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715 results for “folding”
Aparat mieszkowy // Folding camera
Aparat mieszkowy który należał do pierwszego poznańskiego tramwajarza. Posiada plakietkę słynnego dystrybutora Kazimierza Gregera, który sam był fotografem. Podczas powstania wielkopolskiego dokumentował to wydarzenie historyczne. Source: Objaverse 1.0 / Sketchfab
Dispersion of the folded waveguide and output power of the Travelling Wave Tube amplifier in W band.
<p>Datasets of Dispersion of the folded waveguide and beam line (Fig1) and output power (Fig 2) of the paper "Fabrication of W-band TWT for 5G small cells backhaul" for IVEC 2017.</p> <p>Both MAGIC3D and CST- Particle StudioS were used for particle in cell simulations of the whole amplifier. Both the the simulators confirmed more that than 40 W on the full band 923 – 95 GHz as shown in Fig.2 The simulations included the couplers and the RF windows. Specific simulations for the design of the electron optics, the windows and the collector were performed.</p> <p> </p> <p> </p>
Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species
<p>Dorsal view of the reconstructed cerebral hemispheres of 34 different primate species.</p> <p>This figure is from our open access paper:</p> <p>Heuer, K., Gulban, O. F., Bazin, P.-L., Osoianu, A., Valabregue, R., Santin, M., Herbin, M., & Toro, R. (2018). Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 33 primate species. bioRxiv. <a href="https://doi.org/10.1101/379750">https://doi.org/10.1101/379750</a>. </p> <p>Abstract</p> <p>We present a comparative analysis of cerebral size and neocortical folding. Magnetic resonance imaging data was collected from 66 individuals belonging to 34 different primate species. We measured several neocortical folding parameters and studied their evolution using phylogenetic comparative methods. Our results suggest that the most likely model is one where phenotypical differences vary randomly through evolution (the Brownian Motion model). We present estimations of the ancestral primate phenotypes as well as estimations of the rates of phenotypic change.</p> <p> </p>
Supporting dataset underlying "Human cortical folding across regions within individual brains follows universal scaling law"
<p>This is the dataset underlying "Human cortical folding across regions within individual brains follows universal scaling law", the matlab scripts enable the user to direct reproduce the figures in the paper.</p> <p>2020 update: The matlab code for extraction of lobe-wise measures from Freesurfer subjects is now published on <a href="https://doi.org/10.5281/zenodo.3608675">Zenodo</a> and <a href="https://github.com/cnnp-lab/CorticalFoldingAnalysisTools">Github</a>.</p>
Figure 3 in Two-fold increase in White Stork (Ciconia ciconia) population in Lithuania: a consequence of changing agriculture?
Figure 3. Distance from recorded White Stork nests to the nearest neighbouring nest.
Figure 2 in Two-fold increase in White Stork (Ciconia ciconia) population in Lithuania: a consequence of changing agriculture?
Figure 2. Distance from recorded White Stork nests to the nearest building.
Figure 1 in Two-fold increase in White Stork (Ciconia ciconia) population in Lithuania: a consequence of changing agriculture?
Figure 1. Distribution of densities of occupied White Stork nests and colonies in Lithuania.
Fig. 1 in Suraqalatia Brasieri Görmuş, Lawa & Nuaimy, 2017 (Larger Benthic Foraminifera; Suraqalatiidae N. Fam.) From The Late Maastrichtian Of The Tarbur Formation (Zagros Fold-Thrust-Belt) And Remarks On Dicyclina Munier-Chalmas, 1887
Fig. 1 Location map of the Naghan and Mandegan sections (B: from google maps).
Regional thermal history trends from the Idaho-Montana fold thrust belt using multiple low-T thermochronometers
<p><span>Low-temperature thermochronometric data can reveal the long-term evolution of erosion, uplift, and thrusting in fold-thrust-belts. We present results from central-Idaho and southwestern-Montana, where the close spatial overlap of the Sevier fold-thrust-belt and Laramide-style, basement-involved foreland uplifts signify a complex region with an unresolved, long-term tectono-thermal history. Inverse QTQt thermal-history modeling of new zircon (U-Th)/He (ZHe, n=106), and apatite (U-Th)/He dates (AHe, n=43) collected from hanging walls of major thrusts systems along a central-Idaho to southwestern-Montana transect, and apatite fission track (AFT) results from 6 basement samples, reveal regional thermal and spatial trends related to Sevier and Laramide orogenesis. Inverse modeling of foreland basement uplift samples suggest Phanerozoic exhumation initiated as early as ~80 Ma and continued through the early-Paleogene. Inverse modeling of interior Idaho fold-thrust-belt ZHe samples documents mid-Cretaceous cooling at ~125 Ma in the Lost River Range (western transect), and a younger cooling episode in the Lemhi Arch region (mid-transect) from as early as ~100 Ma through the late-Paleogene. This cooling in the Lemhi Arch temporally overlaps with cooling in southwestern-Montana’s basement-cored uplifts, which we interpret as roughly synchronous exhumation related to contractional tectonics and post-orogenic collapse. These data and models, integrated with independent timing constraints from foreland basin strata and previously published thermochronometric results, suggests that mid-Cretaceous deformation of southwestern-Montana’s basement-cored uplifts was low-magnitude and preceded tectonism along the classic California-Wyoming Laramide “corridor”. In contrast, late-Cretaceous and Paleogene thrust-related exhumation was more significant and largely complete by the Eocene. The basement-involved deformation was contemporaneous with and younger than along-strike Sevier belt thrusting in</span><span> </span><span>central-Idaho. </span></p>
Rainout shelter in a Walnut-Sorghum agroforestry system with the tarpaulin folded
<p>Picture of a rainout shelter with a fixed tunnel structure, a folded tarpaulin, and gutters to evacuate water, used in a 28 year old agroforestry system with walnut trees and arable crops in plot A2 of Domaine de Restinclières (coordinates: 43.704274 , 3.860958). Picture taken on 2023-06-29</p>
Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny
An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Brachiopoda+Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. Yet, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a 'total evidence' philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.
Folding-unfolding asymmetry and a RetroFold computational algorithm
<p>We treat protein folding as the molecular self-assembly, while unfolding is viewed as disassembly. Self-assembly and disassembly (fracture) are two opposite non-equilibrium dynamic processes; however, they cannot be converted to each other by a simple time variable reversal. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture may be a constant rate process as the driving force is opposed by damping. Typically, protein folding takes two orders of magnitude longer time than unfolding, and it consumes a lot of computational resources to model folding. Based on energy dissipation rates, we suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modeling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns while unfolding (denaturation) takes only about 5.0 ns, and therefore, fewer computational resources are needed for its simulation. This "RetroFold" approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.</p>
Tissue-engineered vocal fold replacement in swine: Methods for functional and structural analysis.
<p>S2 Data. 5534 pig squeal events investigated in this study, provided in a folder structure sorted by pigs, pre- / post-treatment and recording date as .wav files.</p>
Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence
<p>Dataset for paper: Z. Qin, L. Wu, H. Sun, S. Huo, T. Ma, E. Lim, P.-Y. Chen, B. Marelli, M.J. Buehler, Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence, Extreme Mechanics Letters, Vol. 36, 100652, 2020. <a href="https://doi.org/10.1016/j.eml.2020.100652">https://doi.org/10.1016/j.eml.2020.100652</a>.</p> <p>Code: https://github.com/lamm-mit/MNNN/ </p>
Comparative Study of Molecular Mechanics Force Fields for β-peptidic Foldamers: Folding and Self-Association
<p>Molecular dynamics simulation input files and Python scripts used for preparing the runs and analyzing the trajectories.</p>
Memory kernel extraction and mean first-passage time for fast-folding proteins (Q - trajectories)
<p>Fraction of native contacts reaction coordinate (Q) trajectories for the 8 proteins that appear in the Dalton et. al. PNAS 2023. For the original all-atom data from which the Q(t) were calculated, contact the group of David E. Shaw at Shaw Research (see the paper - K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, How fast-folding proteins fold. Science 334, 517–520 (2011))</p> <p>Data contains:<br> - Q(t) trajectories for 8 proteins <br> - Corresponding free energy profiles<br> <br> Example analysis codes (written in C++) are included for:<br> - Free energy calculation<br> - Mean first-passage times<br> - Velocity-velocity correlation function and position-force correlation function calculations, needed for memory kernel extraction<br> - Memory kernel extraction (see Ayaz et. al. PNAS 2021)</p>
Inverse folding for antibody sequence design using deep learning
<p>Model weights of the <a href="https://arxiv.org/abs/2310.19513">AbMPNN model (arXiv:2310.19513)</a> presented at the <a href="https://icml-compbio.github.io/">2023 ICML Workshop on Computational Biology</a>, and csv files with the split between train, test and validation across the <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/">SAbDab</a> and <a href="https://zenodo.org/record/7258553">ImmuneBuilder</a> datasets.</p><p>This model is based on <a href="https://www.biorxiv.org/content/10.1101/2022.06.03.494563v1">ProteinMPNN</a> and can be run using the corresponding code: <a href="https://github.com/dauparas/ProteinMPNN">https://github.com/dauparas/ProteinMPNN</a>.</p>
The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea
<p>The shown folders contain the molecular dynamics simulation data, used tools, and scripts for the study of "The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea". The simulation data includes the force field and simulation setup for both AWSEM-MD and atomistic MD in OpenMM, the data analyses that are presented in the related paper, and the representative conformations from each simulation. Due to the large file size, the original trajectory files are available upon separate request.</p> <p>The tools and scripts folder includes the specific version of the AWSEM model, implemented in the LAMMPS package, and the scripts used to analyze the simulations. For detailed instructions on using AWSEM model, please refer to our Github: <a href="https://github.com/adavtyan/awsemmd/wiki">https://github.com/adavtyan/awsemmd/wiki</a>. For detailed instructions on using the LAMMPS package, please refer to <a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>. For detailed instructions on using the OpenMM package, please refer to <a href="https://openmm.org/">https://openmm.org/</a>. For any questions about using this data repository, please feel free to contact the author.</p> <p> </p> <p> </p>
Dataset for Peptide binder design with inverse folding and protein structure prediction
<p>Dataset for a paper on peptide design</p> <p> </p> <p><br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)</p> <p> </p> <p> </p>
095 Klappsonnenuhr / Folding sundial
# **Fundort / Site** Dülmen, Kreis Coesfeld (Germany) # **Fundumstände / Circumstances of discovery** Stadt / City 30. März 2016 ## **Objekt / Object** Elefantenelfenbein / Elephant ivory Länge / Length: 3,6 cm Breite / Width: 2,9 cm Höhe / Height: 0,25 cm # **Datierung / Dating** 1600–1650 Frühneuzeit / Early Modern Age Barock / Baroque # **Fundverbleib / Repository** Zentrales Fundarchiv der LWL-Archäologie für Westfalen, Münster # **3-D-Modell / 3D model** Fotokamera / Photo camera: Nikon D850 Modellberechnung / Model processing: Reality Capture Modell / Model: LWL-Archäologie für Westfalen/Florian Westphal Source: Objaverse 1.0 / Sketchfab
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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.
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DANDI Archive for NWB 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.