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621 results for “methodologies”
Figure S1 in Development of experimental mesocosms for cicada nymphs Graptopsaltria nigrofuscata: methodology and research recommendations
Figure S1. Mean daily soil temperature during the mesocosm experiment (16 April to 6 July 2021).
FIGURE 5 in Application of shell spiral deviation methodology to fossil brachiopods: Implications for obtaining specimen ontogenetic ages
FIGURE 5. Spiral deviations from three specimens of the species Terebratula terebratula.
FIGURE 7 in Application of shell spiral deviation methodology to fossil brachiopods: Implications for obtaining specimen ontogenetic ages
FIGURE 7. Spiral deviations from three specimens of the species Pseudoatrypa sp.
FIGURE 6 in Application of shell spiral deviation methodology to fossil brachiopods: Implications for obtaining specimen ontogenetic ages
FIGURE 6. Spiral deviations from three specimens of the species Platystrophia ponderosa.
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
Methodological approach to generate reflection and reflective notes
<p class="MsoNoSpacing">The objective of this data note is twofold: 1) to illustrate the methodological approach used to generate guided reflections at undergraduate level aided by a patient-based vignette portraying an individual with a history of substance use and mental health disorders; 2) to provide a summary of the raw data set in the form brief educational reflections submitted anonymously by undergraduate dental and dental hygiene students. These reflections were used in our recent publication titled 'The role of an educational vignette to teach dental students on issues of substance use and mental health disorders at the University of British Columbia: An exploratory Qualitative study. By offering the reader with a <i>road map</i> to generate such reflections, and a summary of the reflections themselves, we hope to engage other dental schools in planning their educational teaching activities on issues pertaining to mental health and substance use for dental and dental hygiene students as we have advocated over the years.</p>
Methodological advances for hypothesis‐driven ethnobiology
<p>Ethnobiology as a discipline has evolved recently to increasingly embrace theory-inspired and hypothesis driven approaches to study why and how local people choose plants and animals they interact with and use for their livelihood. However, testing complex hypotheses or a network of ethnobiological hypotheses is challenging, particularly for datasets with non-independent observations due to species phylogenetic relatedness or socio-relational links between participants. Further, to fully account for the dynamics of local ecological knowledge, it is important to account for the spatially explicit distribution of knowledge, the changes in knowledge, knowledge transmission and use. To promote the use of advanced statistical modeling approaches that address these limitations, we synthesize methodological advances for hypothesis-driven research in ethnobiology while highlighting the need for more figures than tables and more tables than text in ethnobiological literature. We present the ethnobiologicalmotivations for conducting generalized linear mixed-effect modeling, structural equation modeling, phylogenetic generalized least squares, social network analysis, species distribution modeling, and predictive modeling. For each element of the proposed ethnobiologists quantitative toolbox, we present practical applications along with script for a widespread implementation. Because these statistical modeling approaches are rarely taught in most ethnobiological programs but are essential for careers in academia or industry, it is critical to promote specialized workshops organized during annual professional meetings and focused on these advanced methods. By embracing these quantitative modeling techniques without sacrificing qualitative approaches which provide essential context, ethnobiology will further progress toward an expansive interaction with other disciplines.</p>
How are software repositories mined? A systematic literature review of workflows, methodologies, reproducibility, and tools
<p>This is the excel spreadsheet dataset containing our analysis of papers performing mining software repositories research from the conferences ICSE, ESEC/FSE, and MSR from the years 2018 - 2020. The data is broken into columns and can be explained at a high-level as follows:</p> <p>Column Content</p> <p>1 The paper being analyzed</p> <p>2 Does the paper state the data they analyzed is available</p> <p>3 Does the paper perform some sort of data analysis or sampling using data others have compiled in the past</p> <p>4 Does the paper state a timestamp for when they begin their work</p> <p>5 Does the paper state the use of systems pre-built to help with MSR work</p> <p>6 - 18 Forms of sampling researchers may have employed to select their data</p> <p>19 What datasets (if any) were used in the analysis</p> <p>20 What tools (if any) were used in the analysis</p> <p>21 How they performed their data sampling workflow</p> <p>22 How they performed their data filtering workflow</p> <p>23 How they performed their data retrieval workflow</p> <p>24 Did they create any scripts in each of these workflows</p> <p>25 - 33 Did they publish a replication package and what is contained within</p> <p>34 Is the paper describing a tool for research or not</p> <p>35 Short description of the paper read</p> <p>36 A high-level category of the work performed in each paper</p>
Development of the multi-dimensional Mobility Divide Index as a methodology to assess the accessibility level of public transport systems
<p>This paper presents the development of a multi-dimensional Mobility Divide Index (MDI) for assessing the accessibility of public transport developed using a co-design approach, directly involving end-users in the index design process. The index measures the gap that persons with disabilities feel they need to over-come to use public transport in the same way non-disabled citizens do. The MDI covers six accessibility-related dimensions: 1) safety, 2) convenience, 3) comfort, 4) affordability, 5) travel time, 6) autonomy. The method paper describes the step-by-step approach to create the MDI as a set of indicators to be rated by people with different access needs to a) provide evidence of the main criticalities to be addressed through the design and implementation of new inclusive mobility solutions, b) guide the design of new inclusive mobility solutions and measure their impacts and c) inform the transport sector encouraging positive changes in transport by providing recommendations for policy-making, new directions for service innovation, improvements and practical advice or highlighting investment priorities to pave the way for a more inclusive mobility. We present our findings in ways that can inform universal design and provide actionable information to researchers, policymakers, transport and urban planners, operators and stakeholders’ representatives to promote inclusive and equitable mobility solutions for all. Finally, we suggest follow up research and innovation, as well as recommendations for its uptake and utilisation in the pursuit of European accessibility standards and requirements for products and services in the mobility sector. </p>
Data for How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland
<p>Raw and processed data for the paper "<em>How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland"</em></p> <p>The raw trade data file is named TradeDataAggregated.rds</p> <p>The raw greenhouse gas footprint data is contained in Output_all.xlsx</p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Data for: Validation of a nutria (Myocastor coypus) environmental DNA assay highlights considerations for sampling methodology
<p>Nutria (<em>Myocastor coypus</em>) is a semi-aquatic rodent species that is invasive across multiple regions within the United States. Here we evaluated a qPCR assay previously described for use in Japan for application across invasive populations in the United States. We also compared two environmental DNA sampling methodologies for this assay: field filtration of large volumes of water passed through filters versus direct sampling of small volumes of water. We validated assay specificity, generality, and sensitivity, compared assay performance between two independent laboratories, and successfully tested the assay<em> in situ </em>on a known wild population. The filtration method required fewer samples for environmental DNA detection than direct sampling, but the choice of methods should be assessed based on specific field conditions and time and budget considerations. Our extensive assay validation and comparison across laboratories suggests that the assay is ready to be applied in environmental DNA monitoring of nutria throughout the United States.</p>
Adapting Clinical Practice Guidelines for Chronic Kidney Disease: Blood Pressure Management and Kidney Replacement Therapy in Adults and Children in the Saudi Arabian context using the GRADE-ADOLOPMENT methodology
<p>This compressed ZIP file includes three components</p> <p>The Full Guideline Document (FINAL COPY) for the <strong>2022 Saudi Guideline for Chronic Kidney Disease: Blood Pressure Management and Kidney Replacement Therapy in Adults and Children</strong></p> <p>In addition to two guideline reporting checklists to ensure the quality of this adoloped guideline:-</p> <p><strong>1- AGREE Reporting Checklist</strong></p> <p><strong>2- RIGHT-Ad@pt Checklist</strong></p> <p>As a supplementary to the submitted article entitled:_</p> <p><strong>Adapting Clinical Practice Guidelines for Chronic Kidney Disease: Blood Pressure Management and Kidney Replacement Therapy in Adults and Children in the Saudi Arabian context using the GRADE-ADOLOPMENT methodology</strong></p>
Tracking marine tetrapod carcasses using a low-cost mixed methodology with GPS trackers, passive drifters, and citizen science
<div> <ol> <li> <span><span>Drift experiments are essential to understand stranding patterns and to estimate the mortality of beached animals.</span><span> Most studies do not use telemetry technology due to the high costs of this methodology. </span></span><span><span>The objective of this paper is to describe the possibilities of tracking marine tetrapod carcasses with a low-cost and replicable methodology.</span> <span>The study was conducted </span></span><span><span>in the Southern Subtropical Shelf (~ 28º–34º S), </span><span>a highly productive and key ecological </span><span>region of the southwestern Atlantic Ocean (SWA).</span></span><span> </span> </li> <li> <p><span><span>W</span></span><span><span>e designed and tested a low-cost mixed methodology including </span><span>Global Positioning System </span><span>trackers, passive drifters (reused glass bottles), and Citizen Science (through instant message platform and email) for tracking carcasses of marine </span><span>tetrapods</span><span>. We performed four drift experiments, </span><span>during the</span><span> four seasons </span><span>of</span><span> 2019</span><span>.</span> </span><span><span>We released 787 drifters (600 non-biological and 187 carcasses</span><span> of seabirds, </span><span>sea turtles</span><span>, and cetaceans</span><span>)</span></span><span><span> at sea, at five</span><span> equally</span> <span>separated </span><span>distances (5</span><span>–</span><span>25 km) from the coast.</span> <span>Beach surveys and Citizen Science were implemented to </span><span>recover </span><span>the beached drifters.</span></span></p> </li> <li> <p><span><span>We</span><span> re</span><span>covered </span><span>71.83% of non-biological </span><span>and 27.27% of carcasses </span><span>released</span><span>. We tracked the movements of 38 carcasses </span><span>(25 sea turtles and 13 </span><span>cetaceans</span><span>) with 17 GPS devices. The drift</span><span>ing</span><span> time</span><span>,</span><span> until reaching the beach</span><span>,</span><span> ranged from 12h to 17 days</span><span> for carcasses and 12h to 406 days for bottles</span><span>. </span></span><span><span>Citizen Science was the most important source of rec</span><span>overies </span><span>of non-biological drifters, representing 66.67% of the total bottles rec</span><span>ove</span><span>r</span><span>ed</span><span>.</span> <span>For carcasses, active search was the most important recovery source, representing 64.7% of the total carcasses</span><span> recovered</span><span>.</span></span></p> </li> <li> <p><span>Our study contributes with new findings about drift patterns of marine tetrapods in the SWA and describes an accessible low-cost mixed methodology for small and medium-budget projects that can be </span><span>replicated in other coastal regions of the world for tracking a wide range of marine tetrapod species.</span></p> </li> </ol> </div>
Data from: Integrated survey methodologies provide process-driven framework for marine renewable energy environmental impacts
<p>Data from: Integrated survey methodologies provide process-driven framework for marine renewable energy environmental impacts</p>
Research Methodology
<p><strong>Six Days Online Workshop on “Research Methodology” organized by </strong>Changu Kana Thakur College in association with RUSA, <strong>5-10 April 2021.</strong></p>
Multi‐species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds
<p>Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practical applications, however, still requires significant standardisation and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs high-capacity capsules), number of sampling sites, volume of water filtered and environmental factors affected amphibian detection in Mediterranean temporary ponds. The study involved water filtering until clogging at one (capsules) and five (discs) sites from 16 small and shallow ponds, where three urodele and seven anuran species were recorded through sweep-netting and adult observations. Detection probabilities were estimated from site occupancy models based on replicate sampling and from an adaptation of time-to-detection models relating detection probability to volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with detection probabilities of the two abundant species (<em>Pelobates</em> <em>cultripes</em>, <em>Hyla</em> <em>meridionalis</em>) increasing rapidly with sample size and water volume, reaching almost perfect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively. However, reaching high detection probabilities for rare species (<em>Pelodytes</em> <em>atlanticus</em>, <em>Pleurodeles</em> <em>waltl</em>, <em>Triturus</em> <em>pygmaeus</em>) would require larger sampling effort than that used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with capsules at a single site per pond provided lower detection probabilities for abundant species than filtering with discs at five sites. Rarer species showed no difference between methods, which may be due to small sample sizes and reduced statistical power for species with few detection. The effect of conductivity on species detectability was largely negative, while the influence of water clarity varied across species, and pH had no effects. Overall, our results suggest that eDNA amphibian surveys in Mediterranean temporary ponds need to consider filter clogging, heterogeneous DNA distribution, and highly conductive waters.</p>
Data from: Optimisation design and analysis of mobile pump truck frame using response surface methodology
<p><span>In order to realize the lightweight design of mobile pump truck, this paper takes the frame of a certain type of mobile pump truck as the research object. The response surface method is used to carry out lightweight design of the longitudinal beam structure of the frame, and the finite element method is used to establish the finite element model to analyze and compare the frame before and after optimization.The results show that the height, width and thickness of the optimized longitudinal beam section are reduced by 10 mm, 11 mm, and 0.8 mm respectively, and the weight of the whole frame is reduced by 35.8 kg.</span> <span>Before and after optimization, the displacement and stress changes of the frame are small in four motion situations, which meet the lightweight requirements of optimization design.</span></p>
Dataset for: Estimating pregnancy rate from blubber progesterone levels of a blindly biopsied beluga population poses methodological, analytical and statistical challenges
<p class="MsoBodyText"><span>Beluga (<em>Delphinapterus leucas</em>) from the St. Lawrence Estuary, Canada, have been declining since the early 2000s, suggesting recruitment issues as a result of low fecundity, abnormal abortion rates or poor calf or juvenile survival. Pregnancy is difficult to observe in cetaceans, making the ground-truthing of pregnancy estimates in wild individuals challenging. Blubber progesterone concentrations were contrasted among 62 SLE beluga with a known reproductive state (i.e., pregnant, resting, parturient, and lactating females), that were found dead in 1997–2019. The suitability of a threshold obtained from decaying carcasses to assess reproductive state and pregnancy rate of freshly-dead or free-ranging and blindly-sampled beluga was examined using three statistical approaches and two datasets (135 freshly-harvested carcasses in Nunavik, and 65 biopsy-sampled SLE beluga). Progesterone concentrations in decaying carcasses were considerably higher in known-pregnant (mean </span><span>±</span><span> sd: </span><span>365 </span><span>±</span><span> 244 ng g<sup>-1</sup> of tissue) </span><span>than resting (</span><span>3.1 </span><span>±</span><span> 4.5 ng g<sup>-1</sup> of tissue</span><span>) or lactating (</span><span>38.4 </span><span>±</span><span> 100 ng g<sup>-1</sup> of tissue</span><span>) females. An approach based on statistical mixtures of distributions and a logistic regression was compared to the commonly-used, fixed threshold approach (here, 100 ng g<sup>-1</sup>) for discriminating pregnant from non-pregnant females. The error rate for classifying individuals of known reproductive status was the lowest for the fixed threshold and logistic regression approaches, but the mixture approach required limited <em>a priori</em> knowledge for clustering individuals of unknown pregnancy status. Mismatches in assignations occurred at lipid content <10% of sample weight. Our results emphasize the importance of reporting lipid contents and progesterone concentrations in both units (ng g<sup>-1 </sup>of tissue and ng g<sup>-1</sup> of lipid) when sample mass is low. By highlighting ways to circumvent potential biases in field sampling associated with capturability of different segments of a population, this study also enhances the usefulness of the technique for estimating pregnancy rate of free-ranging population. </span></p>
Data from: Sampling methodology influences habitat suitability modeling for Chiropteran species
<p>Technological advances increase opportunities for novel wildlife survey methods. With increased detection methods, many organizations and agencies are creating habitat suitability models (HSMs) to identify critical habitats and prioritize conservation measures. However, multiple occurrence data types are utilized independently to create these HSMs with little understanding of how biases inherent to those data might impact HSM efficacy.</p> <p>We sought to understand how different data types can influence HSMs using three bat species (<em>L. borealis</em>, <em>L. cinereus</em>, and <em>P. subflavus</em>). We compared the overlap of models created from passive-only (acoustics), active-only (mist-netting and wind turbine mortalities), and combined occurrences to identify the effect of multiple data types and detection bias.</p> <p>For each species, the active-only models had the highest discriminatory ability to tell occurrence from background points and for two of the three species, active-only models performed best at maximizing the discrimination between presence and absence values. By comparing the niche overlaps of HSMs between data types, we found a high amount of variation with no species having over 45% overlap between the models. Passive models showed more suitable habitat in agricultural lands, while active models showed higher suitability in forested land, reflecting sampling bias.</p> <p>Overall, our results emphasize the need to carefully consider the influences of detection and survey biases on modeling, especially when combining multiple data types or using single data types to inform management interventions. Biases from sampling, behavior at the time of detection, false positive rates, and species life history intertwine to create striking differences among models. The final model output should consider biases of each detection type, particularly when the goal is to inform management decisions, as one data type may support very different management strategies than another. </p>
ScienceDex guides
Understand access before you commit
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.