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7,378 results for “case”
The aeroecology of atmospheric convergence zones: the case of Pallid swifts
<p>Trans-Saharan migratory bird species encounter large scale seasonal atmospheric convergence zones, where opposing monsoon and continental air masses meet. These macro-scale atmospheric conditions determine local weather, influence migratory and foraging behaviour and seasonal bird survival rates. Here we investigate the flight behaviour of Pallid swifts (<em>Apus pallidus</em>), a small aerial insectivore, in relation to non-breeding season atmospheric conditions using state-of-the-art GPS logged data. Our analysis suggests that pallid swift prey on insects by catching them where they are most densely concentrated within the atmosphere. Residence of birds in West Africa well past the vegetation minimum suggests that the state of the vegetation and associated local insect populations are not necessarily limiting. Migration events within, to and from, the non-breeding season foraging locations might therefore not only be guided by a decline in vegetation as common metric for prey availability, but also by shifting wind directions and their concentrating effects.</p> <p><strong>Supporting materials</strong></p> <p>This repository includes all data to reproduce the statistics in the described study, above. Certain omissions were made due to the data volumes involved. The latter mostly pertain to the visualization of the processes involved using transects through the atmosphere.</p> <p><strong>Data structure</strong></p> <p>Key data is saved in compressed R serial files (.rds) in the <code>data</code> folder. The <code>position_data.rds</code> file contains bird positions, headings and ancillary data to support most of the analysis in the study. Additional rds files are included which cover spatial analysis in support of the analysis (in the analysis folder).</p> <p><strong>Code execution</strong></p> <p>It is best to execute code in the numeric sequence as provided in the filename. Although it should not matter for the statistical analysis.</p> <p><strong>Licensing</strong></p> <p>For the data include be mindful of the Open Database License (ODbL) which is a copyleft license. Reuse is permitted on the condition that any database (including aggregated working data for analysis) in which our database is used remains open as well. The authors will enforce this policy. All other material such as figures and draft manuscripts are distributed under a CC-BY-SA-4.0 license.</p> <p><strong>Referencing</strong></p> <p>When referencing the data cite both the data repository as: Kearsley, L. et al. 2022. Data from: The aeroecology of atmospheric convergence zones: the case of pallid swifts. – Zenodo Repository, <https://doi.org/10.5281/zenodo.6320888>) and the original paper (Kearsley et al. 2022, <a href="https://doi.org/10.1111/oik.08594">doi.org/10.1111/oik.08594</a>).</p>
Assimilation of NASA's Airborne Snow Observatory snow measurements for improved hydrological modeling: A case study enabled by the coupled LIS/WRF-Hydro system
<p>Data Analysis Scripts and Post-Processed Model Data for a case study using assimilation of ASO Snow Data into the NASA LIS/WRF-Hydro Model. </p> <p>Manuscript Citation:</p> <p>Lahmers T. M., S. V. Kumar, D. Rosen, A. L Dugger, D. Gochis, J. A. Santanello, C. Gangodagamage<sup>,</sup> and R. Dunlap,<strong> </strong>2020: Assimilation of NASA’s Airborne Snow Observatory snow measurements for improved hydrological modeling: A case study enabled by the coupled LIS/WRF-Hydro system,<em>Water Resour. Res.,</em></p>
Dataset for "Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet"
<p>This dataset contains all the spectra and OTU table data used in the paper "Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet", plus the R code to import the TXT (ASCII) files into a dataset, preprocess data, analzye data and generate the figures shown in the paper.</p> <p>Spectral data are available in 2 different format:</p> <p>- the original TXT files (as generated from the Raman instrument, 1 file = 1 spectrum)</p> <p>- as RData file (an hyperSpec object including metadata), directly to be opened in R</p> <p>The OTU table is available either as a single XLSX file or as a RData file to be opened in R.</p> <p>The R code used to generate the figures is available as a single file "Rcode.R".</p>
Seismic acquisition parameters to improve imaging beneath mafic igneous units: Case study from Australia's Northwest Shelf; supplementary material
<p>This dataset comprises two supplementary materials. Supplementary Materials A includes seismic processing workflows conducted by industry on the seismic lines used in this study. The seismic processing workflows are not the property of the author but are publicly available on the NOPIMS and WAPIMS databases. Collating these workflows into supplementary materials provides a simple method for readers to access material important for this research paper. Supplementary Materials B is a collection of 2D seismic lines the author conducted stratigraphic horizon mapping on for this study as viewed in 3D. More details on this dataset can be found throughout the research paper "Seismic acquisition parameters to improve imaging beneath mafic igneous units: Case study from Australia’s Northwest Shelf".</p>
Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study
<p>Aim: The abundance-frequency relationship (AFR) is among the most-investigated pattern in biogeography, yet the relative contributions of niche-based processes related to ecological strategies, and of neutral processes related to spatial colonization-extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche-based processes.</p> <p>Location: France and the UK.</p> <p>Taxon: Vascular plants.</p> <p>Methods: We used two arable weed surveys covering 1544 fields in Western Europe (France, UK), along with functional traits related to resource acquisition, flowering phenology and dispersal. We quantified specialization both to arable habitat and to individual crop types, and performed phylogenetic path analyses to test competing models accounting for direct and indirect relationships between traits, specialization, abundance and frequency. We performed the analyses for all species in each country, as well as for a subset of the most abundant species.</p> <p>Results: Local abundance of weeds increased with their regional frequency, but the relationship became negative or null when considering only the most abundant weeds. Specialization to arable habitat and to individual crop type either had a similar or opposite effect on regional frequency and local abundance explaining these positive and negative relationships, respectively. Regional frequency was not directly explained by any trait but indirectly by resource requirement traits conferring specialization to the arable habitat. Conversely, high local abundance was directly related to low seed mass, high SLA, early and short flowering.</p> <p>Main Conclusions: Direct/indirect effects of functional traits on local abundance/regional frequency, respectively, supports a significant role of niche-based processes in AFR. Neutral spillover dynamics could further explain a direct linkage of abundance and frequency. Similar causal paths and consistent influences of traits on specialization and abundance in the two studied regions suggest genericity of these findings.</p>
Case study on an integrated interoperable metadata model for geoscience information resources
<p>An integrated metadata schema was created to promote interoperability and to characterize historically collected geoscience data. The metadata standard describes the steps taken to develop a switching‐across methodology that allows geoscience metadata standards (ISO 19115, CSDGM, ANZLIC and INSPIRE) to communicate with one another. We also demonstrated a real example of one of the switching‐across that was created. A representative metadata schema was created using items from harmonization standards that might be optimally mapped. Semantic interoperability allows users to access equivalent classes across several metadata standards in a uniform and consistent rule. It also tries to provide fundamental aspects that might characterize acquisition information to enhance data reuse and current metadata standards for data preservation and distribution.</p> <p>This dataset contains 5 data and contains the content standard of each of the four metadata schema and the metadata information of integrated metadata schema.</p> <ul> <li>data_ISO19115.xlsx: Core level of metadata elements for geographic resources of ISO 19115</li> <li>data_CSDGM.xlsx: Content Standard for Digital Geospatial Metadata of CSDGM</li> <li>data_INSPIRE.xlsx: Content Standard of INSPIRE metadata modeldata_ANZLIC.xlsx: Content Standard of ANZLIC Metadata Profile</li> <li>data_integrated model.xlsx: metadata class and their elements in the integrated interoperable metadata model</li> </ul>
dataset related to article "EXPANDING THE GENETIC SPECTRUM OF PRIMARY FAMILIAL BRAIN CALCIFICATION DUE TO SLC2OA2 MUTATIONS: A CASE SERIES"
<p>Sanger sequences (.abi files) of all patients of our Fondazione Besta Cohort.</p>
Comparison of the Birth Weights of Infants with Esophageal Atresia and Tracheoesophageal Fistula and Infants with Inguinal Hernia: A Retrospective Case–Control Study
<p>Esophageal atresia with tracheoesophageal fistula is the most common tracheoesophageal malformation. Amniotic fluid swallowing into the upper blind sack and aspiration were observed during fetal life. Tracheoesophageal fistula serves as a sideway passage of amniotic fluid into the gastrointestinal tract. Compared with inguinal hernia, gestational age adjusted birth weights were lower for infants with esophageal atresia. In esophageal atresia with tracheoesophageal fistula nutrition by aspirated amniotic fluid did not fully compensate the intrauterine growth deficit.</p>
Flight milestones extraction and analysis: a case study for Stockholm Arlanda airport
<p>State vector data for movements (arrivals and departures) at <a href="https://en.wikipedia.org/wiki/Stockholm_Arlanda_Airport">Stockholm Arlanda</a> (IATA: ARN, ICAO: <strong>ESSA</strong>) for the month of September 2021 as extracted from The OpenSky Network historical database.</p>
Particle tracks of 3D flow field during the initiation of a fluvial particle (case 6S)
<p>The dataset belongs to experimental work described in the paper "Role of low-order proper orthogonal decomposition modes and large-scale coherent structures on sediment particle entrainment" published in the Journal of Hydraulics Research. The paper has been published as open access: https://doi.org/10.1080/00221686.2020.1869604</p> <p>The dataset consists of particle tracks of the three-dimensional flow field during the entrainment of a fluvial particle of test case 6S.</p> <p> </p> <p> </p>
Data and script for binomial GLMs in "Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications." (Pratt & Guengerich)
<p>This submission contains data and R-script that enable to reproduce the binomial generalized linear models in the paper “Lithic Analysis of Andean Sedentary Societies, a Case Study from the Chachapoyas Region, Peru, and Potential Applications” by Lauren V. Pratt & Anna Guengerich. Please cite the above paper if you use the files included in this Zenodo record in your work.</p>
Fig. 1. A. caliginosa–A in The Alternative Distribution Of Related Earthworms Aporrectodea Caliginosa And A. Trapezoides (Oligochaeta, Lumbricidae) In Ukraine As A Case Of Geographical Parthenogenesis
Fig. 1. A. caliginosa–A. trapezoides sample locations from the territory of Ukraine.
CView: test case dataset
<p><strong>Summary</strong></p> <p>All North American subtype B gp120 sequences, verified to be CCR5-using sequences (n = 636), were downloaded from the<a href="https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html"> Los Alamos HIV sequence database</a> in aligned fasta format [1]. These were loaded into <a href="https://sourceforge.net/projects/cview/">CView</a>, using the “Load (fasta)” option of the “All Sequences” menu, following which they were saved in unaligned format using the “Save (unaligned)” option of the “All Sequences” menu. Additionally, the titles of these sequences were saved to a separate file using the “Save (titles)” option. This was repeated for CXCR4-using sequences (n = 76). In order to make sites directly comparable between the two sets of unaligned sequences, they were combined into a single file and aligned using MUSCLE [2].</p> <p>This alignment was used in the test case example of our CView paper [3] titled “<em>CView: A network based tool for enhanced alignment visualization</em>” <a href="https://doi.org/10.1371/JOURNAL.PONE.0259726">(view)</a>.</p> <p>The CView project page is located at: <a href="https://sourceforge.net/projects/cview/">https://sourceforge.net/projects/cview/</a></p> <p>A poster sumarization presented at <a href="http://www.iscb.org/ismb2022">ISMB 2022</a> is available <a href="https://doi.org/10.5281/zenodo.6798044">here</a>.</p> <p> </p> <p><strong>Tutorials</strong></p> <p>1. A demonstration of CView usage in the form of an mp4 movie is available <a href="https://zenodo.org/record/6514787">here</a>.</p> <p>2. A demonstration of how variants can be identified using CView is available <a href="https://zenodo.org/record/6514972">here</a>.</p> <p> </p> <p>Related software to this project are:<br> 1. <a href="http://sourceforge.net/projects/cstone/">CStone</a> <br> 2. <a href="http://sourceforge.net/projects/csreadgen/">CSReadGen</a><br> 3. <a href="https://sourceforge.net/projects/cview/">CView</a> <<br> 4. <a href="https://sourceforge.net/projects/chimsim/">ChimSim</a><br> 5. <a href="https://sourceforge.net/projects/tvscript/">TVScript</a></p> <p> </p> <p>General details of the project are available <a href="https://cibio.up.pt/en/projects/de-novo-based-sequence-assembly-of-next-generation-sequence-data-without-chimeras-improved-annotation-gene-expression-profiles-and-haplotype-br-reconstruction/">here</a>.</p> <p> </p> <p><strong>References</strong></p> <p>1. Kuiken C, Korber B, Shafer RW. HIV Sequence Databases. AIDS Rev. 2003;5: 52. Available: /pmc/articles/PMC2613779/</p> <p>2. Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi:10.1093/NAR/GKH340</p> <p>3. Linheiro, R., Sabatino, S., LoboID, D., & ArcherID, J. (2022). CView: A network based tool for enhanced alignment visualization. <em>PLOS ONE</em>, <em>17</em>(6), e0259726. https://doi.org/10.1371/JOURNAL.PONE.0259726</p> <p> </p> <p><strong>| linkedIn . web . orcid |</strong><br> | <a href="https://www.linkedin.com/in/raquel-linheiro-50883873/">linheiro</a> . web . <a href="https://orcid.org/0000-0003-2659-0910">orcid</a> |---| sabatino . <a href="https://cibio.up.pt/en/people/details/stephen-joseph-sabatino/">web</a> . <a href="https://orcid.org/0000-0003-2815-2375">orcid</a> |---| <a href="https://www.linkedin.com/in/diana-lobo-6aa63328/">lobo</a> . <a href="https://cibio.up.pt/en/people/details/diana-lobo/">web</a> . <a href="https://orcid.org/0000-0001-6988-9993">orcid</a> |---| <a href="https://www.linkedin.com/in/john-archer-7b872872">archer</a> . <a href="https://cibio.up.pt/en/people/details/john-archer/">web</a> . <a href="https://orcid.org/0000-0001-6212-0962">orcid</a> |</p> <p> </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>
Fig. 1 in An overlooked case for a century: taxonomy and systematics of a new Iberian species of Eumerus Meigen, 1822 (Diptera, Syrphidae)
Fig. 1. Distribution map of E. colladoi sp. nov. in the Iberian Peninsula.
Data from: Encoding laboratory testing data: case studies of the national implementation of HHS requirements and related standards in five laboratories
<p><strong>Objective</strong>: Assess the effectiveness of providing Logical Observation Identifiers Names and Codes (LOINC®)-to-In Vitro Diagnostic (LIVD) coding specification, required by the United States Department of Health and Human Services for SARS-CoV-2 reporting, in medical center laboratories and utilize findings to inform future United States Food and Drug Administration policy on the use of real-world evidence in regulatory decisions.</p> <p><strong>Materials and Methods</strong>: We compared gaps and similarities between diagnostic test manufacturers' recommended LOINC® codes and the LOINC® codes used in medical center laboratories for the same tests.</p> <p><strong>Results</strong>: Five medical centers and three test manufacturers extracted data from laboratory information systems (LIS) for prioritized tests of interest. The data submission ranged from 74 to 532 LOINC® codes per site. Three test manufacturers submitted 15 LIVD catalogs representing 26 distinct devices, 6956 tests, and 686 LOINC® codes. We identified mismatches in how medical centers use LOINC® to encode laboratory tests compared to how test manufacturers encode the same laboratory tests. Of 331 tests available in the LIVD files, 136 (41%) were represented by a mismatched LOINC® code by the medical centers (chi-square 45.0, 4 df, P &lt; .0001).</p> <p><strong>Discussion</strong>: The five medical centers and three test manufacturers vary in how they organize, categorize, and store LIS catalog information. This variation impacts data quality and interoperability. </p> <p><strong>Conclusion</strong>: The results of the study indicate that providing the LIVD mappings was not sufficient to support laboratory data interoperability. National implementation of LIVD and further efforts to promote laboratory interoperability will require a more comprehensive effort and continuing evaluation and quality control.</p>
Case Study - Performance Changes of Apache Tomcat at Code Level
<p>This dataset provides the data of the case study on <a href="https://github.com/apache/tomcat">Apache Tomcat</a> that was conducted as part of the bachelor thesis "Extending Peass to Detect Performance Changes of Apache Tomcat". The data was generated by <a href="https://github.com/DaGeRe/peass">Peass</a> and the <a href="https://github.com/stro18/peass-ant">Peass-Ant plugin</a>.</p> <p><strong>Contents</strong></p> <p>The dataset is divided into case_study_1v-100v.tar.xz and case_study_100v-200v.tar.xz. Both parts contain the following data:</p> <ul> <li>select/ - Results of regression test selection, especially: <ul> <li>results/traceTestSelection_tomcat.json - Tests selected based on static code analysis and trace analysis</li> </ul> </li> <li>3 x measure_p*_100vm_400iter/ - Results of performance measurements, especially: <ul> <li>clean/ - Mean of measurements per VM</li> <li>results/changes.json - Tests containing performance changes, computed with t-test</li> </ul> </li> <li>rca_p3_100vm_400iter/ - Results of root cause analysis, especially: <ul> <li>rca/tree/ - Measurements results per called method</li> <li>results/*/*.html - Visualization of root cause analysis</li> </ul> </li> </ul> <p>Additionally, f1_score.tar.xz is included in this dataset, It contains heatmaps visualizing the F<sub>1</sub>-score that were used to compare different measurement configurations.</p> <p><strong>Extraction of Data</strong></p> <p>Move all .tar.xz files to an empty directory and execute for each file:</p> <pre><code class="language-bash">tar -Jxf <file></code></pre> <p> </p>
REIP: a Reconfigurable Environmental Intelligence Platform and Software Framework for Fast Sensor Network Prototyping - use case dataset
<p>Sensor networks have dynamically expanded our ability to monitor and study the world. Their presence and need keep increasing, and new hardware configurations expand the range of physical stimuli that can be accurately recorded. Sensors are also no longer simply recording the data, they process it and transform into something useful before uploading to the cloud. However, building sensor networks is costly and very time consuming. It is difficult to build upon other people’s work and there are only a few open-source solutions for integrating different devices and sensing modalities. We introduce REIP, a Reconfigurable Environmental Intelligence Platform for fast sensor network prototyping. REIP’s first and most central tool, implemented in this work, is an open-source software framework, an SDK, with a flexible modular API for data collection and analysis using multiple sensing modalities. REIP is developed with the aim of being user-friendly, device-agnostic, and easily extensible, allowing for fast prototyping of heterogeneous sensor networks. Furthermore, our software framework is implemented in Python to reduce the entrance barrier for future contributions. We show the potential and versatility of REIP in real world applications, along with performance studies and benchmark REIP SDK against similar systems.</p> <p>This dataset was created for the case study in Section 5 of the paper.</p>
Code of "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation"
<p>Code used to prepare a paper entitled "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation" which was submitted to Hydrology and Earth System Sciences.</p>
Objective identification of high-wind features within extratropical cyclones using a probabilistic random forest (RAMEFI). Part I: Method and illustrative case studies - Video Supplement
<p>These videos provide examples of application of RAMEFI (RAndom-forest based MEsoscale wind Feature Identification), a new objective identification of high-wind features within extratropical cyclones, for twelve selected case studies.</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.