gebhart/patrepeval huggingface dataset:
Ester-linked ubiquitin sites formed by HOIL-1 in TLR7 signaling include four novel ubiquitin dimers (2022)

Abstract The E3 ligase HOIL-1 forms ester bonds in vitro between ubiquitin and serine/threonine residues in proteins. Here, we exploit UbiSite technology to identify serine and threonine residues undergoing HOIL-1 catalysed ubiquitylation in macrophages stimulated with R848, an activator of the TLR7/8 heterodimer. We identify Thr12, Thr14, Ser20 and Thr22 of ubiquitin as amino acid residues forming ester bonds with the C-terminal carboxylate of another ubiquitin molecule, increasing from 8 to 12 the different types of ubiquitin dimer formed in cells. We also identify Ser175 of IRAK4, Ser136, Thr163 and Ser168 of IRAK2 and Thr141 of MyD88 as further sites of HOIL-1-catalysed ubiquitylation together with lysine residues in these proteins that also undergo R848-dependent ubiquitylation. These findings establish that the ubiquitin chains attached to components of myddosomes are initiated by both ester and isopeptide bonds. Ester bond formation takes place within the proline, serine, threonine-rich (PST) domains of IRAK2 and IRAK4 and the intermediate domain of MyD88. The ubiquitin molecules attached to Lys162, Thr163 and Ser168 of IRAK2 are attached to different IRAK2 molecules.
Modeling of the bryostatins to the phorbol ester pharmacophore on protein kinase C. (1988)

The bryostatins are macrocyclic lactones that represent an additional structural class of potent activators of protein kinase C. These marine animal biosynthetic products are of unusual interest because they induce only a subset of the biological responses induced by the phorbol esters. We have now determined the binding affinities of naturally occurring and semisynthetic bryostatins for protein kinase C by competition analysis with [26-3H]bryostatin 4 as the radioactive ligand. Esterification of the hydroxyl group at C26 caused dramatic loss of activity as did inversion of the asymmetric center at this position. In contrast, neither of the ester groups at C7 and C20 had a major influence on activity. Computer modeling of the phorbol esters, related diterpenes, and indole alkaloids suggested that the C20, C9, and C4 oxygens of phorbol represented critical elements of the phorbol ester pharmacophore. The C26 oxygen of the bryostatins, together with the C1 and C19 oxygens, gave an excellent spatial correlation with this model, with a root-mean-square deviation of 0.16 A (compared to 0.10-0.35 A among phorbol-related diterpenes). The extension of the phorbol ester pharmacophore model to the bryostatins and its agreement with the structure-activity relations for the bryostatin class of compounds provide additional support for the validity of the model.
Mechanisms of pathogenesis of missense mutations on the KDM6A-H3 interaction in type 2 Kabuki Syndrome (2020)

Mutations in genes encoding for histone methylation proteins are associated with several developmental disorders. Among them, <i>KDM6A</i> is the disease causative gene of type 2 Kabuki Syndrome, a rare multisystem disease. While nonsense mutations and short insertions/deletions are known to trigger pathogenic mechanisms, the functional effects of missense mutations are still uncharacterized. In this study, we demonstrate that a selected set of missense mutations significantly hamper the interaction between KDM6A and the histone H3, by modifying the dynamics of the linker domain, and then causing a loss of function effect.
Chip-based clinical assays: towards analysis of physiological samples (2003)

There are a number of challenges, both engineering and chemical, which still need to be overcome before the use of so-called miniaturized total chemical analysis systems, or /spl mu/TAS, becomes well established in the clinical domain. These are related to the complex nature of physiological media, which are inherently incompatible with microchannels having cross-sectional dimensions on the order of micrometers. The high surface-to-volume ratios of microfluidic devices are the primary concern, since biomolecules are prone to increased adsorption in these systems. Special consideration must therefore be given to analysis of protein-containing matrices in microflow systems, and analysis conditions adjusted to the type of analyte and chip substrate in question.
Experimental evaluation of the separation efficiency in capillary electrophoresis using open tubular and gel-filled columns (1992)

The band dispersion phenomena in capillary zone electrophoresis (CZE) using untreated and surface-treated open tubular and gel-filled capillaries were experimentally evaluated, with emphasis on small capillary diameters (10-100 microns). Laser-induced fluorescence detection was used for high-sensitivity detection of the isoindoles originated from model amino acids. The plots of plate height vs electric field strength were generated for different column radii and compared with a theoretical model for CZE. In addition to the diffusion-controlled band dispersion in the relatively low electric field range, adsorptive interactions between a solute and the capillary wall may play a certain role in band-broadening. The sorption-desorption kinetics become important with increasing electric field strength. Thermal effects appear to contribute little to band-broadening in relatively small capillaries (less than 50-microns i.d.) within normal operating voltages (less than 30 kV), but could become significant in capillaries with larger bores (greater than 75-microns i.d.). With gel-filled capillaries of small diameters (less than 50-microns i.d.), diffusion processes can be minimized. In addition, thermal effects do not appear critical in such columns at reasonable voltages.
High Performance Fiber Optic Temperature Sensor Using Low-Coherence Interferometry (1997)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text H. Choi, H. F. Taylor, and C. E. Lee, "High Performance Fiber Optic Temperature Sensor Using Low-Coherence Interferometry," in 12th International Conference on Optical Fiber Sensors, Vol. 16 of 1997 OSA Technical Digest Series (Optical Society of America, 1997), paper OThD2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
NEUROTROPHINS AND CILIARY NEUROTROPHIC FACTOR - THEIR BIOLOGY AND PATHOLOGY (1994)

Neurotrophins (NTFs) and ciliary neurotrophic factor (CNTF) induce the differentiation of neuronal cells, rescue them from naturally occurring death, and trigger neuronal regeneration. The NTFs bind to two classes of cell surface receptors, whereas CNTF receptor is composed of three subunits. The functions of these polypeptide survival factors with trophic action on nerve cells have recently been approached by the targeted disruption of the CNTF, NTF and their receptor genes by the homologous recombination technique. The embryonic growth and morphogenesis of these gene 'knock-out' mice is normal, but they develop with defects in various subsets of the peripheral nervous system, and the homozygous mutant mice often die during the early postnatal period. Disturbances in the biology of NTFs and CNTF have recently been implicated in the pathogenesis of certain common neurodegenerative disorders, such as Parkinson's disease, motor neurone diseases, and Alzheimer's disease. Intensive research on their pharmaceutical perspective has, therefore, been provoked. All neurotrophins and CNTF can now be synthesized on a large scale as biologically active recombinant proteins, and several alternatives for their local applications to the target tissue have been presented. Their therapeutic potential is discussed.
Introduction:  GlycobiologyUnderstanding the Language and Meaning of Carbohydrates (2002)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTIntroduction: GlycobiologyUnderstanding the Language and Meaning of CarbohydratesRaymond A. Dwek and Terry D. ButtersView Author Information Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UKCite this: Chem. Rev. 2002, 102, 2, 283–284Publication Date (Web):February 13, 2002Publication History Published online13 February 2002Published inissue 1 February 2002https://pubs.acs.org/doi/10.1021/cr010385jhttps://doi.org/10.1021/cr010385jeditorialACS PublicationsCopyright © 2002 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views3029Altmetric-Citations88LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (18 KB) Get e-AlertscloseSUBJECTS:Cancer,Carbohydrates,Oligosaccharides,Peptides and proteins,Post-translational modification Get e-Alerts
Practical approach for AAPSM image imbalance correction for sub-100-nm lithography (2003)

In our previously published work, we investigated alternating-aperture PSM image intensity imbalance as function of various mask and optical parameters using rigorous electro-magnetic field (EMF) simulations. Results suggested that the imbalance could be effectively compensated through application of an optimized combination of undercut and a constant phase-shifter bias. In the effort of development and implementation of a production-ready image imbalance correction methodology, it is important to validate the accuracy of simulation-based predictions through correlation of results to experimental data. For this purpose, a test reticle containing various mask parameters as variables was designed and manufactured. The experimental data was obtained from SEM measurements of the exposed wafers, and results were compared to rigorous EMF simulation data. Based on results obtained, we propose and validate an image imbalance correction methodology to be implemented within the framework of the PSM - OPC manufacturing flow.
Series connection of IGBTs used multilevel clamp circuit and turn off timing adjustment circuit (2004)

Because of its superior switching characteristics, it is useful to connect IGBTs in series in high voltage inverters. In series connected IGBTs, the differences in the switching timing causes a overvoltage and a power loss imbalance. To clamp the overvoltage in the turn-off transient period, a peak-clamp circuit and a dv/dt-clamp circuit were developed. The peak-clamp circuit clamps the overvoltage under the rating of the IGBT. The dv/dt-clamp circuit depresses the dv/dt to be able to clamp the overvoltage by the peak-clamp circuit. By using the above two clamp circuits, the overvoltage is clamped perfectly under the rated voltage of the IGBTs. The collector-emitter voltage in the tailing current period is improved to 2400 V from 3300 V by the tailing current period clamp circuit. To improve the power loss imbalance due to the differences in the turn-off timing, an automatic adjustment circuit for the turn-off timing was developed. The collector-emitter voltage in the tailing current period is used as the signal for the timing adjustment circuit. The timing adjustment circuit can reduce the turn-off timing delay within 100 ns between two series connected IGBTs at the DC-link voltage values from 3300 V to 3700 V. By utilizing these circuits, series connected IGBTs can be applied to high voltage inverters.
Exploring intrinsic MR signal relaxation in acute RF ablation lesions using T2 mapping and IR-SSFP CINE imaging (2013)

Background Cardiac MR has been used successfully in RF ablation therapies for arrhythmias, both for procedural planning and for post-ablation lesion imaging. Non-enhanced imaging, though it has a lower SNR, has advantages over Gdenhanced techniques mainly because contrast kinetics and dosage issues are avoided. Previously T2-weighted imaging was found to be more sensitive than T1-weighted imaging [1]. In this study, we performed non-enhanced T2 mapping and an inversion-prepared SSFP CINE imaging to characterize intrinsic relaxation behavior in acute lesions.
Composition of seismic facies: A case study (2013)

In this case study, we used simulated seismic data from outcrops on Svalbard to analyze what seismic facies are composed of, what the dominating factors in forming the facies are, and which consequences this has for the interpretation results. Seismic facies analyses can be used to interpret environmental setting, depositional processes, and lithology. Here, we found that noise is the most important factor in forming the seismic facies. Noise is defined as all reflections that cannot be ascribed directly to the reservoir model. Effects from overburden and processing dominated, and the low-frequency content of the seismic section complicated the seismic facies analyses. The main reason for this is that the analysis relies heavily on identified internal patterns and low-angle terminations. Such patterns and terminations are easily created by the seismic method itself, by overburden effects, and by artifacts generated when processing the data. External form, strong amplitudes, and continuous reflections are robust seismic observations, whereas the internal pattern and terminations are commonly deceptive. Identification of boundaries based on predefined patterns of terminations does not work here, and uncritical use of seismic facies analysis in this interpretation case will create wrong reservoir models. Because of the size of the outcrops, the results from this analysis are relevant for reservoir-scale seismic interpretation and detailed interpretation for prospect evaluation in mature basins. For seismic interpretation at a more regional scale, it is probably less relevant.
The Function and Integrity of the Neurovascular Unit Rests Upon the Integration of the Vascular and Inflammatory Cell Systems (2005)

The neurovascular unit is composed of a microvascular endothelium, neuron, and glial cell elements that are in physical proximity to the endothelium. The vascular system provides oxygen, glucose, and hormones for brain cells and guides the cells to appropriately respond to the local environment. Conversely, the brain cells, especially glial cells, can regulate the function of blood vessels in response to local requirements. The disruption of the neurovascular coordination was observed in a variety of inflammation-related diseases in brain, such as infectious diseases, stroke, vascular dementia, and multiple sclerosis. Inflammatory responses resulting from infections or injury of the brain activate the endothelium and glial cells to various degrees depending on the type, titer, or strength and duration of exposure to the agents or insults. The activation of endothelial and microglial cells may be modulated by the action of cytokines or other substances secreted from these cells. In an effort to understand the pathogenesis and find rational treatments against inflammatory disorders in brain, studies have been separately carried out using either endothelial cells or microglia. Increasing evidence, however, indicates that a crosstalk between these two cell types is important for the brain inflammation. Here, we review recent advances that provide insights into the coordinated interaction between the vascular and microglial systems, including the role of the specialized endothelium in regulating the immune response that occurs within CNS, the influence of microglial cells on the properties of endothelial cells, and the effects of endothelium on the state of microglial activation.
Olefin Epoxidation by Alkyl Hydroperoxide with a Novel Cross-Bridged Cyclam Manganese Complex:  Demonstration of Oxygenation by Two Distinct Reactive Intermediates (2007)

Olefin epoxidation provides an operative protocol to investigate the oxygen transfer process in nature. A novel\nmanganese complex with a cross-bridged cyclam ligand, Mn&lt;sup&gt;IV&lt;/sup&gt;(Me&lt;sub&gt;2&lt;/sub&gt;EBC)(OH)&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;2+&lt;/sup&gt; (Me&lt;sub&gt;2&lt;/sub&gt;EBC = 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane), was used to study the epoxidation mechanism with biologically important\noxidants, alkyl hydroperoxides. Results from direct reaction of the freshly synthesized manganese(IV) complex,\n[Mn(Me&lt;sub&gt;2&lt;/sub&gt;EBC)(OH)&lt;sub&gt;2&lt;/sub&gt;](PF&lt;sub&gt;6&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;, with various olefins in neutral or basic solution, and from catalytic epoxidation with\noxygen-labeled solvent, H&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;18&lt;/sup&gt;O, eliminate the manganese oxo moiety, Mn&lt;sup&gt;IV&lt;/sup&gt;O, as the reactive intermediate and\nobviate an oxygen rebound mechanism. Epoxidations of norbornylene under different conditions indicate multiple\nmechanisms for epoxidation, and &lt;i&gt;cis&lt;/i&gt;-stilbene epoxidation under atmospheric &lt;sup&gt;18&lt;/sup&gt;O&lt;sub&gt;2&lt;/sub&gt; reveals a product distribution\nindicating at least two distinctive intermediates serving as the reactive species for epoxidation. In addition to alkyl\nperoxide radicals as dominant intermediates, an alkyl hydroperoxide adduct of high oxidation state manganese(IV)\nis suggested as the third kind of active intermediate responsible for epoxidation. This third intermediate functions\nby the Lewis acid pathway, a process best known for hydrogen peroxide adducts. Furthermore, the &lt;i&gt;tert&lt;/i&gt;-butyl\nperoxide adduct of this manganese(IV) complex was detected by mass spectroscopy under catalytic oxidation\nconditions.
How to design catalytic nanocluster by magnetron-sputter gas-aggregation? (2017)

International audience
Novel Etoposide Analogue Modulates Expression of Angiogenesis Associated microRNAs and Regulates Cell Proliferation by Targeting STAT3 in Breast Cancer (2015)

Tumor microenvironment play role in angiogenesis and carcinogenesis. Etoposide, a known topoisomerase II inhibitor induces DNA damage resulting in cell cycle arrest. We developed a novel Etoposide analogue, Quinazolino-4β-amidopodophyllotoxin (C-10) that show better efficacy in regulating cell proliferation and angiogenesis. We evaluated its role on expression of microRNAs-15, 16, 17 and 221 and its targets Bcl-2, STAT3 and VEGF that dictate cell proliferation and angiogenesis. Docking studies clearly demonstrated the binding of Etoposide and C-10 to STAT3. We conclude that combination of Etoposide or C-10 with miR-15, 16, 17 and 221 as a new approach to induce apoptosis and control angiogenesis in breast cancer.
RSK2 Mediates Muscle Cell Differentiation through Regulation of NFAT3 (2007)

RSK2, an ERK downstream kinase, is a novel mediator of skeletal muscle cell differentiation through its regulation of NFAT3 activity. We found that the N-terminal (amino acids (aa) 1-68) and C-terminal (aa 416-674) kinase domains of RSK2 directly interacted with nuclear localization signal 1, the Ser/Pro repeat, and the polyproline domains (aa 261-365) of NFAT3. Upon A23187 stimulation, RSK2 induced nuclear localization of NFAT3. RSK2 phosphorylated NFAT3 in vitro (Km=3.559 microM), and activation of NFAT3 by RSK2 enhanced the promoter activity of NFAT3 downstream target genes in vivo. Furthermore, nuclear accumulation of NFAT3 was attenuated markedly in RSK2-/- cells compared with wild-type RSK2+/+ cells. Notably, RSK2 and NFAT3 induced a significant differentiation of C2C12 myoblasts to multinucleated myotubes. Multinucleated myotube differentiation was inhibited by small interfering RNA against RSK2, ERK1/2, or NFAT3. These results demonstrate that RSK2 is an important kinase for NFAT3 in mediating myotube differentiation.
Improvement in noise characteristics of GaAsSb-based backward diodes by using a modified junction structure (2016)

Summary form only given. The noise performance was improved by modifying the junction structure of GaAsSb-based backward diodes for millimeter and terahertz wave detection. A noise equivalent power (NEP) of 64 pW/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> at 300 GHz was achieved with diodes that consisted of a p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -GaAsSb/n-InGaAs heterojunction. This value was much lower than 303 pW/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> that was obtained from the previously reported diodes consisting of a p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -GaAsSb/i-InAlAs/n-InGaAs heterojunction. The improvement in the NEP resulted from a considerable reduction in the junction resistance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</sub> ) from 17.9 MΩ to 0.41 MΩ by removing the thin i-InAlAs barrier layer. The modified GaAsSb-based backward diodes are applicable for millimeter and terahertz receiver applications.
Substrate non-enantiospecific and product enantioselective reduction of bicyclo[3.2.0]hept-2-en-6-one using yeast (1979)

R. F. Newton, J. Paton, D. P. Reynolds, S. Young and S. M. Roberts, J. Chem. Soc., Chem. Commun., 1979, 908 DOI: 10.1039/C39790000908
Network Coding-Aware Routing in Wireless Networks (2010)

A recent approach-COPE, presented by Katti ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Proc. ACM SIGCOMM 2006, pp. 243-254</i> )-for improving the throughput of unicast traffic in wireless multihop networks exploits the broadcast nature of the wireless medium through opportunistic network coding. In this paper, we analyze throughput improvements obtained by COPE-type network coding in wireless networks from a theoretical perspective. We make two key contributions. First, we obtain a theoretical formulation for computing the throughput of network coding on any wireless network topology and any pattern of concurrent unicast traffic sessions. Second, we advocate that routing be made aware of network coding opportunities rather than, as in COPE, being oblivious to it. More importantly, our model considers the tradeoff between routing flows close to each other for utilizing coding opportunities and away from each other for avoiding wireless interference. Our theoretical formulation provides a method for computing source-destination routes and utilizing the best coding opportunities from available ones so as to maximize the throughput. We handle scheduling of broadcast transmissions subject to wireless transmit/receive diversity and link interference in our optimization framework. Using our formulations, we compare the performance of traditional unicast routing and network coding with coding-oblivious and coding-aware routing on a variety of mesh network topologies, including some derived from contemporary mesh network testbeds. Our evaluations show that a route selection strategy that is aware of network coding opportunities leads to higher end-to-end throughput when compared to coding-oblivious routing strategies.