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47 results for “review process”
[Dataset] Software Process Line as an Approach to Support Software Process Reuse: a Systematic Literature Review
<p>Dataset of a Systematic Literature Review on Software Process Line as an Approach to Support Software Process Reuse</p> <p>Please, read README.txt file before go through dataset.</p>
Literature Datasets for the publication "Systematic Review: Prevalence and Practices of Immunofluorescent Cell Image Processing"
<p>This dataset contains the CSV files returned from PubMed searches used to complete a Systematic Review of Image Processing Publication Practices for methods applied to immunofluorescent images of all CNS cells. <br> <br> The file names are organized "date_supplementarytablenumber" followed by the appropriate search terms. </p>
Data from: Spatial processes and evolutionary models: a critical review
Evolution is a fundamentally population level process in which variation, drift, and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time, using models like Brownian motion, stabilizing selection (Ornstein-Uhlenbeck), and directional selection on traits measured from stratigraphic sequences or on phylogenetic trees. But these models assume that the traits possessed by a species are homogeneous. Spatial processes such as dispersal, gene flow, and geographic range changes can produce patterns of trait evolution that do not fit the expectations of standard models, even when evolution at the local-population level is governed by drift or a typical OU model of selection. The basic properties of population level processes (variation, drift, selection, and population size) are reviewed and the relationship between their spatial and temporal dynamics is discussed. Typical evolutionary models used in palaeontology incorporate the temporal component of these dynamics, but not the spatial. Range expansions and contractions introduce rate variability into drift processes, range expansion under a drift model can drive directional change in trait evolution, and spatial selection gradients can create spatial variation in traits that can produce long-term directional trends and punctuation events depending on the balance between selection strength, gene flow, extirpation probability, and model of speciation. Using computational modelling that spatial processes can create evolutionary outcomes that depart from basic population-level notions from these standard macroevolutionary models.
Structured Literature Review on Traditional Approaches in Current Natural Lanugage Processing
<p>These files contain the foundation for the structured literature review (SLR) on traditional models, approaches and techniques in Natural Language Processing.</p> <p>In order to reproduce the results obtained in this SLR, we have uploaded two files:</p> <ul> <li><em>slr_traditionalmodelsNLP.xlsx</em>:<br>The search strings as well as applied filters used in the SLR can be found in this attached Excel-file.<br>Furthermore, the results of the SLR are also located in this Excel file.</li> <li><em>urls.txt<br></em>Additional URLs for a quantitative analysis are located in this text-file.</li> </ul>
Data-Driven Identification and Analysis of Waiting Times in Business Processes: A Systematic Literature Review
<p>Supplementary Material for Systematic Literature Review titled "Data-Driven Identification and Analysis of Waiting Times in<br> Business Processes: A Systematic Literature Review"</p>
Literature review of the enablers and barriers to stakeholder and citizen engagement in climate change adaptation process (as part of Adaptation AGORA project)
<p>This dataset is the result of collaborative work for Deliverable 4.1 (WP4; T4.1) of the Adaptation AGORA project. This database was used to conduct a literature review of the enablers and barriers to stakeholder and citizen engagement in climate change adaptation process. It contains 123 papers retrived from Web of Science Databse in June 2023. <span>We used a keyword search to identify and select articles that fell within the scope of our research, with each article containing at least one keyword related to climate change adaptation solutions, climate change, co-production, citizen and stakeholder involvement and factors (enablers and barriers). </span></p> <p><span>We divided the coding framework into four main sections:</span></p> <ul> <li> <p><span>Section 1 collected basic information about the paper (i.e., date, journal, authors, type of study and methods for data collection). </span></p> </li> <li> <p><span>Section 2 sought to better understand the adaptation initiatives treated in the paper. Here, we analysed 5 variables (the adaptation solutions type, sectors, benefits, scale, and location). </span></p> </li> <li> <p><span>Section 3 collected characteristics of the climate change adaptation co-production process, including the definition of co-production, the type of the co-production process, its outputs, and the methods used to engage stakeholders. </span></p> </li> <li> <p><span>Section 4 described the factors that enable or hinder the co-production process and their influence on different aspects of the process. After naming and defining each driver, we recorded the main type of factor, its impact, origin, and spatial and temporal scale of influence; the stakeholders who were responsible for and influenced by the factor, and the impacts on the various steps and outcomes of the co-production process.</span></p> <span> </span></li> </ul>
Analysis materials for "Defininig a Knowledge Graph Development Process through a Systematic Review"
<p>This depository stores the analysis materials for the article "Defining a Knowledge Graph Development Process through a Systematic Review". It includes:</p> <ul> <li><strong>Analysis of KG development process - Articles.csv </strong>- a table of summary of the articles included in the systematic review.</li> <li><strong>Analysis of KG development process - Tasks by level (count).csv</strong> - a table of counting the frequency of the tasks in the knowledge graph development process.</li> <li><strong>Analysis of KG development process - Tasks by level count (synonyms) (1).csv </strong>- a table of counting the frequency of the tasks in the knowledge graph development process after its been adjusted to synonyms.</li> <li><strong>Knowledge graph development processes - </strong>a folder of process figures from the articles that have been included in the systematic review.</li> </ul>
Patient and GP experiences of implementing a medication review intervention in older people with multimorbidity: process evaluation of the SPPiRE trial
<p>Abstract</p> <p><strong>Background: </strong>The SPPiRE cluster randomised controlled trial (RCT) found that a GP delivered medication review that incorporated screening potentially inappropriate prescriptions (PIP), a brown bag review and a patient priority assessment, resulted in a significant but small reduction in the number of medicines and no significant reduction in PIP.</p> <p><strong>Objective: </strong>To explore the experiences of GPs and patients engaged in the SPPiRE intervention and the potential for system wide implementation.</p> <p><strong>Design: </strong>Mixed methods process evaluation; quantitative data was collected from the SPPiRE intervention website and qualitative data via semi-structured interviews.</p> <p><strong>Setting and participants:</strong> 51 general practices throughout Ireland, and 404 participants with multimorbidity aged ≥65 years, prescribed ≥15 medicines participated in the RCT. Qualitative data was collected with purposive samples of intervention GPs (18/26) and patients (27/208). </p> <p><strong>Methods: </strong>Quantitative data was analysed descriptively, qualitative data thematically and both were integrated using a triangulation protocol.</p> <p><strong>Results: </strong>The analysis generated three themes, intervention implementation, mechanisms of action, and both were underpinned by the theme of context. One fifth of patients had no review, primarily due to insufficient GP time. The brown bag review component resulted in the most deprescription of medications. GPs felt it easier to change medicines if the patient was well known to them, and patients were generally receptive to change. GPs identified lack of integration into practice software systems and resources as barriers to future implementation.</p> <p><strong>Conclusion: </strong>Consideration of implementation of successful interventions is key to informing policy and integration into clinical practice. GPs and patients viewed the intervention positively, but implementation will depend on resourcing and integration into practice software systems.</p> <p>Trial registration number: <a href="https://doi.org/10.1186/ISRCTN12752680">ISRCTN12752680</a></p>
HarmonEPS modified routines, post-processing scripts and example data used in Tsiringakis, A., Frogner, I.L., de Rooy, W., Andrae, U., Hally, A., Contreras Osorio, S., van der Veen, S. and Barkmeijer, J., An Update to the Stochastically Perturbed Parametrizations Scheme of HarmonEPS. Monthly Weather Review
<p>This dataset contains:</p> <p>- Modified code routines/configurations files used in the EPS of Harmonie-Arome (HarmonEPS) CY43H2.2 version of the model.</p> <p>- Verification scripts from the HARP verification tool, used to verify model output against SYNOP observations.</p> <p>- Post-processing and plotting scripts in python, used in the manuscript.</p> <p>- A subset of the data produced by this study as example input in the verification and post-processing/plotting scripts.</p> <p>This dataset is used in:</p> <p>~Tsiringakis, A., Frogner, I.L., de Rooy, W., Andrae, U., Hally, A., Contreras Osorio, S., van Der Veen, S. and Barkmeijer, J. An Update to the Stochastically Perturbed Parametrizations Scheme of HarmonEPS. Monthly Weather Review</p>
Figure 2. – Computerisation process from 1983 in Historical review of the computerization of the MNHN Fish Collection and its collaboration with FishBase
Figure 2. – Computerisation process from 1983 to 1996 including several steps: 1: Checking the jar, the collection cards, and the ledgers to prepare data in handwritten forms; 2: Data entry using the interface DOC.
Supplementary material for "Business Process Simulation: A Systematic Literature Review"
<p>This material containing a list of the bibliographical data of the final sample and the sample of 300 publications before excluding publications outside of our focus supplements the following literature review:</p> <p>Rosenthal, Kristina; Ternes, Benjamin; Strecker, Stefan, (2018). “Business Process Simulation: A Systematic Literature Review”. In: Proceedings of the 26th European Conference on Information Systems (ECIS), Portsmouth, UK, June 23–28, 2018.</p>
DeepThought DPR: Distributed peer review enhanced with natural language processing and machine learning - Dataset I
<p>This is the anonymized dataset obtained from the DPR Experiment run at ESO in Fall 2018. If this dataset is used both this DOI as well as the main paper need to be cited. </p>
Figs., 12–15. Cheirochela species, dorsomedial process of male genital capsule: 12, C. feana, paratype; 13, C. birmaniensis, holotype; 14, C. tonkina, paratype; 15, C. thailandana, paratype. in A Revision Of The Indochinese Genera Cheirochela And Gestroiella Heteroptera Naucoridae And A Review Of The Tribe Cheirochelini
Figs., 12–15. Cheirochela species, dorsomedial process of male genital capsule: 12, C. feana, paratype; 13, C. birmaniensis, holotype; 14, C. tonkina, paratype; 15, C. thailandana, paratype.
Dataset Literature Review Digital Forensic and Image Processing
<p>Data ini digunakan untuk membuat penelitian sesuai dengan tinjauan literatur dengan kata kunci "<em>digital forensic</em>" dan "<em>image processing</em>"</p>
Dataset Literature Review Digital Forensic AND Image Processing
<p>Data ini digunakan untuk membuat penelitian berdasarkan tinjauan literatur dengan kata kunci "digital forensic" dan "image processing" </p>
[SZESLR] Semi-automated Systematic Literature Review (SLR) Design and P-graph (Process Graph Theory) SLR Database
<p>(c) Széchenyi István University and Artificial Intelligence National Laboratory (MILAB)</p> <p>A proposed semi-automated Systematic Literature Review (SLR) design has been deployed to conduct an exhaustive literature review on contributions concerning applications of the P-graph framework as a case study. The P-graph framework (<a href="https://p-graph.org/">https://p-graph.org</a>) was initially conceived for solving problems related to the synthesis of chemical processes; in particular, the framework has been useful for developing sustainable and resilient systems.</p> <p>The current contribution includes the P-graph SLR database itself, and additionally, the Python scripts used to generate such results. The case study has been selected in view of the authors’ familiarity with the P-graph framework, and because they maintain a manually-collected database of works on the subject. The contributions concerning the framework are easily distinguishable from others involving similar methodologies. It was observed that the implementation of the proposed SLR design extended prior review papers on the P-graph framework and provided additional information on authors and institutions devoted to research on this subject.</p> <p>Generally, it is expected that the dataset will assist researchers, scholars, and practitioners concerned with industrial sustainability in streamlining their literature reviews, thus accelerating the acquisition of pertinent publications that could advance and enrich their own research works on such a subject. Moreover, it is expected that, with proper adaptation, the proposed semi-automated SLR design can be applied to conduct literature reviews in other scientific fields whose results can be validated against existing reviews when available.</p> <p>The normalized P-graph database hereby presented thus can be used as a source of validated information for researchers. The P-graph database was uploaded in various file formats that support database management software (e.g. Zotero .RIS) as well as an "EasyHandle" MS Office (.XLSX) file.</p>
Selection process of articles for a systematic literature review on citizen science initiatives in school contexts
<p>Selection process of articles for a systematic literature review on citizen science initiatives in school contexts. Initial records are extracted from Web of Science database from 2000 to 2021. We used the keyword "citizen science" in the title mixed with some keywords in the topic of the search: “classroom” or “school” or “student*” or “pupil” or “learning”.</p> <p>The different database sheets inform about the application of the inclusion and exclusion criteria applied.</p>
Data from: Spatial processes and evolutionary models: a critical review
Open the record for dataset details and reuse information.
"MiRoR13-P1- A scoping review on the roles and tasks of peer reviewers in the manuscript review process in biomedical journals"
<p>This dataset is related to the publication "A scoping review on the roles and tasks of peer reviewers in the manuscript review process in biomedical journals". All additional data can be found under 'Additional files' in the publication</p>
Knowledge Freedom in computational science: a two stage peer-review process with KF Eligibility Access Review
<p>What is explained below is the <em>peer review process</em> applied by <em>Notes on Transdisciplinar</em><em>y Modelling for Environment </em>(NTMe). Authors and readers are encouraged to understand not only the process, but also the rationale behind the process, which 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 journal. </p> <p> </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. "Typical" data preprocessing, model settings, quality-assessment assumptions (and their "default" 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>"Transdisciplinary" 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 communicate computational methods and data - and their limitations - between multiple disciplinary domains would 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. </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 - or even other time periods - hence calling for a wider perspective. Multiple 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. </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, 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> with a focus on WSTM for environment.</p> <p> </p> <p><span class="math-tex">\(\mathsf{\Large\text{The peer-review process}}\)</span></p> <p><strong>A two-stage peer review process to avoid single-use disposable computational science. </strong>The two-stage peer review process requires discussion papers 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 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: </p> <ul> <li>free software to have been published so as for it to be persistently available;</li> <li>appropriate licensing and source code review to have been done (portable modularisation, with semantics of mathematical data-transformation methods clearly annotated);</li> <li>free data to have been 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 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) 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 referees and the scientific community, while authors are encouraged to interact with pending 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. The second stage of peer review concludes the discussion stage with the submission of a revised manuscript, with final review and corrections. Fulfilment of the eligibility criteria is required over all the publication stages.<br> The published materials might be updated from time to time (at the authors' 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. </p> <p><strong>Scientific opinions, 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 "practical" 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 factual correctness of the objective elements included in the opinion (with adequate bibliographic, tabular, visual support where appropriate). </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. </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> </p> <p><sup>© 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> </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.
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.
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.
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.