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47 results for “surface characterization”
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Peritoneal Surface Malignancies - Characterization, Models and Treatment Strategies
ClinicalTrials.gov study NCT02073500. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
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Figure 1 from: Neamah MJ, Al-Akkam EJM (2024) Preparation and characterization of vemurafenib microemulsion based hydrogel using surface active ionic liquid. Pharmacia 71: 1-9. https://doi.org/10.3897/pharmacia.71.e111178
Figure 1 Pseudoternary phase diagram. A–C. Represent the pseudoternary phase diagram at the Smix ratios of 1:2, 1:3 and 1:4, respectively.
Figure 4 from: Neamah MJ, Al-Akkam EJM (2024) Preparation and characterization of vemurafenib microemulsion based hydrogel using surface active ionic liquid. Pharmacia 71: 1-9. https://doi.org/10.3897/pharmacia.71.e111178
Figure 4 Cumulative amount permeated per square centimetre versus time of different microemulsion-based hydrogel formulas.
Models from "Applying Machine Learning to Characterize and Extrapolate the Relationship Between Seismic Structure and Surface Heat Flow"
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A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth
<p>Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by the temperature gradient of the sample is the main driving force in the growth of well-ordered protein fibrils. Particular attention was devoted to PHF6 peptide and full-length Tau441 protein to form amyloid fibrils. By a combined experimental with the molecular dynamics simulations, the conformational polymorphism of these amyloid fibrils were characterized. The study provided a feasible procedure to optimize the amyloid fibrils formation and characterizations of other types of proteins in future studies.</p>
Surface characterization and biodegradability of sodium hydroxide-treated Moso bamboo substrates
<p>Alkali solution immersion is widely used in pretreatment during bamboo and wood product manufacturing. In this study, we performed a surface analysis on the bamboo chips pretreated by sodium hydroxide with different concentrations at room temperature (25 ℃) and evaluated the surface performance and biodurability. Bamboo surface rapidly changed to darker color at sodium hydroxide concentration (NaOH) of 5% and become rough at 20% NaOH. The K-M curve showed absorption peak near 390-410 nm after alkali treatment, which was due to the presence of chromophore groups derived from lignin, especially from methylene quinone. X-ray diffraction (XRD) showed the area of the crystallization zone was enlarged rapidly at 5% NaOH and then declined. Fourier transform infrared spectroscopy illustrated the conjugate structure of lignin-phenols changed after proton transfer in hydroxyl radical solution and this was the main reason for the surface color changes. During alkali treatment, lignin and hemicellulose in bamboo degraded to some extent, but cellulose was less affected. X-ray photoelectron spectroscopy demonstrated the oxygen-carbon ratio (O/C) and the oxygenated to unoxygenated carbon ratio (C<sub>ox</sub>/C<sub>unox</sub>) all increased, indicating the decrease of extractives and lignin and surface carbon atoms were oxidized in alkali solution and carbon bonds were i more stable. XRD showed sodium hydroxide immersion can not only degrade and dissolve low-polymerization substances in the amorphous zone, increased the crystalline region, but also reached crystalline region, swell the cell wall, which increased the accessibility of fungi and made bamboo more susceptible to fungi infection. Bamboo weight loss of decay after alkali treatment was all larger than the control and maximized at 10% NaOH.</p>
Surface characterization and biodegradability of sodium hydroxide-treated Moso bamboo substrates
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A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth
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Electrochemical selection and characterization of a high current-generating Shewanella oneidensis mutant with altered cell-surface morphology and biofilm-related gene expression
GEO Series GSE50443. Shewanella oneidensis MR-1; Shewanella oneidensis. 6 samples. Type: Expression profiling by array.
Single-cell multiomic characterization of erythroid cells (cultured human BEL-A cell line) with a panel of 118 genes and 7 surface markers on the BD Rhapsody platform
GEO Series GSE287830. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Figure 3 from: Neamah MJ, Al-Akkam EJM (2024) Preparation and characterization of vemurafenib microemulsion based hydrogel using surface active ionic liquid. Pharmacia 71: 1-9. https://doi.org/10.3897/pharmacia.71.e111178
Figure 3 Rheological behaviour of different microemulsion-based hydrogel formulas.
Figure 2 from: Neamah MJ, Al-Akkam EJM (2024) Preparation and characterization of vemurafenib microemulsion based hydrogel using surface active ionic liquid. Pharmacia 71: 1-9. https://doi.org/10.3897/pharmacia.71.e111178
Figure 2 Release profile of vemurafenib from different SAIL-based microemulsion formulas.
Data for Near-Surface Characterization Using Classified Vehicle-Induced Surface Waves from DAS
<p>In this study, we characterize surface waves generated by vehicles of varying sizes and speeds to provide insights into accurate and efficient near-surface imaging using vehicle-induced DAS data. We employ a specialized Kalman filter algorithm to track vehicle locations and classify them into lightweight, midweight, and heavyweight based on the maximum amplitudes of quasi-static DAS records. Vehicles are also classified by their traveling speed (slow, medium, and fast) using their arrival times at DAS channels. Virtual shot gathers for the same class of vehicles are constructed from their surface wave windows selected using the tracked vehicle trajectories. We analyze the dispersion of the phase velocity to investigate the influence of vehicle characteristics on the induced surface waves.</p> <p><code>Put these pickle files into '/das_diff_veh/data/sw_data/' and run the scripts at https://github.com/jingxiaoliu/das_diff_veh</code></p> <p>If you found this useful, please cite our papers:</p> <blockquote> <p>[1] Liu, J., Li, H., Yuan, S., Noh, H. Y., & Biondi, B. (2024). Characterizing Vehicle-Induced Distributed Acoustic Sensing Signals for Accurate Urban Near-Surface Imaging. <em>arXiv preprint arXiv:2408.14320</em>.</p> <p>[2] Yuan, S., Liu, J., Noh, H. Y., Clapp, R., & Biondi, B. (2024). Using vehicle‐induced DAS signals for near‐surface characterization with high spatiotemporal resolution. <em>Journal of Geophysical Research: Solid Earth</em>, <em>129</em>(4), e2023JB028033.</p> <p>[3] Liu, J., Yuan, S., Dong, Y., Biondi, B., & Noh, H. Y. (2023). TelecomTM: A fine-grained and ubiquitous traffic monitoring system using pre-existing telecommunication fiber-optic cables as sensors. <em>Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies</em>, <em>7</em>(2), 1-24.</p> </blockquote>
Characterization of the Edge of Soft Contact Lens and Its Interaction With Ocular Surface
ClinicalTrials.gov study NCT00707291. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterizing and Comparing the Profile of Microorganisms From Specific Body Sites and Environmental Surfaces in Newly Disinfected Patient Rooms
ClinicalTrials.gov study NCT01803100. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4 T cell clones from murine tissues
GEO Series GSE240041. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Characterization of the Filovirus-Resistant Cell Line SH-SY5Y Reveals Redundant Role of Cell Surface Entry Factors
GEO Series GSE104008. Homo sapiens. 13 samples. Type: Expression profiling by array.
Characterization of five novel Pseudomonas aeruginosa cell-surface signaling systems
GEO Series GSE9657. Pseudomonas aeruginosa. 8 samples. Type: Expression profiling by array.
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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.