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621 results for “methodologies”
Understandings of food insecurity in Aotearoa/New Zealand: considering practitioners' perspectives in a neoliberal context using Q methodology
<p>Supplementary material for publication:</p> <p>1 - the list of Q set statements; and</p> <p>2 - the output from PQ Method software for the factor analysis used.</p>
FIGURE 4C in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 4C. General areagrams of Sulawesi species with extralimital distributions. General areagram of Australasian-derived species. 3 and 4 = sections of the Greater Indonesian Arc, 5 = Lydekker's Line. PMB = Philippine Mobile Belt. RI = 0.68 CI = 0.76
FIGURE 3B in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 3B. General areagram of Sulawesi AEEs based on terrane structure of Sulawesi, RI = 0.56 CI = 0.69.
FIGURE 1 in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 1. Locality map showing areas mentioned in the text. Base map from GeoMap (Ryan et al. 2009).
FIGURE 4A in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 4A. General areagram of Sulawesi species. Asia = India+southern China; Inner Banda Arc = Sumbawa–Alor; Outer Banda Arc = Timor–Tanimbar; Melanesian Arc = New Britain+New Ireland+Solomon Islands+Vanuatu; north Maluku = Halmahera; south Maluku = Buru+Seram+Kai; Sunda Shelf = Borneo+Jav+Sumatra; RI = 0.68 CI = 0.68
FIGURE 4B in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 4B. General areagram of Asian-derived species. 1= opening of Makassar Strait c45 Ma, 2 = Eocene rifting of Sunda Shelf margin. RI = 0.77 CI = 0.82.
FIGURE 2 in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 2. Map of Sulawesi showing names of terranes (black lettering) and areas of endemism (white lettering). Dotted lines represent approximate boundaries of terranes (black) and areas of endemism (white). Base map from GeoMap (Ryan et al. 2009).
FIGURE 3C. Composite areagram showing proposed terrane relationships within Sulawesi. 1 in Biotectonics of Sulawesi: Principles, methodology, and area relationships
FIGURE 3C. Composite areagram showing proposed terrane relationships within Sulawesi. 1 = Sula Spur, 2 = Palaeogene Clade.
A novel methodological approach to simultaneously extract high quality total RNA and proteins from cortical and trabecular bone
<p>Molecular differences between cortical and trabecular bone, of relevance to understand the pathophysiological bases of bone diseases, can be determined only throughout effective isolation methods for RNA and proteins. Here we present a TRIzol-based method, combining bone pulverization and homogenization, to extract simultaneously total RNA and proteins from human cortical and trabecular bone from the same carrot. RNA integrity and purity were determined as the 260-to-280 nm and 260-to-230 nm absorbance- ratios, and 28S-to-18S rRNA ratio. Protein integrity and quality were evaluated by Comassie Blue staining. RT-qPCR and immunoblotting for bone-specific genes and proteins were performed to verify the suitability of the isolated material in downstream applications. 260-to-280 nm and 260-to-230 nm absorbance ratios were, on average, ≥1.8. Bands on agarose gel were consistent to an intact RNA, with mean 28S-to-18S ratios of1.68±0.35 and 1.88±0.10 for cortical and trabecular bone, respectively. Band patterns after Comassie Blue staining confirmed protein integrity. Successful gene and protein expression analysis, with relevant differences between the two compartments, highlighted the suitability of the material in downstream applications. The method here presented is appropriate and effective for the study of human bone.</p>
Datasets from the publication "Delineating the geographic context of physical activities: A systematic search and scoping review of the methodological approaches used in social ecological research over two decades"
<p>Data from research article Rinne, T., Kajosaari, A., Söderholm, M., Berg, B., Pesola, A.J., Smith, M., Kyttä, M. (2022). Delineating the geographic context of physical activities: A systematic search and scoping review of the methodological approaches used in social ecological research over two decades, <em>Health and Place</em>.</p> <p>This data includes supplementary materials 1, 2, 3 and 4, PRISMA checklist and a translated research protocol.</p>
Data for "An Ensemble-Based Statistical Methodology to Detect Differences in Weather and Climate Model Executables" Part 1/2
<p>Ensemble simulations from the weather and climate model COSMO. The data has been used for model verification cases in the corresponding paper (https://doi.org/10.5194/gmd-2021-248).</p> <p>The data is partitioned into the following parts:</p> <ol> <li>gpu_dycore.tar.gz<br> 5-day ensemble (600 members) produced with COSMO 5.09 GPU version in double precision.</li> <li>cpu_nodycore.tar.gz<br> 5-day ensemble (200 members) produced with COSMO 5.09 CPU version in double precision.</li> <li>gpu_dycore_sp.tar.gz<br> 5-day ensemble (200 members) produced with COSMO 5.09 GPU version in single precision.</li> </ol> <p>The second part of the dataset with the diffusion ensembles can be found here: https://doi.org/10.5281/zenodo.6355647</p>
Supplementary files for "Building bridges between natural and social science disciplines: A standardised methodology to combine data on ecosystem quality trends"
<p>Data sources and mapping methodology</p>
The effect of methodological considerations on the construction of gene-based plant pan-genomes
<p>Pan-genomics is an emerging approach for studying the genetic diversity within plant populations. In contrast to common resequencing studies that compare whole genome sequencing data to a single reference genome, the construction of a pan-genome involves the direct comparison of multiple genomes to one another, thereby enabling the detection of genomic sequences and genes not present in the reference, as well as the analysis of gene content diversity. While multiple studies describing pan-genomes of various plant species have been published in recent years, our understanding regarding the effect of the computational procedures used for pan-genome construction is still limited.</p> <p>Here we examine the effect of several key methodological factors on the obtained gene pool and on gene presence-absence detections by constructing and comparing multiple pan-genomes of Arabidopsis thaliana and cultivated soybean, as well as conducting a meta-analysis on published pan-genomes. These factors include the construction method, the sequencing depth, and the extent of input data used for gene annotation. We observe substantial differences between pan-genomes constructed using three common procedures (De novo assembly and annotation, Map-to-pan, and Iterative assembly), and that results are dependent on the extent of the input data. Specifically, we report low agreement between the gene content inferred using different procedures and input data. Our results should increase the awareness of the community to the consequences of methodological decisions made during the process of pan-genome construction and emphasize the need for further investigation of commonly applied methodologies.</p>
Assessing the performance and efficiency of environmental DNA/RNA capture methodologies under controlled experimental conditions
<p>Growing interest and affordability of environmental DNA and RNA (eDNA and eRNA) approaches for biodiversity assessments and monitoring of complex ecosystems have led to the emergence of manifold protocols for nucleic acids (NAs) isolation and processing. Although there is no consensus on a standardized workflow, the common practice for water samples is to concentrate NAs via filtration using varying pore size membranes. Using the smallest pore is assumed to be most efficient for NAs capture from a wide range of material (including sub-cellular particles), however a trade-off must occur between detection of a meaningful molecular signal and cost/time effort when processing samples using fine pore membranes.</p> <p>Comparative studies involving formal efficiency assessments are lacking, which restricts informed decision-making around an optimized sampling approach for applications such as biosurveillance (i.e., detection and monitoring of target taxa - nuisance organisms, endangered and indicator taxa or other species of economic or cultural importance). Here, we present an experimental study using an easily cultured microalgal species (<em>Alexandrium pacificum</em>) to test different filter membranes for capturing NAs in the context of cost/time effort and cell fractions encountered in nature (whole cells, partially lysed, and naked NAs).</p> <p>The results showed no statistically significant difference between membrane types for capturing target eDNA signal from intact and partially lysed cell treatments. In terms of time effort and volume processed, higher efficiency ratings were obtained with the larger pore size (5 µm) cellulose membranes. Positively charged nylon demonstrated enhanced capture of naked NAs, and especially eRNA signal, across treatments.</p> <p>Our findings support using coarse pore size filters for adequate capture of target NA signal (from both eDNA and eRNA) with less processing time. The framework presented here can provide a quick and robust feasibility check and comparative assessment of new and existing NA processing technologies, and allows sufficient control over multiple parameters, including physical-chemical water properties, temporal scales, and concentration and type of input material.</p>
Systematic literature review on bioblitzes - Methodology and results
<p>This dataset contains supplementary material to a review paper on bioblitzes (submitted). This dataset contains following files: </p> <p>1a. Systematic literature review methods.pdf</p> <p>1b. Reference list reviewed papers.pdf</p> <p>1c. Reference list reviewed papers_BibTeX.txt</p> <p>1d. Reference list reviewed papers_RIS.txt</p> <p>1e. Reference list reviewed papers.csv</p> <p>1f. Data retrieved from the reviewed papers.csv</p> <p>1g. Ranked importance of each aim per bioblitz record.csv </p> <p>1h. Fig. 1_Map showing the distribution of published bioblitzes considered in the literature review.jpg</p> <p>These files include lists of reviewed papers in different formats (pdf/csv/RIS/BibTeX), the description of the methodology used to search and select this collection of papers, one csv-file containing the extracted data on bioblitzes from the literature and one showing the ranks in respect with the aim of the bioblitz per paper, and one figure showing the geographical distribution of the published records.</p>
Scientific Methodology Course II-Facultad de Medicina, Universidad de la República, Uruguay (2014-2022).
<p>The presented data reflects the information gathered from the Scientific Methodology Course II for advanced medical students from Facultad de Medicina, Universidad de la República, Uruguay (2014-2022). </p> <p>In this course, all the students (600 per year) of the sixth year or the Career perform a research project under the supervision of Faculty mentors. </p> <p>We present general data of the course and all the research projects performed during this period. </p>
Methodological confounds of measuring urinary oxidative stress in wild animals
<p>Biomarkers of oxidative stress (OS) are useful in addressing a wide range of research questions, but thus far, they have had limited application to wild mammal populations due to a reliance on blood or tissue sampling. A shift towards non-invasive measurement of OS would allow field ecologists and conservationists to apply this method more readily. However, the impact of methodological confounds on urinary OS measurement under field conditions has never been explicitly investigated. We combined a cross-sectional analysis with a field experiment to assess the impact of four potential methodological confounds on OS measurements: 1) time of sampling, 2) environmental contamination from foliage; 3) delay between sample collection and flash-freezing in liquid nitrogen; 4) sample storage of up to 15 months below -80C. We measured DNA oxidative damage (8-hydroxy-2'-deoxyguanosine, 8-OHdG), lipid peroxidation (malondialdehyde, MDA), Total Antioxidant Capacity (TAC) and uric acid (UA) in 167 urine samples collected from wild Zanzibar red colobus (Piliocolobus kirkii). We found that MDA was higher in samples collected in the morning than in the afternoon but there were no diurnal patterns in any of the other markers. Contamination of samples from leaf surfaces and time frozen at -80°C for up to 15 months did not affect OS marker concentrations. Freezing delay did not affect OS levels cross-sectionally, but OS values from individual samples showed only moderate to good consistency and substantial rank order reversals when exposed to different freezing delays. We recommend that the impact of storage time on OS marker concentrations and diurnal patterns of OS markers be considered when designing sampling protocols. However, given the high stability we observed for four OS markers subject to a variety of putative methodological confounds, we suggest that urinary OS markers provide a valuable addition to the toolkit of field ecologists and conservationists within reasonable methodological constraints.</p>
Annexes from the paper A Hybrid Methodology for the Facility Re-Layout Problem (FRLP) of Food Production Systems in Industry 5.0 Context
<p>In the attached dataset we present all the data collected and obtained in the case study of our model to improve the redistribution of food production plants. The importance of the attached data lies in the fact that they consist of real data collected in a small snack production plant located in the northern part of Ecuador, and were used to validate the methodology proposed in the article entitled: "A Hybrid Methodology for the Facility Re-Layout Problem (FRLP) of Food Production Systems in Industry 5.0 Context", which is currently in the publication stage.</p>
Methodology based on the MaxEnt algorithm for modelling habitat distribution
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Satellite Images from ASTER TIR and Landsat 9 (RGB+TIR) for evaluation of unmixing methodologies
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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.
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.