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534 results for “scaffold”
Baseline assemblies for "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads" protocol
<p>ntLink is a flexible <em>de novo</em> genome scaffolding toolkit which can be run in various modes depending on the desired user output, with multiple new functionalities recently introduced. Here, we provide the baseline assembly datasets used in the ntLink protocol paper "ntLink: a toolkit for <em>de novo </em>genome assembly scaffolding and mapping using long reads". The provided assemblies are ABySS (short-read) and Flye (long-read) assemblies of <em>Caenorhabditis elegans </em>genome sequencing data. The ABySS (v2.1.4) assembly utilized paired-end short reads (accession DRR008444), and was run with the following parameters: k=64 l=40 s=1000 q=15 B=10G j=8 kc=3 H=4 S=1000-10000 N=9.The <em>C. elegans</em> Flye (v2.5) assembly was run using Oxford Nanopore long reads (accession SRR10028109) and the following parameters: --nano-raw SRR10028109.fastq -g100m -t48.</p>
One scaffold, two conformations: The ring-flip of the messenger InsP8 occurs under cytosolic conditions
<p>Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” axial conformation. Using <sup>13</sup>C-labeled InsPs / PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger InsP<sub>8</sub> readily adopts both conformations at physiological conditions. Environmental factors - such as pH, metal cation composition, and temperature - strongly influence the conformational equilibrium. Thermodynamic data revealed that the transition of InsP<sub>8</sub> from the equatorial to the axial conformation is, in fact, an exothermic process. The speciation of InsPs and PP-InsPs also affects their interaction with protein binding partners; addition of Mg<sup>2+</sup> decreased the binding constant K<sub>d</sub> of InsP<sub>8</sub> to an SPX protein domain. The results illustrate that PP-InsP speciation reacts very sensitively to solution conditions, suggesting it might act as an environment-dependent molecular switch.</p>
AlphaFold-Multimer (v3) model of a complex of Protein Phosphatase 2A catalytic subunit (PP2A/C), PP2A scaffold subunit (PP2A/A), the B55alpha substrate binding subunit, and FAM122A, a PP2A inhibitor protein.
<p>AlphaFold-Multimer (v3) model structure of a complex of Protein Phosphatase 2A catalytic subunit (PP2A/C), PP2A scaffold subunit (PP2A/A), the B55alpha substrate binding subunit, and FAM122A, a PP2A inhibitor protein. The protein sequences were obtained from UniProt:</p> <p>P67775 · PP2AA_HUMAN</p> <p>P30153 · 2AAA_HUMAN</p> <p>P63151 · 2ABA_HUMAN</p> <p>Q96E09 · PBIR1_HUMAN</p> <p>Coordinates are in mmCIF format. A PyMOL session file is included.</p> <p>Modeling was performed with AlphaFold-Multimer v3, downloaded from DeepMind's github. Structure prediction was performed without templates. The model was relaxed with Amber.</p> <p>FAM122A binds using a short linear motif (SLIM) (residues 84-89) first identified in RBL1 (p107) (Fowle et al., eLife, <a href="https://doi.org/10.7554/eLife.63181">https://doi.org/10.7554/eLife.63181</a> in the form of a short alpha helix (residues 84-92). This is followed by a long alpha helix (residues 96-122) which blocks access to the active site of the catalytic subunit. There are further contacts of FAM122A (residues 150-170) with one of the beta sheets of the B55alpha beta propeller domain. FAM122A regulates PP2A activity during the cell cycle.</p> <p> </p>
Regenerative Collagen Scaffold for Breast Volume Restoration in Breast-Conserving Surgery
ClinicalTrials.gov study NCT07219316. IPD Sharing: YES. Countries: 1. Publications: 5.
Re-scaffolded genome and supertranscriptome of the strawberry poison frog (Oophaga pumilio)
<p>Re-scaffolded genome and SuperTranscriptome of<em> Oophaga pumilio</em></p> <p>Supplementary data to the article: "Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (<em>Oophaga pumilio</em>)"</p> <p> </p>
Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media
<p>Raw datasets and media accompanying the manuscript: <strong>Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles</strong>, published in ACS Sensors</p>
Currently available scaffolds and MMP cores in ChEMBL 20
<p>All target-based BM scaffolds (K<sub>i</sub>: 35,872; IC<sub>50</sub>: 74,379), CSKs (K<sub>i</sub>: 23,056; IC<sub>50</sub>: 49,216), MMP cores (K<sub>i</sub>: 42,104; IC<sub>50</sub>: 73,616), and retrosynthetic MMP cores (K<sub>i</sub>: 19,040; IC<sub>50</sub>: 32,382) for high confident bioactive compounds extracted from ChEMBL version 20 are provided herein. </p>
Women's subsistence networks scaffold cultural transmission among BaYaka foragers in the Congo Basin
<p><span>In hunter-gatherer societies, women's subsistence activities are crucial for food provisioning and children's social learning, but they are understudied relative to men's activities. To better understand the structure of women's foraging networks, we present data of 230 days focal-follows in a BaYaka community. To analyze these data, we develop a stochastic block model for repeat observations with uneven sampling. We find that women's subsistence networks are characterized by cooperation between kin, gender homophily, and mixed age-group composition. During early-childhood, individuals preferentially co-forage with adult kin, but those in middle-childhood and adolescence are likely to co-forage with non-kin peers, providing opportunities for horizontal learning. By quantifying the probability of co-foraging ties across age-classes and relatedness levels, our findings provide insights into the scope for social learning during women's subsistence activities in a real-world foraging population and provide ground-truth values for key parameters used in formal models of cumulative cultural change.</span></p>
Input parameters and output trajectory files for manuscript "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLPro: Insights from the Computational and Experimental Investigations"
<p>Input parameters used for molecular dynamics simulations on GROMACS 2022 software and the output trajectory files for calculating binding free energy, in the manuscript with the title: "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CL<sup>Pro</sup>: Insights from the Computational and Experimental Investigations"</p>
Results of the mechanical characterization by tensile tests and the in vitro cell-biomaterial interaction analyses by WST-1 and Live/Dead of 3D-printed scaffolds generated by PLA, PCL, FF, FD and GelMA
<p>Dataset containing the quantitative results of the mechanical characterization, and the in vitro cell-biomaterial interaction analyses with neural cells after 72 hours and 7 days of cell culture of the following 3D printed scaffolds:</p> <ul> <li>Polylactic acid (PLA)</li> <li>Polycaprolactone (PCL)</li> <li>Conductive Filaflex (FF)</li> <li>Flexdym (FD)</li> <li>GelMA (G)</li> </ul> <p>The Live/Dead results were quantified using ImageJ software to determine area fractions corresponding to live (green) and dead (red) cells.</p>
Dataset published in the article: "Electrospun poly(L-lactide-co-DL-lactide) nanofibrous scaffold as substrate for ex vivo limbal epithelial cell cultivation"
Open the record for dataset details and reuse information.
AMaze: fully discrete training with three regimes (direct, scaffolding, interactive) and two algorithms (A2C, PPO)
<p>Dataset containing all training artifacts (final models, training curves, intermediate visualizations, ...) as well as the raw data used to assert generalization capabilities.</p> <p>The associated archive final_behavior.tar.gz provides a visualization of every replicate's final behavior for easier navigation.</p> <p>Distribution files contain a sampling across 1000 seeds, 5 probabilities for traps and lures, 4 sizes and 5 set sizes resulting in 486356 mazes. Descriptive graphs provide an overview of the accessible "maze space".</p> <p> </p> <p>v2: Added script to aggregate run dynamics (mean reward, errors, maze lengths...) and resulting generated dataset (csv) and plots (pdf)</p>
The Effect of Stromal Vascular Fraction (SVF) & Scaffolds Application on Fracture Healing with Bone Defect as Assessed Through Osteocalcin and Bone Morphogenetic Protein-2 (BMP-2) Biomarker Examination: Experimental Study on Murine Model
<p>This data is the raw data for the manuscript with titled The Effect of Stromal Vascular Fraction (SVF) & Scaffolds Application on Fracture Healing with Bone Defect as Assessed Through Osteocalcin and Bone Morphogenetic Protein-2 (BMP-2) Biomarker Examination: Experimental Study on Murine Model.</p>
Contigs scaffolding with Hi-C for plant genomes
<p>Example contigs fasta file use in the protocol: Contigs scaffolding with Hi-C for plant genomes</p>
Data for: Pericytes' Circadian Clock Affects Endothelial Cells' Synchronization and Angiogenesis in a 3D Tissue Engineered Scaffold
<p>Raw data set and analysis files for Mastrullo et al., Frontiers in Pharmacology, 2022 <strong>DOI:</strong> 10.3389/fphar.2022.867070 </p>
Adipose-derived stromal cells preserve pancreatic islet function in a transplantable 3D bioprinted scaffold
<p><span>Intra-portal islet transplantation is the method of choice for treatment of insulin dependent type 1 diabetes, but its outcome is hindered by limited islet survival due to the immunological and metabolic stress post transplantation. Adipose-derived stromal cells (ASCs) promise to improve significantly the islet micro-environment but an efficient long-term delivery method has not been achieved. We therefore explore the potential of generating ASC enriched islet transplant structure by 3D bioprinting. Here, we fabricate a double-layered 3D bioprinted scaffold for islets and ASCs by using alginate-nanofibrillated cellulose bioink. We demonstrate the diffusion properties of the scaffold and report that human ASCs increase the islet viability, preserve the endocrine function, and reduce pro-inflammatory cytokines secretion <em>in vitro</em>. Intraperitoneal implantation of the ASCs and islets in 3D bioprinted scaffold improve the long-term function of islets in diabetic mice. Our data reveals an important role for ASCs on the islet micro-environment. We suggest a novel cell therapy approach of ASCs combined with islets in a 3D structure with a potential for clinical beta cell replacement therapies at extrahepatic sites. </span></p>
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design
<p>Training datasets used for LibINVENT publication <a href="https://doi.org/10.1021/acs.jcim.1c00469">https://doi.org/10.1021/acs.jcim.1c00469</a>.</p> <p>The datasets used for training of the prior:</p> <ul> <li><strong>purged_chembl_sliced.smi.gz:</strong> The CHEMBl 27 compounds, filtered according to the rules described in the manuscript and sliced according to the reaction rules.</li> <li><strong>chembl_train.smi.gz:</strong> The purged, sliced dataset used for model training. The DRD2 compounds are removed as described in the manuscript.</li> </ul>
Compounds with multi-target activity from X-ray structures, corresponding analog series, and associated scaffolds
<p>A total of 702 crystallographic ligands with activity against multiple targets from different protein families (multi-family ligands) were extracted from the Protein Data Bank (PDB). These ligands are made available as aromatic non-stereo SMILES strings together with their target information. A subset of these ligands were also found in the ChEMBL database yielding additional target annotations. Target and family assignments were made following the UniProt classification scheme. In addition, 133 analog-series-based (ASB) scaffolds were derived from series of PDB ligands and structural analogs identified in ChEMBL, which are also made available. For each ASB scaffold, the number of analogs, targets, and target families is provided (union of PDB and ChEMBL annotations).</p>
Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures
Open the record for dataset details and reuse information.
Novel stereological method for estimation of cell counts in 3D collagen scaffolds
<p>Dataset provides all images used for cell number evaluation. The used macros are the part of Supplementary of the article.</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.