Open License Research Articles

THE GLOBAL CONTEXT OF OPEN ACCESS TO SCIENTIFIC PUBLICATIONS

Scientific publications are migrating to the digital environment. This phenomenon is characterized by universal norms determined by specifics of the global context ensuring open access to scientific publications. To investigate these norms in this article the ideal type method is applied, and the research data are extracted with the on-line search engine Google Books Ngram Viewer. The results obtained are: a) the study of dynamics of open science is a priority concerning the topics of open access and license of using open information; b) in the area of open science, the importance of studying the forms of access to pre-published works is prioritized; c) “the green access” is the most investigated model of the open access to scientific publications. The publication of scientific results in open access requires regular adjustment to the global norms of open science.

PriMa: A low-cost, modular, open hardware, and 3D-printed fMRI manipulandum

Motor actions in fMRI settings require specialized hardware to monitor, record, and control the subjects behavior. Commercially available options for such behavior tracking or control are very restricted and costly. We present a novel grasp manipulandum in a modular design, consisting of MRI-compatible, 3D printable buttons and a chassis for mounting. Button presses are detected by the interruption of an optical fiber path, which is digitized by a photodiode and subsequent signal amplification and thresholding. Two feedback devices (manipulanda) are constructed, one for macaques (Macaca mulatta) and one for human use. Both devices have been tested in their specific experimental setting and possible improvements are reported. Design files are shared under an open hardware license.

SoilKsatDB: global database of soil saturated hydraulic conductivity measurements for geoscience applications

Abstract. The saturated soil hydraulic conductivity (Ksat) is a key parameter in many hydrological and climate models. Ksat values are primarily determined from basic soil properties and may vary over several orders of magnitude. Despite the availability of Ksat datasets in the literature, significant efforts are required to combine the data before they can be used for specific applications. In this work, a total of 13 258 Ksat measurements from 1908 sites were assembled from the published literature and other sources, standardized (i.e., units made identical), and quality checked in order to obtain a global database of soil saturated hydraulic conductivity (SoilKsatDB). The SoilKsatDB covers most regions across the globe, with the highest number of Ksat measurements from North America, followed by Europe, Asia, South America, Africa, and Australia. In addition to Ksat, other soil variables such as soil texture (11 584 measurements), bulk density (11 262 measurements), soil organic carbon (9787 measurements), moisture content at field capacity (7382), and wilting point (7411) are also included in the dataset. To show an application of SoilKsatDB, we derived Ksat pedotransfer functions (PTFs) for temperate regions and laboratory-based soil properties (sand and clay content, bulk density). Accurate models can be fitted using a random forest machine learning algorithm (best concordance correlation coefficient (CCC) equal to 0.74 and 0.72 for temperate area and laboratory measurements, respectively). However, when these Ksat PTFs are applied to soil samples obtained from tropical climates and field measurements, respectively, the model performance is significantly lower (CCC = 0.49 for tropical and CCC = 0.10 for field measurements). These results indicate that there are significant differences between Ksat data collected in temperate and tropical regions and Ksat measured in the laboratory or field. The SoilKsatDB dataset is available at https://doi.org/10.5281/zenodo.3752721 (Gupta et al., 2020) and the code used to extract the data from the literature and the applied random forest machine learning approach are publicly available under an open data license.

A Cross-Country Model for End-Use Specific Aggregated Household Load Profiles

End-use specific residential electricity load profiles are of interest for energy system modelling that requires future load curves or demand-side management. We present a model that is applicable across countries to predict consumption on a regional and national scale, using openly available data. The model uses neural networks (NNs) to correlate measured consumption from one country (United Kingdom) with weather data and daily profiles of a mix of human activity and device specific power profiles. We then use region-specific weather data and time-use surveys as input for the trained NNs to predict unscaled electric load profiles. The total power profile consists of the end-use household load profiles scaled with real consumption. We compare the model’s results with measured and independently simulated profiles of various European countries. The NNs achieve a mean absolute error compared with the average load of 6.5 to 33% for the test set. For Germany, the standard deviation between the simulation, the standard load profile H0, and measurements from the University of Applied Sciences Berlin is 26.5%. Our approach reduces the amount of input data required compared with existing models for modelling region-specific electricity load profiles considering end-uses and seasonality based on weather parameters. Hourly load profiles for 29 European countries based on four historical weather years are distributed under an open license.

Towards utilising emerging technologies to address the challenges of using Open Educational Resources: a vision of the future

The rapid advancements in online education have pointed to a new open learning approach using Open Educational Resources (OER). In this approach, educators and learners can freely access or redistribute educational resources that have been released online in the public domain under an open licence. Whereas this approach looks appealing in reducing learning costs, as well as in enhancing learning quality and facilitating knowledge sharing, several challenges might hinder the adoption of OER, such as locating and selecting the most appropriate resources among the thousands that are published and that are available online, and trusting them. This paper elaborates on those challenges and suggests an emerging technologies-based perspective for addressing the efficient inclusion of OER. To this end, this paper discusses how the integration of emerging yet essential technologies, such as Artificial Intelligence (AI) and blockchain, with big learning data and educational data mining algorithms could have a profound impact on enhancing OER-based learning and teaching. The dynamics of incorporating these technologies to solve several OER challenges are demonstrated through numerous examples, and the potential limitations are also discussed. The paper concludes with visions of the future, possible research challenges and directions.

The first FOSD-tacotron-2-based text-to-speech application for Vietnamese

Recently, with the development and deployment of voicebots which help to minimize personnels at call centers, text-to-speech (TTS) systems supporting English and Chinese have attracted attentions of researchers and corporates worldwide. However, there is very limited published works in TTS developed for Vietnamese. Thus, this paper presents in detail the first Tacotron-2-based TTS application development for Vietnamese that utilizes the publicly available FPT open speech dataset (FOSD) containing approximately 30 hours of labeled audio files together with their transcripts. The dataset was made available by FPT Corporation with an open access license. A new cleaner was developed for supporting Vietnamese language rather than English which was provided by default in Mozilla TTS source code. After 225,000 training steps, the generated speeches have mean opinion score (MOS) well above the average value of 2.50 and center around 3.00 for both clearness and naturalness in a crowd-source survey.

Open Access Models, Pirate Libraries and Advocacy Repertoires: Policy Options for Academics to Construct and Govern Knowledge Commons

In this article, I propose exploring open access publishing through the lenses of Knowledge Commons. Instead of focusing on users’ rights to access and reuse the output under open copyright licensing conditions, I study the governance of the academic publishing ecosystem, and its political economy, technical and labour infrastructure. Based on selected examples, I discuss how they comply with the concept of the commons. I use analytical frameworks from the Ostromian literature of the governance of Knowledge Commons to provide insights on the various steps of academic publishing work as a process. I then analyse a scope of open access publishing projects, including gold, green, diamond, platinum and pirate libraries. Finally, I draw from practices a repertoire of advocacy actions and I make recommendations for academics to develop policies supporting Academic Commons.  

Building capacity through open approaches: Lessons from developing undergraduate electrophysiology practicals

Background: Electrophysiology has a wide range of biomedical research and clinical applications. As such, education in the theoretical basis and hands-on practice of electrophysiological techniques is essential for biomedical students, including at the undergraduate level. However, offering hands-on learning experiences is particularly difficult in environments with limited resources and infrastructure. Methods: In 2017, we began a project to design and incorporate electrophysiology laboratory practicals into our Biomedical Physics undergraduate curriculum at the Universidad Nacional Autónoma de México. We describe some of the challenges we faced, how we maximized resources to overcome some of these challenges, and in particular, how we used open scholarship approaches to build both educational and research capacity. Results: We succeeded in developing a number of experimental and data analysis practicals in electrophysiology, including electrocardiogram, electromyogram, and electrooculogram techniques. The use of open tools, open platforms, and open licenses was key to the success and broader impact of our project. We share examples of our practicals and explain how we use these activities to strengthen interdisciplinary learning, namely the application of concepts in physics to understanding functions of the human body. Conclusions: Open scholarship provides multiple opportunities for universities to build capacity. Our goal is to provide ideas, materials, and strategies for educators working in similar resource-limited environments.

A Century of French Railways: The Value of Remote Sensing and VGI in the Fusion of Historical Data

Providing long-term data about the evolution of railway networks in Europe may help us understand how European Union (EU) member states behave in the long-term, and how they can comply with present EU recommendations. This paper proposes a methodology for collecting data about railway stations, at the maximal extent of the French railway network, a century ago.The expected outcome is a geocoded dataset of French railway stations (gares), which: (a) links gares to each other, (b) links gares with French communes, the basic administrative level for statistical information. Present stations are well documented in public data, but thousands of past stations are sparsely recorded, not geocoded, and often ignored, except in volunteer geographic information (VGI), either collaboratively through Wikipedia or individually. VGI is very valuable in keeping track of that heritage, and remote sensing, including aerial photography is often the last chance to obtain precise locations. The approach is a series of steps: (1) meta-analysis of the public datasets, (2) three-steps fusion: measure-decision-combination, between public datasets, (3) computer-assisted geocoding for ‘gares’ where fusion fails, (4) integration of additional gares gathered from VGI, (5) automated quality control, indicating where quality is questionable. These five families of methods, form a comprehensive computer-assisted reconstruction process (CARP), which constitutes the core of this paper. The outcome is a reliable dataset—in geojson format under open license—encompassing (by January 2021) more than 10,700 items linked to about 7500 of the 35,500 communes of France: that is 60% more than recorded before. This work demonstrates: (a) it is possible to reconstruct transport data from the past, at a national scale; (b) the value of remote sensing and of VGI is considerable in completing public sources from an historical perspective; (c) data quality can be monitored all along the process and (d) the geocoded outcome is ready for a large variety of further studies with statistical data (demography, density, space coverage, CO2 simulation, environmental policies, etc.).

New Changes, New Possibilities: China’s Latest Patent Law Amendments

Abstract New amendments to China’s Patent Law feature open licensing which should encourage the use of patents, and promote the more rapid broadcast and dissemination of new technology. They should also offer the possibility of greater transactional visibility, transparency and traceability which has important ramifications for IP valuation and reporting in IPOs, annual and other reports. Other provisions underscore China’s efforts to improve its patent system by introducing new protections for patent holders, mechanisms to reduce abuse, provisions to strengthen patent-related public services and promote the use of patents. There are also a number of changes that should interest pharmaceutical companies, patent litigants, patent holders and app developers.

Building capacity through open approaches: Lessons from developing undergraduate electrophysiology practicals.

Background: Electrophysiology has a wide range of biomedical research and clinical applications. As such, education in the theoretical basis and hands-on practice of electrophysiological techniques is essential for biomedical students, including at the undergraduate level. However, offering hands-on learning experiences is particularly difficult in environments with limited resources and infrastructure. Methods: In 2017, we began a project to design and incorporate electrophysiology laboratory practicals into our Biomedical Physics undergraduate curriculum at the Universidad Nacional Autónoma de México. We describe some of the challenges we faced, how we maximized resources to overcome some of these challenges, and in particular, how we used open scholarship approaches to build both educational and research capacity. Results: We succeeded in developing a number of experimental and data analysis practicals in electrophysiology, including electrocardiogram, electromyogram, and electrooculogram techniques. The use of open tools, open platforms, and open licenses was key to the success and broader impact of our project. We share examples of our practicals and explain how we use these activities to strengthen interdisciplinary learning, namely the application of concepts in physics to understanding functions of the human body. Conclusions: Open scholarship provides multiple opportunities for universities to build capacity. Our goal is to provide ideas, materials, and strategies for educators working in similar resource-limited environments.

A French corpus annotated for multiword expressions and named entities

We present the enrichment of a French treebank of various genres with a new annotation layer for multiword expressions (MWEs) and named entities (NEs).1 Our contribution with respect to previous work on NE and MWE annotation is the particular care taken to use formal criteria, organized into decision flowcharts, shedding some light on the interactions between NEs and MWEs. Moreover, in order to cope with the well-known difficulty to draw a clear-cut frontier between compositional expressions and MWEs, we chose to use sufficient criteria only. As a result, annotated MWEs satisfy a varying number of sufficient criteria, accounting for the scalar nature of the MWE status. In addition to the span of the elements, annotation includes the subcategory of NEs (e.g., person, location) and one matching sufficient criterion for non-verbal MWEs (e.g., lexical substitution). The 3,099 sentences of the treebank were double-annotated and adjudicated, and we paid attention to cross-type consistency and compatibility with thesyntactic layer. Overall inter-annotator agreement on non-verbal MWEs and NEs reached 71.1%. The released corpus contains 3,112 annotated NEs and 3,440 MWEs, and is distributed under an open license.

Developing the Gaois Linguistic Database of Irish-language Surnames

It is now commonplace to see surnames written in the Irish language in Ireland, yet there is no online resource for checking the standard spelling and grammar of Irish-language surnames. We propose a data structure for handling Irish-language surnames which comprises bilingual (Irish–English) clusters of surname forms. We present the first open, data-driven linguistic database of common Irish-language surnames, containing 664 surname clusters, and a method for deriving Irish-language inflected forms. Unlike other Irish surname dictionaries, our aim is not to list variants or explain origins, but rather to provide standard Irish-language surname forms via the web for use in the educational, cultural, and public spheres, as well as in the library and information sciences. The database can be queried via a web application, and the dataset is available to download under an open licence. The web application uses a comprehensive list of surname forms for query expansion. We envisage the database being applied to name authority control in Irish libraries to provide for bilingual access points.

The impact of Plan S on scholarly journals from less developed European countries

In September 2018, Science Europe (https://www.scienceeurope.org/) launched the cOalition S initiative for increasing Open Access (OA) to research data and publications derived from publicly funded scientific research projects. The backbone of the initiative is Plan S with one main goal: With effect from 2021, scholarly publications on the results from research funded by public or private grants provided by national, regional and international research councils and funding bodies, must be published in Open Access Journals, on Open Access Platforms, or made immediately available through Open Access Repositories without embargo (1). Whichever of these three routes is taken, all publications must be published under an open license, preferably the Creative Commons Attribution license (CC BY), in order to fulfil the requirements defined by the Berlin Declaration. Many European research funders have been endorsing cOAlition S from the very beginning and supporting Plan S as one of the paths to science without publication paywalls. Its aims, principles, and scope are a step forward to open science. Despite this boost, it remains to be seen whether Plan S will have unexpected long-term effects on journals from small or peripheral scientific communities. Many researchers in these communities mainly publish in their domestic journals. Despite limited international reception, these journals can play an important role by increasing access to locally relevant information and helping domestic researchers to improve their publication performance. If the diamond OA publishing model of these journals loses stable national financial support, it would be an additional blow to small scientific communities.

Editorial

Dear Readers, It is a great pleasure for me to welcome you to our first regular issue in 2021 covering 3 very relevant and novel articles in various computer science topics. There are also many news and changes with the beginning of the new year that I am excited to report on and share. To start with, we are very happy to welcome two new consortium members and editors-in-chief: California Polytechnic State University San Luis Obispo represented by Prof. Christian Eckhardt from the Department of Computer Science & Software Engineering and the Institute for IDEAS at American University in Washington DC represented by Prof. Krzysztof Pietroszek. On the management side of J.UCS, Dana Kaiser has retired at the end of last year, and on behalf of the journal I want to gratefully thank Dana for her devoted and great work since the foundation of this journal. I also want to give Johanna Zeisberg a warm welcome who will take over the role as Publishing Manager and collaborate and support the whole J.UCS community. On the technical side, our journal has moved to another submission and publishing platform. Since the foundation of J.UCS more than 25 years ago, the journal has offered readers, authors and editors various novel features over the course of the years. In this perspective but also in terms of the visionary view of founding a freely accessibly online journal, I want to express our deep gratitude for the contributions of Prof. Hermann Maurer to the success of J.UCS for almost 20 years. Since beginning of 2021, J.UCS is hosted by Pensoft Publishers Ltd. on the ARPHA Publishing Platform. This allows us not only to offer state-of-the-art publishing features but also to make use of integrated long-time archiving systems and various indexing services. In this context I also want to thank Internet Studio Isser and Photographer Christian Trummer for the kind support in the development of the design update and the J.UCS images. In this first issue of the year, I also want to look back on the journal’s achievements in 2020. We are proud to report a total of 11 issues with 74 articles on novel aspects of various topics in computer science; to be more specific, 51 articles have been published in 7 special issues and 23 articles in 4 regular issues. Since last year, J.UCS publishes under the open access Creative Commons License CC BY-ND 4.0 and therefore provides even more value und openness to a broader community. In 2020, we counted more than 87 thousand unique visits and almost 65 thousand paper downloads. This success is only possible due to the great support of the involved institutions, reviewers and authors, and I want to gratefully thank them all for their valuable support and work. Over the years we have not only offered readers open access to our high-quality journal, but we also do not charge our authors publication fees. This adventurous approach together with a rigorous review process and a broad support by the community resulted in a valuable contribution in the field of computer science, which is reflected in the high number of unique visitors and article downloads. In this context I gratefully thank all consortium members for their financial support of J.UCS. I am looking forward to continuing the cooperation with our editors, the editorial team and the technical support to maintain the success of J.UCS. I would be very grateful for suggestions and feedback on how we can even improve and develop J.UCS in the future. In this regular issue, I am very pleased to introduce 3 accepted papers from 5 different countries. On the occasion of the 25th anniversary of the J.UCS journal, Nelson Baloian, José A. Pino, Gustavo Zurita, Valeria Lobos-Ossandón, and Hermann Maurer analyze and discuss a bibliometric overview of the first 25 years of the journal in their collaboration between Austria and Chile. In a collaborative research between China and Spain, Xin Liu, Xiaoying Song, Wei Gao, Li Zou, and Alvaro Labella Romero report on their decision making approach based on hesitant fuzzy linguistic-valued credibility reasoning. And finally, Christian Moreira Matos, Vitor Kehl Matter, Marcio Garcia Martins, Joao Elison Da Rosa Tavares, Alexandre Sturmer Wolf, Paulo Cesar Buttenbender, and Jorge Luis Victoria Barbosa from Brazil discuss a collaborative model to assist people with disabilities and the elderly people in smart assistive cities. Enjoy Reading!

The Biochemist 2021

Over the last 12 months, the world has seen a lot of change and as we all look ahead now to 2021, with vaccines offering the promise of a return to social normality, we are reminded there is hope. During this time, Portland Press and the Biochemical Society have been working hard behind the scenes to improve The Biochemist, and we would like to take this opportunity to give you an update.In October 2019, we launched a new online offering (https://portlandpress.com/biochemist) as part of our new Portland Press websites, with greater search and sharing functions. All content published in the magazine is made available online to the community for free and published under an open access license so you can share it with your colleagues and reuse it if you wish.During the second half of 2020, we have been looking at processes to make the production of the magazine more efficient (including for authors) and therefore we have brought in an XML-first workflow and submission system. XML-first workflows will help to streamline the publishing process for both the author and the publishing team, while the online manuscript processing system would enable us to track submissions to the magazine and operate an online peer review process.The Biochemist has provided researchers from all over the world and at all career stages the opportunity to share what they feel is important – from work addressing inequality in the STEM fields, to our beginner’s guide series sharing technical knowledge, and we are proud to be able to continue to do so in 2021. Looking ahead to themes we aim to cover in forthcoming issues, including biological symmetry, vaccine strategies, and diabetes and insulin, we hope to bring you something of interest – whatever your current research field.If you read the editorial in our last issue, you will know that Chris Willmott has now stepped down as Science Editor and we would like to introduce you to our new Science Editor, Heather Doran.Heather has been a member of The Biochemist Editorial Board since 2017 and is the Public Engagement Manager for the award winning Leverhulme Research Centre for Forensic Science at the University of Dundee. Her PhD from the University of Aberdeen is in molecular pharmacology and her undergraduate degree is in Molecular Biology and Biochemistry, so she is a biochemist by background and training. Heather has worked in public engagement since 2012 where her efforts have been focused on supporting researchers to engage with the public through face-to-face initiatives, designed citizen science projects and online engagement. Respected in her field, in 2015/2016 she was awarded a Winston Churchill Memorial Trust Travel Fellowship on the communication of science travelling to the USA, Japan and China to explore how major research institutes and individual researchers help foster online engagement through social media.We are always looking for ways we can improve the magazine. If you would like to contribute content or have suggestions for future themes you would like to see covered, please contact us at editorial@PortlandPress.com.

A dataset for evaluating blood detection in hyperspectral images

The sensitivity of imaging spectroscopy to haemoglobin derivatives makes it a promising tool for detecting blood. However, due to complexity and high dimensionality of hyperspectral images, the development of hyperspectral blood detection algorithms is challenging. To facilitate their development, we present a new hyperspectral blood detection dataset. This dataset, published under an open access license, consists of multiple detection scenarios with varying levels of complexity. It allows to test the performance of Machine Learning methods in relation to different acquisition environments, types of background, age of blood and presence of other blood-like substances. We have explored the dataset with blood detection experiments, for which we have used a hyperspectral target detection algorithm based on the well-known Matched Filter detector. Our results and their discussion highlight the challenges of blood detection in hyperspectral data and form a reference for further works.

Galileo Ionospheric Correction Algorithm Integration into the Open-Source GNSS Laboratory Tool Suite (gLAB)

Users of the global navigation satellite system (GNSS) operating with a single-frequency receiver must use an ionospheric correction algorithm (ICA) to account for the delay introduced on radio waves by the upper atmosphere. Galileo, the European GNSS, uses an ICA named NeQuick-G. In an effort to foster the adoption of NeQuick-G by final users, two implementations in C language have been recently made available to the public by the European Space Agency (ESA) and the Joint Research Centre (JRC) of the European Commission (EC), respectively. The aim of the present contribution is to compare the slant total electron content (STEC) predictions of the two aforementioned implementations of NeQuick-G. For this purpose, we have used actual multi-constellation and multi-frequency data for several hundreds of stations distributed worldwide belonging to the Multi GNSS Experiment (MGEX) network of the International GNSS Service (IGS). For each first day of the month during year 2019, the STECs of the two NeQuick-G versions were compared in terms of accuracy, consistency, availability, and execution time. Our study concludes that both implementations of NeQuick-G perform equivalently. Indeed, in over 99.998% of the 2125 million STECs computed, the output is exactly coincident. In contrast, 0.002% of the whole set of STECs for those rays are tangent to the Earth, the behavior of both implementations differs. We confirmed the discrepancy by processing radio-occultation actual measurements from a COSMIC-2 low Earth orbit satellite. We selected the JRC version of the Galileo ICA to be integrated into the GNSS LABoratory (gLAB) tool suite, because its open license and its processing speed (it is 13.88% faster than the ESA version). NeQuick-G outperforms the GPS ICA in STEC residuals up to 12.15 TECUs (percentile 96.23th) and in the 3D position errors, up to 5.76 m (percentile 99.18th) for code-pseudorange positioning.

The Applicable Conditions of Patent Open License System

Patent; Open license; Application of law; Process of establishment

Coastal ocean forecasting on the GPU using a two-dimensional finite-volume scheme

In this work, we take a modern high-resolution finite-volume scheme for solving the rotational shallow-water equations and extend it with features required to run real-world ocean simulations. Our contributions include a spatially varying north vector and Coriolis term required for large scale domains, moving wet-dry fronts, a static land mask, bottom shear stress, wind forcing, boundary conditions for nesting in a global model, and an efficient model reformulation that makes it well-suited for massively parallel implementations. Our model order is verified using a grid convergence test, and we show numerical experiments using three different sections along the coast of Norway based on data originating from operational forecasts run at the Norwegian Meteorological Institute. Our simulation framework shows perfect weak scaling on a modern P100 GPU, and is capable of providing tidal wave forecasts that are very close to the operational model at a fraction of the cost. All source code and data used in this work are publicly available under open licenses.