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2,001 results for “Orders”
Long term responses of first order streams to allochthonous and detrital manipulations at the Coweeta Hydrologic Laboratory, Otto, NC from 1984 to 2006
This dataset examines the long term effects of litter exclusion, small and large wood removal, and the addition of leaf species of varying detrital quality on organic matter standing crop, export of organic and inorganic particles, and invertebrate abundance and biomass in a high-gradient headwater stream. Pre-treatment and stream reference data are also included. This study was conducted at the Coweeta Hydrologic Laboratory watersheds 53, 54, and 55 from years 1988 through 2006.
Point count surveys in order to gain density estimates of birds
Recent evidence suggests that the southern Appalachian Mountains are experiencing increasing spatial and temporal variability in hydroclimate. Specifically, the region is experiencing both increasing frequency of extreme precipitation and a reduced frequency of more moderate precipitation. Moreover, heterogeneity in precipitation among subwatersheds has resulted in neighboring watersheds experiencing large differences in precipitation levels over the past 30 years. This extreme spatial variability creates an opportunity to examine how differences in precipitation relate to the abundances of regional flora or fauna. Breeding bird abundance was measured on areas of intact forest in Macon County, North Carolina, USA that have varied in precipitation over the past 30 years. I hypothesized that long term changes in moisture regimes would cause terrestrial vertebrates to persist in an area where their species specific environmental requirements were being met. Focal passerines of this study have variable life history traits and therefore I hypothesized that vegetation that promotes their respective habitat would be a main factor determining their abundance; furthermore, vegetation is proximally associated with precipitation, therefore some measurable differences among sites may exist. All dry sites in this study have higher estimated avian densities, Black-throated Blue Warblers were found exclusively on dry sites and Black-throated Green Warblers were found almost exclusively on wet sites. These results suggest that a correlation exist between microclimate and avifauna surveyed in this study.
Fig. 3 in Atlas of European millipedes 2: Order Julida (Class Diplopoda)
Fig. 3. Area codes as used in the atlas, from Fauna Europaea guidelines (Jong et al. 2014, supplementary material 1). Reproduced with permission. Note that MN (Montenegro) and SB (Serbia) in the above list and throughout this paper are shown as YU (Yugoslavia) on this map.
Fig. 1. A in Atlas of European millipedes 2: Order Julida (Class Diplopoda)
Fig. 1. A selection of European species of Julida. A. Boreoiulus tenuis (Bigler, 1913) (Blaniulidae) (J. Spelda phot.). B. Trichoblaniulus hirsutus (Brölemann, 1899) (Trichoblaniulidae) (D. Cheung phot.). C–J. Julidae. C. Cylindroiulus boleti (C.L. Koch, 1847) (J. Spelda phot.). D. Leptoiulus belgicus (Latzel, 1884) (J. Spelda phot.). E. Ommatoiulus hoffmani Akkari & Enghoff, 2012 (K. Mohr phot.). F. Ommatoiulus sabulosus (Linnaeus, 1758), colour variety from the Italian Riviera (D. Cheung phot.). G. Pteridoiulus aspidiorum Verhoeff, 1913 (J. Spelda phot.). H. Pachyiulus cattarensis (Latzel, 1884) (D. Antić phot.). I. Serboiulus deelemanni Strasser, 1971 (D. Antić phot.). J. Unciger foetidus (C.L. Koch, 1838) (J. Spelda phot.). Not to scale.
Extending a Brainiac Prover to Lambda-Free Higher-Order Logic -- Evalution Data
<p>This package contains problems used for evalaution and the raw evaluation data for the Extending a Brainiac Prover to Lambda-Free Higher-Order Logic article</p>
Data for: On-the-fly ab initio semiclassical evaluation of third-order response functions for two-dimensional electronic spectroscopy
<p>Data for publication: T. Begusic, J. Vanicek, On-the-fly ab initio semiclassical evaluation of third-order response functions for two-dimensional electronic spectroscopy, <em>J. Chem. Phys.,</em> <strong>153</strong>, 184110 (2020).</p> <p>Contains simulated linear and two-dimensional spectra of the S<sub>1</sub> - S<sub>0</sub> electronic transition of phenol, excited-state and ground-state ab initio trajectories at the PBE0/6-311G(d,p) level of theory, and other supporting data related to the abovementioned publication.</p>
Supporting voucher images for Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales
<p>A compressed directory of images of voucher specimens used for sequencing and phylogenetic analysis.</p>
Accurate modeling of plasma acceleration with arbitrary order pseudo-spectral particle-in-cell methods
<p>This is supplementary material to the publication "Accurate modeling of plasma acceleration with arbitrary order pseudo-spectral particle-in-cell methods" by S. Jalas et. al.</p> <p>Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo- spectral solvers featuring infinite order stencils can strongly reduce NCR – or even suppress it – and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be prone to NCR. Here, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for parallel computation by domain decomposition.</p> <p>The given script can be run with the open source particle in cell codes FBPIC (https://github.com/fbpic/fbpic) and Warp (https://bitbucket.org/berkeleylab/warp)</p> <p>The produced data is conformant with the openPMD standard (openpmd.org) and can be analysed for example with the openPMD-viewer (https://github.com/openPMD/openPMD-viewer).</p>
A geometry preserving, conservative, mesh-to-mesh isogeometric interpolation algorithm for spatial adaptivity of the multigroup, second-order even-parity form of the neutron transport equation
<p>In this paper a method is presented for the application of energy-dependent spatial meshes applied to the multigroup, second-order, even-parity form of the neutron transport equation using Isogeometric Analysis (IGA). The computation of the inter-group regenerative source terms is based on conservative interpolation by Galerkin projection. The use of Non-Uniform Rational B-splines (NURBS) from the original computer-aided design (CAD) model allows for efficient implementation and calculation of the spatial projection operations while avoiding the complications of matching different geometric approximations faced by traditional finite element methods (FEM). The rate-of-convergence was verified using the method of manufactured solutions (MMS) and found to preserve the theoretical rates when interpolating between spatial meshes of different refinements. The scheme’s numerical efficiency was then studied using a series of two-energy group pincell test cases where a significant saving in the number of degrees-of-freedom can be found if the energy group with a complex variation in the solution is refined more than an energy group with a simpler solution function. Finally, the method was applied to a heterogeneous, seven-group reactor pincell where the spatial meshes for each energy group were adaptively selected for refinement. It was observed that by refining selected energy groups a reduction in the total number of degrees-of-freedom for the same total L2 error can be obtained.</p>
Linear Time Varying System Examples for Model Order Reduction
<p>Three linear time varying system benchmarks implemented in MATLAB. </p> <p>1.) a time varying version of the Oberwolfach Steel Cooling Benchmark</p> <p>2.) a one dimensional heat equation with a moving point heat source</p> <p>3.) a linearized Burgers equation</p> <p>Model 1 comes in the same 5 resolutions as the original time-invariant version. the other two are freely scalable.</p> <p> </p>
Orientation anisotropy of quantitative MRI relaxation parameters in ordered tissue
<p>This dataset contains all the raw source data and MATLAB analysis functions that comprise the study:</p> <p><br> <strong>Orientation anisotropy of quantitative MRI relaxation parameters in ordered tissue</strong></p> <p>Scientific Reports | DOI:10.1038/s41598-017-10053-2</p> <p>Hänninen Nina(1,2), Rautiainen Jari(1), Rieppo Lassi(2,3), Saarakkala Simo(2,3,4) and Nissi Mikko Johannes(1*)</p> <ol> <li>Department of Applied Physics, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland</li> <li>Research Unit of Medical Imaging, Physics and Technology, University of Oulu, POB 5000, FI-90014 Oulu, Finland</li> <li>Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland</li> <li>Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland</li> </ol> <p> </p> <p>*Corresponding author:<br> Mikko J. Nissi<br> Department of Applied Physics,<br> University of Eastern Finland<br> POB 1627<br> FI-70211, Kuopio, Finland<br> mikko.nissi@uef.fi<br> +358-50-5955517</p> <p><br> Keywords: relaxation anisotropy, orientation, cartilage, MRI, quantitative</p> <p> </p> <p><br> Included folders and files are:</p> <ul> <li>article_figures: all figures published in the manuscript</li> <li>data: MRI measurement data and pre-processed PLM measurement data</li> <li>matlab_functions: matlab functions used in data analysis with subfolders: <ul> <li>aedes_plugins: plugins for aedes (http://aedes.uef.fi) for calculation of relaxation time maps</li> <li>fitting_functions: miscellaneous functions for fitting relaxation times etc, used by the functions in above folder</li> <li>miscellaneous_functions: small helper functions for a number of small tasks utilized by the other scripts and functions</li> </ul> </li> <li>plm_new_data: histological data measured by quantitative polarized light microscopy.</li> <li>sample_holder_3D_model: .stl files for the 3-D printable sample-holder which allows rotation of the specimen</li> <li>carbon_data_collector_ROT_for_publication.m: master data collection and analysis script that reads in all the data and performs all the calculations to produce the images of the study. This function relies on all the matlab-functions in the subfolder (i.e. the subfolders need to be indexable by matlab) and Aedes analysis software (http://aedes.uef.fi) and matlab R2013b or later.</li> <li>README.txt: this file</li> </ul> <p><br> Notes for setting up Aedes correctly for this dataset:<br> Run Aedes -> Tools -> Edit VNMR Defaults:</p> <ul> <li>Return: FT + K-space</li> <li>DC: off</li> <li>Zeropadding: off</li> <li>Sorting & fastread: on</li> <li>Precision: single</li> <li>Read_fcn: readfid (old)</li> <li>Orient: no</li> </ul> <p>See more info in separate readme files included in each folder.</p> <p><br> (Mikko Nissi, Aug 15, 2017)</p> <p> </p>
Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
<p>A better understanding of the relationship between plant specialized metabolism and traditional medicine has the potential to aid in bioprospecting and untangling of cross-cultural use patterns. However, given the limited information available for metabolites in most plant species, understanding medicinal use-metabolite relationships can be difficult. The order Caryophyllales has a unique pattern of lineages of tyrosine- or phenylalanine-dominated specialized metabolism, represented by mutually exclusive anthocyanin and betalain pigments, making Caryophyllales a compelling system to explore the relationship between medicine and metabolites by using pigment as a proxy for tyrosine- vs phenylalanine-dominant metabolism. We compiled a list of medicinal species in select tyrosine- or phenylalanine-dominant families of Caryophyllales (Nepenthaceae, Polygonaceae, Simmondsiaceae, Microteaceae, Caryophyllaceae, Amaranthaceae, Limeaceae, Molluginaceae, Portulacaceae, Cactaceae, and Nyctaginaceae) by searching scientific literature until no new medicinal uses were recovered. We then tested for phylogenetic clustering of uses using a "hot nodes" approach. To test potential non-metabolite drivers of medicinal use, like how often humans encounter a species (apparency), we repeated the analysis using only North American species across the entire order and performed phylogenetic generalized least squares regression (PGLS) with occurrence data from the Global Biodiversity Information Facility (GBIF). We hypothesized families with tyrosine-enriched metabolism would show clustering of different types of medicinal use compared to phenylalanine-enriched metabolism. Instead, wide-ranging, apparent clades in Polygonaceae and Amaranthaceae are overrepresented across nearly all types of medicinal use. Our results suggest that apparency is a better predictor of medicinal use than metabolite profile, although metabolism type may still be a contributing factor.</p>
Dataset: Fano meets Stokes: Four-order-of-magnitude enhancement of asymmetric Brillouin light scattering spectra
<p>Dataset accompanying publication:</p> <p>Rafał Białek, Thomas Vasileiadis, Mikołaj Pochylski, Bartłomiej Graczykowski, Fano meets Stokes: Four-order-of-magnitude enhancement of asymmetric Brillouin light scattering spectra, Photoacoustics, Volume 30, 2023, 100478, ISSN 2213-5979, https://doi.org/10.1016/j.pacs.2023.100478.</p>
PHC. 4. Belondira muhiauicu. n in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
PHC. 4. Belondira muhiauicu. n. sp.: /I -cïpymypa rononııoro Kouua uemaronu; E _ noııonme opraııbı caııııa; B - xßocr ca-MKn
Pnc. l in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
Pnc. l Laurop /ıragus lauri, n. sp A _ |poclmno-ccncopubxíi omen Tena, B-ııepeilımfl, B B-aaııııflfl 1331111 ï1 fl ' \lflCTH mcm T Tuna 0113; f-nononue opraum caxmm ı
Pm". 3. Bulundiru nmlrluvicu, n. sp .. fl-oöuuıü mul ııexıaroım; 13 -- cßmımep ııpokopnyca rımııeßo1a, B-¬ aanunñ xoneu Tema camua ı in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
Pm". 3. Bulundiru nmlrluvicu, n. sp .. fl-oöuuıü mul ııexıaroım; 13 -- cßmımep ııpokopnyca rımııeßo1a, B-¬ aanunñ xoneu Tema camua ı
PHC. 5 in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
PHC. 5 Thorncnc / nu urulifu, n.:p A ncpeïuuñ Koııeıı Tena; B —- xnocT ueuaronbl, B -ıınııonue IIOIIODLIC oprauu cınııuı; I` ~ Tpoıbııuo-ceıicopııbıñ omcn ı 1011a; LI - mencóncrafl uacn. nnmenona
Puc. 6 in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
Puc. 6. Erıclıodelııs arcticııs, n. sp.: / 1- crpymypa ıonomıoro Kolnla rena, 1 5 _ TpoqıııKo-ceııcopııbıü Omen; B-Jzıııımı Iıacn, Term ncuaronu; f- lıünøßuß Opraııbı czmua
PHC. 2 in New species of plant nematodes of the order Dorylaimida, found in Moldavia and other areas of the USSR
PHC. 2. Craleronenza lozovensís, n sp.: A -crpy'i‹rypa nepcnneñ lxacTH Tena; 5 - xnocr ııeııaToııbı; B — rpoclnıxo-ceııcopııbıñ omen rena; 1`- nouepeunafl ncuepueuuocrb Kyrnxyııbı
Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
<p>Parrots (Order: Psittaciformes) are a diverse clade that are easily distinguishable from other birds. Despite the clear characters that define the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024; Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus <em>Probosciger</em> and we restrict usage of the recently introduced tribe Touitini to its type-genus <em>Touit</em>. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades and we further reinstate five valid, available generic names not widely used in recent literature if at all (<em>Licmetis</em>, <em>Gymnopsittacus</em>, <em>Clarkona</em>, <em>Suavipsitta</em>, <em>Cardeos</em>). We advocate the retention of <em>Vini</em> Lesson, 1833 over <em>Coriphilus</em> Wagler, 1832 based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., <em>Bolborhynchus</em> parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the <em>Psittacula</em> <em>sensu lato</em> ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields.</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.