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456 results for “motifs”
Do expectation-maximization algorithms have to make use of 'background distribution' for de novo motif search?
<p>Data for the article "Do expectation-maximization algorithms have to make use of ‘background distribution’ for de novo motif search?". The preprint is live on Research Square (DOI: <a href="https://www.researchsquare.com/article/rs-1725972/v2">10.21203/rs.3.rs-1725972/v2</a>).</p>
A twin capital with decoration of plant motifs
The presented twin capital is one of four such column capitals discovered over the years 1947–1953 during archaeological research carried out while reconstructing the eastern wing of the monastery. It is considered to be one of the best examples of Romanesque masonry in Poland. It comes from the first monastic complex in Tyniec. However, researchers do not agree whether the twin capitals were originally located in the church or in the cloisters. The twin capital has the shape of two truncated pyramids turned upside down and connected in the upper part by a high cuboidal abacus. Due to some damage and numerous abrasions on the surface of the capital, the decorations are barely visible. Recognisable elements include a bipartite ribbon and plant motifs in the form of a trefoil and a half-palmette. 4th quarter of the 11th century, Tyniec Museum of the Benedictine Abbey in Tyniec Inventory number: DA/163/2012 Source: Objaverse 1.0 / Sketchfab
Vessel with Frog Motif, 1st C BCE - 1st C CE
Thai Vessel with Frog Motif, 1st century BCE - 1st century CE, now in the collection of the Minneapolis Institute of Art. More information at https://collections.artsmia.org/art/99897/vessel-with-frog-motif-thailand Source: Objaverse 1.0 / Sketchfab
Half of a twin capital with a motif of hearts
Half of a twin capital with a motif of three hearts The presented capital is one of seven halves of twin capitals uncovered during the years 1947–1953 by archaeologists during research in the course of reconstructing eastern wing of the monastery. The head is considered as one of the best examples of Romanesque masonry in Poland. It comes from the first monastic complex in Tyniec. However, researchers do not agree whether the twin capitals discovered in Tyniec were originally located in the church or in the cloisters. The capital has the shape of a truncated pyramid turned upside down. The obverse is filled by ornamentation consisting of little stalks, but the pattern is barely discernible due to some defects and abrasion of the surface. On the reverse, there is decoration in the form of palmettes enclosed by a floral scroll, which forms the shape of three large hearts. 4th quarter of the 11th century, Tyniec Museum of the Benedictine Abbey in Tyniec Inventory number: DA/168/2012 Source: Objaverse 1.0 / Sketchfab
Snake Motif Incised Pottery Fragment
A large pottery fragment with a repeating snake or vine pattern. Coles Creek Period, 700 - 1200 CE. Found in Tensas Parish, LA. 2022 PS_05 Source: Objaverse 1.0 / Sketchfab
A twin capital with decoration of plant motifs
The presented twin capital is one of four such column capitals discovered over the years 1947–1953 during archaeological research carried out while reconstructing the eastern wing of the monastery. The double capitals in the collections of the Museum of the Benedictine Abbey in Tyniec are among the best examples of Romanesque masonry in Poland. They come from the first monastic foundation in Tyniec. However, researchers do not agree whether the twin capitals were originally located in the church or in the cloisters. The fully preserved twin capital has the shape of two truncated pyramids turned upside down and connected in the upper part by a high cuboidal abacus. At the base, both segments are surrounded by an echinus. The surface of the capitals is covered by clearly visible plant motif decoration consisting of large, deeply carved and sharply outlined leaves. 11th/12th century, Tyniec Museum of the Benedictine Abbey in Tyniec Inventory number: DA/153/2012 Source: Objaverse 1.0 / Sketchfab
Chinese jar with dragon-and-tiger motif
Ceramic with black glaze. Dated Eastern Han dynasty (25-220). Zhejiang Provincial Museum Gushan Branch, Hangzhou, China. At the shoulder of the long-neck jar are two humanoid figures with their animal campanions--a dragon (with horns) and a tiger (no horns)--and two winged creatures (wild geese or cranes?) among them, all marching in a counter-clockwise direction around the neck of the jar. Attached to the neck are two acrobats, three projected animal heads (tigers or monkeys?), and at least five small birds (some broken or missing). Source: Objaverse 1.0 / Sketchfab
Vamos motif set v2.0
<p>This is an updated motif set on 953,875 loci including both VNTR and STR loci. This uses an updated clustering algorithm to ensure that redundant, repetitive motifs are not included.</p>
Photoenzymatic asymmetric incorporation of fluorinated motifs into olefins
<p>Enzymes capable of assimilating fluorinated feedstocks are scarce, which poses a challenge for the biosynthesis of fluorinated compounds used in pharmaceuticals, agrochemicals, and materials. We develop a photoenzymatic hydrofluoroalkylation that adeptly integrates fluorinated motifs into olefins. The photoinduced promiscuity of flavin-dependent ene-reductases enables generation of carbon-centered radicals from iodinated fluoroalkanes, which are directed by the photoenzyme to engage enantioselectively with olefins. This approach facilitates stereocontrol through interaction between a singular fluorinated unit and the enzyme, securing high enantioselectivity at β-, γ-, or δ-positions of fluorinated groups via enzymatic hydrogen atom transfer, a process notably challenging with conventional chemocatalysis. This work advances enzymatic strategies for integrating fluorinated chemical feedstocks and opens new avenues for asymmetric synthesis of fluorinated compounds.</p>
Fig. 3 in A Ladybird (Coleoptera: Coccinellidae) Motif In Crocheted Towel End Lace: The First Example Of Cultural Entomology In Latvia
Fig. 3. Adalia bipunctata (Linneus, 1758) – The Latvian national insect.
Automated recognition of RNA structure motifs by their SHAPE data signatures
<p>Datasets, code and results supporting the manuscript:</p> <p>Radecki P., Ledda M. & Aviran S., Automated recognition of RNA structure motifs by their SHAPE data signatures</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
<p>This repository contains the representative structures of the 20 clusters obtained, which constitute the “MD-adapted structure ensemble”: i.e., sets of atomic coordinates that capture the flexibility and the pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n7x.pdb?versionId=310a80f6-aa64-445d-8641-45faf9f1ac03">ensemble_MD_2n7x.pdb</a>) and Rbfox/pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n82.pdb?versionId=82d7afcb-8a92-4daa-8150-789dbd7b2474">ensemble_MD_2n82.pdb</a>) conformers suggested by MD simulations while still retaining the highest possible level of agreement with the primary NMR data.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.-PART 8
<p>Simulations of the miR20b RNA with the Case vdW modification to amber force field and OPC water molecules.</p>
[Dataset] Lattice Metamaterials with Mesoscale Motifs: Exploration of Property Charts by Bayesian Optimisation
<p>[Dataset] Lattice Metamaterials with Mesoscale Motifs: Exploration of Property Charts by Bayesian Optimisation</p> <p>Roman Kulagin*, Patrick Reiser, Kyryl Truskovskyi, Arnd Koeppe, Yan Beygelzimer, Yuri Estrin, Pascal Friederich, Peter Gumbsch</p> <p>[*] Dr. R. Kulagin, Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. E-Mail: roman.kulagin@kit.edu</p> <p>Dr. Patrick Reiser, Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Engler-Bunte-Ring 8, 76131 Karlsruhe, Germany.</p> <p>Kyryl Truskovskyi, Georgian, Toronto, Canada</p> <p>Dr. Arnd Koeppe, Institute for Applied Materials (IAM-MMS), Karlsruhe Institute of Technology, Straße am Forum 7, 76131 Karlsruhe, Germany.</p> <p>Prof. Pascal Friederich, Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Engler-Bunte-Ring 8, 76131 Karlsruhe, Germany.</p> <p>Prof. Y. Beygelzimer, Donetsk Institute for Physics and Engineering named after A.A. Galkin, National Academy of Sciences of Ukraine, Nauki ave., 46, 03028 Kyiv, Ukraine.</p> <p>Prof. Y. Estrin, Department of Materials Science and Engineering, Monash University, 22 Alliance Lane, Clayton 3800, Australia; Department of Mechanical Engineering, The University of Western Australia, Crawley 6009, Australia.</p> <p>Prof. P. Gumbsch, Institute for Applied Materials, Karlsruhe Institute of Technology, Straße am Forum 7, 76131, Karlsruhe, Germany; Fraunhofer Institute for Mechanics of Materials, Freiburg, Wöhlerstraße 11, 79108 Freiburg, Germany.</p> <p>Part of the work was supported by the German Research Foundation (DFG, Deutsche Forschungsgemeinschaft) through the POLiS Cluster of Excellence (grant no. UP 33/1) under project ID 390874152 and by the Helmholtz association under the KNMFi program (grant no. 43.31.01).</p>
Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
<p>To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.</p>
Frozen feather and motif files for Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue.
<p>Frozen feather and motif files for manuscript "Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue" by Espinoza DA, et al. Data was downloaded from cisTarget database from aertslab.org.</p>
FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation
<p>Amyloid deposition of the microtubule-associated protein tau is a unifying theme in a multitude of neurodegenerative diseases. Disease-associated missense mutations in tau are associated with frontotemporal dementia (FTD) and enhance tau aggregation propensity. However, the molecular mechanism of how mutations in tau promote tau assembly into amyloids remains obscure. There is a need to understand how tau folds into pathogenic conformations to cause disease. Here we describe the structural mechanism for how an FTD-tau S320F mutation drives spontaneous aggregation. We use recombinant protein and synthetic peptide systems, computational modeling, cross-linking mass spectrometry, and cell models to investigate the mechanism of spontaneous aggregation of the S320F FTD-tau mutant. We discover that the S320F mutation drives the stabilization of a local hydrophobic cluster which allosterically exposes the <sup>306</sup>VQIVYK<sup>311</sup> amyloid motif. We identify a suppressor mutation that reverses the S320F aggregation phenotype through the reduction of S320F-based hydrophobic clustering <em>in vitro</em> and in cells. Finally, we use structure-based computational design to engineer rapidly aggregating tau sequences by optimizing nonpolar clusters in proximity to the S320 site revealing a new principle governing the regulation of tau aggregation. We uncover a mechanism for regulating aggregation that balances transient nonpolar contacts within local protective structures or in longer-range interactions that sequester amyloid motifs. The introduction of a pathogenic mutation redistributes these transient interactions to drive spontaneous aggregation. We anticipate that more profound knowledge of this process will permit control of tau aggregation into discrete structural polymorphs to aid the design of reagents that can detect disease-specific tau conformations.</p>
Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase
<p>We have provided all the necessary files, outputs, as well as the ReadMe file for this work to be redone.</p>
Geometrical frustration and incommensurate magnetic order in Na3RuO4 with two triangular motifs
<p>Auxiliary data for the frustrated magnet Na3RuO4: magnetic susceptibility, specific heat, lattice parameters, magnetic moments, and the results of DFT calculations for the magnetic exchange couplings</p>
Mapped data: Transcription factor stoichiometry, motif affinity and syntax regulate single cell chromatin dynamics during fibroblast reprogramming to pluripotency
<p>This record contains mapped sequencing data for the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen <em>et al</em>. It contains single-cell RNA-seq (scRNA) and single-cell ATAC-seq (scATAC) data from a time course of human dermal fibroblasts induced with Yamanaka factors OSKM using a Sendai virus based delivery system. The scRNA and scATAC data is performed at days 0, 2, 4, 6, 8, 10, 12, 14 and the final iPSCs. The experiment was re-performed and single-nucleus multiome (ATAC+RNA) was collected on days 1 and 2. </p> <p>The data is as follows:</p> <p><strong>scATAC</strong>: We used Chromap (commit <a href="https://github.com/haowenz/chromap/tree/6e97125b9">https://github.com/haowenz/chromap/tree/6e97125b9</a>, <a href="https://doi.org/10.1038/s41467-021-26865-w">https://doi.org/10.1038/s41467-021-26865-w</a>) to perform barcode correction, alignment and filtering for each of our samples. The corresponding fragment files (tab separated file containing mapped fragments with columns: chr, start, end, barcode, number of reads) and their tabix indices are available for each sample.</p> <p><strong>scRNA</strong>: We used cellranger v6.0.2 for read mapping and quantification to obtain the counts matrix. We used the GRCh38 2020-A reference. For each sample, the raw and filtered counts matrices are provided. E.g. `D0/raw_feature_bc_matrix.h5` contains an HDF5 object containing gene counts for each barcode and associated metadata for the Day 0 sample. Similarly, the files in `D0/raw_feature_bc_matrix/` contain the same gene x barcode matrix, with the counts matrix in Matrix Market format (`matrix.mtx.gz`), and gene (`features.tsv.gz`) and barcode names (`barcodes.tsv.gz`). </p> <p><strong>multiome</strong>: The ATAC and RNA components are separately processed using the same tools as mentioned above for scATAC and scRNA. Outputs are in the `snATAC` and `snRNA` subdirectories respectively. In addition, the `ATAC.RNA.bc.map.tsv` file contains a map to link snATAC barcodes to snRNA barcodes. </p>
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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)
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.