gebhart/patrepeval huggingface dataset:
Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2 (2009)

Emodin (1,3,8-trihydroxy-6-methyl-anthraquinone) is a moderately potent and poorly selective inhibitor of protein kinase CK2, one of the most pleiotropic serine/threonine protein kinases, implicated in neoplasia and in other global diseases. By virtual screening of the MMS (Molecular Modeling Section) database, we have now identified quinalizarin (1,2,5,8-tetrahydroxyanthraquinone) as an inhibitor of CK2 that is more potent and selective than emodin. CK2 inhibition by quinalizarin is competitive with respect to ATP, with a Ki value of approx. 50 nM. Tested at 1 microM concentration on a panel of 75 protein kinases, quinalizarin drastically inhibits only CK2, with a promiscuity score (11.1), which is the lowest ever reported so far for a CK2 inhibitor. Especially remarkable is the ability of quinalizarin to discriminate between CK2 and a number of kinases, notably DYRK1a (dual-specificity tyrosine-phosphorylated and -regulated kinase), PIM (provirus integration site for Moloney murine leukaemia virus) 1, 2 and 3, HIPK2 (homeodomain-interacting protein kinase-2), MNK1 [MAPK (mitogen-activated protein kinase)-interacting kinase 1], ERK8 (extracellular-signal-regulated kinase 8) and PKD1 (protein kinase D 1), which conversely tend to be inhibited as drastically as CK2 by commercially available CK2 inhibitors. The determination of the crystal structure of a complex between quinalizarin and CK2alpha subunit highlights the relevance of polar interactions in stabilizing the binding, an unusual characteristic for a CK2 inhibitor, and disclose other structural features which may account for the narrow selectivity of this compound. Tested on Jurkat cells, quinalizarin proved able to inhibit endogenous CK2 and to induce apoptosis more efficiently than the commonly used CK2 inhibitors TBB (4,5,6,7-tetrabromo-1H-benzotriazole) and DMAT (2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole).
Forward to 2014 (2013)

The New Year tends to bring change and new developments, and such includes this journal. Entering its seventh year is an achievement in its own right and the journal continues to receive strong aca...
Thiol–maleimide “click” chemistry: evaluating the influence of solvent, initiator, and thiol on the reaction mechanism, kinetics, and selectivity (2015)

The mechanism and kinetics of thiol–maleimide “click” reactions have been modeled computationally under a variety of conditions and further investigated using experimental competition reactions.
CELLULAR UPTAKE AND INTRACELLULAR QUANTIFICATION OF FLUORESCENT LABELED T<sub>20</sub>ME-SATE PROOLIGONUCLEOTIDES (2001)

Fluorescein labeled Me-SATE T20 models were synthesized. The high uptake of these prooligos in HeLa cells was confirmed by fluorescence microscopy, flow cytometry and by spectrofluorometry.
Effect of Fibre Distribution on Infiltration Processing and Fracture Behaviour of Carbon Fibre-Reinforced Aluminium Composites (1991)

Article Effect of Fibre Distribution on Infiltration Processing and Fracture Behaviour of Carbon Fibre-Reinforced Aluminium Composites was published on October 1, 1991 in the journal International Journal of Materials Research (volume 82, issue 10).
Spherical Stereo for the Construction of Immersive VR Environment (2006)

By representing projection of a point at space on a spherical image, called spherical projection, the conventional stereo algorithm can be reformulated. This means that we can acquire the whole surrounding 3D structure of environments for the construction of immersive VR (virtual reality) environment by full view spherical images, called spherical stereo, instead of the conventional approach that uses a normal camera with a limited view to take multiple plane images, reconstructs parts of the environment structure from multiple image pairs, respectively, and finally fuses them as the whole surrounding 3D structure of environments. In this paper we give the concrete approach to realize this spherical stereo method and show the effectiveness of this method.
Vorinostat Enhances the Activity of Temsirolimus in Renal Cell Carcinoma Through Suppression of Survivin Levels (2009)

Vorinostat augmented the anticancer activity of temsirolimus in both in vitro and in vivo models of RCC. The effectiveness of the combination was due to a decrease in survivin levels and corresponding induction of apoptosis, and enhanced inhibition of angiogenesis. Targeting survivin may be a promising therapeutic strategy to improve RCC therapy.
Measurement and stability of plasma reduced, oxidized and total coenzyme Q10 in humans (1999)

There are findings indicating that a decreased ratio of plasma coenzyme Q10 (Q10) to LDL cholesterol could be associated with an increased risk of atherosclerosis. Furthermore, the proportion of plasma Q10H2 (reduced Q10, ubiquinol) of total Q10 has been shown to be attenuated in major diseases, such as hyperlipidemia and coronary artery disease. These observations suggest that measurement of plasma total Q10 and the proportion of plasma Q10H2 of total Q10 would be of clinical significance. However, epidemiological studies addressing this issue require large numbers of subjects, and measurements from unfrozen samples are unfeasible. For this reason, we evaluated the stability of Q10 samples during sample storage and processing. We also compared solid phase and hexane pre-treatments prior to high-performance liquid chromatographic determination of Q10. Our results indicate that samples for plasma total Q10 measurement can be pre-treated in normal laboratory lighting conditions, thawed and frozen several times, and stored deep frozen for a couple of years without changes in measured Q10 values. If purification of the samples by silica and C18 is needed, the best reproducibility tends to be achieved with powder treatment (not with cartridges). However, to measure successfully the proportion of plasma ubiquinol of total Q10, samples must be thawed, extracted, and analysed one at a time and quickly to ensure minimal ubiquinol oxidation during the measurement process.
Why Surface Nanobubbles Live for Hours (2013)

We present a theoretical model for the experimentally found but counterintuitive exceptionally long lifetime of surface nanobubbles. We can explain why, under normal experimental conditions, surface nanobubbles are stable for many hours or even up to days rather than the expected microseconds. The limited gas diffusion through the water in the far field, the cooperative effect of nanobubble clusters, and the pinned contact line of the nanobubbles lead to the slow dissolution rate.
Cannabinoids: Occurrence and Medicinal Chemistry (2011)

With an inventory of several hundreds secondary metabolites identified, Cannabis sativa L. (hemp) is one of the phytochemically best characterized plant species. The biomedical relevance of hemp undoubtedly underlies the wealth of data on its constituents and their biological activities, and cannabinoids, a class of unique meroterpenoids derived from the alkylation of an olivetollike alkyl resorcinol with a monoterpene unit, are the most typical constituents of Cannabis. In addition to the well-known psychotropic properties of Δ(9)-THC, cannabinoids have been reported to show potential in various fields of medicine, with the capacity to address unmet needs like the relief of chemotherapy-derived nausea and anorexia, and symptomatic mitigation of multiple sclerosis. Many of the potential therapeutic uses of cannabinoids are related to the interaction with (at least) two cannabinoid G-protein coupled receptors (CB1 and CB2). However, a number of activities, like the antibacterial or the antitumor properties are non totally dependent or fully independent from the interaction with these proteins. These pharmacological activities are particularly interesting since, in principle, they could be easily dissociated by the unwanted psychotropic effects. This review aims at giving readers a survey of the more recent advances in both phytochemistry of C. sativa, the medicinal chemistry of cannabinoids, and their distribution in plants, highlighting the impact that research in these hot fields could have for modern medicinal chemistry and pharmacology.
Gold cluster-laden polydiacetylenes: novel materials for nonlinear optics (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGold cluster-laden polydiacetylenes: novel materials for nonlinear opticsAllan W. Olsen and Zakya H. KafafiCite this: J. Am. Chem. Soc. 1991, 113, 20, 7758–7760Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://doi.org/10.1021/ja00020a046RIGHTS & PERMISSIONSArticle Views234Altmetric-Citations73LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
Workpiece placement optimization for machining operations with a KUKA KR270-2 robot (2013)

Roboticists are faced with new challenges in robotic-based manufacturing. Up to now manufacturing operations that require both high stiffness and accuracy have been mainly realized with computer numerical control machine tools. This paper aims to show that manufacturing finishing tasks can be performed with robotic cells knowing the process cutting conditions and the robot stiffness throughout its Cartesian workspace. It makes sense that the finishing task of large parts should be cheaper with robots. However, machining robots have not been adapted for such operations yet. As a consequence, this paper introduces a methodology that aims to determine the best placement of the workpiece to be machined knowing the elastostatic model of the robot and the cutting forces exerted on the tool. Therefore, a machining quality criterion is proposed and an optimization problem is formulated and solved. The KUKA KR270-2 robot is used as an illustrative example throughout the paper.
Differential inhibition of the Fas- and granule-mediated cytolysis pathways by the orthopoxvirus cytokine response modifier A/SPI-2 and SPI-1 protein. (1996)

Cytotoxic T lymphocytes are important effectors of antiviral immunity, and they induce target cell death either by secretion of cytoplasmic granules containing perforin and granzymes or by signaling through the Fas cell surface antigen. Although it is not known whether the granule-mediated and Fas-mediated cytolytic mechanisms share common components, proteinase activity has been implicated as an important feature of both pathways. The orthopoxviruses cowpox virus and rabbitpox virus each encode three members of the serpin family of proteinase inhibitors, designated SPI-1, SPI-2, and SPI-3. Of these, SPI-2 (also referred to as cytokine response modifier A in cowpox virus) has been shown to inhibit the proteolytic activity of both members of the interleukin 1 beta converting enzyme family and granzyme B. We report here that cells infected with cowpox or rabbitpox viruses exhibit resistance to cytolysis by either cytolytic mechanism. Whereas mutation of the cytokine response modifier A/SPI-2 gene was necessary to relieve inhibition of Fasmediated cytolysis, in some cell types mutation of SPI-1, in addition to cytokine response modifier A/SPI-2, was necessary to completely abrogate inhibition. In contrast, viral inhibition of granule-mediated killing was unaffected by mutation of cytokine response modifier A/SPI-2 alone, and it was relieved only when both the cytokine response modifier A/SPI-2 and SPI-1 genes were inactivated. These results suggest that an interleukin 1 beta converting enzyme-like enzymatic activity is involved in both killing mechanisms and indicate that two viral proteins, SPI-1 and cytokine response modifier A/SPI-2, are necessary to inhibit both cytolysis pathways.
Pyrrolidinoindoline Alkaloids from <i>Psychotria </i><i>o</i><i>leoides </i>and <i>Psychotria </i><i>l</i><i>yciiflora</i> (1999)

The chemical study of two Rubiaceae from New Caledonia, Psychotria lyciiflora and Psychotria oleoides, led to the isolation of several pyrrolidinoindoline alkaloids. Two dimers, the known meso-chimonanthine (9) and the new Nb-desmethyl-meso-chimonanthine (5), and a known trimer, hodgkinsine (1), have been isolated from P. lyciiflora. Hodgkinsine (1), quadrigemine C (2), isopsychotridine B (3), psychotridine (4), and three new alkaloids, quadrigemine I (6), oleoidine (7), and caledonine (8), have been isolated from P. oleoides. Structural assignments of the compounds were based on mass spectra analysis and 2D NMR experiments. A tentative stereochemical determination is made from 2D NMR experiments, circular dichroism study and chemical correlations. Some of these compounds are functional antagonists of somatostatine (SRIH).
Cathodoluminescent Properties of the Rare Earths in Yttrium Oxide (1968)

The cathodoluminescent properties of eleven trivalent rare earths in yttrium oxide (Y2O3) have been studied. Total intensities and selected line intensities were measured as a function of activator concentration. Emission spectra from 2000–30 000 Å, decay times, and energy efficiency are reported.
Reaching out for signals (2005)

ErbB1 receptors situated on cellular filopodia undergo systematic retrograde transport after binding of the epidermal growth factor (EGF) and activation of the receptor tyrosine kinase. Specific inhibitors of the erbB1 receptor tyrosine kinase as well as cytochalasin D, a disruptor of the actin cytoskeleton, abolish transport but not free diffusion of the receptor-ligand complex. Diffusion constants and transport rates were determined with single molecule sensitivity by tracking receptors labeled with EGF conjugated to fluorescent quantum dots. Retrograde transport precedes receptor endocytosis, which occurs at the base of the filopodia. Initiation of transport requires the interaction and concerted activation of at least two liganded receptors and proceeds at a constant rate mediated by association with actin. These findings suggest a mechanism by which filopodia detect the presence and concentration of effector molecules far from the cell body and mediate cellular responses via directed transport of activated receptors.
Group A streptococcal growth phase‐associated virulence factor regulation by a novel operon (Fas) with homologies to two‐component‐type regulators requires a small RNA molecule (2001)

A novel growth phase‐associated two‐component‐type regulator, Fas ( f ibronectin/fibrinogen binding/haemolytic a ctivity/ s treptokinase regulator), of Streptococcus pyogenes was identified in the M1 genome sequence, based on homologies to the histidine protein kinase (HPK) and response regulator (RR) part of the Staphylococcus aureus Agr and Streptococcus pneumoniae Com quorum‐sensing systems. The fas operon, present in all 12 tested M serotypes, was transcribed as polycystronic message ( fasBCA ) and contained genes encoding two potential HPKs (FasB and FasC) and one RR (FasA). Downstream of fasBCA , we identified a small 300 nucleotide monocistronic transcript, designated fasX , that did not appear to encode true peptide sequences. Measurements of luciferase promoter fusions revealed a growth phase‐associated transcription of fasBCA and fasX , with peak activities during the late exponential phase. Insertional mutagenesis disrupting fasBCA and fasA led to a phenotype similar to agr ‐null mutations in S . aureus , with prolonged expression of extracellular matrix protein‐binding adhesins and reduced expression of secreted virulence factors such as streptokinase and streptolysin S. In addition, fasX transcription was dependent on the RR FasA; however, deletion mutagenesis of fasX resulted in a similar phenotype to that of the fasBCA or fasA mutants. Complementation of the fasX deletion mutant, with the fasX gene expressed in trans from a plasmid, restored the wild‐type fasBCA regulation pattern. This strongly suggested that fasX , a putative non‐translated RNA, is the main effector molecule of the fas regulon. However, using spent culture supernatants from wild‐type and fas mutant strains, we were not able to show an influence on the logarithmic growth phase expression of fas and dependent genes. Thus, despite structural and functional similarities between fas and agr , to date the fas operon appears not to be involved in group A streptococcal (GAS) quorum‐sensing regulation.
Noninvasive assessment of liver fibrosis (2010)

Liver biopsy has long been an important tool for assessing the degree of liver fibrosis. Information on the presence and degree of liver fibrosis is useful before making therapeutic decisions or predicting disease outcomes. The need to stage liver fibrosis, however, should decrease as treatment options become more successful (as has occurred with viral hepatitis). In recent years, noninvasive tests have demonstrated a reasonable ability to identify significant fibrosis, cirrhosis in particular, nor is it surprising that liver disease specialists and patients favor a noninvasive approach. However, only those tests with the highest diagnostic accuracy, cost-effectiveness, and availability should be implemented. Apart from their diagnostic accuracy, the potential ability of these tests to predict disease outcomes (a more relevant endpoint) should be compared with that of liver biopsy. Indeed, the use of a standardized system to evaluate the utility of biomarkers would facilitate their implementation in clinical practice.
Iron ochre – a pre‐catalyst for the cracking of methane (2014)

The application of two waste products - iron ochre and methane - to generate two useful products - hydrogen and a magnetic carbon-containing composite - has been demonstrated. Furthermore, the ochre has been shown to comprise tubular morphology extra-cellular biogenic iron oxide which may be of interest in terms of other applications. © 2014 The Authors. <i>Journal of Chemical Technology & Biotechnology</i> published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Certificate revocation list distribution in vehicular communication systems (2008)

The need to evict compromised, faulty, or illegitimate nodes is well understood in prominent projects designing security architectures for Vehicular Communication (VC) systems. The basic approach envisioned to achieve this is via distribution of Certificate Revocation Lists (CRLs). Nonetheless, the problem of how to distribute CRLs effectively and efficiently has not been investigated. In this paper, we addresses exactly this problem. We propose a flexible, simple, and scalable design that leverages on road-side VC infrastructure. Our scheme can distribute large CRLs across wide VC regions within minutes, by utilizing a bandwidth of only a few Kbps at each road-side infrastructure unit.
Nanocluster Nucleation, Growth, and Then Agglomeration Kinetic and Mechanistic Studies:  A More General, Four-Step Mechanism Involving Double Autocatalysis (2005)

The discovery of the four-step, double autocatalytic mechanism by which transition-metal organometallic and metal-salt precursors self-assemble into zerovalent transition-metal nanoclusters under reductive conditions is reported. The prototype system investigated is (1,5-COD)PtCl2 reduction under hydrogen plus 2 equiv of Bu3N and 2 equiv of Proton Sponge (1,8-bis(dimethylamino)naphthalene). The reaction stoichiometry is established by TEM, XPS, NMR, and GLC. A concomitant, fast, cyclohexene hydrogenation reporter reaction is employed to monitor the kinetics of Pt0 product/catalyst formation and agglomeration. After 15 alternative mechanisms were ruled out, a minimalistic (“Ockham's Razor”) mechanism is proposed consisting of four steps: slow continuous nucleation, A → B (rate constant k1), fast autocatalytic surface growth, A + B → 2B (rate constant k2), bimolecular agglomeration, B + B → C (rate constant k3), and a new, unprecedented autocatalytic agglomeration step between small (B) and larger, bulk-metal-like (C) particles, B + C → 1.5C (rate constant k4). The results provide the following: a rare case of a mechanism with two autocatalytic steps in the same reaction scheme (“double autocatalysis”); the most general mechanism to date by which transition-metal nanoparticles nucleate, grow, and agglomerate to bulk metal under reductive conditions; probably the best understood self-assembly mechanism to date for such a large system in which the extensive kinetic studies required for reliable mechanistic deduction also exist; kinetic curves that can have step-function-like shapes; and insights for the synthesis of nanoclusters vs bulk-metal films (notably that higher temperature and lower concentrations favor nanocluster formation, while the opposite conditions favor bulk-metal production). A summary section details the main conclusions plus caveats and remaining questions/future research goals.
The impact of crystalloidal and colloidal infusion preparations on coronary vascular integrity, interstitial oedema and cardiac performance in isolated hearts (2013)

It appears important to maintain the pH value within a physiological range to maintain optimal myocardial contractility. Using colloids prepared in calcium-containing, balanced solutions for volume replacement therapy may attenuate the breakdown of vascular barrier competence in the critically ill.
Cholesteryl Ester Storage Disease: Case Report during Childhood (1999)

Cholesteryl ester storage disease (CESD) is rare and characterized by accumulation of cholesteryl esters and triglycerides in many tissues due to the deficiency of lysosomal acid lipase. We report a 3(1/2)-year-old child with CESD. The diagnosis was indicated by liver biopsy and confirmed by reduced acid lipase activity in leukocytes.
The Influence of Chemical Structure on Polyolefin Melt Rheology and Miscibility (2005)

Abstract The ability to predict polymer properties from a knowledge of the chemical architecture of the chains is one of the main goals of polymer science, and achievement of this can be very useful in the development of new polymeric materials. In this paper the connection between dimensions of polyolefin chains and some of their most fundamental properties, such as the degree of entanglement and miscibility, are described. The experimental and theoretical justifications of these relations are outlined in the first sections, and then the ways these can be used to predict the performance of polyolefins are demonstrated. Finally, other areas where such connections may be found in the future are suggested. Keywords: chemical architecturepolyolefin chainsrheologymiscibilityentanglement Acknowledgments As can be seen from the list of references, the results described in this paper have come from collaborations with many coworkers, both inside and outside of ExxonMobil. Chief among these are Bill Graessley, Nikos Hadjichristidis, Lew Fetters, and César García‐Franco, whom I want to especially thank. I am also grateful to Bryan Chapman for useful suggestions on this manuscript.