gebhart/patrepeval huggingface dataset:
Enzyme kinetics in reversed micelles (1990)

Enoate reductase (EC 1.3.1.31) can stereospecifically reduce a variety of alpha,beta-unsaturated carboxylates. Its use was extended to apolar media by incorporating the enzyme into a reversed micellar medium. The kinetics of the enzyme in such a medium have been investigated using 2-methylbutenoic acid as substrate and NADH as a cofactor and compared with the reaction rates in aqueous solution. In aqueous solution the enzyme obeys a ping pong mechanism [Bühler et al. (1982) Hoppe-Seyler's Z. Physiol. Chem 363, 609-625]. In 50 mM Hepes pH = 7.0 with ionic strength of 0.05 M the Michaelis constants for NADH and 2-methylbutenoic acid are 20 microM and 6.0 mM respectively. In reversed micelles the kinetics of the reaction (Michaelis constant, maximum velocity as well as inhibitory effects) were markedly different. The rate of the enzymatic reaction of enoate reductase was studied using various concentrations of 2-methylbutenoic acid and various NADH concentrations. In reversed micelles composed of the anionic detergent sodium di(ethylhexyl)sulphosuccinate, the enzymatic reaction deviates substantially from the values in aqueous solution. Using our model (see preceding paper in this issue of the journal), all kinetics could be explained as evolving from enclosure in reversed micelles without any change in the intrinsic rate parameters of the enzyme. So the enzyme itself is unaffected by incorporation in reversed micelles, but the rate of intermicellar exchange as well as the microheterogeneity of the medium, resulting in very high local concentrations of the substrate, are the most important factors altering the reaction pattern. The effect of the composition of the reversed micellar medium was also investigated using either a nonionic or a cationic surfactant. In these solutions too, exchange and microheterogeneity of the medium proved to be the most important parameters influencing the enzymatic reaction. In all reversed micellar solutions inhibition by the enoate was observed at an overall concentration of 0.5-5 mM, implying that a concentration of substrate equal to the Km value in aqueous solution may already cause inhibition in reversed micelles. At this level no inhibition by NADH was observed. The microheterogeneity of the medium also explains this inhibition of the enzyme at relatively low 2-methylbutenoic acid concentrations.
Characterization of A-kinase-anchoring disruptors using a solution-based assay (2006)

Subcellular localization of PKA (cAMP-dependent protein kinase or protein kinase A) is determined by protein-protein interactions between its R (regulatory) subunits and AKAPs (A-kinase-anchoring proteins). In the present paper, we report the development of the Amplified Luminescent Proximity Homogeneous Assay (AlphaScreen) as a means to characterize AKAP-based peptide competitors of PKA anchoring. In this assay, the prototypic anchoring disruptor Ht31 efficiently competed in RIIalpha isoform binding with RII-specific and dual-specificity AKAPs (IC50 values of 1.4+/-0.2 nM and 6+/-1 nM respectively). In contrast, RIalpha isoform binding to a dual-specific AKAP was less efficiently competed (IC50 of 156+/-10 nM). Characterization of two RI-selective anchoring disruptors, RIAD (RI-anchoring disruptor) and PV-38 revealed that RIAD (IC50 of 13+/-1 nM) was 20-fold more potent than PV-38 (IC50 of 304+/-17 nM) and did not compete in the RIIalpha-AKAP interaction. We also observed that the kinetics of RII displacement from pre-formed PKA-AKAP complexes and competition of RII-AKAP complex formation by Ht31 differed by an order of magnitude when the component parts were mixed in vitro. No such difference in potency was seen for RIalpha-AKAP complexes. Thus the AlphaScreen assay may prove to be a valuable tool for detailed characterization of a variety of PKA-AKAP complexes.
TRANSPLANTATION IN HUMANS OF ENCAPSULATED XENOGENEIC CELLS WITHOUT IMMUNOSUPPRESSION (1994)

Aebischer, P; Buchser, E; Joseph, J M; Favre, J; de Tribolet, N; Lysaght, M; Rudnick, S; Goddard, M Author Information
Targeting the epidermal growth factor receptor in cancer: apoptosis takes center stage. (2003)

Aberrant activation of the epidermal growth factor receptor (EGFR) is frequently observed in neoplasia,notably in tumors of epithelial origin. Attempts to treat such tumors with EGFR antagonists have met with remarkable initial successes, particularly when EGFR antagonists were used in combination with chemotherapy or ionizing radiation. Considering the almost ubiquitous expression of the EGFR in normal epithelial tissues, these clinical trials also revealed a surprisingly low rate of adverse side effects associated with EGFR blockade. This review highlights antiapoptotic effects of EGFR activation as they relate to therapeutic efficacy of EGFR blockade. We introduce the concept that control of cell survival through EGFR activation is conditional in the sense that it is rate limiting to tumor cell survival but not to survival of normal epithelial cells. Specifically, normal epithelial cells are provided with a full complement of physiological cell-cell contacts and cell-matrix interactions that lessen their dependence on survival signals provided by the EGFR. By contrast, malignant tumor cells faced with inadequate cell-matrix contacts critically depend on EGFR activation for survival, rendering them more susceptible to apoptosis induction by EGFR blockade. Redundant control of cell survival by the EGFR and extracellular matrix/cell adhesion receptors is enabled, in part, by shared signal transduction pathways that control expression and activation states of members of the Bcl-2 family of apoptosis regulators.
A pore way to heal and regenerate: 21st century thinking on biocompatibility (2016)

This article raises central questions about the definition of biocompatibility, and also about how we assess biocompatibility. We start with the observation that a porous polymer where every pore is spherical, ∼40 microns in diameter and interconnected, can heal into vascularized tissues with little or no fibrosis and good restoration of vascularity (i.e., little or no foreign body reaction). The same polymer in solid form will trigger the classic foreign body reaction characterized by a dense, collagenous foreign body capsule and low vascularity. A widely used definition of biocompatibility is 'the ability of a material to perform with an appropriate host response in a specific application'. With precision-porous polymers, in direct comparison with the same polymer in solid form, we have the same material, in the same application, with two entirely different biological reactions. Can both reactions be 'biocompatible?' This conundrum will be elaborated upon and proposals will be made for future considerations and measurement of biocompatibility.
Identification of a gp130 Cytokine Receptor Critical Site Involved in Oncostatin M Response (2000)

Gp130 cytokine receptor is involved in the formation of multimeric functional receptors for interleukin-6 (IL-6), IL-11, leukemia inhibitory factor (LIF), oncostatin M (OSM), ciliary neurotrophic factor, and cardiotrophin-1. Cloning of the epitope recognized by an OSM-neutralizing anti-gp130 monoclonal antibody identified a portion of gp130 receptor localized in the EF loop of the cytokine binding domain. Site-directed mutagenesis of the corresponding region was carried out by alanine substitution of residues 186-198. To generate type 1 or type 2 OSM receptors, gp130 mutants were expressed together with either LIF receptor beta or OSM receptor beta. When positions Val-189/Tyr-190 and Phe-191/Val-192 were alanine-substituted, Scatchard analyses indicated a complete abrogation of OSM binding to both type receptors. Interestingly, binding of LIF to type 1 receptor was not affected, corroborating the notion that in this case gp130 mostly behaves as a converter protein rather than a binding receptor. The present study demonstrates that positions 189-192 of gp130 cytokine binding domain are essential for OSM binding to both gp130/LIF receptor beta and gp130/OSM receptor beta heterocomplexes.
Potential for patient harm from intrathecal administration of preserved solutions (2000)

Intrathecal drug administration is an important component of the management of malignancy and symptom control. This route of administration reduces systemic adverse effects, but can increase the risk of local adverse effects such as arachnoiditis. It is accepted practice that any spinal injection should not contain any preservatives (such as benzyl alcohol and parabens-containing compounds). The intrathecal administration of solutions preserved with benzyl alcohol has been shown in case studies to increase the risk of adverse neurological events. Available data do not support the safety of intrathecal injection of products preserved with parabens; rather, they demonstrate a need for further investigation. Steps should be taken to ensure that preservative-free products are used. Staff involved with the preparation and administration of intrathecal preparations need to be educated about the risks associated with preservatives in this setting.
Mesocellular Siliceous Foams with Uniformly Sized Cells and Windows (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMesocellular Siliceous Foams with Uniformly Sized Cells and WindowsPatrick Schmidt-Winkel, Wayne W. Lukens,, Dongyuan Zhao, Peidong Yang, Bradley F. Chmelka, and Galen D. StuckyView Author Information Department of Chemistry, Materials Research Laboratory and Department of Chemical Engineering University of California, Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 1999, 121, 1, 254–255Publication Date (Web):December 19, 1998Publication History Received9 September 1998Published online19 December 1998Published inissue 1 January 1999https://pubs.acs.org/doi/10.1021/ja983218ihttps://doi.org/10.1021/ja983218irapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views6348Altmetric-Citations735LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Emulsions,Liquids,Nitrogen,Phase transitions Get e-Alerts
Brain Trauma Leads to Enhanced Lung Inflammation and Injury: Evidence for Role of P4504Fs in Resolution (2006)

Traumatic brain injury is known to cause several secondary effects, which lead to multiple organ dysfunction syndrome. An acute systemic inflammatory response seems to play an integral role in the development of such complications providing the potential for massive secondary injury. We show that a contusion injury to the rat brain causes large migration of inflammatory cells (especially macrophages and neutrophils) in the major airways and alveolar spaces at 24 h post-injury, which is associated with enhanced pulmonary leukotriene B4 (LTB4) production within the lung. However, by 2 weeks after injury, a temporal switch occurs and the resolution of inflammation is underway. We provide evidence that 5-lipoxygenase and Cytochrome P450 4Fs (CYP4Fs), the respective enzymes responsible for LTB4 synthesis and breakdown, play crucial roles in setting the cellular concentration of LTB4. Activation of LTB4 breakdown via induction of CYP4Fs, predominantly in the lung tissue, serves as an endogenous signal to ameliorate further secondary damage. In addition, we show that CYP4Fs are localized primarily in the airways and pulmonary endothelium. Given the fact that adherence to the microvascular endothelium is an initial step in neutrophil diapedesis, the temporally regulated LTB4 clearance in the endothelium presents a novel focus for treatment of pulmonary inflammation after injury.
Control of beta-interferon expression in murine embryonal carcinoma F9 cells. (1989)

Murine embryonal carcinoma F9 cells, a tissue culture model for early embryonic development, do not produce interferon (IFN) in response to poly(I-C), as determined by an antiviral assay. RNase protection analyses were used to examine total RNA extracted from the cells for the presence of beta-IFN RNA. Whereas F9 cells differentiated in vitro with retinoic acid produced a biologically active protein as well as beta-IFN RNA in response to poly(I-C), undifferentiated F9 cells produced no detectable beta-IFN RNA even in the presence of cycloheximide, an IFN-superinducing agent. These results show that undifferentiated embryonal carcinoma cells do not accumulate beta-IFN RNA in response to an IFN-inducing agent, suggesting a transcriptional regulatory mechanism. However, this control mechanism is altered upon differentiation, since the gene can be transcriptionally activated in retinoic acid-differentiated cells.
Changes in conformation and antimicrobial properties caused by replacement ofD-amino acids with α-aminoisobutyric acid in the gramicidin backbone: synthesis and circular dichroic studies (1992)

In an attempt to mimic the stable helical structures of proteins with possible pore-forming ability in membranes, the linear gramicidin backbone has been changed by inserting achiral α-aminoisobutyric acids (Aib) in place of all of the alternatively sequenced D-amino acids. The conformation and biological activity of the synthetic gramicidin A and B analogues have been studied. CD measurements have been used to determine the conformation in solution. The original conformation of gramicidin clearly changes and its antimicrobial activity is reduced in Aib analogues. Although α-helical motifs can be clearly distinguished in analogues, the CD spectra show inherent complexities. The possibility of superposition of different conformations is considered. The potential pore-forming ability of analogues is briefly discussed.
Making waves by time reversal (2005)

We present a methodology that provides a new perspective on modeling and inversion of wave propagation satisfying time‐reversal invariance and reciprocity in generally inhomogeneous media. The approach relies on a representation theorem of the wave equation to express the Green's function between points in the interior as an integral over the response in those points due to sources on a surface surrounding the medium. Following a predictable initial computational effort, Green's functions between arbitrary points in the medium can be computed as needed using a simple cross correlation algorithm.
Apache flink : Stream and batch processing in a single engine (2015)

Modern enterprise applications are currently undergoing a complete paradigm shift away from traditional transactional processing to combined analytical and transactional processing. This challenge of combining two opposing query types in a single database management system results in additional requirements for transaction management as well. In this paper, we discuss our approach to achieve high throughput for transactional query processing while allowing concurrent analytical queries. We present our approach to distributed snapshot isolation and optimized two-phase commit protocols.
Cardiac Safety of Neuromuscular Incapacitating Defensive Devices (2005)

Neuromuscular incapacitation (NMI) devices discharge a pulsed dose of electrical energy to cause muscle contraction and pain. Field data suggest electrical NMI devices present an extremely low risk of injury. One risk of delivering electricity to a human is the induction of ventricular fibrillation (VF). We hypothesized that inducing VF would require a significantly greater NMI discharge than a discharge output by fielded devices. The cardiac safety of NMI discharges was studied in nine pigs weighing 60 +/- 28 kg. The minimum fibrillating level was defined as the lowest discharge that induced VF at least once, the maximum safe level was defined as the highest discharge which could be applied five times without VF induction, and the VF threshold was defined as their average. A safety index was defined as the ratio of the VF threshold to the standard discharge level output by fielded NMI devices. A VF induction protocol was applied to each pig to estimate the VF threshold and safety index. The safety index for stored charge ranged from 15X to 42X as weight increased from 30 to 117 kg (P < 0.001). Discharge levels above standard discharge and weight were independently significant for predicting VF inducibility. The safety index for an NMI discharge was significantly and positively associated with weight. Discharge levels for standard electrical NMI devices have an extremely low probability of inducing VF.
Golimumab, a new human tumor necrosis factor α antibody, administered every four weeks as a subcutaneous injection in psoriatic arthritis: Twenty‐four–week efficacy and safety results of a randomized, placebo‐controlled study (2009)

Treatment with golimumab at doses of 50 mg and 100 mg significantly improved active PsA and associated skin and nail psoriasis through week 24.
Metal-Mediated Synthesis of Medium-Sized Rings (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-Mediated Synthesis of Medium-Sized RingsLarry YetView Author Information Albany Molecular Research, Incorporated, 21 Corporate Circle, P.O. Box 15098, Albany, New York 12212−5098 Cite this: Chem. Rev. 2000, 100, 8, 2963–3008Publication Date (Web):June 17, 2000Publication History Received30 September 1999Published online17 June 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/cr990407qhttps://doi.org/10.1021/cr990407qresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views8560Altmetric-Citations764LEARN 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 Other access optionsGet e-Alertsclose SUBJECTS:Anions,Catalysts,Cyclization,Ethers,Metathesis Get e-Alerts
Phase retrieval with masks using convex optimization (2015)

Signal recovery from the magnitude of the Fourier transform, or equivalently, from the autocorrelation, is a classical problem known as phase retrieval. Due to the absence of phase information, some form of additional information is required in order to be able to uniquely identify the underlying signal. In this work, we consider the problem of phase retrieval using masks. Due to our interest in developing robust algorithms with theoretical guarantees, we explore a convex optimization-based framework. In this work, we show that two specific masks (each mask provides 2n Fourier magnitude measurements) or five specific masks (each mask provides n Fourier magnitude measurements) are sufficient for a convex relaxation of the phase retrieval problem to provably recover almost all signals (up to global phase). We also show that the recovery is stable in the presence of measurement noise. This is a significant improvement over the existing results, which require O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> n) random masks (each mask provides n Fourier magnitude measurements) in order to guarantee unique recovery (up to global phase). Numerical experiments complement our theoretical analysis and show interesting trends, which we hope to explain in a future publication.
Atomic Layer Deposition of Lithium Niobium Oxides as Potential Solid-State Electrolytes for Lithium-Ion Batteries (2017)

The development of solid-state electrolytes by atomic layer deposition (ALD) holds unparalleled advantages toward the fabrication of next-generation solid-state batteries. Lithium niobium oxide (LNO) thin films with well-controlled film thickness and composition were successfully deposited by ALD at a deposition temperature of 235 °C using lithium tert-butoxide and niobium ethoxide as Li and Nb sources, respectively. Furthermore, incorporation of higher Li content was achieved by increasing the Li-to-Nb subcycle ratio. In addition, detailed X-ray absorption near edge structure studies of the amorphous LNO thin films on the Nb L-edge revealed the existence of Nb as Nb<sup>5+</sup> in a distorted octahedral structure. The octahedrons in niobium oxide thin films experienced severe distortions, which could be gradually alleviated upon the introduction of Li atoms into the thin films. The ionic conductivities of the as-prepared LNO thin films were also measured, with the highest value achieving 6.39 × 10<sup>-8</sup> S cm<sup>-1</sup> at 303 K with an activation energy of 0.62 eV.
Phosphate-specific fluorescence labeling under aqueous conditions (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphate-specific fluorescence labeling under aqueous conditionsPoguang. Wang and Roger W. GieseCite this: Anal. Chem. 1993, 65, 23, 3518–3520Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/ac00071a032https://doi.org/10.1021/ac00071a032research-articleACS PublicationsRequest reuse permissionsArticle Views538Altmetric-Citations17LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
The First Controlled Reduction of the High Explosive RDX. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.