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621 results for “methodologies”
Dataset for neutron and gamma-ray pulse shape discrimination: radiation pulse signals and discrimination methodologies
<p>This dataset provides neutron and gamma-ray pulse signals for pulse shape discrimination experiments. Serval traditional and recently proposed pulse shape discrimination algorithms are utilized to conduct pulse shape discrimination under raw pulse signals and noise-enhanced datasets. These algorithms include zero-crossing (ZC), charge comparison (CC), falling edge percentage slope (FEPS), frequency gradient analysis (FGA), pulse-coupled neural network (PCNN), ladder gradient (LG), and heterogeneous quasi-continuous spiking cortical model (HQC-SCM). This dataset also provides the source code of all these pulse shape discrimination methods, together with the source code of schematic pulse shape discrimination performance evaluation and anti-noise performance evaluation. Detailed descriptions of this dataset can be found at: https://doi.org/10.48550/arXiv.2305.18242.</p>
Environmental impact assessment for large carnivores: a methodological review of the wolf (Canis lupus) monitoring in Portugal
<p>The continuous growth of the global human population results in increased use and change of landscapes, with infrastructures like transportation or energy facilities, being a particular risk to large carnivores. Environmental Impact Assessments were established to identify the probable environmental consequences of any new proposed project, find ways to reduce impacts, and provide evidence to inform decision making and mitigation. Portugal has a wolf population of around 300 individuals, designated as an endangered species with full legal protection. They occupy the northern mountainous areas of the country which has also been the focus of new human infrastructures over the last 20 years. Consequently, dozens of wolf monitoring programs have been established to evaluate wolf population status, to identify impacts, and to inform appropriate mitigation or compensation measures. We reviewed Portuguese wolf monitoring programs to answer four key questions: do wolf programs examine adequate biological parameters to meet monitoring objectives? is the study design suitable for measuring impacts? are data collection methods and effort sufficient for the stated inference objectives? and do statistical analyses of the data lead to robust conclusions? Overall, we found a mismatch between the stated aims of wolf monitoring and the results reported, and often neither aligns with the existing national wolf monitoring guidelines. Despite the vast effort expended and the diversity of methods used, data analysis makes almost exclusive use of relative indices or summary statistics, with little consideration of the potential biases that arise through the (imperfect) observational process. This makes comparisons of impacts across space and time difficult and is therefore unlikely to contribute to a general understanding of wolf responses to infrastructure-related disturbance. We recommend the development of standardized monitoring protocols and advocate for the use of statistical methods that account for imperfect detection to guarantee accuracy, reproducibility, and efficacy of the programs.</p>
Methodology of diachronic analysis of old prints and its validation by tracing the changing meaning of key concepts in the intellectual debate of 16th century Italy
<p>This dataset in corpus.zip file contains OCR texts for 16th century Italian books available from BNF (folder gallica) and archive.org (folder internetarchive). Source URL is given in 1st line of each text file. The pages within each document may come in order different than in the source, however, the order of lines in each page is preserved. The archive is protected with password, which will be made public immediately after the publication of the related research paper under the same title.</p> <p>Samples of three documents along with images of their initial pages are provided at the current time.</p>
Supplemental idf files used for paper "Refurbishmet Methodology to Attain Thermally Comfortable near-Zero Energy Buildings Using Customizable Solutions"
<p>These are the idf files used to study different technology alternatives offered by the Reco2st project on an idealized dormitory room located in London, UK. The files are presented "as is" and were done for EnergyPlus v8.9. Includes files that might have not made it to the final paper.</p> <p>Geometry: One zone room with one external window.<br> Materials: External construction is cavity wall, with bricks on both sides, gypsum plaster on internal side<br> Internal walls brick single layer with gypsum plaster.<br> Ceiling and floor reinforced concrete. Plaster finish on ceiling, nylon carpet on floor<br> Double glazed window. Five panes available: one large central fixed, two small clerestory opening, and two large side opening.<br> For simulation purposes a single equivalent area of all openings modelled.<br> Material data sources: gov.scot, puravent.co.uk, nature.com. SHGC from LBL.</p> <p>This is part of work done for ReCO2ST - Residential Retrofit assessment platform and demonstrations for near zero energy and CO2 emissions with optimum cost, health, comfort and environmental quality. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 768576.</p>
The National Composite Index for Family Planning (NCIFP): results and methodological issues
<p>This dataset accompanies a paper under consideration for publication in Gates Open Research by Rebecca Rosenberg, John Ross, Karen Hardee and Imelda Zosa-Feranil. The file includes raw data, as well as a tab for each table and figure in the paper.</p>
Case study data of the paper: A methodological guide to observe local-scale geodiversity for biodiversity research and management
<p><span>Current global environmental change calls for comprehensive and complementing approaches for biodiversity conservation. According to recent research, consideration of the diversity of Earth's abiotic features (i.e., geodiversity) could provide new insights and applications into the investigation and management of biodiversity. However, methods to map and quantify geodiversity at local scale have not been developed although this scale is important for conservation planning. </span><span>Here, we introduce a field methodology for observing plot-scale geodiversity, pilot the method in an Arctic-alpine tundra environment, provide empirical evidence on the plot-scale biodiversity-geodiversity relationship and give guidance for practitioners on the implementation of the method</span><span>.</span></p> <p><span>The field method is based on observation of geofeatures, i.e., elements of geology, geomorphology, and hydrology, from a given area surrounding a location of species observations. As a result, the method provides novel information on the variation of abiotic nature for biodiversity research and management. The method was piloted in northern Norway and Finland by observing geofeatures from 76 sites at three scales (5, 10 and 25 m radii). To explore the relationship between measures of biodiversity and geodiversity, the occurrence of vascular plant species was recorded from 2 m x 2 m plots at the same sites.</span></p> <p><span>According to the results, vascular plant species richness was positively correlated with the richness of geofeatures (R<sub>s</sub> = 0.18–0.59). The connection was strongest in habitats characterized by deciduous shrubs. The method has a high potential for observing geofeatures without extensive geological or geomorphological training or field survey experience and </span><span>could be applied by conservation practitioners</span><span>.</span></p> <p><span>Consideration of geodiversity in understanding, analysing and conserving biodiversity could facilitate environmental management and ensure the long-term sustainability of ecosystem functions. With the developed method, it is possible to cost-efficiently observe the elements of geodiversity that are useful in ecology and biodiversity conservation. Our approach can be adapted in different ecosystems and biodiversity investigations. The method can be adjusted depending on the abiotic conditions, expertise of the observer(s), and the equipment available.</span></p>
A new tree-based methodological framework to infer the evolutionary history of Mesopolyploid lineages: An application to the Brassiceae tribe (Brassicaceae)
<p>Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework, we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e., genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multilabelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.</p>
fNIRS Brain Imaging in Motor Paradigms: Evidence-Based Methodological Recommendations
<p>Anonymized behavioural, physiological, motion-capture, and <em>f</em>NIRS data and associated codes supporting the analyses reported in the paper "<em>f</em>NIRS Brain Imaging in Motor Paradigms: Evidence-Based Methodological Recommendations".</p>
Supplementary material to the article "Finding a way into an interpreter's heart: Methodological considerations on heart-rate variability building on an exploratory study"
<p>Supplementary material to the article "Finding a way into an interpreter's heart: Methodological considerations on heart-rate variability building on an exploratory study" by Nicoletta Spinolo, Christian Olalla-Soler & Ricardo Muñoz Martín. </p> <p>The ZIP file contains the four texts that were used in the study reported in the article. </p> <p>Reference:</p> <p>Spinolo, Nicoletta; Olalla-Soler, Christian, Muñoz Martín, Ricardo (202X). "Finding a way into an interpreter's heart: Methodological considerations on heart-rate variability building on an exploratory study". </p>
Data from: A field experiment exploring disturbance-and-recovery, and restoration methodology of Zostera capensis to support its role as a coastal protector
<p>This DRYAD data set covers statistical analysis for the study, "Seagrass restoration experiment to support coastal protection." </p> <p>Dataset attached covers row data regarding field experiments carried out to demonstrate the time needed for the seagrass to recover after disturbance (imitation of anthropogenic impact). The data is centered on showing the evolution (increase) of seagrass shoot density after a quantified period (time series over a year) where the pressure to seagrass is halted. Halting of pressure would resemble a total ban or reduction of anthropogenic impact of digging and revolving of seagrass; action carried out by communities, aiming to collect clams and other shellfish. This data covers also variation in sediments and epiphytes. </p> <p>Additional data is provided on the seagrass restoration methodology that was added to the above-mentioned experiment. The IUCN Red listed Vulnerable seagrass species, <em>Zostera capensis</em> was tested using the plug method (a sediment-based methodology). Two size plugs, made of PVC tube, were tested: 4.5 cm and 7.5 cm diameter size, over a 12-month period (measurements carried out on four occasions). The 7.5 PVC tube experiment revealed a higher survival rate and is therefore a more suitable method for future <em>Z. capensis </em>restoration in impacted areas.</p> <p>These data can be re-used as long as it cites the original data (this paper). To comply with best practices, we recommend mentioning the source of the data.</p>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
EU Biotransform - Repository on existing impact assessment methodologies
<p>A thorough review of already existing methodologies to assess environmental/social/economic impacts of fossil/bio-based and linear/circular economies, as well as their transitions, e.g. impact forecasting through theory of change, full or simplified LCAs, material flow analyses, and outlook like<br>automated data extraction with AI, at macro level (country or regional level).</p>
FIGURE 1 in The Integrated Plant Record (IPR) analysis: Methodological advances and new insights into the evolution of European Palaeogene/Neogene vegetation
FIGURE 1. Zelkova zelkovifolia is a representative of the broad-leaved deciduous component.
In-Plume Profiling Methodology: Ensuring Firefighter Safety During Pyroconvective Extreme Wildfire Events
<p>dataset for the paper: <span>In-Plume Profiling Methodology: Ensuring Firefighter Safety During Pyroconvective Extreme Wildfire Events</span></p> <p> </p> <p><span>It includes the radiosonde flight files used in the methodology</span></p> <p><span>It includes the videos of radiosondes launching as complementary materials</span></p>
Methodology data of "A qualitative and quantitative citation analysis toward retracted articles: a case of study"
<p>This document contains the datasets and visualizations generated after the application of the methodology defined in our work: <em>"A qualitative and quantitative citation analysis toward retracted articles: a case of study"</em>. The methodology defines a citation analysis of the Wakefield et al. [1] retracted article from a quantitative and qualitative point of view. The data contained in this repository are based on the first two steps of the methodology. The first step of the methodology (i.e. “Data gathering”) builds an annotated dataset of the citing entities, this step is largely discussed also in [2]. The second step (i.e. "Topic Modelling") runs a topic modeling analysis on the textual features contained in the dataset generated by the first step. </p> <p><strong>Note:</strong> the data are all contained inside the "<strong><em>method_data.zip"</em> </strong>file. You need to unzip the file to get access to all the files and directories listed below.</p> <p> </p> <p><strong>Data gathering</strong></p> <p>The data generated by this step are stored in <strong>"<em>data/</em>"</strong>:</p> <ol> <li><em><strong>"cits_features.csv": </strong></em>a dataset containing all the entities (rows in the CSV) which have cited the Wakefield et al. retracted article, and a set of features characterizing each citing entity (columns in the CSV). The features included are: DOI ("doi"), year of publication ("year"), the title ("title"), the venue identifier ("source_id"), the title of the venue ("source_title"), yes/no value in case the entity is retracted as well ("retracted"), the subject area ("area"), the subject category ("category"), the sections of the in-text citations ("intext_citation.section"), the value of the reference pointer ("intext_citation.pointer"), the in-text citation function ("intext_citation.intent"), the in-text citation perceived sentiment ("intext_citation.sentiment"), and a yes/no value to denote whether the in-text citation context mentions the retraction of the cited entity ("intext_citation.section.ret_mention").<br> <strong>Note: </strong>this dataset is licensed under a <a href="https://creativecommons.org/publicdomain/zero/1.0/legalcode">Creative Commons public domain dedication (CC0)</a>.<br> </li> <li><em><strong>"cits_text.csv": </strong>this dataset stores the abstract ("abstract") and the in-text citations context ("intext_citation.context") </em>for each citing entity identified using the DOI value ("doi").<br> <strong>Note: </strong>the data keep their original license (the one provided by their publisher). This dataset is provided in order to favor the reproducibility of the results obtained in our work.</li> </ol> <p> </p> <p><strong>Topic modeling</strong><br> We run a topic modeling analysis on the textual features gathered (i.e. abstracts and citation contexts). The results are stored inside the <em><strong>"topic_modeling/"</strong></em> directory. The topic modeling has been done using MITAO, a tool for mashing up automatic text analysis tools, and creating a completely customizable visual workflow [3]. The topic modeling results for each textual feature are separated into two different folders, <em><strong>"abstracts/"</strong></em> for the abstracts, and <em><strong>"intext_cit/"</strong></em> for the in-text citation contexts. Both the directories contain the following directories/files: <strong> </strong></p> <ol> <li> <p><em><strong>"mitao_workflows/"</strong></em>: the workflows of MITAO. These are JSON files that could be reloaded in MITAO to reproduce the results following the same workflows.</p> </li> <li> <p><em><strong>"corpus_and_dictionary/": </strong></em>it contains the dictionary and the vectorized corpus given as inputs for the LDA topic modeling.</p> </li> <li> <p><em><strong>"coherence/coherence.csv":</strong></em> the coherence score of several topic models trained on a number of topics from 1 - 40.</p> </li> <li> <p><em><strong>"datasets_and_views/": </strong></em>the datasets and visualizations generated using MITAO. </p> </li> </ol> <p> </p> <p><strong>References</strong></p> <ol> <li>Wakefield, A., Murch, S., Anthony, A., Linnell, J., Casson, D., Malik, M., Berelowitz, M., Dhillon, A., Thomson, M., Harvey, P., Valentine, A., Davies, S., & Walker-Smith, J. (1998). RETRACTED: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. <em>The Lancet</em>, <em>351</em>(9103), 637–641. <a href="https://doi.org/10.1016/S0140-6736(97)11096-0">https://doi.org/10.1016/S0140-6736(97)11096-0</a></li> <li> <p>Heibi, I., & Peroni, S. (2020). A methodology for gathering and annotating the raw-data/characteristics of the documents citing a retracted article v1 (protocols.io.bdc4i2yw) [Data set]. In protocols.io. ZappyLab, Inc. <a href="https://doi.org/10.17504/protocols.io.bdc4i2yw">https://doi.org/10.17504/protocols.io.bdc4i2yw</a></p> </li> <li> <p> </p> Ferri, P., Heibi, I., Pareschi, L., & Peroni, S. (2020). MITAO: A User Friendly and Modular Software for Topic Modelling [JD]. PuntOorg International Journal, 5(2), 135–149. <a href="https://doi.org/10.19245/25.05.pij.5.2.3">https://doi.org/10.19245/25.05.pij.5.2.3</a> <p> </p> </li> </ol>
ToyLabs - A new toy development methodology
<p>Enabling an Open Innovation Model for EU Toy Industry SMEs through Co-Creation with FabLabs, Safety Experts and Customer Communities</p> <p>This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 732559.</p> <p>The scope of ToyLabs is to introduce a new innovation model realised via an open ICT platform supporting the creativity processes and production cycles of the Toy Industry SMEs, putting into the picture Fabrication Laboratories (FabLabs), Toy Safety Experts and End Customers in terms of co-creation, co-design and decentralised product prototyping. ToyLabs will act as a collaboration bus interconnecting the aforementioned stakeholder types, towards the direction of changing the market positioning and the prospects of SMEs in the Toy Industry, overcoming obstacles like geographical barriers and fragmented markets.</p> <p><br> </p>
Flow diagram depicting an overview of the proposed layer optimisation methodology for Li-ion pouch cells
<p>Flow diagram depicting an overview of the proposed layer optimisation methodology for Li-ion pouch cells.</p>
Binary asteroseismic modelling: isochrone-cloud methodology and application to Kepler gravity mode pulsators
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018MNRAS.tmp.2555J/abstract">Johnston et al. (2019)</a>. MESA version 10108.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/sty2671">10.1093/mnras/sty2671</a></p>
'No results or wrong' - Methodological Challenges in Computational Literary Studies
<p>4th lecture</p>
Single-pass STEM-EMCD on a zone axis using apatterned aperture: Data and methodology
<p>Raw data and code accompanying the paper "Experimental progress towards single-pass STEM-EMCD on a zone axis using a patterned aperture"</p>
ScienceDex guides
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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.