation coeffecient = 0.925), though automated scoring resulted in significantly more 1–49% scores than manual scoring (p = 0.012). At both 1% and 50% thresholds, automated scores showed a level of concordance with our ‘gold standard’ (the average of three pathologists’ manual scores) similar to that of individual pathologists. Automated scoring showed high sensitivity (95%) but lower specificity (84%) at a 1% threshold, and excellent specificity (100%) but lower sensitivity (71%) at a 50% threshold. We conclude that our automated PD-L1 scoring system for NSCLC has an accuracy similar to that of individual pathologists. The detailed protocol we provide for free open source scoring software and our discussion of the limitations of this technology may facilitate more effective integration of automated scoring into clinical workflows.

Use of volumetric CT scanning to predict tumor staging and survival in pancreatic cancer patients that are to be administered curative resection.

This study evaluates the achievability of CT volumetry of pancreatic cancer and its correlation with pTNM stage and survival. Tumor volume was measured from contrast enhanced CT images of 58 patients who undergo curative resection for pancreatic cancer using the Segment Editor module implemented in 3D-Slicer-a free open source software platform. Receiver operating characteristic (ROC) analysis was used to evaluate correlation between Tvol and pTNM staging. The preoperative images of 58 pancreatic adenocarcinoma patients were included. The mean Tvol of pancreatic cancer is an increasing trend with T stage (The mean T1vol = 1.75 cm3 , the mean T2vol = 11.43 cm3 , the mean T3vol = 14.98 cm3 , the mean T4vol = 19.6 cm3 ). There were statistical differences between volumes (p = .000). On ROC analysis, the area under the ROC curve (Az) of Tvol to differentiate T1 stage from ≥T2 stage was 0.966 (p = .000). At a cut-off value of 3.050 cm3 , sensitivity of 92.3%, and specificity of 83.3% were achieved. Az value of Tvol to differentiate ≤T2 from ≥T3 stage was 0.750 (p = .010). At a cut-off value of 10.250 cm3 , sensitivity of 72.7% and specificity of 66% were achieved. In addition Az value of Tvol to differentiate ≤T3 from ≥T4 stage was 0.652 and was not significant (p = .380). At a cut-off value of 11.2 cm3 , sensitivity of 66.7% and specificity of 63.6% were achieved. CT volumetry in pancreatic cancer is feasible with excellent reproducibility. It is one of the prognostic factors affecting survival in operated patients with pancreatic cancer.

Evaluate the Use of Moodle Platforms for Education in University of Duhok Using Online Survey Application

Development countries uses E-Learning as a form of education to cooperate with the challenges of globalization, the birth of the internet and so on. Moodle is a Learning Management System (LMS) which is a free open source platform designed to assist educators in creating online courses with opportunities for dynamic interaction. In this paper the meaning of Moodle was carried out, then the web form (Google Form) is created as a Database to store the answers, gathering feedback and as statistical software to provide analytics of the effect of using Moodle by the lecturer’s opinion or perspective in College of Engineering, University of Duhok (UoD), Kurdistan Region of Iraq; their questioners are completed on the internet. The study results point out that 72.55% of lecturers were interested in services provided by Moodle@uod, mostly utilized as a depot for getting the course’s materials but the interactive learning tools are not effectively invested. Where 29.73% used the application in making quizzes; 32.43% for communicating with their students this is because of the instability of internet services. For that, the authors suggest satisfying academic staff desires in taking training courses to be more familiar with using Moodle Platform.

Fast Open-Source Toolkit for Water T2 Mapping in the Presence of Fat From Multi-Echo Spin-Echo Acquisitions for Muscle MRI.

Imaging has become a valuable tool in the assessment of neuromuscular diseases, and, specifically, quantitative MR imaging provides robust biomarkers for the monitoring of disease progression. Quantitative evaluation of fat infiltration and quantification of the T2 values of the muscular tissue's water component (wT2) are two of the most essential indicators currently used. As each voxel of the image can contain both water and fat, a two-component model for the estimation of wT2 must be used. In this work, we present a fast method for reconstructing wT2 maps obtained from conventional multi-echo spin-echo (MESE) acquisitions and released as Free Open Source Software. The proposed software is capable of fast reconstruction thanks to extended phase graphs (EPG) simulations and dictionary matching implemented on a general-purpose graphic processing unit. The program can also perform more conventional biexponential least-squares fitting of the data and incorporate information from an external water-fat acquisition to increase the accuracy of the results. The method was applied to the scans of four healthy volunteers and five subjects suffering from facioscapulohumeral muscular dystrophy (FSHD). Conventional multi-slice MESE acquisitions were performed with 17 echoes, and additionally, a 6-echo multi-echo gradient-echo (MEGE) sequence was used for an independent fat fraction calculation. The proposed reconstruction software was applied on the full datasets, and additionally to reduced number of echoes, respectively, to 8, 5, and 3, using EPG and biexponential least-squares fitting, with and without incorporating information from the MEGE acquisition. The incorporation of external fat fraction maps increased the robustness of the fitting with a reduced number of echoes per datasets, whereas with unconstrained fitting, the total of 17 echoes was necessary to retain an independence of wT2 from the level of fat infiltration. In conclusion, the proposed software can successfully be used to calculate wT2 maps from conventional MESE acquisition, allowing the usage of an optimized protocol with similar precision and accuracy as a 17-echo acquisition. As it is freely released to the community, it can be used as a reference for more extensive cohort studies.

A Brief History of Free, Open Source Software and Its Communities

Free, open source software (FOSS) has a long history, beginning with the origins of software itself, when the terms free software and open source software were not yet defined. Learning about the milestones of this history may help to understand FOSS today.

Free Open Source Software for Protein and Peptide Mass Spectrometry- based Science.

In the field of biology, and specifically in protein and peptide science, the power of mass spectrometry is that it is applicable to a vast spectrum of applications. Mass spectrometry can be applied to identify proteins and peptides in complex mixtures, to identify and locate post-translational modifications, to characterize the structure of proteins and peptides to the most detailed level or to detect protein-ligand non-covalent interactions. Thanks to the Free and Open Source Software (FOSS) movement, scientists have limitless opportunities to deepen their skills in software development to code software that solves mass spectrometric data analysis problems. After the conversion of raw data files into open standard format files, the entire spectrum of data analysis tasks can now be performed integrally on FOSS platforms, like GNU/Linux, and only with FOSS solutions. This review presents a brief history of mass spectrometry open file formats and goes on with the description of FOSS projects that are commonly used in protein and peptide mass spectrometry fields of endeavor: identification projects that involve mostly automated pipelines, like proteomics and peptidomics, and bio-structural characterization projects that most often involve manual scrutiny of the mass data. Projects of the last kind usually involve software that allows the user to delve into the mass data in an interactive graphics-oriented manner. Software projects are thus categorized on the basis of these criteria: software libraries for software developers vs desktop-based graphical user interface, software for the end-user and automated pipeline-based data processing vs interactive graphics-based mass data scrutiny.

A Comprehensive Roadmap to 50 Years of (Satellite) Earth Observation Resources for the Island of Ireland (1972 – 2023)

A comprehensive review of optical (panchromatic, multispectral and hyperspectral) and synthetic aperture radar satellite imagery coverage for terrestrial and near-shore areas of interest on the island of Ireland. The review spans 50 years and includes approximately 170+ retired and operational Earth Observation (EO) satellite sensors, and a further 60+ EO satellite sensors which are planned to be launched over the next five years. Satellite characteristics and sensor capabilities are listed in tabular form and the extents of the spatial and temporal coverage of the island of Ireland are estimated for each sensor (as available). Guidance on how to access this data is provided, with an emphasis on gaining free or reduced cost access for research and scientific purposes. Information on free open source software tools for viewing, processing and analysing EO imagery is provided, along with a selection of online resource and reference materials.

A Comprehensive Roadmap to 50 Years of (Satellite) Earth Observation Resources for the Island of Ireland (1972 – 2023)

A comprehensive review of optical (panchromatic, multispectral and hyperspectral) and synthetic aperture radar satellite imagery coverage for terrestrial and near-shore areas of interest on the island of Ireland. The review spans 50 years and includes approximately 170+ retired and operational Earth Observation (EO) satellite sensors, and a further 60+ EO satellite sensors which are planned to be launched over the next five years.Satellite characteristics and sensor capabilities are listed in tabular form and the extents of the spatial and temporal coverage of the island of Ireland are estimated for each sensor (as available). Guidance on how to access this data is provided, with an emphasis on gaining free or reduced cost access for research and scientific purposes.Information on free open source software tools for viewing, processing and analysing EO imagery is provided, along with a selection of online resource and reference materials.

Technology provides better document search results on Slovak legislation webpage as result of a simulation of webpage performance parameters

This article acquaints the public with the insights gained from conducting document searches in the Slovak public administration information system, when supported by knowledge of its management. Additionally, it discusses the advantages of simulating performance parameters and comparing the obtained results with the real parameters of the eZbierka (eCollection) legislation webpage. This comparison was based upon simulated results, obtained through the Gatling simulation tool, versus those obtained from measuring the properties of the public administration legislation webpage. Both sets of data (simulated and real), were generated via the the document search technologies in place on the eZbierka legislation webpage. The webpage provides users with binding laws and bylaws available in an electronically signed PDF file format. It is free open source. In order to simulate the accessing of documents on the webpage, the Gatling simulation tool was used. This tool simulated the activity, performed in the background of the information system, as a user attempted to read the data via the steps mentioned in the scenario. The settings of the simulated environment corresponded as much as possible to the hardware parameters and network infrastructure properties used for the operation of the respective information system. Based on this data, through load changing, we determined the number of users, the response time to queries, and their number; these parameters define the throughput of the server of the legislation webpage. The required parameter determination and performance of search technology operations are confirmed by a suitable hardware design and the webpage property parameter settings. We used the data from the eZbierka legislation webpage from its operational period of January 2016 to January 2019 for comparison, and analysed the relevant data to determine the parameter values of the legislation webpage of the slov-lex information system. The basic elements of the design solution include the technology used, the technology for searching the legislative documents with support of a searching tool, and a graphic database interface. By comparing the results, their dependencies, and proportionality, it is possible to ascertain the proper determination and appropriate applied search technology for selection of documents. Further, the graphic interface of the real web database was confirmed.

Open source text visualization tools: A comparative analysis

Text visualization is usefulfor researchersfrom many fields like social media analysts, information graphics, digital libraries, linguistics, marketing etc. who often use tools to obtain visualization of their textual data. Though there are a lot of open source tools for this purpose, especially for creating word clouds, most of the free open source tools employ straightforward frequency based approach and consideration ofword significance is user's responsibi lity. Users from interdisciplinary researches are not equipped with adequate knowledge or free tools to summarize text corpus into single text file or identify significant words. The main idea behind this paper is to provide a summary of all those popular open source visualization tools available for text visualization. We provide a comparative analysis of these tools with their pros and cons. Experimental results are provided for visual comparison to serve as quick reference for a user to help in selection of tool.

Monitoring Next Cloud sebagai Private Cloud Storage dengan Notifikasi Telegram

Penyimpanan online seperti Cloud Computing merupakan platform yang paling banyak digunakan sebagai media penyimpanan online yang dapat diakses dimanapun dan kapanpun. Saat ini Cloud Computing mengalami perkembangan pesat. Salah satu diantaranya adalah menyediakan media penyimpanan yang dapat digunakan user untuk menyimpan data dengan aman. Salah satu Open Source yang menyediakan layanan media penyimpanan adalah Nextcloud. Nextcloud merupakan penyedia layanan penyimpanan gratis dan Open Source yang memiliki fitur keamanan dan kemampuan monitoring cloud. Informasi monitoring cloud disampaikan oleh Bot Telegram. User Telegram dapat berkomunukasi dengan bot telegram untuk mendapatkan informasi monitoring tentang Nextcloud. Terdapat beberapa perintah yang digunakan untuk mendapatkan informasi Monitoring

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.

Patents information for humanities research: Could there be something?

Latour and co-authors proposed, in the Science and Technology Translation theory, to target the many SHS (Social and Human Science) questions addressed by social studies of sciences by considering, in complement to traditional academic matters, the complete social environment (political, economic or societal). Patents obviously are a potential primary information source to do so. We propose to extend this considering that recent changes have evolved in our capacity to do so. We propose three preliminary steps: (a) patent documents as providing a structured information source, (b) a patent database as a technical encyclopedia and (c) the recent expansion of the variety of uses and users in patent domains. We underline, furthermore, that minority research in the academic space does effectively use patent information, especially in SHS compared to other disciplines. We deliver an experiment to estimate the amount of data unconsidered by not questioning the huge database of the European Patent Office. By comparatively considering the terminology of the two branches of the Unesco thesaurus, namely the micro thesauri “Social and Human Sciences" and the “Information and Communication Science” branches, we evaluate a database response to the whole vocabulary. An in-depth analysis of one selected concept will complete the study. Results show that patent information may provide a quantity of documents for a wide range of academic research questions, from strategic to state of the art, and position advances aside from the Social Studies of Science. The free open source tool is also a way to practice digital humanities expected skills on real world corpora.

Post-Failure Dynamics of Rainfall-Induced Landslide in Oltrepò Pavese

Prediction of landslide hazard risk at hill slope induced by intense rainfall requires the appropriate modeling of the interactions between soil and weather phenomena, leading to failure as well as a reliable prediction of post-failure dynamics. In the peculiar case of fast shallow landslides behaving like dense granular flows, a suitable modeling approach for large and rapid deformations is necessary to estimate potential related damage. The impact force exerted by the leading edge of the earth-flow on the downstream structure should be estimated for both damage prediction and design of effective protection measures. In this paper, a free open source 3D research code based on standard weakly compressible smoothed particle hydrodynamics (WCSPH) method is validated by modeling a full-scale rainfall-induced shallow landslide which occurred in Oltrepò Pavese (Northern Italy). The code allows resolving the vertical velocity gradients, potentially providing a more reliable representation of the landslide dynamics and impact force. Mechanical parameters are consistent with average soil characteristics, avoiding calibration analysis. The final landslide profile is compared with an experimental survey for model validation, showing good fit. Influence of uncertainties of geotechnical parameters on the landslide front velocity and impact force on the downstream wall is evaluated.

The Signals of Opportunity Coherent Bistatic Scattering Simulator: A Free Open Source Framework [Software and Data Sets

Signals of opportunity (SoOp) has the potential to offer cost-effective global remote sensing for land applications. Because of the complexity of SoOp scattering over land, comprehensive bistatic scattering models and simulators can help demonstrate its feasibility. To investigate this potential, we have developed a generalized, fully polarimetric forward model: the SoOp Coherent Bistatic Scattering (SCoBi) model. We have also developed a simulator framework, employing the SCoBi model to create an analysis environment for a community of researchers, scientists, and users with little or no electromagnetic background. We aim to enable studying and analyzing new SoOp methods with varying configurations; determining the optimal cases for specific missions; and generating, visualizing, and analyzing test data with the help of SCoBi.

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.

Estimation of forest cover change using Sentinel-2 multi-spectral imagery in Georgia (the Caucasus)

Abstract: Our objective was to use Sentinel-2A multispectral data in order to cost-effectively detect change in forest cover in Georgia (the Caucasus). Generalized additive models (GAMs) were used to fit forest cover measures to Sentinel-2A spectral band values modified using different topographic correction methods. Canopy closure (calculated from upward-looking fisheye photographs taken beneath forest canopy) was the best forest cover measure accounted for by the Sentinel-2 spectral data that were topographically corrected using the Minnaert Correction (R2 = 0.882). Spectral bands best explaining canopy closure were Band 3 (Green), Band 8 (NIR) and Band 12 (SWIR). Our model is able to reasonably detect spatial and temporal changes in canopy closure, even in highly rugged terrain and diverse vegetation cover, and it has potential to be improved to the extent that it can be applied by managers of natural resources. Based on free open source applications in combination with cheap gadgets our approach might play an important role in monitoring the forests of countries with low economic indicators.

Target toxicity design for phase I dose-finding

We propose a new two-/three-stage dose-finding design called Target Toxicity (TT) for phase I clinical trials, where we link the decision rules in the dose-finding process with the conclusions from a hypothesis test. The power to detect excessive toxicity is also given. This solves the problem of why the minimal number of patients is needed for the selected dose level. Our method provides a statistical explanation of traditional ‘3+3’ design using frequentist framework. The proposed method is very flexible and it incorporates other interval-based decision rules through different parameter settings. We provide the decision tables to guide investigators when to decrease, increase or repeat a dose for next cohort of subjects. Simulation experiments were conducted to compare the performance of the proposed method with other dose-finding designs. A free open source R package tsdf is available on CRAN. It is dedicated to deriving two-/three-stage design decision tables and perform dose-finding simulations.