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230 results for “structure determination”
Accelerated lignocellulosic molecule adsorption structure determination dataset
<p>Dataset containing all structures from the accelerated structure search for lignocellulosic molecules. Part of the data corresponds to DFT data, while the largest portion of structures correspond to data acquired using a machine learned interatomic potential (NequIP) trained on the former. The energies attached to each structure are atomisation energies. Contains both isolated adsorbates and adsorption structures. The dataset also contains configuration files for the NequIP training. </p>
Networking nutrients: how nutrition determines the structure of ecological networks - Dataset
<p>Raw sequencing data and other metadata files are associated with Cuff et al. (2021a, 2022a), available at https://doi.org/10.5281/zenodo.4708418</p> <p>Data/code relating to the macronutrient contents and delineation of tropho-species clusters are associated with Cuff et al. (2021b, 2022b), available at https://doi.org/10.5281/zenodo.5738016</p> <p>Cuff, Jordan P. (2021a). A molecular analysis of the diet and biocontrol potential of spiders in cereal crops - Dataset. <em>Zenodo</em>. doi: 10.5281/zenodo.4708419</p> <p>Cuff, Jordan Patrick, Tercel, M. P., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. (2021b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Zenodo</em>. doi: 10.5281/zenodo.5738015</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Drake, L. E., Vaughan, I. P., Bell, J. R., Orozco-terWengel, P., … Symondson, W. O. C. (2022a). Density-independent prey choice, taxonomy, life history and web characteristics determine the diet and biocontrol potential of spiders (Linyphiidae and Lycosidae) in cereal crops. <em>Environmental DNA</em>, in press. doi: 10.1002/edn3.272</p> <p>Cuff, Jordan P., Tercel, M. P. T. G., Vaughan, I. P., Drake, L. E., Wilder, S. M., Bell, J. R., … Symondson, W. O. C. (2022b). Evidence for nutrient-specific foraging of predators under field conditions. <em>Authorea</em>. doi: 10.22541/au.164908092.21266343/v1</p>
Rapid structure determination of microcrystalline molecular compounds using electron diffraction (nanoArgovia Project A3EDPI)
<p>The are the data linked to the publication "Rapid structure determination of microcrystalline molecular compounds using electron diffraction", <a href="https://doi.org/10.1002/anie.201811318">10.1002/anie.201811318</a>. Electron Diffraction data collected with an EIGER X 1M detector (DECTRIS Ltd.).</p> <p>Each tar file contains the raw files in HDF5 format, together with the XDS.INP file used for data integration. Images of the respective crystals have '_img_' in their file names. The log files for recording the stage alpha angle are included with the same name and suffix .txt. See publication for details.</p> <p>NB: The meta-data in the HDF5 files have no meaning, please refer to the respective XDS.INP file for respective information.</p> <p>The crystallographic data (CIF-files) have been uploaded to the ICSD (High--throughput Structural Chemistry with Electron Diffraction) and CSD (https://www.ccdc.cam.ac.uk/) respectively:</p> <p>Paracetamol from Grippostad CCDC 1856579<br> electron structure of MBBF4 CCDC 1856580</p> <p>ZSM-5 x227 CSD 1856581</p> <p>ZSM-5 x331 CSD 1856582</p> <p>ZSM-5 x79 CSD 1856583<br> ZSM-5 x811 CSD 1856584</p> <p> </p>
17O-EPR determination of the structure and dynamics of copper single-metal sites in zeolites
<p><strong>Description of the dataset: </strong></p> <ul> <li><strong>Data type</strong>: Experimental spectroscopic measurements, computer simulation and analysis</li> <li>Files are with filename extensions: <strong>DSC</strong>, <strong>DAT</strong>, <strong>spc</strong>, <strong>par</strong>, <strong>m</strong>, <strong>f34</strong>,<strong> xyz</strong>, <strong>out</strong>, <strong>in</strong></li> <li>Information on <strong>origin of the data</strong>:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions <strong>DSC</strong>, <strong>DTA</strong>,<strong> spc </strong>and<strong> par.</strong></li> <li>EPR spectroscopic simulation and analyses with filename extension <strong>m</strong>.</li> <li>Periodic DFT computations with(out) filename extensions <strong>out</strong> and <strong>f34</strong> in ASCII format.</li> <li>Molecular cluster DFT computations with filename extensions <strong>in</strong> and <strong>out</strong> in ASCII format.</li> <li>Geometry information of cluster models is stored in <strong>xyz</strong> files in ASCII format.</li> </ul> <ul> <li>X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with SHQ cavity produced by Bruker.</li> <li>Q-band and X-band Pulsed-EPR spectroscopic measurements were generated by ELEXYS 580 EPR spectrophotometer equipped with SHQ cavity and ER035 M NMR gaussmeter produced by Bruker.</li> <li>Periodic DFT computations were generated using distributed parallel version of CRYSTAL17 code.</li> <li>Molecular cluster DFT computations were generated using the ORCA (v4.2.1) code.</li> <li><strong>If t</strong> <ul> <li>Files in <strong>PARACAT_WP3_20210625_01_CW</strong> folder includes X-band CW-EPR spectroscopic measurements; original data are in DTA/DSC and spc/par formats.</li> <li>Files in <strong>PARACAT_WP3_20210625_02_HYSCORE</strong> folder includes HYSCORE spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in <strong>PARACAT_WP3_20210625_03_ESE</strong> folder includes ESE spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in <strong>PARACAT_WP3_20210625_04_ENDOR</strong> folder includes ENDOR spectroscopic measurements; original data are in DTA/DSC formats.</li> <li>Files in <strong>PARACAT_WP3_20210625_05_MATLAB</strong> folder includes computer simulations/analyses of the EPR measurements; data are in m formats.</li> <li>Files in <strong>PARACAT_WP3_20210625_06_DFT </strong>folder includes periodic and cluster DFT computation inputs, outputs and geometries in ASCII format.</li> </ul> </li> </ul> <ul> <li><strong>Information on</strong>: <ul> <li>specialized abbreviations: <strong>EPR</strong> – Electron Paramagnetic Resonance, <strong>CW</strong> – Continuous Wave EPR, <strong>ESE</strong> – Electron Spin Echo detected EPR, <strong>HYSCORE</strong> – HYperfine Sublevel CORrelation spectroscopy, <strong>ENDOR</strong> – Electron Nuclear DOuble Resonance spectroscopy, <strong>DFT </strong>– Density Functional Theory, <strong>CHA </strong>– Chabazite, zeolite topology.</li> <li>definitions of variables: <strong>Magnetic field, Temperature.</strong></li> <li>units of measurement: <strong>Gauss (G), K, degree (°), milliTesla (mT)</strong>.</li> <li>abbreviations: <strong>6MR, 8MR </strong>are the Cu docking sites; <strong>2Al-3NN</strong>, <strong>2Al-2NN</strong>, <strong>1Al</strong> are the different aluminium distributions analysed; <strong>1w</strong>, <strong>2w</strong>, <strong>3w, 4w</strong> indicates the number of water ligands considered in the models; <strong>eq</strong> and <strong>ax</strong> indicates equatorial and axial ligands. Periodic DFT computations with filename extension <strong>.f34</strong> include structural/symmetry information of optimized structure. Molecular cluster DFT computations with filename extension <strong>.in</strong>/<strong>.out</strong>/<strong>.xyz</strong> are inputs, outputs, and structure of cluster models.</li> </ul> </li> </ul>
Integrative structure determination of PTBP1-viral IRES complex in solution
<p>Ensemble structure model of the RNA-binding protein PTBP1 in complex with the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV) RNA and data underlying these models.</p> <ul> <li>Main ensemble based on all restraints (corresponding to Figure 2 in the associated paper)</li> <li>Ensemble obtained with only DEER distance distribution restraints corresponding to Figure S7(A) in the Supplementary Material of the associated paper</li> <li>Validation ensemble obtained with all restraints after removing the conformers of the main ensemble from the raw ensemble corresponding to Figure S7(B) inthe Supplementary Material of the associated paper</li> <li>Ensemble obtianed with all restraints by fitting populations with a non-negative linear least squares (NNLLSQ) approach corresponding to Figure S8(A) in ths Supplementary Material of the associated paper</li> <li>Primary DEER-EPR data underlying site-to-site distance distributions for 35 spin-label pairs and corresponding distanace distributions</li> <li>Small-angle neutron scattering (SANS) curves a two detector distances with corresponding resolution files and a small-angle x-ray scattering (SAXS) curve</li> <li>Restraint file for the ensemble fit with MMMx software, specifying the mean distances and standrad deviations of distance distributions that were also used for specifying lower and upper distance bounds in CYANA generation of the raw ensemble</li> <li>Source data for the figures in the associated paper</li> <li>Source data for the tables in the associated paper</li> </ul> <p>All ensembles are ZIP files containing single PDB files for all conformers and an ensemble specification that reports populations for all conformers.</p>
Critical Assessment of automated Structure Determination of Proteins by NMR
<p>The community-wide initiative "Critical Assessment of Automated Structure Determination of Proteins by NMR (<strong>CASD-NMR</strong>)" was launched in 2009 to to evaluate the ability of automated methods to produce 3D protein structures from NMR data that closely match structures manually determined by experts.</p> <p>This dataset includes all the experimental data made available to the participants of CASD-NMR in the two completed rounds of the initiative.</p> <p>Also refer to http://www-nmr.cabm.rutgers.edu/blindtest/blind.html for additional details, including first release date and link to each final PDB entry</p>
Diffraction data underpinning the structure of StayGold determined by X-ray crystallography (PDB code 8BXT)
<p>Raw diffraction data underpinning the crystal structure of StayGold fluorescent protein.</p> <p>This is the raw data underpinning PDB entry 8BXT.</p>
Structural equation modeling reveals determinants of fitness in a cooperatively breeding bird
<p>Even in well-studied organisms, it is often challenging to uncover the social and environmental determinants of fitness. Typically, fitness is determined by a variety of factors that act in concert, thus forming complex networks of causal relationships. Moreover, even strong correlations between social and environmental conditions and fitness components may not be indicative of direct causal links, as the measured variables may be driven by unmeasured (or unmeasurable) causal factors. Standard statistical approaches, like multiple regression analyses, are not suited for disentangling such complex causal relationships. Here, we apply structural equation modeling (SEM), a technique that is specifically designed to reveal causal relationships between variables, and which also allows to include hypothetical causal factors. Therefore, SEM seems ideally suited for comparing alternative hypotheses on how fitness differences arise from differences in social and environmental factors. We apply SEM to a rich data set collected in a long-term study on the Seychelles warbler (Acrocephalus seychellensis), a bird species with facultatively cooperative breeding and a high rate of extra-group paternity. Our analysis reveals that the presence of helpers has a positive effect on the reproductive output of both female and male breeders. In contrast, per capita food availability does not affect reproductive output. Our analysis does not confirm earlier suggestions on other species that the presence of helpers has a negative effect on the reproductive output of male breeders. As such, both female and male breeders should tolerate helpers in their territories, irrespective of food availability.</p>
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Tree size, microhabitat diversity and landscape structure determine the value of isolated trees for bats in farmland
<p>Isolated trees are increasingly recognised as playing a vital role in supporting biodiversity in agricultural landscapes, yet their occurrence has declined substantially in recent decades. Most bats in Europe are tree-dependent species that rely on woody elements in order to persist in farmlands. However, isolated trees are rarely considered in conservation programs and landscape planning. Further investigations are therefore urgently required to identify which trees – based on both their intrinsic characteristics and their location in the landscape – are particularly important for bats. We acoustically surveyed 57 isolated trees for bats to determine the relative and interactive effects of size, tree-related microhabitat (TreM) diversity and surrounding landscape context on bat activity. Tall trees with large diameter at breast height and crown area positively influenced the activity of <em>Pipistrellus pipistrellus</em> and small Myotis bats (<em>Myotis</em> spp.) while smaller and thinner trees favoured <em>M. myotis</em> activity. The diversity of TreMs that can be used as roosts had a positive effect on (i) <em>Barbastella barbastellus</em> activity only when trees were relatively close (10% within 100 radius scale). The potential benefits of isolated trees for bats result from ecological mechanisms operating at both tree and landscape scales, underlining the crucial need for implementing a multi-scale approach in conservation programs. Maintaining the largest and most TreM-diversified trees located in the most heterogeneous agricultural landscapes will provide the greatest benefits.</p>
Research data in support of: An Interplay of Mechanical and Structural Properties of DNA Determines Its Electrostatic Interactions with Lipids
<p>The data collected and reported for the publication entitled: An Interplay of Mechanical and Structural Properties of DNA Determines Its Electrostatic Interactions with Lipids. by Diana Morzy et al.</p> <p>Data is divided by the technique used, with folders named accordingly. Each dataset has a readme file, explaining the basic technical details, as well as how to open each file type.</p> <p>Please do not hesitate to contact the corresponding author (MMCB) for further details.</p>
Crystal structures determination of CtUGGT-N aka CtUGGT S180C:T742C
<p>Two crystal structures of the double Cys mutant <em>Ct</em>UGGT-N <em>aka</em> <em>Ct</em>UGGT S180C:T742C have been determined by X-ray crystallography. The trigonal one, in space group P3<sub>2</sub>12 was determined at 4.7 Å resolution by molecular replacement using PDB ID 5NV4 as a search model, against the data collected by Mario Hensen and Roberta Ibba on I24@Diamond on 08.08.2018. The orthorhombic one, in space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>, was determined to 4.6 Å resolution by molecular replacement using the P3<sub>2</sub>12 <em>Ct</em>UGGT-N model as a search model, against the data collected by Pietro Roversi and Roberta Ibba on I03@Diamond on 05.05.2018. Both structures show the disulphide bridge across the engineered double mutation S180C:T742C, and the TRXL1 and TRXL3 domains clamped shut. In the P3<sub>2</sub>12 form the orientation of TRXL2 with respect to the rest of the protein is the most opened ever observed so far (a rotation of 60 degrees away from the TRXL2 in PDB ID). The orthorhombic form proves that the clamped shut structure (<em>Ct</em>UGGT-N P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>) is compatible with the bent shut structure (<em>Ct</em>UGGT-H, P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>, PDB ID 5NV) <em>i.e.</em> both clamping and bending movements can close at the same time. A quadruple <em>Ct</em>UGGT mutant, containing both D611C:G1050C and S180C:T742C, should be feasible and its human UGGT1 equivalent could provide the best rigidification of the human structure conceivable so far.</p>
Example structure of data sent from a citizen science platformback to a collection management system, multi-determined case
<p>Illustrative example of data format following Darwin Core sent back from a citizen science platform to the relevant collection management system. Multi-determined herbarium sheet case : http://coldb.mnhn.fr/catalognumber/mnhn/p/p01978557</p> <p>Illustration of the milestone28 document, worpackage 5.2 of the ICEDIG project.</p>
WASHTREET. Application of Structure from Motion (SfM) photogrammetric technique to determine surface elevations in an urban drainage physical model.
<p><strong>WASHTREET</strong><strong> - </strong><strong>Application of Structure from Motion (SfM) photogrammetric technique to determine surface elevations in an urban drainage physical model.</strong></p> <p>This dataset contains raw data and surface elevations results from the application of the Structure from Motion (SfM) photogrammetric technique in a 36 m<sup>2</sup> full-scale urban drainage physical model, which is placed in the Hydraulic Laboratory of the Centre for Technological Innovation in Construction and Civil Engineering (CITEEC) at the University of A Coruña (Spain). This work is part of the <a href="https://zenodo.org/communities/washtreet">WASHTREET project</a>, where a series of high-resolution experiments were performed measuring urban surface wash-off and sediment transport through gully pots and pipes under laboratory-controlled conditions. The accurately measurement of the surface elevations is needed for a proper representation of surface flow, which is key in the detachment and transport of solids in the model surface. The dataset was used in the work developed in Naves et al. (2019) (DOI: <a href="https://doi.org/10.1016/j.jhydrol.2019.05.003">https://doi.org/10.1016/j.jhydrol.2019.05.003</a>)</p> <p>A detailed description of experimental procedure and data collected can be consulted in ‘<em>1_ExperimentalProcedure.pdf’</em>. Raw images taken as input for the SfM software are included in ‘<em>2_RawImages.zip’</em>. Then, the point cloud resulted is provided in ‘<em>3_SFM_RawPointCloud.ply</em>’. This point cloud was processed and the final elevation map with a resolution of 5 mm is included in ‘<em>4_SfM_ElevationMap(m).xyz</em>’.</p> <p>Further details of the physical model and hydraulic and sediment transport experiments can be consulted in the dataset <a href="http://doi.org/10.5281/zenodo.3233918"><em>WASHTREET - Hydraulic, wash-off and sediment transport experimental data</em></a>. In addition, raw data and runoff velocities results obtained using seeded and unseeded Particle Image Velocimetry (PIV) techniques are provided in the dataset <a href="http://www.doi.org/10.5281/zenodo.3239401">WASHTREET - PIV data</a>.</p> <p>The WASHTREET project is being developed in the scope of the PhD thesis of the first author, which is in receipt of a Spanish Ministry of Science, Innovation and Universities predoctoral grant [FPU14/01778]. The project also receive funding from the Spanish Ministry of Science, Innovation and Universities under POREDRAIN project RTI2018-094217-B-C33 (MINECO/FEDER-EU)</p> <p>Derived publications:</p> <ul> <li>Naves, J., Anta, J., Puertas, J., Regueiro-Picallo, M., & Suárez, J. (2019). Using a 2D shallow water model to assess Large-Scale Particle Image Velocimetry (LSPIV) and Structure from Motion (SfM) techniques in a street-scale urban drainage physical model. <em>Journal of Hydrology</em>, <em>575</em>, 54-65. <a href="https://doi.org/10.1016/j.jhydrol.2019.05.003">https://doi.org/10.1016/j.jhydrol.2019.05.003</a></li> <li>Naves, J., Anta, J., Suárez, J., & Puertas, J. (2020). Hydraulic, wash-off and sediment transport experiments in a full-scale urban drainage physical model. <em>Scientific Data</em>, <em>7</em>(1), 1-13.<a href="http://doi.org/10.1038/s41597-020-0384-z"> https://doi.org/10.1038/s41597-020-0384-z</a></li> </ul>
Fig. 2 in CCDC 204627: Experimental Crystal Structure Determination
Fig. 2. Thaumastosaurus sulcatus, partial right squamosal (lamella alaris squamosi), paratype (MSUVP 2021). Late Eocene "Rodent Bed" of the Hordle Cliff Locality, Hampshire, England. A, B. Lateral views. C. Medial view.
Fig. 1 in CCDC 204627: Experimental Crystal Structure Determination
Fig. 1. Thaumastosaurus sulcatus sp. nov., partial left maxilla, holotype (MSUVP 1976), Late Eocene "Mammal Bed", Hordle Cliff Locality, Hampshire, England. A, B. Lingual view. C. Enlarged view of tooth indicated by arrow at B. D, E. Labial views.
Fig. 2 in CCDC 651299: Experimental Crystal Structure Determination
Fig. 2. Nemestrinid fly Ahirmoneura neimengguensis Zhang, Yang, and Ren, gen. et sp. nov., holotype CNU−B−NN2006003, from the Daohugou Village, Inner Mongolia, China; Aalenian−Bajocian Jiulongshan Formation, Middle Jurassic. A. Body with wings photograph in dorsal view. B. Camera lucida drawing, based on the original photograph, in dorsal view. C. Camera lucida drawing, base of vein C details.
Fig. 1 in CCDC 651299: Experimental Crystal Structure Determination
Fig. 1. Location of the type locality of Ahirmoneura neimengguensis Zhang, Yang, and Ren, gen. et sp. nov. Daohugou Village, Shantou Township, Ningcheng County, Inner Mongolia, China. A. Outlined location. B. Detailed location. Abbreviations: Chc, Changchougou Formation; Chch, Chuanlinggou Formation; Chd, Dahongyu Formation; Cht, Tuanshanzi Formation; J2j, Jiulongshan Formation; J2t, Tiaojishan Formation; Ky, Yixian Formation; Q, Quaternary; Dms, Dalaiyingzi erosion surface; Mgn, Maanshan gneiss.
Fig. 4 in CCDC 615855: Experimental Crystal Structure Determination
Fig. 4. Distribution of Cenozoic marsupials in North−Africa and Eurasia. Peradectidae: 1, Chambi, Tunisia (early Eocene); 2, Fayum, Egypt (early Oligocene); 3, Taqah, Oman (early Oligocene); 4, Li Basin, Thailand (middle Miocene); 5, Sonlinzhuang, China (early Miocene). Herpetotheriidae: 6, Zaissan Basin, Kazakhstan (late Eocene – early Oligocene); 7, Vastan lignite mine, India (early Eocene); 8, Bugti Hills, Pakistan (early Oligocene); 9, Shanghuang fissure fillings B and C, Jiangsu, China (middle Eocene). Localities that yielded remains of disputable marsupial affinity (see text): 7, Vastan lignite mine, India (early Eocene); 10, Kartal Formation, Turkey (Eocene).
Fig. 1 in CCDC 615855: Experimental Crystal Structure Determination
Fig. 1. Geographic location of the marsupial−bearing locality of Paali Nala−DBC2 (denoted by an asterisk), the lowermost part of the Chitarwata Formation (Bugti Member, Oligocene), in the Bugti Hills (Central Pakistan, eastern Balochistan).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.
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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.