gebhart/patrepeval huggingface dataset:
Label‐Free Detection of Protein–Protein Interactions on Biochips (2005)

Eliminating the middle-man: The combination of MALDI-TOF mass spectrometry and self-assembled monolayers on gold (SAMDI) offers a new detection method for protein–ligand (shown) and protein–protein interactions. Proteins and protein complexes are selectively bound to biochips and then directly analyzed by MALDI-TOF MS without the need for labels. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501363_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Quenching of [Ru(bpy)3]2+Fluorescence by Binding to Au Nanoparticles (2002)

Gold nanoparticles coated with stabilizing thiolate monolayers of N-(2-mercaptopropionyl)glycine (tiopronin) and N, N-trimethyl(undecylmercapto)ammonium quench the fluorescence of [Ru(bpy)3]2+ in aqueous solution. The tiopronin monolayer protected clusters (MPCs) exert energy-transfer quenching by both collisional quenching and by static quenching in electrostatic complexes formed between [Ru(bpy)3]2+ and the tiopronin carboxylate groups. The electrostatic binding is pH-dependent and can be released by addition of electrolyte (e.g., K+, Bu4N+, and Ca2+ salts, which are increasingly effective in the order given). The tiopronin MPC quenching of [Ru(bpy)3]2+ fluorescence follows Stern−Volmer relations for plots of Fo/F against MPC concentration and Fo/F against electrolyte concentration at constant MPC concentration. Quenching and electrolyte binding constants were derived. MPCs with average Au core diameters of 2.2 nm (average) exhibited quenching constants that are 20-fold larger than those for 1.8-nm diameter.
Compressive Wideband Power Spectrum Estimation (2012)

In several applications, such as wideband spectrum sensing for cognitive radio, only the power spectrum (a.k.a. the power spectral density) is of interest and there is no need to recover the original signal itself. In addition, high-rate analog-to-digital converters (ADCs) are too power hungry for direct wideband spectrum sensing. These two facts have motivated us to investigate compressive wideband power spectrum sensing, which consists of a compressive sampling procedure and a reconstruction method that is able to recover the unknown power spectrum of a wide-sense stationary signal from the obtained sub-Nyquist rate samples. It is different from spectrum blind sampling (SBS), which aims at reconstructing the original signal instead of the power spectrum. In this paper, a solution is first presented based on a periodic sampling procedure and a simple least-squares reconstruction method. We evaluate the reconstruction process both in the time and frequency domain. Then, we examine two possible implementations for the compressive sampling procedure, namely complex Gaussian sampling and multicoset sampling, although we mainly focus on the latter. A new type of multicoset sampling is introduced based on the so-called minimal sparse ruler problem. Next, we analyze the statistical properties of the estimated power spectrum. The computation of the mean and the covariance of the estimates allows us to calculate the analytical normalized mean squared error (NMSE) of the estimated power spectrum. Further, when the received signal is assumed to contain only circular complex zero-mean Gaussian i.i.d. noise, the computed mean and covariance can be used to derive a suitable detection threshold. Simulation results underline the promising performance of our proposed approach. Note that all benefits of our method arise without putting any sparsity constraints on the power spectrum.
TNF-alpha and IL-1 sequentially induce endothelial ICAM-1 and VCAM-1 expression in MRL/lpr lupus-prone mice. (1999)

Dysfunctional leukocyte-endothelial interactions are thought to play a key role in systemic lupus erythematosus pathogenesis. We questioned the importance of TNF-alpha and IL-1 for endothelial activation in MRL/lpr lupus-prone mice. Endothelial ICAM-1 and VCAM-1 expression increased significantly with disease evolution in kidney, heart, and brain, as shown by i.v. injected radiolabeled Ab uptake. Lung endothelial VCAM-1 also increased, while lung endothelial ICAM-1 did not rise above a high basal level. Immunoassays showed a significantly raised circulating level of TNF-alpha by 14 wk, with levels of circulating IL-1alpha and IL-1beta being additionally raised by 20 wk. With 14-wk-old MRL/lpr, anti-TNF-alpha antiserum inhibited expression of ICAM-1 and VCAM-1 by endothelial cells cultured with sera in vitro, and uptake of anti-ICAM-1 and anti-VCAM-1 mAb in lung, kidney, brain, and heart in vivo. In contrast, both anti-TNF-alpha and anti-IL-1 antisera were required for maximal inhibition in vitro and in vivo at 20 wk. These data indicate that TNF-alpha is largely responsible for the early up-regulation of endothelial ICAM-1 and VCAM-1, but that IL-1 enhances expression in late disease. Our observations provide novel insights of possible relevance to understanding endothelial activation in systemic lupus erythematosus, and highlight an approach that can be extended to dissecting other chronic inflammatory diseases.
A hingeless Fc fusion system for site-specific cleavage by IdeS (2016)

Fusion of proteins to the Fc region of IgG is widely used to express cellular receptors and other extracellular proteins, but cleavage of the fusion partner is sometimes required for downstream applications. Immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) is a protease with exquisite specificity for human IgG, and it can also cleave Fc-fusion proteins at a single site in the N-terminal region of the CH2 domain. However, the site of IdeS cleavage results in the disulfide-linked hinge region partitioning with the released protein, complicating downstream usage of the cleaved product. To tailor the Fc fragment for release of partner proteins by IdeS treatment, we investigated the effect of deleting regions of IgG-derived sequence that are upstream of the cleavage site. Elimination of the IgG-derived hinge sequence along with several residues of the CH2 domain had negligible effects on expression and purity of the fusion protein, while retaining efficient processing by IdeS. An optimal Fc fragment comprising residues 235-447 of the human IgG1 heavy chain sufficed for efficient production of fusion proteins and minimized the amount of residual Ig-derived sequence on the cleavage product following IdeS treatment. Pairing of this truncated Fc fragment with IdeS cleavage enables highly specific cleavage of Fc-fusion proteins, thus eliminating the need to engineer extraneous cleavage sequences. This system should be helpful for producing Fc-fusion proteins requiring downstream cleavage, particularly those that are sensitive to internal miscleavage if treated with alternative proteases.
Constrained Bithiazoles: Small Molecule Correctors of Defective ΔF508–CFTR Protein Trafficking (2014)

Conformationally constrained bithiazoles were previously found to have improved efficacy over nonconstrained bithiazoles for correction of defective cellular processing of the ΔF508 mutant cystic fibrosis transmembrane conductance regulator (CFTR) protein. In this study, two sets of constrained bithiazoles were designed, synthesized, and tested in vitro using ΔF508-CFTR expressing epithelial cells. The SAR data demonstrated that modulating the constraining ring size between 7- versus 8-membered in these constrained bithiazole correctors did not significantly enhance their potency (IC50), but strongly affected maximum efficacy (Vmax), with constrained bithiazoles 9e and 10c increasing Vmax by 1.5-fold compared to benchmark bithiazole corr4a. The data suggest that the 7- and 8-membered constrained ring bithiazoles are similar in their ability to accommodate the requisite geometric constraints during protein binding.
Quantification of Endospore-Forming Firmicutes by Quantitative PCR with the Functional Genespo0A (2013)

Bacterial endospores are highly specialized cellular forms that allow endospore-forming Firmicutes (EFF) to tolerate harsh environmental conditions. EFF are considered ubiquitous in natural environments, in particular, those subjected to stress conditions. In addition to natural habitats, EFF are often the cause of contamination problems in anthropogenic environments, such as industrial production plants or hospitals. It is therefore desirable to assess their prevalence in environmental and industrial fields. To this end, a high-sensitivity detection method is still needed. The aim of this study was to develop and evaluate an approach based on quantitative PCR (qPCR). For this, the suitability of functional genes specific for and common to all EFF were evaluated. Seven genes were considered, but only spo0A was retained to identify conserved regions for qPCR primer design. An approach based on multivariate analysis was developed for primer design. Two primer sets were obtained and evaluated with 16 pure cultures, including representatives of the genera Bacillus, Paenibacillus, Brevibacillus, Geobacillus, Alicyclobacillus, Sulfobacillus, Clostridium, and Desulfotomaculum, as well as with environmental samples. The primer sets developed gave a reliable quantification when tested on laboratory strains, with the exception of Sulfobacillus and Desulfotomaculum. A test using sediment samples with a diverse EFF community also gave a reliable quantification compared to 16S rRNA gene pyrosequencing. A detection limit of about 10(4) cells (or spores) per gram of initial material was calculated, indicating this method has a promising potential for the detection of EFF over a wide range of applications.
Cause of spectral variation in the luminescence of semisynthetic aequorins (1995)

Aequorin emits light in the presence of Ca2+, decomposing into apoaequorin, coelenteramide and CO2. Semisynthetic aequorins, produced by replacing the coelenterazine moiety in aequorin with analogues of coelenterazine, showed widely different sensitivities to Ca2+ as well as certain spectral variations. A group of semisynthetic aequorins, e-type aequorins, showed bimodal luminescence, with peaks at 400-405 nm and 440-475 nm in various intensity ratios, whereas all other aequorins luminesced with only one peak, in the range 440-475 nm. The cause of the spectral variation was studied by various experiments including: (1) comparison with the fluorescence of the spent solution and the luminescence of the spent solution produced by added coelenterazine; (2) luminescence in 2H2O; (3) the rate of conformational change of apoaequorin; (4) the rates of regeneration in the presence and absence of O2. The results suggested that the spectrum of Ca(2+)-triggered luminescence is strongly affected by the ionic charge on the amide N atom of the coelenteramide that is bound to apoaequorin. When the amide N atom is negatively charged, light is emitted with a 440-475 nm peak. In the case of e-type aequorins, the negative charge on the amide N atom is less because of the structure of e-coelenterazine involved, resulting in the emission of a 400-405 nm peak from the uncharged form of coelenteramide; the intensity ratio of 400-405 nm peak to 440-475 nm peak is determined by the amount of negative charge resting on the amide N atom of e-coelenteramide at the time of light emission. Most of the spectral variations in luminescence and fluorescence can be explained on the basis of ionic and hydrophobic interaction between a coelenteramide and apoaequorin.
Mycolic Acid Analysis by High-Performance Liquid Chromatography for Identification ofMycobacteriumSpecies (2001)

Mycobacterium tuberculosis is the etiologic agent of tuberculosis and can be accurately detected by laboratories using commercial genetic tests. Nontuberculosis mycobacteria (NTM) causing other mycobacterioses can be difficult to identify. The identification processes are confounded by an increasing diversity of newly characterized NTM species. The ubiquitous nature of NTM, combined with their potential to be opportunistic pathogens in immunocompromised as well as nonimmunodeficient patients, further complicates the problem of their identification. Since clinical case management varies depending on the etiologic agent, laboratories must identify the species in a timely manner. However, only a few identification methods can detect the species diversity within the Mycobacterium genus. Over the last decade, high-performance liquid chromatography analysis of the mycolic acids has become an accepted method for identification of mycobacteria. In this review, we assess its development and usefulness as an identification technique for Mycobacterium species.
Induced hypothermia in critical care medicine: A review (2003)

Induced hypothermia has a role in selected patients in the intensive care unit. Critical care physicians should be familiar with the physiologic effects, current indications, techniques, and complications of induced hyperthermia.
Isoelectric focusing of monoclonal immunoglobulin G, A and M followed by detection with the avidin‐biotin system (1985)

Abstract The sera of 49 subjects with IgG, IgA or IgM benign monoclonal gammopathy‐components were examined by agarose gel isoelectric focusing followed by Coomassie Brilliant Blue R‐250 staining as well as avidin‐biotin amplified double‐antibody peroxidase labelling after nitrocellulose blotting. IgG‐components gave 2–10 distinct bands within the isoelectric point (p I )‐range of pH 6.5–9.5, IgA‐components were focused into 10–15 bands with p I ‐values of pH 4.5–6.5 and the IgM‐components gave 1–2 fractions within the p I ‐range of pH 4.5–6.5. The avidin‐biotin peroxidase complex (ABC) technique exhibited some tendency to non‐specific labeling related to the avidin‐biotin component and depending on the relative amounts of the individual proteins. However, the method has a definite potential for the visualization of submicrogram quantities of immunoglobulins blotted to nitrocellulose membranes after isoelectric focusing.
Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7–RILP–p150Glued and late endosome positioning (2009)

Late endosomes (LEs) have characteristic intracellular distributions determined by their interactions with various motor proteins. Motor proteins associated to the dynactin subunit p150(Glued) bind to LEs via the Rab7 effector Rab7-interacting lysosomal protein (RILP) in association with the oxysterol-binding protein ORP1L. We found that cholesterol levels in LEs are sensed by ORP1L and are lower in peripheral vesicles. Under low cholesterol conditions, ORP1L conformation induces the formation of endoplasmic reticulum (ER)-LE membrane contact sites. At these sites, the ER protein VAP (VAMP [vesicle-associated membrane protein]-associated ER protein) can interact in trans with the Rab7-RILP complex to remove p150(Glued) and associated motors. LEs then move to the microtubule plus end. Under high cholesterol conditions, as in Niemann-Pick type C disease, this process is prevented, and LEs accumulate at the microtubule minus end as the result of dynein motor activity. These data explain how the ER and cholesterol control the association of LEs with motor proteins and their positioning in cells.
Forced convection boiling in a microchannel heat sink (2001)

Micromachining technology was utilized to fabricate a transparent microchannel heat-sink system by bonding glass to a silicon wafer. The micro heat sink consisted of a microchannel array, a heater, and a temperature sensor array. This integrated microsystem allowed simultaneous qualitative visualizations of the flow pattern within the microchannels and quantitative measurements of temperature distributions, flow rates, and input power levels. Boiling curves of temperature as a function of the input power were established. No boiling plateau was observed in the boiling curves, consistent with our previously reported data but different from results reported for macrochannel heat sinks. Three stable boiling modes, depending on the input power level, have been distinguished from the flow patterns. Local nucleation boiling was observed in microchannels with a hydraulic diameter as small as 26 /spl mu/m at the lower input power range. At the higher input power range, a stable annular flow was the dominant boiling mode. Bubbly flow, commonly observed in macrochannels, could not be developed in the present microchannels. Consequently, no boiling plateau was detected in the boiling curves.
TRRAP-Dependent and TRRAP-Independent Transcriptional Activation by Myc Family Oncoproteins (2002)

We demonstrate that transformation-transactivation domain-associated protein (TRRAP) binding and the recruitment of histone H3 and H4 acetyltransferase activities are required for the transactivation of a silent telomerase reverse transcriptase (TERT) gene in exponentially growing human fibroblasts by c-Myc or N-Myc protein. However, recruitment of TRRAP by c- or N-Myc is dispensable for the partial induction of several basally expressed genes in exponentially growing primary and immortalized fibroblasts. Furthermore, recruitment of TRRAP is required for c-Myc- or N-Myc-mediated oncogenic transformation but not for the partial restoration of the growth defect in myc-null fibroblasts. A segment of the adenovirus E1A protein fused to a transformation-defective N-Myc protein carrying a small deletion in the transactivation domain specifically restores interaction with TRRAP, activates the silent TERT gene, induces acetylation of histones H3 and H4 at the TERT promoter, and transforms primary cells. Accordingly, wild-type L-Myc is much less efficient in TRRAP binding, activation of the silent TERT gene, and transformation of primary fibroblasts. Nevertheless, L-Myc is a potent activator of several basally expressed genes and can fully restore the growth defect of myc-null cells. These results suggest a differential requirement for TRRAP for several Myc-mediated activities.
ROS1 Fusions in Cancer: A Review (2016)

The ROS1 gene belongs to the sevenless subfamily of tyrosine kinase insulin receptor genes. A literature review identified a ROS1 fusion in 2.54% of the patients with lung adenocarcinoma and even higher frequencies in spitzoid neoplasms and inflammatory myofibroblastic tumors. At present, 26 genes were found to fuse with ROS1, some of them already known to fuse with RET and ALK. All the fusion proteins retain the ROS1 kinase domain, but rarely its transmembrane domain. Most of the partners have dimerization domains that are retained in the fusion, presumably leading to constitutive ROS1 tyrosine kinase activation. Some partners have transmembrane domains that are retained or not in the chimeric proteins. Therefore, different ROS1 fusions have distinct subcellular localization, suggesting that they may activate different substrates in vivo.
Finite‐difference iterative migration by linearized waveform inversion in the frequency domain (2002)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2002Finite‐difference iterative migration by linearized waveform inversion in the frequency domainAuthors: S. ØstmoW. A. MulderR.‐E. PlessixS. ØstmoSintef, Norway, W. A. MulderShell International E&P, The Netherlands, and R.‐E. PlessixShell International E&P, The Netherlandshttps://doi.org/10.1190/1.1816917 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816917FiguresReferencesRelatedDetailsCited ByFast least-squares reverse time migration via a superposition of Kronecker productsWenlei Gao, Gian Matharu, and Mauricio D. Sacchi12 February 2020 | GEOPHYSICS, Vol. 85, No. 2Higher-order source-wavefield reconstruction for reverse time migration from stored values in a boundary strip just one point wideWim A. Mulder1 December 2017 | GEOPHYSICS, Vol. 83, No. 1Elastic least-squares reverse time migration via linearized elastic full-waveform inversion with pseudo-Hessian preconditioningKe Chen and Mauricio D. Sacchi27 July 2017 | GEOPHYSICS, Vol. 82, No. 5Least-squares migration in the presence of velocity errorsSimon Luo* and Dave Hale5 August 2014Least-squares migration in the presence of velocity errorsSimon Luo and Dave Hale3 July 2014 | GEOPHYSICS, Vol. 79, No. 4Separating traveltimes and amplitudes in waveform inversionSimon Luo and Dave Hale19 August 2013Seismic attenuation imaging with causality17 November 2010 | Geophysical Journal International, Vol. 184, No. 1Velocity and attenuation perturbations can hardly be determined simultaneously in acoustic attenuation scatteringW.A. Mulder and B. Hak14 October 2009Automatic migration velocity analysis and multiplesWim A. Mulder and Tristan van Leeuwen15 December 2008A comparison between one‐way and two‐way wave‐equation migrationGEOPHYSICS, Vol. 69, No. 6Frequency-domain finite-difference amplitude-preserving migrationGeophysical Journal International, Vol. 157, No. 3 SEG Technical Program Expanded Abstracts 2002ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2002 Pages: 2478 publication data© 2002 Copyright © 2002 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 03 Jan 2005 CITATION INFORMATION S. Østmo, W. A. Mulder, and R.‐E. Plessix, (2002), "Finite‐difference iterative migration by linearized waveform inversion in the frequency domain," SEG Technical Program Expanded Abstracts : 1384-1387. https://doi.org/10.1190/1.1816917 Plain-Language Summary PDF DownloadLoading ...
Emotional reactions of haemophilia health care providers (1999)

This study investigated the prevalence and impact of job burnout and job satisfaction among health care professionals working with HIV-infected patients with haemophilia, using a survey that included the Maslach Burnout Inventory (MBI). A minority (7.4%) of the 213 respondents met the criteria for job burnout as assessed by the MBI. Nearly 90% of the respondents reported 'liking' their job, although only 46% anticipated being in the same job in 5 years. The following factors were associated with increased degrees of burnout: greater perceived colleague stress, less overall job satisfaction, greater perceived stress in the working environment, fewer team meetings and fewer years of career experience. Mental health professionals were also less likely than physicians to report burnout. A multiple logistic regression found that providers who reported stress with colleagues were 42% more likely than their peers to be classified as experiencing a high level of job burnout. This study underscores the importance of a well-functioning team in buffering the inevitable stresses of caring for haemophilia patients with HIV.
OpenFluor– an online spectral library of auto-fluorescence by organic compounds in the environment (2013)

An online repository of published organic fluorescence spectra has been developed, which can be searched for quantitative matches with any set of unknown spectra.
Mortality at Low and High Estimated Glomerular Filtration Rate Values: A ‘U’ Shaped Curve (2008)

As a marker of mortality, both low and high eGFRs are equally predictive of increased mortality in community patients, exhibiting a 'U' shaped curve. Thus, current CKD guidelines which recommend inaction or even the non-reporting of eGFR values greater than 60-90 ml/min/1.73 m(2) may not identify patients who are at an equally high risk of dying as those where intervention is recommended.