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zenodo44/100

2023 Utrecht University Open Access Monitor (peer reviewed journal articles)

<p>Results of the OA monitor of Utrecht University (UU) and University Medical Center Utrecht(UMCU) for the year 2023. It lists the open access availability of all peer reviewed journal articles registered in the CRIS (Pure) of Utrecht University and/or University Medical Center Utrecht.&nbsp;</p>

opencc-zeroJun 2024View details →
zenodo44/100

Open Access levels of Dutch universities' output 2016-2017 (articles & reviews): green, gold, hybrid and bronze - May 2018

<p>Using Web of Science and Unpaywall data, we here provide an update of Open Access (OA) levels of Dutch universities, for 2016 and 2017.</p> <p>Our previous analysis&nbsp;&nbsp;(<a href="http://doi.org/10.5281/zenodo.1133759">10.5281/zenodo.1133759</a> and <a href="http://doi.org/10.7287/peerj.preprints.3520v1">10.7287/peerj.preprints.3520v1</a>)&nbsp;looked at OA classification as included in Web of Science (gold and green OA, based on Unpaywall data), and supplemented that with a breakdown of gold OA into pure gold, hybrid and bronze, taken from Unpaywall data (formerly OADOI) directly. Here, we improve on this by running all DOIs retrieved from WoS through Unpaywall data (using their web interface that allows batch checking of up to 10,000 DOIs at a time). Unlike WoS, Unpaywall data itself includes author-submitted versions in their green OA classification, resulting in more complete green OA levels.&nbsp;</p> <p>In addition, since our initial analysis of December 2017, Unpaywall data has considerably expanded its coverage of institutional repositories&nbsp; (IRs) (see <a href="https://unpaywall.org/sources">https://unpaywall.org/sources</a>). This now includes coverage of the IRs from all Dutch universities.&nbsp;</p> <p>Taken together, the current data show higher levels of green open access, including author-submitted versions, compared to our previous analysis.&nbsp;</p> <p>In this update, we include output (articles and reviews) from 2016 and 2017 for all 14 universities in the Netherlands.&nbsp;</p> <p>The following categories are distinguished (description taken from&nbsp;Piwowar at al., 2018, doi:&nbsp;<a href="https://doi.org/10.7717/peerj.4375">10.7717/peerj.4375</a>)</p> <ul> <li><strong>Pure gold</strong>: Published in an open-access journal (as defined by the DOAJ)</li> <li><strong>Hybrid</strong>: Free under an open license in a toll-access journal</li> <li><strong>Bronze</strong>: Free to read on the publisher page, but without a license</li> <li><strong>Green:&nbsp;</strong>Available from an institutional or disciplinary repository (including PubMedCentral)</li> </ul> <p>Data for Dutch universities were collected from Web of Science using the organization-enhanced field. Only articles and reviews were included. DOIs were extracted from the Web of Science export, run through the Unpaywall data <a href="https://unpaywall.org/products/simple-query-tool">Simple Query Tool</a>. From the resulting data from Unpaywall, OA classification was done using a simple formula in Excel (to be replaced by an R script in a future update). The Excel template used is included in this dataset, as is the OADOI API output for each Dutch university&#39;s article subset, and the lists of DOIs derived from Web of Science. The dataset also includes summarized data and three charts generated from these data, showing levels of different types of OA for 2016, 2017 and the two years compared.&nbsp;&nbsp;</p> <p>----------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p>

opencc-by-4.0May 2018View details →
zenodo44/100

Project "Public services management system to improve the quality and accessibility of services" (01.2.2-LMT-K-718-03-0019) literature review screening results

<p>The results of the keyword query in Scopus search with the abstracts were screened using <i>abstractr </i>platform at&nbsp;<a href="http://abstrackr.cebm.brown.edu">http://abstrackr.cebm.brown.edu</a>. Four reviewers reviewed intersecting subsets of the overall list of publications in separate reviews, therefore duplicate records in the file are possible. The results from four reviews were combined into one file using functionality of <i>abstractr </i>platform. The reviews were finalized in February, 2022. Majority of the publications from the Scopus query results were automatically assigned low relevance scores thanks to the active learning algorithm used by <i>abstractr</i> and therefore were not reviewed manually.</p><p>Notes on the columns of the dataset:</p><ul><li>(internal) id&nbsp; - internal id added by <i>abstractr.</i></li><li>(source) id&nbsp; - Scopus document id followed by underscore and '1' (if publication has DOI)&nbsp; or 'n' (if publication has no DOI).</li><li>keywords - authors' keywords and Scopus keywords concatenated from the Scopus query results.</li><li>abstract - an abstract of a publication from the Scopus query results.</li><li>title - title of a publication from the Scopus query results.</li><li>journal - journal of a publication from the Scopus query results.</li><li>authors - authors of a publlication from the Scopus query results.</li><li>consensus - for publications reviewed by multiple reviewers the consensus decision is signified by '1', no consensus - by 'x' and unable to asses consensus by 'o'. These codes are generated by <i>abstrackr.</i></li><li>eg - the first reviewer id. Code '1' means the publication was selected based on title and abstract, '0' - unsure, '-1' rejected.</li><li>dj - the second reviewer id.&nbsp;Code '1' means the publication was selected based on title and abstract, '0' - unsure, '-1' rejected.</li><li>rp - the third reviewer id. Code '1' means the publication was selected based on title and abstract, '0' - unsure, '-1' rejected.</li><li>mp - the fourth reviewer id. Code '1' means the publication was selected based on title and abstract, '0' - unsure, '-1' rejected.</li><li>count (+1) - integer, the number of reviewers selecting the publication for fulltext reading. Calculated from 'eg ','dj ','rp' and 'mp' columns.</li><li>count (0) - integer, the number of reviewers not sure of selecting the publication for fulltext reading.&nbsp;Calculated from 'eg ','dj ','rp' and 'mp' columns.</li><li>count (-1)&nbsp; - integer, the number of reviewers not selecting the publication for fulltext reading.&nbsp;Calculated from 'eg ','dj ','rp' and 'mp' columns.</li><li>at leat once selected - binary integer, representing the final decision rule to select publications for fulltext reading and further analysis.</li></ul><p>The data were collected as a part of the project "Public services management system to improve the quality and accessibility of services" ("Viešųjų paslaugų vadybos sistema paslaugų kokybei ir prieinamumui gerinti"), grant no. 01.2.2-LMT-K-718-03-0019, funded by the Lithuanian research council.</p>

opencc-by-4.0Jun 2023View details →
zenodo40/100

Proportion of Open Access Papers Published in Peer-Reviewed Journals in Austria 2008-2013

<p>In 2014, Archambault et al. published a report which provided data about Open Access publishing for the years 2008-2013 for all countries of the European Research Area (ERA) as well as for Brazil, Canada, Japan and the USA. They differentiated not only by disciplines but also by three OA categories: Golden, Green and a residual category. For the dataset, the data for Austria and the whole area examined has been extracted and modified. The results show above-average rates for Austria in almost all disciplines.</p>

opencc-by-4.0May 2015View details →
zenodo40/100

User participation in digital accessibility evaluations: reviewing methods and objectives

<p><span>Although laws and standardization bodies promote user participation in digital accessibility evaluations, people with disabilities still consider themselves excluded from this process. One reason could be the lack of systematized knowledge about evaluation methods involving users. This article seeks to understand how and for what purpose digital accessibility evaluations with user participation were conducted in the scientific literature from 2018 to 2021. Three types of user participation emerged: 1) user-based usability testing to evaluate task accomplishment, user reactions and interface qualities; 2) interviewing users to assess the local and social factors impacting digital service accessibility; 3) using questionnaires or crowdsourcing to check the compliance of certain interfaces with accessibility standards. Participants are primarily chosen based on their functional impairments and, to a lesser degree, their project-related skills, biographical information, technology habits, among other criteria. The comprehensive user insights gained with these methods are judged to be positive whereas the lack of representativeness of the selected user samples is found to be regrettable. The article finally discusses the definitions of accessibility and disability that underpin these methodologies.</span></p>

opencc-by-4.0Mar 2024View details →
zenodo40/100

Review of Recent Trends in Measuring the Computing Systems Intelligence-Figure 3. Intelligence of different living creature (accessed 01.11.2017). 3.1. A painting elephant (http://www.wittyfacts.com/suda-the-painting-elephant/); 3.2. A common octopus (https://en.wikipedia.org/wiki/Octopus). 3.3. An African grey parrot (https://en.wikipedia.org/wiki/Grey_parrot)

<p>Many observations proved that octopus species have an impressive spatial learning capacity, advanced navigational abilities, and advanced predatory techniques. The dexterity is important for using and manipulating tools. Zullo, Sumbre, Agnisola, Flash, &amp; Hochner, (2009) studied the successful dexterity of octopuses. They have highly sensitive suction cups and prehensile arms, squid, and cuttlefish. This allows them to hold and manipulate objects. The motor skills of octopuses (Figure 3.2) do not seem to depend upon mapping their body. Some species of parrots are able to mimic very well the human speech. There were performed many studies with parrots that shown that some individuals are able to associate words with their meanings. Another observed ability is to form simple sentences. It has been shown that some grey parrots perform at the cognitive level of a 3-year-old child in some tasks. Pepperberg (2006) proved that some parrots can count up to 6. Figure 3.3 presents a frequently studied species of parrots, called African grey parrot.</p>

opencc-by-4.0Apr 2018View details →
zenodo40/100

Review of Recent Trends in Measuring the Computing Systems Intelligence-igure 2. Intelligence of different living creature (accessed 01.11.2017). 2.1. A crow solving a complex task (https://www.disclose.tv/spooky-genius-crow-had-to-be-removed-from-scientific-experiment- 314886). 2.2. A group of dolphins with a social behaviour (http://www.sciencemag.org/news/2012/04/teamwork-builds-big-brains); 2.3. An orangutan that use a spear to fish (https://primatology.net/2008/04/29/orangutan-photographed-using-tool-as-spear-to-fish)

<p>Some species of birds have been shown capable of using different tools. Many studies consider the crows as very intelligent. Smirnova, Lazareva, and Zorina (2000) suggested that crows have some kind of numerical ability. Figure 2.1 presents a crow that uses a tool, a small stone in order to catch a worm from a glass of water.The dolphins in many studies are considered intelligent at the individual level. An advanced ability of dolphins is the self-awareness. Marten and Psarakos (1995) presented an interesting study based on self-view television to distinguish between self-examination and social behavior in the Bottlenose dolphin. The most well-known abilities of dolphins are to teach, learn and cooperate. Dolphins have a complex communication and social behaviour. Figure 2.2 presents the image of a common group of dolphins. Some studies prove that primates are one of the most intelligent in the class of animals (Reader, Hager, &amp; Laland, 2011). Orangutans are one of the most intelligent primates. The ability of orangutans to use different types of tools in order to perform tasks is well-known. Figure 2.3 presents an orangutan that uses a spear to catch fish. The orangutans can be considered intelligent at individual level.</p>

opencc-by-4.0Apr 2018View details →
zenodo40/100

Review of Recent Trends in Measuring the Computing Systems Intelligence-Figure 1. Intelligence of different simple living creature (accessed 01.11.2017). 1.1. A carnivorous plants catching an insect (https://phys.org/news/2016-05-colombia-peace-reveal-jungle-species.html); 1.2. A colony of ants solving a very complex task (https://mappingignorance.org/2016/05/27/rafting-ants); 1.3. The collective behaviour of a school of fish (https://simple.wikipedia.org/wiki/Shoaling_and_schooling)

<p>The biological intelligence of different life forms, ranging from very simple (such as plants) to very complex (such as humans) is the subject of many studies and a large amount of research. Frequent studies related to different kind of biological intelligence include: the intelligence of horses (Krueger, &amp; Heinze, 2008; Krueger, Farmer, &amp; Heinze, 2014; Schuetz, Farmer, &amp; Krueger, 2016), intelligence of pigs (Broom, Sena, &amp; Moynihan, 2009), intelligence of dogs (Coren, 1995), intelligence of primates (Reader, Hager, &amp; Laland, 2011) and so one. Figures 1, 2, and 3 present some biological life forms that are frequently considered intelligent. Trewavas (2002; 2005) considered that plants intelligence should be based on principles such as their ability to adjust their morphology, and phenotype accordingly to ensure self- preservation and reproduction. Figure 1.1 presents an intelligent plant (carnivorous) that uses a strategy for catching very fast flying insects. In order to eat the insect, it makes a movement. Figure 1.1 presents the catching of an insect by a carnivorous plant. The intelligence of colonies of ants, termites and other insects that live in large colonies is considered at the colony level (Brady, Fisher, Schultz, &amp; Ward, 2014; Johnson, Borowiec, Chiu, Lee, Atallah, &amp; Ward, 2013). Figure 1.2 presents the coherent intelligent surviving behaviour of a colony of a species of ants. The ants make a structural reorganization in order to move on the surface of the water. Figure 1.3 presents a very large school of fish with an intelligent coherent collective feeding and self-protecting behaviour. Each individual fish has a very simple behavior. Based on this it cannot be considered intelligent. The intelligence in large schools of fish emerges at the collective level (Shaw, 1978; Parrish, Viscedo, &amp; Grunbaum, 2002).</p>

opencc-by-4.0Apr 2018View details →
zenodo40/100

Review of Recent Trends in Measuring the Computing Systems Intelligence-Figure 4. Intelligent robots (accessed 01.11.2017). 4.1. Erica, a humanoid robot (https://www.tech-review.com/erica-is-the-latest-japanese-robot-with-human-appearance.html). 4.2. Atlas, a bipedal humanoid robot developed by Boston Dynamics (https://en.wikipedia.org/wiki/Atlas_(robot))

<p>One of the most highly quoted and interesting definitions of machine intelligence was presented by Alan Turing (1950). Turing considered a computing system intelligent if a human assessor could not decide the nature of the system (being human or artificial) based on questions asked from a room hidden from a human assessor. Until recently there were performed different discussions and comments on the Turing test. Hern&aacute;ndez-Orallo (2000) presents an interesting study related to the Turing Test. Dowe and Hajek, (1998) propose a computational extension of the Turing Test. The design and development of intelligent systems are historically very recent. But, even if the advance of hardware and software is very fast, it will take a longer time until the artificial computing systems will attain a similar intelligence with the humans. Based on this fact, we consider that is not appropriate to formulate the problem of the direct comparison at a general level of human intelligence with the machine intelligence. Different definitions were proposed for the intelligence of the agents (Russell, &amp; Norvig, 2003; Iantovics, &amp; Zamfirescu, 2013). Many authors (Russell, &amp; Norvig, 2003; Iantovics, 2005) argue that the intelligence of the agents cannot be defined universally. The impossibility to give a universal definition to the human intelligence is based mostly on the enormous complexity of the human brain and complexity of the human thinking and decision making. Similarly, we may consider the impossibility of universal definition of intelligence of the agents based on the very large variety (by type and complexity) of intelligent agents. The machine intelligence frequently is defined based on different abilities such as (Iantovics, 2005; Sharkey, 2006): autonomous learning, self-adaptation, and evolution. These principles of considering the intelligence are inspired by biological life forms able to learn autonomously during their life cycle, to adapt to the environment and to evolve during more generations. We would like to outline that not all the designed agents are intelligent. There is not a required property of an agent to be intelligent.</p>

opencc-by-4.0Apr 2018View details →
zenodo40/100

Review of Recent Trends in Measuring the Computing Systems Intelligence-Figure 5. What machine intelligence is (accessed 01.11.2017) http://www.ibmbigdatahub.com/blog/measuring-artificial-intelligence-quotient)

<p>There are many developed cooperative systems composed of very simple agents that at the system&rsquo;s level are considered intelligent. Yang, Galis, Guo, and Liu (2003) presented an intelligent cooperative mobile multiagent system composed of simple reactive agents. The mobile agents are specialized in a computer network administration. They are endowed with knowledge retained as a set of rules which describe network administration tasks. The multiagent system could be considered intelligent based on the fact that it simulates the behavior of a human network administrator. In some cooperative systems, the member agents can organize themselves into cooperative coalitions/groups. Each coalition being able to solve cooperatively problems. Iantovics and Zamfirescu (2013) presented such an adaptive cooperative multiagent system, able to reorganize autonomously the coalitions in order to solve more intelligently problems. The biological and artificial intelligence are by a completely different type (Figure 5). Recently, the biological intelligence is the source of inspiration for the development of many intelligent artificial systems and different problem-solving algorithms.</p>

opencc-by-4.0Apr 2018View details →
zenodo40/100

Evaluating Institutional Commitments to Open Scholarly Infrastructure: A Review of Open Access Collection Development Policies

<p>Data prepared for the publication &quot;Evaluating Institutional Commitments to Open Scholarly Infrastructure: A Review of Open Access Collection Development Policies.&quot;</p> <p><strong>oa-cd-policies.csv</strong></p> <p>Scope: This data represents collection development policies that contain substantial mention of open access.</p> <p>Data collection: The policies were sourced using an Advanced Google Search for &quot;open access&quot; AND &quot;collection development policy&quot; at &quot;.edu&quot; domains.</p> <p>Variables:</p> <ul> <li>institution: Free text, name of the institution.</li> <li>carnegie_class: One of <a href="https://carnegieclassifications.acenet.edu/carnegie-classification/classification-methodology/basic-classification/">these options</a>;&nbsp;the Carnegie classification of the institution.</li> <li>institution_type: One of public or private; the funding source of the institution.</li> <li>policy_name: Free text; the title of the policy.</li> <li>supplemental_policy: Link to a supplemental open access policy if linked in the collection development policy.</li> <li>cd_policy_link: Link to the policy.</li> <li>infrastructure: TRUE or FALSE; whether the policy includes a commitment to open access scholarly&nbsp;infrastructure development, including open source platforms, locally hosted platforms, consortia, or an institutional repository.</li> <li>excerpt: Free text; text from the policy that mentions infrastructure.</li> </ul> <p><strong>principles-policies.csv</strong></p> <p>Scope:&nbsp;This data represents those collection development policies from oa-cd-policies.csv&nbsp;that contain commitments in line with the <a href="https://openscholarlyinfrastructure.org/">Principles for Open Scholarly Infrastructure</a>.</p> <p>Variables:</p> <ul> <li>institution: Free text, name of the institution.</li> <li>carnegie_class: One of <a href="https://carnegieclassifications.acenet.edu/carnegie-classification/classification-methodology/basic-classification/">these options</a>;&nbsp;the Carnegie classification of the institution.</li> <li>institution_type: One of public or private; the funding source of the institution.</li> <li>policy_name: Free text; the title of the policy.</li> <li>supplemental_policy: Link to a supplemental open access policy if linked in the collection development policy.</li> <li>cd_policy_link: Link to the policy.</li> <li>principle: One of the three main <a href="https://openscholarlyinfrastructure.org/">Principles</a>.</li> <li>sub_principle: One of the <a href="https://openscholarlyinfrastructure.org/">Sub-Principles</a>.</li> <li>excerpt: Free text; text from the policy that illustrates the sub_principle.</li> </ul>

opencc-by-4.0May 2023View details →
zenodo36/100

Knowledge Freedom in computational science: a two stage peer-review process with KF Eligibility Access Review

<p>What is explained below is the&nbsp;<em>peer review process</em>&nbsp;applied by&nbsp;<em>Notes on Transdisciplinar</em><em>y Modelling for Environment&nbsp;</em>(NTMe). Authors and readers are encouraged to understand not only the process, but also the rationale behind the process, which&nbsp;is closely connected with the peculiar challenges faced by the scientific problems (computational-science modelling under uncertainty, in broad and heterogeneous contexts) in the scope of the&nbsp;journal.&nbsp;</p> <p>&nbsp;</p> <p><span class="math-tex">\(\mathsf{\Large\text{The rationale behind the peer-review process}}\)</span></p> <p><strong>Computational research problems for more than one discipline. </strong>Research specific to a particular disciplinary domain is typically authored, and then studied, by experts in that domain. Several conventions, assumptions, fundamental protocols and methodology practices, are shared by domain experts as a common ground. Given that proficiency in these aspects is a precondition for domain experts, this kind of knowledge is often implicit, and not well communicated within domain-specific literature. &quot;Typical&quot; data preprocessing, model settings, quality-assessment assumptions (and their &quot;default&quot; simplifications and shortcuts), in this literature are often minimally reported or omitted, because the domain-specific community of researchers and practitioners knows them so well that they may resemble a sort of acquired conditioned response. However, when in a wider research more than one disciplinary domain is connected among each other, then implicit unexpressed knowledge may lead to ambiguity, misuse of results, and avoidable errors - sometimes challengly difficult to detect. The more and more diverse the domains, the higher this risk might be.</p> <p><strong>Useful cross-domain building blocks. </strong>&quot;Transdisciplinary&quot; research may risk being misinterpreted as just the final summary list of results grabbed by autonomous disciplinary silos run in parallel. However, a poor ability to&nbsp;communicate computational methods and data - and their limitations - between multiple disciplinary domains&nbsp;would&nbsp;jeopardise the collective (cross-domain) ability to distill truly integrated computational science. Computational science for transdisciplinary problems requires a pragmatic, engineered, but reasonably simple and modular approach to break and connect disciplinary silos - when appropriate for the problems investigated. Publishing <em>useful</em> cross-domain building blocks of this approach is the aim of the peer-review process in NTMe.</p> <p><strong>Connecting disciplines, space and time scales under uncertainty: the need for a shared semantics.&nbsp;</strong>Wide-scale transdisciplinary modelling (WSTM) relies on methods proper to computational science for connecting multiple scientific disciplines, and shedding light on broad, complex problems. Several of the most pressing problems we face as a human society are only partially known in their chain of consequences, and hopelessly difficult to address by a single discipline and a narrow perspective. Some of these problems capture the specific interest by particularly exposed regions, but their mechanism is more general, with essential knowledge often lying in other spatial areas -&nbsp;or even other time periods - hence calling for a wider perspective. Multiple&nbsp;spatial and temporal scales, with dissimilar data resolution, are frequent in WSTM problems, since they are often dictated by the complexity of reality and the available data. A wide-scale extent typically implies uneven quality and availability of data, and many sources of uncertainty - which increases when assumptions, methods and semantics by different disciplines or research institutions do not easily merge. A truly transdisciplinary communication of this essential semantics requires the <em>freedom </em>to communicate scientific knowledge, accurately and transparently, between disciplinary and corporate barriers.</p> <p><strong>Real knowledge sharing in computational science.&nbsp;</strong>As a consequence, wide-scale transdisciplinary modelling demands a focus on reproducible research and real scientific knowledge freedom. Data and software freedom are essential aspects of knowledge freedom in computational science. Therefore, ideally published articles should also provide the readers with the data and source code of the described mathematical modelling. To maximise transparency, replicability,&nbsp;reproducibility and reusability, published data should be made available as open data while source code should be made available as free software. Communicating semantics even to non-experts in a given domain requires that mathematical assumptions, otherwise obvious within a specific discipline, are duly annotated in a portable and concise way. Accordingly, brief but semantically clear documentation of data, methods and software is a key precondition. Here, a two-stage peer review process is described in which scientific knowledge freedom is considered with a dedicated Eligibility Access Review. This new peer review process is applied by <em>Notes on Transdisciplinary Modelling for Environment</em>&nbsp;with a focus on WSTM for environment.</p> <p>&nbsp;</p> <p><span class="math-tex">\(\mathsf{\Large\text{The peer-review process}}\)</span></p> <p><strong>A&nbsp;two-stage peer review process to avoid single-use disposable&nbsp;computational science.&nbsp;</strong>The two-stage peer review process requires discussion papers&nbsp;to be published so as to receive feedback from the scientific community before their possible finalisation. Initial manuscript submission is subject to the soundness review outlined above, also ensuring eligibility criteria to be fulfilled so as to support&nbsp;scientific knowledge freedom. Although this concept is multifaceted, some few dimensions might be emphasised which broadly apply in computational science and engineering (CSE). Among the many possible eligibility criteria in CSE, it should be highlighted at least the need for:&nbsp;</p> <ul> <li>free software to have been&nbsp;published so as for it to be persistently available;</li> <li>appropriate licensing and source code review to have been&nbsp;done (portable modularisation, with semantics of mathematical data-transformation methods clearly annotated);</li> <li>free data&nbsp;to have been&nbsp;published so as for it to be persistently available (with semantics of quantities clearly annotated);</li> <li>a minimal share of free-access core references to be selected&nbsp;in order for scientists and research organisations not to be discriminated on the basis of their funding availability, when they try to access the core literature cited in the manuscript.</li> </ul> <p>Before acceptance for discussion, a manuscript (and its potential data, parameters and software)&nbsp;may be revised, without exposing to the public immature versions, until it becomes able to fulfil the eligibility criteria. These iterations between author(s) and editors/reviewers remain confidential, and a potential manuscript rejection does not preclude resubmission. Acceptance of the manuscript to the discussion stage is followed by the permanent publication of the accepted version. This does not preclude, and actually encourages, further revised versions to be resubmitted. Any new revision is subject to eligibility access review, which takes into account the submission history of the manuscript and the already accepted public older versions.</p> <p><strong>Not a static publication. </strong>The discussion stage of the peer review process allows short comments to be submitted by&nbsp;referees and the scientific community, while authors are encouraged to interact with pending&nbsp;comments by providing their responses. During this stage, the paper accepted for discussion is already citable. Depending on the specific goals of each research problem, the discussion may remain open for a short time interval, or instead for a noticeably longer period of time (even indefinitely, if appropriate: for example, whenever authors do consider publishing cumulative milestone versions as important). There is not an a-priori limit to the duration of this first stage, and to the number of intermediate public revisions (which are optional), for a paper accepted for discussion.&nbsp;The second stage of peer review concludes the discussion stage with the&nbsp;submission of a revised manuscript, with final review&nbsp;and corrections. Fulfilment of the eligibility criteria is required over all the&nbsp;publication stages.<br> The published materials might be updated from time to time (at the authors&#39; discretion), and - after peer-reviewing the changes - published so that the evolution is clear and available to others. Although preferred and encouraged in the discussion stage, updates are possible even after the final stage. Revisions offering a noticeably different content, compared with the previous versions, might sometime be recommended by editors/reviewers as deserving the status of a new publication - not to confuse the readers. This implies the full two-stage review process has to be applied to the new publication (as an independent publication), while the previous accepted publication is considered as the final permanent version. Recalling an analogy with the typical evolution of free-software, a software package is frequently subject to future improvements and corresponding new versions. If a new version is too different from the original package, it may become a new independent package.&nbsp;</p> <p><strong>Scientific opinions,&nbsp;perspectives, and overviews.</strong> Manuscripts focusing on computational science methods, data, parameters, and software are expected to contribute practical components of scientific knowledge which can be adapted, modified, or generally integrated within the future body of knowledge - potentially in unexpected ways. Therefore, the aforementioned two-stage review is, overall, meant to ease the future invention of derivative works. On the other hand, manuscripts offering expert opinions on these topics do not contribute &quot;practical&quot; components to be directly modified. Instead, they contribute organised ideas to support the evolution of scientific knowledge. Therefore, the peer review process for this typology of manuscripts focuses on:</p> <ul> <li>the broad understandability and potential interest of the expert opinions, and</li> <li>the&nbsp;factual&nbsp;correctness of the objective elements included in the opinion (with adequate bibliographic, tabular, visual support where appropriate).&nbsp;</li> </ul> <p><strong>Preregistration, protocols and methods. </strong>NTMe accepts a third typology of manuscripts, focusing on anticipated results (hence not yet computed) which are expected following a modelling procedure to transform input data and parameters into the desired output. As data and software are only anticipated in this typology of manuscripts, the peer-review process focuses on:</p> <ul> <li>the broad understandability and potential interest of the proposed protocol or methodology,</li> <li>the correctness and clarity of the mathematical formulation of the proposed computational-modelling steps (data-transformation modules),</li> <li>the discussion of anticipated results, pitfalls, sources of uncertainty and their proper management, bifurcations of the methodology depending on the potential variants that a user may desire to apply (depending on available data and their quality, and on the desired specialisation of the proposed general method), and</li> <li>the adequacy of bibliographic, tabular, visual supports where appropriate.&nbsp;</li> </ul> <p><strong>Abstract, and plain language summary. </strong>Each article includes a technical abstract. Although the topics of published content might deal with domain-specific aspects of computational/environmental science, their focused analysis is expected to support wider research in a transdisciplinary context. Therefore, the abstract is expected to be accessible beyond the domain-specific research community. Each article, either in the discussion or in the final stage, in addition to a technical abstract needs a <em>plain language summary</em> so that non-experts and readers with a basic scientific and technical literacy can understand the main contributions of the article. The aim of the plain language summary is to support educational dissemination. The summary is not a simpler abstract, and typically offers a longer, more comprehensive description. It is realised with an editorial support to authors, so as to respect a general structure (unless otherwise agreed):</p> <ul> <li>first, the general context of the work is presented (the general topics in which the work is situated);</li> <li>second, the general open questions are introduced to which the work aims to contribute;</li> <li>third, the specific way is described in which the work contributes to progress on the general open questions;</li> <li>fourth, the implications, new opportunities or suggested lines of research, and potential limitations and unaswered questions are summarised.</li> </ul> <p><strong>Constructive peer review.</strong> The ultimate aim of the peer review process is to support authors, and future readers, in sharing useful, durable, and understandable notes of transdisciplinary knowledge. Given the very nature of the topics in NTMe, the need for a cogent peer review on a multiplicity of expertise fields is essential. Rarely a single reviewer is able to cover all the aspects of transdiciplinary computational science. Even so, different opinions by different reviewers may emerge on specific points. Therefore, a <em>constructive </em>approach is promoted during each step of the peer review process, so that authors are guided to understand the peer review, and a compendium of recommandations may be presented in a consistent way.</p> <p>&nbsp;</p> <p><sup>&copy; 2012-2020 Daniele de Rigo. This work is licensed under a </sup><a href="http://creativecommons.org/licenses/by-nd/4.0/legalcode"><sup>Creative Commons Attribution No Derivatives 4.0 International</sup></a><sup> license. Please, cite as<br> de Rigo, D., 2012. </sup><strong><sup>Knowledge Freedom in computational science: a two stage peer-review process with KF eligibility access review</sup></strong><sup>. </sup><em><sup>Zenodo, </sup></em><sup>CERN. </sup><a href="https://doi.org/10.5281/zenodo.7578"><sup>https://doi.org/10.5281/zenodo.7578</sup></a><sup> </sup></p> <p>&nbsp;</p>

opencc-by-nd-4.0Dec 2012View details →
zenodo36/100

Accessibility Reviews Associated with Visual Disabilities or Eye Conditions

<p>A dataset of nearly 180 million user reviews from which we extracted 4,999 accessibility reviews that express concerns that affect users with visual disabilities or eye conditions.&nbsp;</p> <p>This data is related to the following paper:</p> <p>Alberto Dumont Alves Oliveira, Paulo S&eacute;rgio Henrique Dos Santos, Wilson Est&eacute;cio Marc&iacute;lio J&uacute;nior, Wajdi M Aljedaani, Danilo Medeiros Eler, and Marcelo Medeiros Eler. 2023. Analyzing Accessibility Reviews Associated with Visual Disabilities or Eye Conditions. In Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI '23). Association for Computing Machinery, New York, NY, USA, Article 37, 1&ndash;14.&nbsp;<a href="https://doi.org/10.1145/3544548.3581315" rel="nofollow">https://doi.org/10.1145/3544548.3581315</a></p>

opencc-by-4.0Aug 2024View details →
zenodo36/100

Accessibility Reviews Related to BBC Mobile Accessibility Guidelines

<p>This dataset comprises accessibility user reviews from the Android App Store, categorized according to the accessibility principles, topics, and guidelines outlined in the <a href="https://www.bbc.co.uk/accessibility/forproducts/guides/mobile/" target="_blank" rel="noopener">BBC Mobile Accessibility Guidelines</a>.</p>

opencc-by-4.0Nov 2024View details →
ClinicalTrials.gov36/100

PARTNERS HF: Program to Access and Review Trending Information and Evaluate Correlation to Symptoms in Patients With Heart Failure

ClinicalTrials.gov study NCT00279955. IPD Sharing: Not stated. Countries: 1. Publications: 2.

restrictedIPD-UNDECIDEDFeb 2026View details →
dryad32/100

Data from: Systematic review on barriers and enablers for access to diabetic retinopathy screening services in different income settings

Background: Diabetic retinopathy (DR) can lead to visual impairment and blindness if not detected and treated in time. Knowing the barriers/enablers in advance in contrasting different country income settings may accelerate development of a successful DR screening (DRS) program. This would be especially applicable in the low-income settings with the rising prevalence of DR. Objectives: The aim of this systematic review is to identify and contrast the barriers/enablers to DRS for different contexts using both consumers i.e., people with diabetes (PwDM) and provider perspectives and system level factors in different country income settings. Methods: We searched MEDLINE, Embase, CENTRAL in the Cochrane Library from the databases start date to December 2018. We included the studies reported on barriers and enablers to access DRS services based at health care facilities. We categorised and synthesized themes related to the consumers (individuals), providers and the health systems (environment) as main dimensions according to the constructs of social cognitive theory, supported by the quantitative measures i.e., odds ratios as reported by each of the study authors. Main Results: We included 77 studies primarily describing the barriers and enablers. Most of the studies were from high income settings (72.7%, 56/77) and cross sectional in design (76.6%, 59/77). From the perspectives of consumers, lack of knowledge, attitude, awareness and motivation were identified as major barriers. The enablers were fear of blindness, proximity of screening facility, experiences of vision loss and being concerned of eye complications. In providers' perspectives, lack of skilled human resources, training programs, infrastructure of retinal imaging and cost of services were the main barriers. Higher odds of uptake of DRS services was observed when PwDM were provided health education (odds ratio (OR) 4.3) and having knowledge on DR (OR range 1.3-19.7). Conclusion: Knowing the barriers to access DRS is a pre-requisite in development of a successful screening program. The awareness, knowledge and attitude of the consumers, availability of skilled human resources and infrastructure emerged as the major barriers to access to DRS in any income setting.

opencc-zeroApr 2020View details →
zenodo32/100

Accessibility Update Reviews Related to WCAG 2.2

<p>This dataset consists of user reviews from the Android App Store, specifically selecting those that mention app updates and their impact on digital accessibility, as well as their relation to the accessibility principles and guidelines of the Web Content Accessibility Guidelines (WCAG) version 2.2.</p>

opencc-by-4.0Jul 2024View details →
dryad32/100

Systematic review of marine environmental DNA metabarcoding studies: Toward best practices for data usability and accessibility

<p>The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer-reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.</p>

opencc-zeroFeb 2023View details →
dryad32/100

Systematic review of marine environmental DNA metabarcoding studies: Toward best practices for data usability and accessibility

Open the record for dataset details and reuse information.

publicFeb 2023View details →
dryad32/100

Data from: Systematic review on barriers and enablers for access to diabetic retinopathy screening services in different income settings

Open the record for dataset details and reuse information.

publicApr 2020View details →

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas
neuroscienceopenDocumentation, web resources, and API references are available online.
Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage
behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.
Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb
electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.
Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl
behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.
Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro
neuroscienceopenPublished datasets are available on demand over the internet.
Last verified 2026-04-29Open record