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64 results for “nomadism”
Third FAIRmat users meeting Nov2023 - FAIR Data Principles in Perovskite Solar Cell Research using NOMAD - Daniel Baumann
<p>Daniel Baumann (doctoral research project at KIT in the group of Ulrich Paetzold) highlights how NOMAD Oasis supports experimental materials researchers in the field of perovskite photovoltaics. A live demonstration of experimental planning, documentation, as well as automated data evaluation is presented. Particularly, in conjunction with a highly repeatable robotic spin-coating setup, the realization of this vast potential may be closer than anticipated. </p>
FAIRmat Tutorial 14: Developing schemas and parsers for FAIR computational data storage using NOMAD-Simulations
<p><a href="https://nomad-lab.eu"><u>NOMAD</u></a> is an open-source, community-driven data infrastructure, focusing on materials science data. Originally built as a repository for data from DFT calculations, the NOMAD software can automatically extract data from the output of a large variety of simulation codes. Our previous computation-focused tutorials (<a href="https://fairmat-nfdi.github.io/AreaC-Tutorial-CECAM-2023/"><u>CECAM workshop</u></a>, <a href="https://fairmat-nfdi.github.io/AreaC-Tutorial10_2023/"><u>Tutorial 10</u></a>, and <a href="https://www.fairmat-nfdi.eu/events/fairmat-tutorial-7/tutorial-7-materials"><u>Tutorial 7</u></a>) have highlighted the extension of NOMAD’s functionalities to support advanced many-body calculations, classical molecular dynamics simulations, and complex simulation workflows. <br>But how can you utilize this infrastructure and associated suite of tools if your simulation code or method is not yet supported? <strong>This tutorial will provide foundational knowledge for customizing NOMAD to fit the specific needs of your computational research project</strong>. The following provides an outline of the major topics that will be covered:</p> <ul> <li>Introduction to the NOMAD software and repository</li> <li>Working with the NOMAD-Simulations schema plugin</li> <li>Extending NOMAD-Simulations to support custom methods and outputs</li> <li>Creating parser plugins from scratch</li> <li>Extra: Interfacing complex simulation and analysis workflows with NOMAD</li> </ul> <p><strong>Disclaimer:</strong> NOMAD is being continuously developed based on input and feedback from the scientific community. Hence the features, services or interface may have changed since the time of recording of this video. For up-to-date information please consult our latest tutorials and the NOMAD documentation <a href="https://nomad-lab.eu/prod/v1/docs/">https://nomad-lab.eu/prod/v1/docs/</a></p>
Dataset of the Volkswagen Fond Project no. 90 216 " Early mounted nomads and their vessels Ceramic analysis project aimed at supporting the reconstruction of socio-economic conditions in mobile populations north of the Black Sea between 1100 and 600 BC"
<p>The Excel-Sheet contains information (location of the site, chronological position, type of site, archaeological culture, literature, photographies and drawings, analysis made, results of the analysis, etc.) about the samples taken in the Volkswagen Fond Project no. 90 216 "Early mounted nomads and their vessels Ceramic analysis project aimed at supporting the reconstruction of socio-economic conditions in mobile populations north of the Black Sea between 1100 and 600 BC".</p> <p>The project itself focuses on contacts and interactions between groups with different material culture remains in two vegetation zones to the north of the Black Sea.The investigation takes a complex archaeometric approach to characterise the pottery of communities that lived in the forest steppe zone and steppe zone to the north of the Black Sea between the Dniester and Dnieper rivers between 1100 and 600 BC. By using an multidisciplinary approach to study the material culture of these communities with mobile lifeways, this project will allow the comparison of the natural science and archaeological data for the first time.</p> <p>The Excel-Sheet presents the results of various analyses performed during the project and serves as the database for publications of the project members.</p>
Body mass and triglycerides predict departure of free-living nomadic pine siskins
<p>1. Facultative migrations are observed across vertebrate taxa, include irruptive and nomadic movements, and occur in response to ephemeral and unpredictably variable resources. While the physiology underlying seasonal, obligate migrations is thoroughly studied, much less is known about the physiological mechanisms of facultative movements. We test two hypotheses in a free-living, nomadic bird, the pine siskin (Spinus pinus).</p> <p>2. The Prepare Hypothesis predicts that, like obligate migrants, siskins increase fuel stores to prepare for migratory movements and elevations of baseline corticosterone (CORT) support departure. The Escape Hypothesis predicts that siskins do not prepare for departure, body condition declines as food availability declines, and stress-related levels of CORT induce escape from resource-poor areas.</p> <p>3. Under the controlled lab conditions of previous studies, food restriction induces declines in body condition and increases in CORT and locomotor activity, supporting the Escape Hypothesis. This study evaluates the ecological relevance of these captive findings by testing the Prepare and Escape Hypotheses in the field for the first time.</p> <p>4. During two fall field seasons, we radio-tagged siskins and tracked their local movements using handheld and automated telemetry. We assess how body condition and CORT relate to feeding behavior (estimated via plasma triglycerides (TRIG)), space use, and departure.</p> <p>5. We do not find support for either the Prepare or Escape Hypothesis, but rather observe an intermediate pattern. Birds with higher TRIG, and therefore greater food intake, are more likely to depart. Birds in poor condition stay longer near the field site; however, above a threshold body mass, body condition does not predict departure.</p> <p>6. These findings suggest moderate energy stores are necessary for departure but movement decisions depend on other factors among birds with sufficient fuel. Siskin movements are physiologically distinct from both obligate and fugitive movements, and we discuss how food availability and body condition interact to drive different types of movement.</p>
German NFDI, FAIRmat-NFDI, NOMAD, NOMAD OASIS, pynxtools, example datasets for atom probe microscopy and electron microscopy
<p>The following repository contains a collection of data and metadata files in different vendor formats which were collected in the fields of atom probe microscopy (LEAP instruments) and electron microscopy (Nion instruments). These files are meant for development and testing purposes of the nomad north-remote-tools-hub and the related nomad-nexus-parser software tools within the FAIRmat project.FAIRmat is a consortium lead by the Humboldt-Universität zu Berlin. FAIRmat is a member of the German Research Data Infrastructure (NFDI) initiative.</p> <p>A detailed description of the background and content of the individual files follows:</p> <p><strong>ger_berlin_haas_nionswift_multimodal.zip</strong><br> This is a dataset for testing how to load entire data and metadata from compressed NionSwift project files directly.<br> This is a dataset for testing the em_nion reader which handles files from Nion microscopes and NionSwift software.<br> The data were collected by Benedikt Haas from Humboldt-Universität zu Berlin. The parser was developed together<br> with Sherjeel Shabih also from Humboldt-Universität zu Berlin. Both work in the group of Prof. Christoph Koch.<br> EM.STEM.Nion.Dataset.1.zip is a dataset we used for an earlier version of this parser</p> <p><strong>APM.LEAP.Datasets.*.zip:</strong><br> This is a collection of two datasets for testing the generic nx_apm reader which handles commercial and community file formats for reconstructed ion position and ranging data from atom probe microscopy experiments. The datasets were collected by different authors.<br> <br> <strong>APM.LEAP.Datasets.1.zip:</strong><br> <em>R31_06365-v02.pos</em>, was shared by Jing Wang and Daniel Schreiber (both at PNNL). Details to the dataset are available<br> under the following DOIs:<br> https://doi.org/10.1017/S1431927618015386<br> https://doi.org/10.1017/S1431927621012241<br> <em>70_50_50.apt</em>, was a shared by Xuyang Zhou at his time with the Max-Planck-Institut für Eisenforschung GmbH as a open-source test data to the publication he lead on machine-learning-based techniques for composition profiling.<br> The dataset and publication is available via the following DOI and resources:<br> https://doi.org/10.1016/j.actamat.2022.117633<br> The dataset specifically is also available here:<br> https://github.com/RhettZhou/APT_GB/tree/main/example/Cropped_70_50_50<br> The range files <em>*.rng </em>and<em> *.rrng</em> range serve as examples to develop tools for parsing them and handle the formatting of range files. The scientific content of the range files was inspired by experiments but is not related to the above-mentioned atom probe datasets<br> and should not be used to analyze these test data for more than pure development purposes.<br> Use instead your own data and matching range files for scientific analyses.</p> <p><strong>APM.LEAP.Datasets.2.zip</strong><br> <em>R18_53222_W_18K-v01.epos</em>, was shared with Markus Kühbach by Andrew Breen<br> during their time at the Max-Planck-Institut für Eisenforschung GmbH.<br> <br> We would like to invite the community to use the nomad infrastructure and support us with<br> sharing data and dataset which we can then use to improve the file format parsing, the reading capabilities,<br> and analyses services of the nomad infrastructure so that the community can profit again from these developments.</p> <p><strong>aut_leoben_leitner.zip</strong><br> is the dataset associated to the grain boundary solute segregation case study discussed in https://arxiv.org/abs/2205.13510</p> <p><strong>usa_portland_wang.zip</strong><br> is the dataset associated with the ODS steel specimen dataset, which is a good example for testing and learning iso-surface<br> based analyses with the paraprobe-toolbox. This dataset was mentioned as one of the test cases in https://arxiv.org/abs/2205.13510</p> <p><strong>ger_erlangen_felfer_ck10.zip</strong><br> is the Ck10 for fundamentals dataset from the atom-probe-toolbox<br> https://github.com/peterfelfer/Atom-Probe-Toolbox/tree/master/test%20data/Ck%2010%20steel%20for%20fundamentals</p> <p><strong>usa_denton_smith_apav_gbco.zip</strong><br> is the GBCO-type dataset from J. Smith and M. Young discussed in their following publications:<br> https://doi.org/10.1017/S1431927621012794 and https://github.com/openjournals/joss-reviews/issues/4862<br> <br> <strong>usa_denton_smith_apav_si.zip</strong><br> is a very small dataset in POS, ePOS, APT, RNG, and RRNG for development and testing purposes.<br> The dataset is a part of APAV mentioned here<br> https://gitlab.com/jesseds/apav/-/tree/JOSS/apav/tests</p>
Data from: A hierarchical population model for the estimation of latent prey abundance and demographic rates of a nomadic predator
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Social environment influences termination of nomadic migration
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Body mass and triglycerides predict departure of free-living nomadic pine siskins
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Data from: Declining food availability alters vocal behavior of a nomadic finch
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Data for: Telomere length predicts timing and intensity of migratory behavior in a nomadic songbird
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Continental-scale shift in foraging habitat use by a highly nomadic species following Australia’s Black Summer megafires
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Movement rules determine nomadic species' responses to resource supplementation and degradation
<p>1. In environments that vary unpredictably, many animals are nomadic, moving in an irregular pattern that differs from year to year. Exploring the mechanisms of nomadic movement is needed to understand how animals survive in highly variable environments, and to predict behavioral and population responses to environmental change. 2. We developed a network model to identify plausible mechanisms of nomadic animal movement by comparing the performance of multiple movement rules along a continuum from nomadism to residency. Using simulations and analytical results, we explored how different types of habitat modifications (that augment or decrease resource availability) might affect the abundance and movement rates of animals following each of these rules. 3. Movement rules for which departure from patches depended on either resource availability or competition performed almost equally well and better than residency or uninformed movement under most conditions, even though animals using each rule moved at substantially different rates. Habitat modifications that stabilized resources, either by resource supplementation or degradation, eroded the benefits of informed nomadic movements, particularly for movements based on resource availability alone. 4. These results suggest that simple movement rules can explain nomadic animal movements and determine species' responses to environmental change. In particular, landscape stabilization and supplementation might be useful strategies for promoting populations of resident animals, but would be less beneficial for managing highly mobile species, many of which are threatened by habitat disruption and changes in climate. </p>
Overlap in the wing shape of migratory, nomadic and sedentary grass parrots
Bird wing shape is highly correlated with mobility, and vagile species have more pointed wing tips than sedentary ones. Most studies of bird wing shape are biased to the northern hemisphere, and consider only two migratory syndromes (north-south migrants or sedentary species). There are major gaps in knowledge about the wing shapes of different taxa with other movement strategies (e.g. nomads) in the southern hemisphere. Parrots are a prominent southern hemisphere bird order with complex movement patterns, but their wing shapes are mostly unstudied. We test whether three metrics of wing shape of grass parrots (Neophema and Neopsephotus spp.) correspond to their purported migration syndromes (and other factors). We show that two strongly migratory grass parrots and an arid-adapted nomad had pointed wings, with flight feather longer distally and shorter proximally. However, purportedly sedentary species overlapped extensively with migrants and nomads in all aspects of wing shape, and taxonomic relationships, purported migratory syndromes and ecological barriers did not explain the variation we recorded. The most distantly related species (Neopsephotus) had most dissimilar wing shape to the others, but broadly conformed to the expectations of long pointed wings of a nomad. Why purportedly sedentary grass parrots had unexpectedly pointed wings is unclear. We propose the hypothesis that this wing shape may persist in sedentary populations if individuals experience strong but intermittent selection to disperse when environmental conditions are poor. If pointed wings are not costly during good times when individuals are sedentary, this wing shape may persist in populations as a 'back up' in bad times. Our study highlights the interesting migration patterns in the southern hemisphere that remain largely unstudied. Wing shape offers an interesting way to identify potentially undiscovered capacity for movement in data deficient species, which may also have implications for conservation.
Data from: Matching habitat choice in nomadic crossbills appears most pronounced when food is most limiting
Of the various forms of non-random dispersal, matching habitat choice, whereby individuals preferentially reside in habitats where they are best adapted, has relatively little empirical support. Here I use mark-recapture data to test for matching habitat choice in two nomadic ecotypes of North American Red Crossbills (Loxia curvirostra complex) that occur in the lodgepole pine (Pinus contorta) forests in the South Hills, Idaho every summer. Crossbills are adapted for foraging on seeds in conifer cones, and in the South Hills the cones are distinctive, favoring a relatively large bill. During a period when seed was most limiting, only the largest individuals approximating the average size of the locally adapted ecotype remained for a year or more. During a period when seed was less limiting, proportionately more individuals remained and the trend for larger individuals to remain was weaker. Although matching habitat choice is difficult to demonstrate, it likely contributed to the observed patterns. Otherwise, nearly unprecedented intensities of natural selection would be needed. Given the nomadic behavior of most crossbill ecotypes and the heterogeneous nature of conifer seed crops, matching habitat choice should be favored and likely contributes to their adaptation to alternative conifers and rapid diversification.
Burial bed of the leader of the nomads AIK3B3.
Russia, Republic of Bashkortostan, Abzelilovsky district. Avlasovsky necropolis. Excavations 2011. Kurgan №3. Burial №3. Burial bed for a deceased nomad leader. Early Iron Age. Chronology: V-VI centuries BC. Early Sarmatian culture. Россия, Республика Башкортостан, Абзелиловский район. Некрополь Авласовский. Курган №3. Захоронение №3. Погребальное ложе. Ранний железный век. Хронология: V-VI века до н.э. Ранняя сарматская культура. Source: Objaverse 1.0 / Sketchfab
Burial of a nomad NB1K1B3
Krasnodar Territory, Timashevsky District. Necropolis Brick-1. Mound No. 1. Burial No. 3. Chronology: Middle Ages. Краснодарский край, Тимашевский район. Некрополь Кирпичный-1. Курган №1. Захоронение №3. Хронология: средневековье. Region Krasnodar, Bezirk Timashevsky. Necropolis Brick-1. Hügel Nr. 1. Bestattung Nr. 3. Chronologie: Mittelalter. Source: Objaverse 1.0 / Sketchfab
NOMAD element annotation bowtie2 indices
<p>Default list of bowtie2 annotations used in NOMAD manuscript</p>
Element annotations indices for NOMAD
<p>Default set of bowtie2 annotations, used in the element annotation step of the NOMAD pipeline</p>
Nomad-FAIR North-Remote-Tool Example Dataset Electron Microscopy
<p><strong>Dataset.Objective.Aperture.Energy.Slit.cdf.nx5.zip<br> Dataset.Objective.Aperture.Energy.Slit.dm3.cdf.zip<br> parser-focalseries-gatandm-cdf2nx5.py</strong><br> An example dataset for focus-series reconstruction (in-line holography).<br> The dataset supplements/comes from a research study <a href="https://doi.org/10.1016/j.ultramic.2021.113264">https://doi.org/10.1016/j.ultramic.2021.113264</a></p> <p><strong>em-sprint09-example.zip</strong></p> <p>This archive contains an example YAML file how metadata to e.g. 1613_Si_HAADF_610_kx.emd<br> (see below) are stored internally in a NOMAD OASIS when saving entries into the customized<br> ELN schema of the EM example that was developed in Sprint09 Area B in the FAIRmat project.<br> This eln_data.yaml file serves as an input to the dataconverter/em reader tool to supplement<br> the numerical data from the 1613_Si_HAADF_610_kx.emd file with metadata during the creation<br> of the emd.nxs file.</p> <p>Furtermore, this archive contains a Bruker BCF, a Velox EMD, and a Digital Micrograph v3 DM3<br> file. These file formats can be used as input to the dataconverter/em reader tool to inject<br> specific numerical data while creating an instance of an NXem-compliant NeXus file.</p> <p>The files have the following SHA256 checksum to verify their integriety:</p> <p>sha256sum eln_data.yaml<br> c0fd230336ce7cd8e2715445ea6af404202b4ab9d7e7186838748bd0559d536f</p> <p>sha256sum 46_ES-LP_L1_brg.bcf<br> bf5ca0f862af49726b848a8a60d73af6f1669990131288ac4b4ca6cb57e58aff</p> <p>sha256sum 1613_Si_HAADF_610_kx.emd<br> 6ed0e8b8c170a0ed307e5c877fd891767a38e636f4680632e9b00c46a2b963b9</p> <p>sha256sum EELS_map_2_ROI_1_location_4.dm3<br> b97850f6c6b100740813c34d20eda294ef66a6130daa42a6cf975c4572ff599c</p> <p> </p>
Quiver with arrows of a nomad warrior AIK2B2
Russia, Republic of Bashkortostan, Abzelilovsky district. Avlasovsky necropolis. Kurgan №2. Burial №2. Fragment of the collective burial of soldiers. Quiver with bronze arrowheads. The wooden details of the quiver and arrow shaft are visible. Early Iron Age. Chronology: V-VI centuries BC. Early Sarmatian culture. Россия, Республика Башкортостан, Абзелиловский район. Некрополь Авласовский. Курган №2. Захоронение №2. Фрагмент коллективного захоронения воинов. Колчан с бронзовыми наконечниками стрел. Видно деревянные детали колчана и древка стрел. Ранний железный век. Хронология: V-VI века до н.э. Ранняя сарматская культура. Source: Objaverse 1.0 / Sketchfab
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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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.