gebhart/patrepeval huggingface dataset:
Dual role of B7 costimulation in obesity-related non-alcoholic steatohepatitis (NASH) and metabolic dysregulation (2014)

The inflammatory state present in obesity contributes to obesity-related metabolic dysregulation, including non-alcoholic steatohepatitis (NASH) and insulin resistance. Intercellular interactions between immune cells or between immune cells and hepatic parenchymal cells contribute to the exacerbation of liver inflammation and steatosis in obesity. The co-stimulatory molecules B7.1 and B7.2 are important regulators of cell-cell interactions in several immune processes; however, the role of B7 co-stimulation in obesity-related liver inflammation is still unknown. Here, diet-induced obesity (DIO) studies in mice with genetic inactivation of both B7.1 and B7.2 (Dko) revealed aggravated obesity-related metabolic dysregulation, glucose intolerance and enhanced progression to steatohepatitis due to B7.1/B7.2-double deficiency. The metabolic phenotype of B7.1/B7.2-double deficiency upon DIO was accompanied by increased hepatic and adipose tissue inflammation, associated with largely reduced numbers of regulatory T cells (Tregs) in these organs. In order to assess the role of B7co-stimulation in DIO in a non-Treg lacking environment, we performed antibody-mediated inhibition of B7 molecules in wild-type mice in DIO. Antibody-blockade of both B7.1 and B7.2, but not of either one alone, improved the metabolic phenotype of DIO-mice, which was linked to amelioration of hepatic steatosis and reduced inflammation in liver and adipose tissue. Our study demonstrates a dual role of B7 co-stimulation in the course of obesity-related sequelae, particularly NASH. The genetic inactivation of B7.1/B7.2 deteriorates obesity-related liver steatosis and metabolic dysregulation likely due to the intrinsic absence of Tregs in these mice rendering Dko mice a novel murine model of NASH in future studies. In contrast, inhibition of B7 co-stimulation under conditions, where Tregs are present, may provide a novel therapeutic approach for obesity-related metabolic dysregulation and especially NASH.
Chemical vapor deposition of graphene on thin-metal films (2021)

Metal foils, particularly copper and copper-nickel alloy, are commonly used to grow large-area crystalline mono- or bi-layer graphene domains and films by chemical vapor deposition (CVD) methods. Thin-metal films, which are usually made by depositing metals on various substrates such as single-crystal sapphire, have also been reported as catalytic substrates for high-quality graphene growth. Thin-metal films can also serve as intermediates to grow graphene on catalytically inactive substrates, such as dielectrics for electronic devices. Focusing on the CVD growth of graphene on thin-metal films, we review the history of CVD graphene growth, the growth on different single-metals and alloy thin films, and the reported performance of such graphene in electronic devices. We also comment on current challenges and opportunities for the further development of this field.
Macrophages: The Potent Immunoregulatory Innate Immune Cells (2019)

Macrophages are ubiquitously present innate immune cells in humans and animals belonging to both invertebrates and vertebrates. These cells were first recognized by Elia Metchnikoff in 1882 in the larvae of starfish upon insertion of thorns of tangerine tree and later in Daphnia magna or common water flea infected with fungal spores as cells responsible for the process of phagocytosis of foreign particles. Elia Metchnikoff received the Noble prize (Physiology and Medicine) for his discovery and describing the process of phagocytosis in 1908. More than 130 years have passed and different subtypes and roles of macrophages as innate immune cells have been established by the researchers. In addition to their immunoregulatory role in immune homeostasis and pathogenic infection, they also play a crucial role in the pathogenesis of sterile inflammatory conditions including autoimmunity, obesity, and cancer. The present chapter describes the immunoregulatory role of macrophages in the homeostasis and inflammatory diseases varying from autoimmunity to metabolic diseases including obesity.
Statistical properties of local extrema in two-dimensional Gaussian random fields (1998)

This paper is concerned with the statistical properties of the local extrema and local maxima of two-dimensional (2D) Gaussian random fields (GRFs). A GRF may be represented by a linear filtering operation on a white noise field; the spatial properties of the GRF are then determined by the shape of the filter kernel function. New expressions are derived for the mean spatial density of local extrema and for the distribution of local extrema in a 2-D random field. The work is motivated by the problem of detecting known structures in images using 2D matched filters. The new results enable accurate performance predictions to be made of the reliability of such filters in the presence of noise. Case studies are presented for several well-known 2-D filter kernel functions.
Trends in Protein-Based Biosensor Assemblies for Drug Screening and Pharmaceutical Kinetic Studies (2014)

The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.
Learning Protein-Ligand Binding Affinity with Atomic Environment Vectors (2020)

&lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;Scoring functions for the prediction of protein-ligand binding affinity have seen renewed interest in recent years when novel machine learning and deep learning methods started to consistently outperform classical scoring functions. Here we explore the use of atomic environment vectors (AEVs) and feed-forward neural networks, the building blocks of several neural network potentials, for the prediction of protein-ligand binding affinity. The AEV-based scoring function, which we term AEScore, is shown to perform as well or better than other state-of-the-art scoring functions on binding affinity prediction, with an RMSE of 1.22 pK units and a Pearson’s correlation coefficient of 0.83 for the CASF-2016 benchmark. However, AEScore does not perform as well in docking and virtual screening tasks. We therefore show that the model can be combined with the classical scoring function AutoDock Vina in the context of ∆-learning, where corrections to the AutoDock Vina scoring function are learned instead of the protein-ligand binding affinity itself. Combined with AutoDock Vina, ∆-AEScore has an RMSE of 1.32 pK units and a Pearson’s correlation coefficient of 0.80 on the CASF-2016 benchmark, while retaining the good docking and screening power of the underlying classical scoring function. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt;
MnOx−CeO2 Binary Oxides for Catalytic NOx Sorption at Low Temperatures. Sorptive Removal of NOx (2000)

Interactions of nitrogen oxides (NOx) with (n)MnOx−(1 − n)CeO2 binary oxides were studied to use them for sorptive NOx removal at low temperatures (≃150 °C). The formation of MnOx−CeO2 solid solutions with the fluorite-type structure at n ≃ 0.5 was found to be quite effective in accelerating NOx sorption from flowing mixtures of 0.08% NO, 2% O2, and He balance (W/F = 0.24 g·s/cm3). The cumulative NOx uptake was increased by decreasing the reaction temperature and/or by increasing O2 concentration, indicative of chemisorption via oxidation of NO/NO2. In situ FT-IR diffuse reflectance spectrometry demonstrated that adsorption of NOx as bidentate, monodentate, and ionic nitrates is responsible for the large uptake. These adsorbates are produced by oxidative adsorption, which is caused by NO oxidation to NO2 by lattice oxygens bound to Mn and subsequent coordination to Ce in adjacent surface sites. XPS and O2-TPD studies suggested that the active site for NO oxidation should be related to the redox of Mn and accompanying reversible sorption/desorption of lattice oxygens.
Corrosion of high temperature materials in AFBC environments. Part 1 (1500-h tests) (1981)

Candidate heat exchanger tube materials have been tested for times to 1500 h in a small-scale atmospheric fluidized-bed combustor (AFBC) operated by the FluiDyne Corporation of Minneapolis, Minnesota. The materials included alloys 800H and 600; types 304, 310, and 316 stainless steel; and aluminized alloy 800 and type 310 stainless steel. These air-cooled tubes were exposed to the AFBC environment with wall temperatures ranging from 810 to 875/sup 0/C, a Ca/S molar ratio of 3.3 to 5.3, 2.5 to 3.5% excess O/sub 2/, and a fluidizing velocity of 0.7 m/s (2.3 fps). Tubes were removed for examination after 500 h of exposure and at the conclusion of the 1500-h test. In general, the materials performed well with moderate fireside scale formation and slight intergranular corrosion. The notabe exception was catastrophic corrosion of three alloy 600 tubes shortly after resumption of the test following the 500-h segment.
[The atrial contribution to ventricular filling in mitral stenosis. An evaluation by Doppler echocardiography]. (1991)

Using Doppler echocardiography, we have quantified the atrial contribution to ventricular filling in 22 patients with mitral stenosis in sinus rhythm without or with minimal mitral and/or aortic regurgitation. With continuous wave Doppler from apex we obtained the ventricular filling flow from which the valvular area was calculated. The product of the integrated ventricular filling waves multiplying by the valvular area was called total volume (TV). Assuming that the deceleration of the ventricular filling flow is linear and remain constant, we integrated the transmitral flow, this time without considering the atrial filling wave as if the patient was entering into atrial fibrillation. Multiplying this integration by the valvular area we obtained a second volume, atrial fibrillation volume (AFV). The atrial contribution was calculated by: 1) absolute value: TV-AFV and in 2) percent value or fraction: (TV-AFV/TV) x 100. When we correlate absolute and percent values with mitral valve area, the results were statistically significant in both cases (p less than 0.001), with an excellent regression factor both with absolute value r = 0.90 and the percent one r = 0.72. In mitral stenosis the atrial contribution to ventricular filling has an inverse relation with the grade of severity, being very low in the more severe lesions. This is why it would be doubtful that its lost (atrial contribution) is the only cause of hemodynamic deterioration that has been observed in patients who suddenly present atrial fibrillation.
Development and design of DC‐GIS (1999)

In order to realize a reliable, compact, and economical converter station for HVDC transmission, applications of gas insulated switchgear (GIS) for dc transmission lines are considered. The characteristics of dc gas insulation differ from those of ac. The behavior of metallic particles left in the enclosure is one of the largest differences. The accumulation of electrical charges on solid insulators is another essential factor in designing a DC-GIS. Also, degradation of metal oxide arrester blocks under dc stress must be deliberated. Based on the fundamental studies, we developed the components of ± 500-kV DC-GIS. Electrical and mechanical performances of these components have been tested and proven to be satisfactory. Finally these components have been assembled into a full DC-GIS and subjected to a long-term voltage endurance test. In this paper, the design philosophy of ± 500-kV DC-GIS, details of the components, and the test results are described. © 1999 Scripta Technica, Electr Eng Jpn, 129(2): 51–61, 1999
Quantification of fatigue cracking in CT specimens with passive and active piezoelectric sensing (2010)

Monitoring of fatigue cracks in steel bridges is of interest to bridge owners and agencies. Monitoring of fatigue cracks has been attempted with acoustic emission using either resonant or broadband sensors. One drawback of passive sensing is that the data is limited to that caused by growing cracks. In this work, passive emission was complemented with active sensing (piezoelectric wafer active sensors) for enhanced detection capabilities. Passive and active sensing methods were described for fatigue crack monitoring on specialized compact tension specimens. The characteristics of acoustic emission were obtained to understand the correlation of acoustic emission behavior and crack growth. Crack and noise induced signals were interpreted through Swansong II Filter and waveform-based approaches, which are appropriate for data interpretation of field tests. Upon detection of crack extension, active sensing was activated to measure the crack size. Model updating techniques were employed to minimize the difference between the numerical results and experimental data. The long term objective of this research is to develop an in-service prognostic system to monitor structural health and to assess the remaining fatigue life.
Aero-Optical Environment Around a Conformal-Window Turret (2007)

This paper presents the aero-optical environment around a generic conformal-window turret formed from a hemisphere on a short cylindrical base. A suite of optical instruments consisting of a Malley probe, a conventional two-dimensional Shack-Hartmann wave-front sensor, and a new high-bandwidth, lower-resolution Hartmann wave-front sensor were used to measure the aberrations on the wave front of a laser beam emanating from the turret at various angles in both the forward and aft direction in the turret's zenith plane. The measurements were made over a range of Mach numbers from 0.35 to 0.45. Complementary steady- and unsteady-pressure measurements over a slightly larger range of Mach numbers were also made, along with a surface-flow-visualization study of the complex flowfield over and around the turret. The use of the suite of sensors allowed for the recognition and separation of the aberrating optical environment into components associated with stationary disturbances and convecting disturbances at the frequency of the turret's separated wake and at order-of-magnitude-higher frequencies associated with structures that form in the separated shear layers, respectively. The optical data separated in this way are valuable because of the implications for adaptive optics.
The Direct Metalation and Subsequent Functionalization of Trifluoromethyl‐Substituted Pyridines and Quinolines (2003)

Abstract Depending on the choice of the reagent, 2‐(trifluoromethyl)pyridine can be selectively metalated and subsequently carboxylated or otherwise functionalized either at the 3‐ or at the 6‐position. “Optional site selectivity” can also be achieved with 4‐(trifluoromethyl)pyridine, which may be deprotonated either at the 2‐ or at the 3‐position. In contrast, 3‐(trifluoromethyl)pyridine undergoes nucleophilic addition and ensuing decomposition whatever the base. Depending on the reaction conditions, 2‐(trifluoromethyl)quinoline displays reactivity toward lithium reagents at its 3‐, 4‐, or 8‐positions, 3‐(trifluoromethyl)quinolines at the 2‐ or 4‐positions, and 4‐(trifluoromethyl)quinoline at the 2‐ or 3‐positions. It was therefore possible to prepare four trifluoromethyl‐substituted pyridinecarboxylic acids ( 1 , 4 , 9 , and 10 ) and six trifluoromethyl‐substituted quinolinecarboxylic acids ( 11 , 13 , 14 , 15 , 17 , and 18 ) regioisomerically uncontaminated and in a most straightforward way. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
High Q Single-Mode High-Tone Bulk Acoustic Resonator Integrated With Surface-Micromachined FBAR Filter (2005)

This paper describes a novel high-tone bulk acoustic resonator (HBAR) integrated with a surface micromachined FBAR (film bulk acoustic resonator) filter on sapphire substrate. The single-mode HBAR exhibited a quality factor (Q) of 3,580 at 2.5 GHz with total size (including the contact pads) of 0.8×0.4×0.4mm <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> . The integrated narrow band FBAR filter provides adequate suppression (>4dB) of the unwanted modes in the HBAR. This high Q and small size resonator is ideally suited for Pierce oscillator for voltage controlled oscillator (VCO) above 2 GHz.
Permeability of Human Isolated Airways Increases After Hydrogen Peroxide and Poly-L-Arginine (1996)

In asthma, the airway epithelium may be damaged by oxidants and cationic proteins produced by eosinophils. The degree of epithelial damage correlates with the level of bronchial hyperreactivity. An increase in airway permeability to bronchoactive agonists may be one of the factors responsible for airway hyperresponsiveness in asthma. We investigated the effects of the oxidant hydrogen peroxide and the major basic protein (MPB) analogue poly-L-arginine on the permeability and morphology of nonasthmatic human peripheral airways. In addition, we examined whether airway permeability depends on airway size. Human airway tubes (generation 7 to 12) mounted in an organ bath were luminally perfused with Krebs-Henseleit buffer containing the hydrophilic tracer 111In-diethyletriamine pentaacetic acid (111In-DTPA) or the lipophilic tracer 14C-antipyrine (14C-AP). Permeability of the airways was calculated from the fluxes of the tracer molecules across the airway wall. After experiments, light- and electromicroscopic examination of the airway epithelium was performed. Baseline permeability to 14C-AP was five times greater than to 111In-DTPA. Luminal exposure of the airways to 100 mmol/L H2O2 produced a significant, sixfold increase in permeability to 111In-DTPA but not to 14C-AP, indicating the opening of paracellular pathways. The H2O2-induced increase in permeability was partly reversible. Luminal exposure to polyarginine for 3 h and 16 h produced a significant 4.5- and 7-fold increase in permeability to 111In-DTPA, respectively. Histologic examination of epithelium exposed to H2O2 of poly-L-arginine showed focal loss of superficial cells with preservation of basal cells. Baseline airway permeability increased with decreasing airway size (rs = -0.75, p < 0.01). These results suggest that epithelial damage due to eosinophil products may increase airway permeability, and that this may at least partly explain the increased responsiveness to inhaled stimuli in asthma.
Elastolysis Induces Collagenolysis in a Gingival Lamina Propria Model (2006)

Elastin peptides were previously reported to increase MMP expression in several cell types. We found binding of these peptides to their receptors led to enhanced MMP-3 and MMP-1 expression, but not activation, in human gingival fibroblasts cultured on plastic dishes. We hypothesized that these peptides, in a more physiological environment, might additionally trigger an MMP-3/MMP-1 activation cascade, leading to matrix lysis, as occurs in periodontitis. To test this hypothesis, we used contracted and attached lattices as gingival lamina propria equivalents. In such 3D models, supplementation of elastin peptides and plasminogen triggered an MMP-3/MMP-1 activation cascade and significant down-regulation of TIMPs production, further leading to intense collagen degradation. We propose that elastolysis, as occurs in periodontitis, potentiates collagenolysis, thus promoting disease progression.
A Capping Step During Automated Glycan Assembly Enables Access to Complex Glycans in High Yield (2018)

The products of multi-step automated solid phase syntheses are purified after release from the resin. Capping of unreacted nucleophiles is commonplace in automated oligonucleotide synthesis to minimize accumulation of deletion sequences. To date, capping was not used routinely during automated glycan assembly (AGA) since previous capping protocols suffered from long reaction times and conditions incompatible with some protective groups. Here, a method using methanesulfonic acid and acetic anhydride for the fast and quantitative capping of hydroxyl groups that failed to be glycosylated is reported. Commonly used protective groups in AGA are stable under these capping conditions. The introduction of a capping step into the coupling cycle drastically improved overall yields by decreasing side-products and simplifying purification, while reducing building block consumption. To illustrate the method, the biologically important tetrasaccharide Lc4, as well as a 50-mer polymannoside were prepared.
Arginine Methylation of hnRNP A2 Does Not Directly Govern Its Subcellular Localization (2013)

The hnRNP A/B paralogs A1, A2/B1 and A3 are key components of the nuclear 40S hnRNP core particles. Despite a high degree of sequence similarity, increasing evidence suggests they perform additional, functionally distinct roles in RNA metabolism. Here we identify and study the functional consequences of differential post-translational modification of hnRNPs A1, A2 and A3. We show that while arginine residues in the RGG box domain of hnRNP A1 and A3 are almost exhaustively, asymmetrically dimethylated, hnRNP A2 is dimethylated at only a single residue (Arg-254) and this modification is conserved across cell types. It has been suggested that arginine methylation regulates the nucleocytoplasmic distribution of hnRNP A/B proteins. However, we show that transfected cells expressing an A2(R254A) point mutant exhibit no difference in subcellular localization. Similarly, immunostaining and mass spectrometry of endogenous hnRNP A2 in transformed cells reveals a naturally-occurring pool of unmethylated protein but an exclusively nuclear pattern of localization. Our results suggest an alternative role for post-translational arginine methylation of hnRNPs and offer further evidence that the hnRNP A/B paralogs are not functionally redundant.
Self-Assembly of Chiral Nematic-Like Films with Chiral Nanorods Directed by Chiral Molecules (2021)

Chiral superstructures are ubiquitous in nature and display intriguing and elegant performances, which inspired us to realize multiscale chiral mesostructured inorganics. Here, we report cholic acid-induced anisotropic epitaxial growth of chiral CdSe/CdS nanorods (CCCNs) and their self-assembly into chiral nematic-like films (CNFs) via an evaporation-induced self-assembly route. Three levels of chirality exist in the CNFs assembled with CCCNs: a primary chiral distortion of the nanorod, a secondary chiral nematic-like phase in which layered nanobelts are stacked to form with a side-by-side arrangement of the CCCNs, and tertiary helical planks with stacking of the layered chiral nematic-like phase creating a banded spherulite structure. The CNFs exhibited excitonic absorption- and scattering-based optical activities and circularly polarized luminescence due to their hierarchical chirality. © 2021 American Chemical Society.