gebhart/patrepeval huggingface dataset:
Arrestin‐3 binding to JNK1alpha1/JNK2alpha2: modulation of JNK1 and JNK2 activity via scaffolding (2013)

Non‐visual arrestins scaffold mitogen‐activated protein kinase (MAPK) cascades, bringing together three components of MAPK signaling modules. The c‐Jun N‐terminal kinases (JNKs) are members of MAPK family and three JNKs isoforms (JNK1, JNK2, and JNK3) have been identified. JNK1 and JNK2 are ubiquitously expressed, whereas JNK3 is expressed mainly in testes and neuronal tissues. Arrestin‐3 isoform has been shown to enhance JNK3 activity by scaffolding JNK3 with upstream kinases. However, it has not been documented whether arrestin‐3 can modulate the activity of JNK1 and JNK2 isoforms. Using purified proteins we found that arrestin‐3 directly binds JNK1α1 and JNK2α2. Reconstitution of JNK1α1 or JNK2α2 signaling module with either MKK4 or MKK7 in the presence of different arrestin‐3 concentrations showed that arrestin‐3 acts as scaffold, facilitating JNK1α1 and JNK2α2 phosphorylation at optimal concentration. Arrestin‐3 also enhanced phosphorylation of endogenous JNK1 and 2 isoforms when upstream kinases MKK4 or MKK7 were overexpressed together with arrestin‐3 in COS‐7 cells. Thus, the data suggest that arrestin‐3 also modulates JNK1 and JNK2 activity in non‐neuronal cells acting as a scaffold for these JNK isoforms and upstream kinases. Support: NIH Grants NS065868 and DA030103 (EVG), GM077561, GM081756, and EY011500 (VVG), GM059802 and Welch Foundation Grant F‐1390 (KND).
Role of Hydrophobicity on Structure of Polymer−Metal Complexes (2001)

Metal complexation of a series of polymeric gels, with different degrees of ionization, prepared from acrylic acid and acryloyl amino acid monomers (CH2CHCONH(CH2)nCOOH, where n = 4, 6 and 8), were investigated. The binding of Cu(II) ions to the gels was studied by means of swelling, quantitative determination of the amount of “bound” or complexed Cu(II), and EPR spectroscopy of Cu(II) complexes. Both the amount of Cu(II) and the structure of polymer−Cu(II) complex were influenced by the length of the pendent chain, i.e., “hydrophobicity” of the polymer gels. The metal uptake by the gels increases with increasing “hydrophobicity”. Two types of polymer−Cu(II) complexes (monomer and dimer, respectively) were identified by EPR spectroscopy, their concentrations were found to be a function of hydrophilic−hydrophobic balance of the polymer gels.
Combustion Performance of Methane Fermentation Gas with Hydrogen Addition under Various Ignition Timings (2022)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Hydrogen (H2) addition is widely used for natural gas combustion to improve the engine efficiency. However, less attention was paid on the various ignition timings for the maximum brake torque (MBT) and brake thermal efficiency (BTE). In order to check the ignition timing effect, experiments were performed in a spark ignition engine with engine speed fixed on 1500 revolutions per minute (rpm). Firstly, CH4 was only used for combustion with excess air ratio (λ) changing from 0.8 to 1.4. Then, co-combustion of 50 vol% CH4 and 50 vol% CO2 was checked to simulate methane fermentation gas. Finally, H2 was added with volume percentage varying from 5% to 20%. Among these discussions, torque, brake mean effective pressure (BMEP), BTE and cylinder pressure were evaluated. Based on the results, high efficiency can be achieved by advancing the ignition timing with H2 addition at λ=1.4. However, with H2 addition, the ignition timing should be retarded to obtain higher BTE. At the lean-burn condition, through delaying the ignition timing at -20° CA TDC, BTE of 20% H2 addition reaches to 22%, which is even higher than that of CH4 only combustion at stoichiometric condition. Furthermore, the optimal working region for the mixed gas combustion is mapped under various conditions. Besides, H2 addition could improve the combustion stability and decreases CCV and COV in &lt;i&gt;Pmax.&lt;/i&gt;&lt;/div&gt;&lt;/div&gt;
Synthesis and Cytotoxicity of Y2O3 Nanoparticles of Various Morphologies (2009)

As the field of nanotechnology continues to grow, evaluating the cytotoxicity of nanoparticles is important in furthering their application within biomedicine. Here, we report the synthesis, characterization, and cytotoxicity of nanoparticles of different morphologies of yttrium oxide, a promising material for biological imaging applications. Nanoparticles of spherical, rod-like, and platelet morphologies were synthesized via solvothermal and hydrothermal methods and characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), light scattering, surface area analysis, thermogravimetric analysis (TGA), and zeta potential measurements. Nanoparticles were then tested for cytotoxicity with human foreskin fibroblast (HFF) cells, with the goal of elucidating nanoparticle characteristics that influence cytotoxicity. Cellular response was different for the different morphologies, with spherical particles exhibiting no cytotoxicity to HFF cells, rod-like particles increasing cell proliferation, and platelet particles markedly cytotoxic. However, due to differences in the nanoparticle chemistry as determined through the characterization techniques, it is difficult to attribute the cytotoxicity responses to the particle morphology. Rather, the cytotoxicity of the platelet sample appears due to the stabilizing ligand, oleylamine, which was present at higher levels in this sample. This study demonstrates the importance of nanoparticle chemistry on in vitro cytotoxicity, and highlights the general importance of thorough nanoparticle characterization as a prerequisite to understanding nanoparticle cytotoxicity.
Online sensing of volatile organic compounds in groundwater using mid-infrared fibre optic evanescent wave spectroscopy: a pilot scale test (2003)

A prototype sensing system for in-situ monitoring of volatile organic compounds in contaminated groundwater was tested at a pilot scale plant. The sensor consists of a commercially available Fourier transform infrared spectrometer, connected to a 6 m long infrared transparent silver halide fibre optic cable. A 10 cm long core-only section at the centre of the fibre is mounted on a sensor head and coated with a hydrophobic polymer layer, while the remaining fibre is protected by Teflon tubing and thus not in contact with the surrounding media. The sensor head was immersed into the monitoring wells of the pilot plant testing the sensor system under circumstances close to field conditions and typical for in-situ measurements. The pilot plant consists of a 1 m3 cubic tank filled with gravel. A pump is used to circulate water horizontally through the tank, simulating a natural aquifer. The evolution of the concentration of analytes injected into the system is monitored with time using the developed prototype sensing system. The results are validated by corresponding sampling and analysis with headspace gas chromatography.
Examining &lt;I&gt;Cuphea&lt;/I&gt; as a Potential Host for Western Corn Rootworm (Coleoptera: Chrysomelidae): Larval Development (2008)

In previous crop rotation research, adult emergence traps placed in plots planted to Cuphea PSR-23 (a selected cross of Cuphea viscosissma Jacq. and Cuphea lanceolata Ait.) caught high numbers of adult western corn rootworms, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), suggesting that larvae may have completed development on this broadleaf plant. Because of this observation, a series of greenhouse and field experiments were conducted to test the hypothesis that Cuphea could serve as a host for larval development. Greenhouse-grown plants infested with neonates of a colonized nondiapausing strain of the beetle showed no survival of larvae on Cuphea, although larvae did survive on the positive control (corn, Zea mays L.) and negative control [sorghum, Sorghum bicolor (L.) Moench] plants. Soil samples collected 20 June, 7 July, and 29 July 2005 from field plots planted to Cuphea did not contain rootworm larvae compared with means of 1.28, 0.22, and 0.00 rootworms kg(-1) soil, respectively, for samples collected from plots planted to corn. Emergence traps captured a peak of eight beetles trap(-1) day(-1) from corn plots on 8 July compared with a peak of 0.5 beetle trap(-1) day(-1) on 4 August from Cuphea plots. Even though a few adult beetles were again captured in the emergence traps placed in the Cuphea plots, it is not thought to be the result of successful larval development on Cuphea roots. All the direct evidence reported here supports the conventional belief that rootworm larvae do not survive on broadleaf plants, including Cuphea.
Shear-Dependent Interactions in Hydrophobically Modified Ethylene Oxide Urethane (HEUR) Based Rheology Modifier–Latex Suspensions: Part 1. Molecular Microstructure (2014)

We have studied the microstructure of latex suspensions formulated with hydrophobically modified ethylene (oxide) urethane (HEUR) thickener (or rheology modifier, RM) using small-angle neutron scattering under shear (rheo-SANS). Within the shear rate range studied (0–1000 s–1), the neutron scattering profiles are consistent with a polydisperse core–shell model, with the latex particles comprising the core and an adsorbed layer of water-swollen RM on the latex surface forming the shell. The core–shell structure is isotropic under quiescent conditions but becomes anisotropic under shear (with the major axis along the vorticity direction). During shear, the solvent (D2O/H2O) is expelled (hydrodynamic squeezing) from the swollen polymer chains, and the shell structure becomes denser. The anisotropic shell is a result of differing degrees of compression along the flow and vorticity directions. With increasing shear rate, the shell thickness (in both the flow and vorticity direction) tends toward asymptotic values (with the shell thickness in the vorticity direction greater than the shell thickness in the flow direction) independent of the RM hydrophobe density (defined as the average number of hydrophobes per polymer chain). The RM concentration (w/w) in the adsorbed layer varies from ∼0.05–0.1 (at low shear) to ∼0.25–0.4 (high shear, ∼1000 s–1) with higher values for the RM polymer with higher hydrophobe density. The swollen RM-water shell substantially increases the effective volume fraction of the dispersed latex particles. We find, however, that accounting for this increase within the conventional effective hard-sphere (Krieger–Dougherty) dispersion rheology model does not fully explain the higher viscosity of the formulated mixture. We hypothesize the existence of latex–latex interactions mediated by RM polymer bridges even at high shear. The large-scale structure of the particle assembly will be reported in a subsequent manuscript.
Uromodulin Levels Associate with a Common UMOD Variant and Risk for Incident CKD (2009)

Common variants in the region of the UMOD gene, which encodes uromodulin (Tamm-Horsfall protein), associate with chronic kidney disease (CKD) and estimated GFR (eGFR). Whether uromodulin levels associate with UMOD variants or with the risk for developing CKD is unknown. We conducted an age- and gender-matched case-control study (n = 200) of incident CKD (eGFR <60 ml/min per 1.73 m(2)) within the Framingham Heart Study (FHS). Baseline urinary uromodulin concentrations were related to case-control status 9.9 yr later and to genotype at rs4293393. As a replication set, we tested the genotype association with uromodulin concentration in the Atherosclerosis Risk in Communities (ARIC) Study (n = 42). Geometric means of uromodulin concentrations were 51% higher in case than in control subjects (P = 0.016). The adjusted odds ratio of CKD per 1-SD higher concentration of uromodulin was 1.72 (95% confidence interval 1.07 to 2.77; P = 0.03) after accounting for CKD risk factors and baseline eGFR. We observed lower urinary uromodulin concentrations per each copy of the C allele at rs4293393 in both cohorts. In summary, elevated uromodulin concentrations precede the onset of CKD and associate with a common polymorphism in the UMOD region.
The ABCs (and Ds) of Class I Terpene Cyclase (αC), Trans- Head-to-Tail (αHT) and Head-to-Head (αHH) Prenyltransferase Structures and Mechanisms of Action (2019)

We report the structures of the terpene cyclases Santalum album L. sesquisabinene synthases 1 and 2 and of santalene synthase, in apo forms, and with the sesquisabinene synthases, bound to either farnesyl diphosphate (FPP), farnesyl S-thiolo-diphosphate, FPP containing a POP bridging O-to-CCl2 substitution, or to sabinene, leading to a sequential mechanism for substrate binding and catalysis. We trapped early pre-catalytic inactive open forms that show how ligands initially bind to the apo-proteins, then when the pocket closes, catalysis can proceed. We also show that there are strong structural similarities between the most highly conserved residues in class I cyclases and those in head-to-tail (aHT) trans-prenyl transferases—outside the well-known DDXXD-like and NSE/DTE-like domains. In the aHT prenyltransferases there is a highly conserved Thr>Gln>Asp>Tyr motif and in the cyclases, a similar Thr>Arg>Asp>Tyr domain, these residues forming very similar, extended H-bond networks (rmsd ~1.4 Å) that are involved in catalysis, leading to the proposal that there are 3 key domains in both the cyclases and the aHT prenyltransferases: The AC-domain that binds MgA and MgC; the B domain that binds MgB and leads to pocket closure, ionization, and condensation or cyclization; and the D-domain H-bond network, involved in H+ elimination. In aHH prenyltransferases the overall folds and MgABC motifs are similar to those found in the cyclase and aHT proteins, but the full Thr>Arg/Gln>Asp>Tyr domain is absent and instead there are Tyr/Asp or Tyr/Glu residues that bind to MgC and are highly conserved. Overall, the results are of general interest since they show unexpected similarities between the enzymes that produce the most diverse molecules on Earth: aHT and aHH prenyltransferases, and terpenoid cyclases.
Protecting the Ocular Surface and Improving the Quality of Life of Dry Eye Patients: A Study of the Efficacy of an HP-Guar Containing Ocular Lubricant in a Population of Dry Eye Patients (2009)

The improvements in ocular surface staining and dry eye symptoms with the HPG containing ocular lubricant -- evident as early as the first follow-up visit (Day 7) and continued throughout the 28 days of the study with a concurrent, increase in OPI to a level greater than unity -- indicate that this preparation is a fast-acting, long-lasting, and effective treatment for dry eye. In concurrence with the results from previously published clinical studies, the HPG containing ocular lubricant has shown efficacy in alleviating the signs and symptoms of dry eye as well as affording improved ocular surface protection.
Structure and compressibility of the high-pressure molecular phase II of carbon dioxide (2014)

The structure and equation of state of the crystalline molecular phase II of carbon dioxide have been investigated at room temperature from 15.5 to 57.5 GPa using synchrotron x-ray diffraction methods. The CO${}_{2}$ samples were embedded in neon pressure medium in order to provide quasihydrostatic conditions. The x-ray diffraction patterns of phase II are best described by a tetragonal structure, with space group $P{4}_{2}/mnm$ and 2 molecules per unit cell, in accordance with a previous study [Yoo et al., Phys. Rev. B 65, 104103 (2002)]. There is however a large (15%) difference in the intramolecular C=O bond length between the present study, 1.14(3) \AA{}, and the latter work (1.329--1.366 \AA{}). The present value is similar to that of the free molecule and is in very good agreement with predictions based on density functional theory. The compressibility of CO${}_{2}$-II determined here also disagrees with the previous study: our value for the zero-pressure bulk modulus, ${B}_{0}=8.5(3)$ GPa [with ${B}_{0}^{\ensuremath{'}}={(\ensuremath{\partial}B/\ensuremath{\partial}P)}_{0}=6.29$], is 15.5 times smaller. These findings oppose the view that CO${}_{2}$-II is an intermediate state between the low-pressure molecular phases and the high-pressure nonmolecular forms, consistent with our previous results for phase IV [Datchi et al., Phys. Rev. Lett. 103, 185701 (2009)]. The x-ray diffraction patterns of CO${}_{2}$-II above 15 GPa indicate the presence of a large orthorhombic microstrain. Carrying out density functional theory calculations of the elastic tensor and stress-strain relation, we interpret this as due to the softness of the crystal against deviatoric stress in the [110] and symmetry-related directions. Unlike the other dioxides of the group-14 elements, there is however no mechanical or dynamical instability of the $P{4}_{2}/mnm$ structure in CO${}_{2}$ up to 57.5 GPa at 295 K, and therefore no symmetry lowering to $Pnnm$.
Higher consumption of red and processed meat is associated with adverse cardiovascular magnetic resonance morpho-functional phenotypes: A study of 19,408 UK Biobank participants (2021)

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): British Heart Foundation Clinical Research Training Fellowship No. FS/17/81/33318 European Union’s Horizon 2020 research and innovation programme under grant agreement No 825903 (euCanSHare project). Background Multiple epidemiological studies link greater red and processed meat consumption with poorer cardiovascular outcomes. However, the impact of these exposures on directly measured cardiovascular phenotypes has not been examined in large cohorts. Limited existing studies suggest that the observed associations may be mediated by cardiometabolic diseases and/or novel mechanisms acting via the heart-gut axes. However, few studies systematically examine potential confounding and mediating mechanisms. Purpose We assessed, in the UK Biobank, the association between meat intake and cardiovascular structure and function incorporating a comprehensive range of confounders and mediators. Methods We studied 19,408 participants with cardiovascular magnetic resonance (CMR) data. We determined average daily red and processed meat intake using food frequency questionnaires. We used oily fish as a comparator linked to favourable cardiac health. We considered conventional CMR measures (ventricular volumes, left ventricular mass, ejection fraction, stroke volume), novel CMR radiomics features (shape, texture), and arterial stiffness metrics (arterial stiffness index, aortic distensibility). Multivariable linear regression models were used to investigate associations between meat/fish intake and cardiovascular phenotypes, adjusting for age, sex, deprivation, educational level, smoking, alcohol intake, and exercise. In separate models, we investigated the mediating role of cardiometabolic morbidities. Results Higher intake of red and processed meat was associated with an adverse overall pattern of right and left ventricular remodelling, poorer cardiac function, and higher arterial stiffness. Conversely, higher oily fish intake was associated with a healthy cardiovascular phenotype (better ventricular function, greater arterial compliance). Radiomics analysis showed association of the different dietary habits with unique overall geometry of the ventricles and myocardial texture. These associations were partially mediated by cardiometabolic morbidities. Conclusions Higher red and processed meat consumption is associated with adverse cardiovascular phenotypes. These relationships are not fully explained by mediation through cardiometabolic morbidities suggesting importance of alternative disease pathways. Understanding these potential novel disease mechanisms is important for optimising cardiovascular disease prevention strategies.
Oxidized low-density lipoprotein as a risk factor of thrombosis in antiphospholipid syndrome (2003)

Beta2-Glycoprotein I (beta2-GPI) is a major antigen for anticardiolipin antibodies (aCL, Abs) present in patients with antiphospholipid syndrome (APS). We recently reported that oxidized LDL(oxLDL) is subsequently targeted by beta2-GPI and anti-beta2-GPI auto-Abs and that-carboxyl variants of 7-ketocholesteryl esters, such as 7-ketocholesteryl-9-carboxynonanoate (oxLig-1) and 7-ketocholesteryl-12-carboxy (keto) octadodecanoate (oxLig-2), are ligands for beta2-GPI (J Lipid Re 2001; 42: 697; J Lipid Res 2002; 43: 1486). These beta2-GPI ligands provide an electrostatic interaction between oxLDL and beta2-GPI followed by forming stable complexes (such as Schiff base adducts). The omega-carboxyl function in these ligand is responsible for beta2-GPI binding to oxLDL and the oxLDL-beta2-GPI complexes are anti-beta2-GPI auto-Ab-dependently taken up by macrophages (i.e., by phagocytosis). Our recent observations are consistent with the evidence that beta2-GPI co-localizes with lymphocytes and mononuclear cells in human athero-plaques. Thus, autoimmune thrombogenesis (atherogenesis) is linked to interaction of anti-beta2-GPI Abs with the beta2-GPI-oxLDL complexes. We propose an alternative idea, that an immune response against the beta2-GPI-oxLDL complexes may be involved in mechanisms in the development of atherosclerosis, which has been explained by the theory of 'the response to injury'.
Template Polymerization in Lignin Biosynthesis (1998)

The primary structures of lignins are determined by the sequences not of the constituent monomer residues, which are very similar to one another, but rather of the interunit linkages, which are about ten in number. This configurational determinant has usually been thought to vary randomly among macromolecular lignin chains: the final step in the assembly of the biopolymer, namely the coupling of radical intermediates produced during the dehydrogenative polymerization of monolignols, is not under direct enzymatic control. However, it has now been found that, without covalent participation in radical coupling, lignin macromolecules in vitro cogently promote formation of high molecular weight species from the enzymecatalyzed dehydropolymerization of monolignols. In lignifying tissues such an effect could provide the organization necessary for replicating sequences of interunit linkages along macromolecular lignins chains by a direct template polymerization mechanism. The configurations of the progenitorial lignin chains are presumably established by proteins which proffer arrays of dirigent sites comparable to those that prescribe regio- and stereoselectivity in the phenoxy-radical coupling processes responsible for lignan formation. Among the major families of structural proteins so far described in plant cell walls, the proline-rich proteins (PRPs) would most closely approach the plausible manifestation of such characteristics.
Extensive Supersonic Natural Laminar Flow on the Aerion Business Jet (2007)

Few aircraft are specifically designed to emphasize passive laminar flow at the preliminary design stage. The Aerion natural laminar flow supersonic business jet concept requires just that. This paper discusses some details of the unique technology developed for the design of Aerion’s revolutionary jet. An overview of the laminar flow features of the configuration are presented, along with a summary of the design-oriented transition prediction methodology used for aerodynamic design of the airplane. Results from aerodynamic shape optimizations of the business jet and of a new high Reynolds number supersonic laminar flow experiment are also presented.
Supplementary Figure 1 from Pivotal Roles of Snail Inhibition and RKIP Induction by the Proteasome Inhibitor NPI-0052 in Tumor Cell Chemoimmunosensitization (2023)

Supplementary Figure 1 from Pivotal Roles of Snail Inhibition and RKIP Induction by the Proteasome Inhibitor NPI-0052 in Tumor Cell Chemoimmunosensitization