gebhart/patrepeval huggingface dataset:
Improving the Nicotinic Pharmacophore with a Series of (Isoxazole)methylene-1-azacyclic Compounds:  Synthesis, Structure−Activity Relationship, and Molecular Modeling (1999)

A series of (isoxazole)methylene-1-azacyclic compounds was prepared. The compounds were tested for affinity to central nicotinic acetylcholine receptors (nAChRs) and central muscarinic receptors. The compounds covered a broad range of affinities for the nAChRs (IC(50) = 0.32 to >1000 nM), with selectivities for the nAChRs over the muscarinic receptors in the range of 3-183. The high-affinity compound (Z)-26 (3-(4-methyl-5-isoxazolyl)methylene-1-azabicyclo[2.2. 2]octane, IC(50) = 3.2 nM) having only one energy minimum was used as the reference structure in a computational study. This ligand has enabled definition of an important distance parameter, and the existence of this parameter was supported by showing that other potent nicotinic ligands (for example, nicotine and epibatidine) fit the model.
Design and analysis of transitions from rectangular waveguide to layered ridge dielectric waveguide (1996)

Transitions from rectangular waveguide to layered ridge dielectric waveguide are studied both experimentally and theoretically. In addition, a design procedure is given for each transition. The analysis and design procedures are valid for transitions between rectangular waveguide and other open dielectric waveguides such as image guide, insulated image guide, dielectric ridge guide, and inverted strip dielectric waveguide. It is shown that for small dielectric waveguides such as layered ridge dielectric waveguide, a transition which is comprised of a tapered ridge waveguide reduces the radiation loss by at least 1 dB.
Quantum Electrodynamical Metamaterials (2022)

Recent experiments have revealed ultrastrong coupling between light and matter as a promising avenue for modifying material properties, such as electrical transport, chemical reaction rates, and even superconductivity. Here, we explore (ultra)strong coupling as a means for manipulating the optical response of metamaterials based on ensembles of constituent units individually in the ultrastrong coupling regime. We develop a framework based on linear response for quantum electrodynamical systems to study how light-matter coupling affects the optical response. We begin by applying this framework to find the optical response of a two-level emitter coupled to a single cavity mode, which could be seen as a "meta-atom" of a metamaterial built from repeated units of this system. We find optical behaviors ranging from that of a simple two-level system (Lorentz-oscillator) to effectively transparent, as the coupling goes from the weak to deep strong coupling regimes. We explore a one-dimensional chain of these meta-atoms, demonstrating the tunability of its optical behavior. Our scheme may ultimately provide a framework for designing new metamaterials with low-loss, highly-confined modes, as well as tunable (single-photon) nonlinearities.
Distributed Adaptive Output Feedback Control Design and Application to a Formation Flight Experiment (2005)

An approach for augmenting existing distributed controller designs for large-scale interconnected systems with neural network based adaptive elements is proposed. It is assumed that the controllers are interconnected in the same way as the plant and based on the available measurements, a single hidden layer neural network is introduced for each subsystem to partially cancel the effects of the sub-system interconnections and modeling errors on tracking performance. Boundedness of error signals is shown through Lyapunov's direct method. Effectiveness of the approach is demonstrated on a wind tunnel experiment representing aerial vehicles flying in a highly aerodynamically coupled formation. Copyright © 2005 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.
Investigation of Sand Ripple Dynamics with Combined Particle Image and Tracking Velocimetry (2018)

Abstract Accurately assessing the response of sediments to oscillatory flows requires high-resolution fluid velocity and sediment transport measurements at the fluid–sediment interface. Fluid and sediment grain velocities were measured simultaneously with combined particle image and tracking velocimetry under oscillatory flows over movable sand ripples. Three high-speed cameras equipped with varying optical filters were used to distinguish between fluorescent fluid tracers and the grains, from which the fluid and grain velocities were determined, respectively. Individual grains were tracked during transport to determine velocities and trajectories. Sediment grains were first mobilized by a vortex impacting the bed during flow reversal and suspended into the water column just prior to vortex ejection from the ripple crest, similar to previous observations. During phases of maximum flow velocity, additional grains were mobilized by the shear stress and were subsequently suspended. The flow reversed and similar observations were made in the opposite direction. Consequently, four peaks in suspended sediment concentration were observed throughout the flow cycle, consistent with previous observations. However, some previous researchers attributed peaks in suspended sediment concentration occurring during phases of maximum flow velocity to sediment-laden vortices that were shed from adjacent ripples. The measured sediment grain velocities were of similar magnitude and phase to the near-bed fluid velocities when the grains were being advected with the flow. Measurements of suspended sediment concentration agreed well with semiempirical formulations having an average root-mean-square deviation of approximately 4 × 10 −5 m 3 m −3 . Predictions of settling velocity also compared well with the laboratory estimates, agreeing to within 90%.
ChemInform Abstract: A Practical and Catalytic Reductive Olefin Coupling. (2014)

Abstract The described protocol allows the direct C‐C bond formation between alkenes using a readily available iron source as catalyst.
The Human Werner Syndrome Protein Stimulates Repair of Oxidative DNA Base Damage by the DNA Glycosylase NEIL1 (2007)

The mammalian DNA glycosylase, NEIL1, specific for repair of oxidatively damaged bases in the genome via the base excision repair pathway, is activated by reactive oxygen species and prevents toxicity due to radiation. We show here that the Werner syndrome protein (WRN), a member of the RecQ family of DNA helicases, associates with NEIL1 in the early damage-sensing step of base excision repair. WRN stimulates NEIL1 in excision of oxidative lesions from bubble DNA substrates. The binary interaction between NEIL1 and WRN (K(D) = 60 nM) involves C-terminal residues 288-349 of NEIL1 and the RecQ C-terminal (RQC) region of WRN, and is independent of the helicase activity WRN. Exposure to oxidative stress enhances the NEIL-WRN association concomitant with their strong nuclear co-localization. WRN-depleted cells accumulate some prototypical oxidized bases (e.g. 8-oxoguanine, FapyG, and FapyA) indicating a physiological function of WRN in oxidative damage repair in mammalian genomes. Interestingly, WRN deficiency does not have an additive effect on in vivo damage accumulation in NEIL1 knockdown cells suggesting that WRN participates in the same repair pathway as NEIL1.
Correction (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Preparation of Barium Strontium Titanate Thin Film by Spray Deposition (2002)

Barium strontium titanate ((Ba,Sr)TiO 3 ; BST) thin films were prepared on platinum-coated silicon substrates using spray deposition. The spray condition (substrate temperature and chamber pressure) dependence on surface roughness for the fired BST thin films was investigated. We obtained BST films thinner than 100 nm on the following properties. Average roughness (Ra) and peak-to-valley value (Rmax) were 3.9 and 130 nm. Dielectric constant and dissipation factor at 1 kHz were 250 and 1.6%. These excellent properties were obtained with even thickness. This method is considered to be advantageous for use with electronic devices that have thin dielectric layers, which make for thin films.
Raman study of nano‐crystalline Ge under high pressure (2006)

Abstract We investigated high pressure behaviour of nano‐crystalline Ge that is free of substrate up to 17 GPa using Raman scattering. Nano‐crystalline Ge has been prepared by stain‐etching of 100 oriented Ge wafer and then lifted off. Electron diffraction measurements revealed that after etching particles retain diamond structure of original mono‐crystalline wafer. The Raman peak corresponding to zone‐center optical phonons mode was found to be shifted at ambient conditions from 300 cm –1 found in c‐Ge to around 280(1) cm –1 in nano‐crystalline Ge. Particle size was estimated from Raman and TEM measurements to be ∼5 nm. We observed no pressure transformation from the diamond to a high pressure phase as expected for bulk Ge (at around 10 GPa) in our Raman measurements. The pressure dependence of the Raman peak position was found to be highly nonlinear with d ω /d P = 3.9(1) cm –1 /GPa and d 2 ω /d P 2 = –0.14(2) cm –1 /GPa 2 . We discuss the microscopic origins of observed high pressure behavior of nano‐crystalline Ge. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
PATH-11. PROGNOSTIC SIGNIFICANCE OF EPIGENETIC SUBTYPES AND CpGs ASSOCIATED WITH PROGRESSION TO G-CIMP LOW IN THE EORTC RANDOMIZED PHASE III INTERGROUP CATNON (2020)

Abstract BACKGROUND Uncontrolled studies have suggested that methylation-based epigenetic subtypes can be used for prognostication of glioma. We used the prospective randomized CATNON trial to validate the clinical relevance of these epigenetic subtypes. METHODS The phase III CATNON trial randomized 751 adult patients with newly diagnosed 1p/19q non-codeleted anaplastic glioma to 59.4 Gy radiotherapy +/- concurrent and/or adjuvant TMZ. CNV data and methylation data were derived from Infinium MethylationEPIC arrays. Epigenetic subtyping and risk of progression to G-CIMP low were determined from random forest models and 7 specific CpGs (PMID: 29642018). IDH1/2 status was determined with a glioma-tailored NGS panel. Overall survival (OS) was measured from date of randomization. RESULTS Methylation analysis was performed on 654 tumors: 440 were IDH1/2mt, 204 IDH1/2wt and of 10 IDH1/2 status was unknown; 8 IDH1/2mt were 1p/19q codeleted. Based on methylation, tumors were classified as G-CIMP high (n=409), G-CIMP low (n=19), codel-like (n=18), mesenchymal-like (n=107), classic-like (n=48), and PA-like tumors (n=53). Median OS between these epigenetic subtypes varied considerably: codel-like 9.1 yrs, G-CIMP high 9.5 yrs, G-CIMP low 2.8 yrs, mesenchymal-like 1.3 yrs, classic-like 1.6 yrs, and PA-like 2.8 yrs. The difference in OS of the IDH1/2mt astrocytoma subgroup patients was prominent [G-CIMP low vs G-CIMP high: HR 4.12, 95% CI 2.37-7.19, p &amp;lt; 0.001]. Within the IDH1/2mt G-CIMP high astrocytoma patients, 115 tumors were predicted to have risk of progression to G-CIMP low and patients with such tumors indeed had poorer survival [risk vs no-risk: HR 1.59, 95% CI 1.10-2.31, p = 0.02]. Median OS in G-CIMP high tumors with (n=37) and without (n=366) CDKN2A/B HD was 3.3 yrs versus not reached [p&amp;lt; 0.001], in G-CIMP low tumors it was 1.2 yrs (n=6) versus 4.4 yrs (n=12) [p=0.008]. CONCLUSIONS In IDH1/2mt anaplastic astrocytoma, G-CIMP status and CDKN2A/B HD are of independent prognostic value.
Novel Murine Model To Study Modulation of Genes and Molecular Pathways Induced Following In Vivo Interaction between Multiple Myeloma Cells and Human BM Milieu. (2006)

Abstract Interaction between multiple myeloma (MM) cells and the bone marrow (BM) microenvironment plays a critical role in promoting MM cell growth, survival, migration and development of drug resistance. This interaction within the bone marrow milieu is unique and its understanding is important in evaluating effects of novel agents in vitro and in vivo. We here describe a novel murine model that allows us to study the expression changes in vivo in MM cells within the human BM milieu. In this model, the green fluorescent protein (INA-6 GFP+) transduced IL-6-dependent human MM cell line, INA-6, was injected in human bone chip implanted into SCID mice. At different time points the bone chip was retrieved, cells flushed out and GFP+ MM cells were purified by CD138 MACS microbeads. Similar isolation process was used on INA-6 GFP+ cells cultured in vitro and used as control. Total RNA was isolated from these cells and gene expression profile analyzed using the HG-U133 array chip (Affymetrix) and DChip analyzer program. We have identified significant changes in expression of several genes following in vivo interaction between INA-6 and the BM microenvironment. Specifically, we observed up-regulation of genes associated with cytokines (IL-4, IL-8, IGFB 2–5) and chemokines (CCL2, 5, 6, 18, 24, CCR1, 2, 4), implicated in cell-cell signalling. Moreover genes implicated in DNA transcription (V-Fos, V-Jun, V-kit), adhesion (Integrin alpha 2b, 7, cadherin 1 and 11) and cell growth (CDC14, Cyclin G2, ADRA1A) were also up-regulated and genes involved in apoptosis and cell death (p-57, BCL2, TNF1a) were down-regulated. Using the Ingenuity Pathway Analysis the most relevant pathways modulated by the in vivo interaction between MM cells and BMSCs were IL-6, IGF1, TGF-beta and ERK/MAPK-mediated pathways as well as cell-cycle regulation and chemokine signalling. These results are consistent with previously observed in vitro cell signalling studies. Taken together these results highlight the ability of BM microenvironment to modulate the gene expression profile of the MM cells and our ability to in vivo monitor the changes. This model thus provides us with an ability to study in vivo effects of novel agents on expression profile of MM cells in BM milieu, to pre-clinically characterize their activity.
Preparation of overlapping peptides of bovine retinal S-antigen and their localization by immunoblotting with peptide-specific antibodies (1988)

Bovine retinal S-antigen was cleaved by three chemical cleavage procedures including o-iodosobenzoic acid (IBA), mile acid and cyanogen bromide. The resultant peptides were used to study antibody-defined epitopes. Treatment with IBA, which cleaves primarily at tryptophanyl peptide bonds, produced at least 4 major fragments and several minor fragments. The peptides have been identified by their migration on SDS-PAGE and tested for their immunoreactivity to several affinity-purified anti-CNBr-peptide antibodies and to affinity-purified anti-IBA peptide antibodies. The presence of a single tryptophan residue 194 residues from the amino-terminus should result in 2 fragments of approximately 23,000 and 26,000 molecular weight based on the known size of intact S-antigen. The additional fragmentation is due to the presence of acid labile bonds and cleavage at IBA-sensitive tyrosyl residues associated with a side reaction. Western immunoblots using affinity-purified antibodies against the various IBA and CNBr peptides have allowed location of these peptides within the intact molecule. Specifically, IBA23K and IBA21K are overlapping fragments on the carboxy end, mutally exclusive of all other peptides. IBA15K and IBA5.6K overlap, and IBA18K and IBA10K overlap within IBA26K which comprises the N-terminal half of S-Ag. Additionally, IBA10K contains an antibody epitope destroyed by CNBr cleavage of the methionyl residue between CB53 and CB56. Further characterization of these IBA peptides will expedite the location of possible additional uveitogenic epitopes in the amino-terminal half of S-Ag as well as epitopes lost by other peptide generating techniques.
Springback in Metal Cutting with High Cutting Speeds (2015)

In metal forming springback is a widely researched topic. It is generally referred to as the change of part shape that occurs upon removal of constraints after forming. In cutting this also occurs but on a much smaller level. Literature [1], [2], [3] shows divers results for mostly static or quasi-static experiments leading to simulations without velocityinfluence. Experiments done at IWF of ETH Zürich provide results with cutting speeds from vc =10 to 450 m/min for Aluminiumand Titanium. A cutting speed dependency is shown. Capacitive sensors mounted on a custom made tool holder while oblique cutting on a lathe provide online measurements. Experiments include different cutting edge radii, materials and cutting speeds demonstrating the influence of the springback on cutting forces, tool wear and surface roughness.
Spectroscopic ellipsometry analysis of multilayered TiO<sub>2</sub>‐Ag thin films for photochromic application (2008)

Abstract By altering the surrounding media of metal particles, the wavelength of surface plasma resonance can be tailored, which offers the potential for utilizing of plasma resonance related phenomenon, such as photochromism. Both sandwiched (TiO 2 /Ag/TiO 2 ) and overcoated (TiO 2 /Ag) films with different thicknesses were deposited on quartz substrate by rf helicon magnetron sputtering method. The structure of multilayered TiO 2 ‐Ag films and the concentration of loaded metal Ag in each layer were determined by spectroscopic ellipsometry in high accuracy. The spectral dependent dielectric functions of each layer were obtained, which exhibited typical semiconductor TiO 2 , metal Ag and mixture TiO 2 ‐Ag behaviors, respectively. The surface plasma resonance peak was observed for several extremely thin mixture layers. The apparent redshift of SPR peak from 700 nm to 780 nm was happened with increasing of Ag amount from 35% to 50%. The broadening of SPR peak was found for layer 3 in sample 1 with low concentration Ag embedded in TiO 2 media. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Cycloaddition (2023)

This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.
ChemInform Abstract: Improved Synthesis of 5,11,17,23,29‐Penta‐t‐butylcalix(5)arene‐31,32, 33,34,35‐pentol and Immobilization of the Conformation by O‐Alkylation. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cap‐Dependent Translation Initiation Factor e<scp>IF4E</scp>: An Emerging Anticancer Drug Target (2012)

Cancer cells tend to be more highly dependent on cap-dependent translation than normal tissues. Thus, proteins involved in the initiation of cap-dependent translation have emerged as potential anti-cancer drug targets. Cap-dependent translation is initiated by the binding of the factor eIF4E to the cap domain of mRNA. Detailed x-ray crystal and NMR structures are available for eIF4E in association with cap-analogs, as well as domains of other initiation factors. This review will summarize efforts to design potential antagonist of eIF4E that could be used as new pharmacological tools and anti-cancer agents and. Insights drawn from these studies should aid in the design of future inhibitors of eIF4E dependent translation initiation.
Genomic imprinting effects on complex traits in domesticated animal species (2015)

Monoallelically expressed genes that exert their phenotypic effect in a parent-of-origin specific manner are considered to be subject to genomic imprinting, the most well understood form of epigenetic regulation of gene expression in mammals. The observed differences in allele specific gene expression for imprinted genes are not attributable to differences in DNA sequence information, but to specific chemical modifications of DNA and chromatin proteins. Since the discovery of genomic imprinting some three decades ago, over 100 imprinted mammalian genes have been identified and considerable advances have been made in uncovering the molecular mechanisms regulating imprinted gene expression. While most genomic imprinting studies have focused on mouse models and human biomedical disorders, recent work has highlighted the contributions of imprinted genes to complex trait variation in domestic livestock species. Consequently, greater understanding of genomic imprinting and its effect on agriculturally important traits is predicted to have major implications for the future of animal breeding and husbandry. In this review, we discuss genomic imprinting in mammals with particular emphasis on domestic livestock species and consider how this information can be used in animal breeding research and genetic improvement programs.
Recommendation Based on Opportunistic Information Sharing Between Tourists (2008)

We propose a new approach to collaborative filtering in mobile tourist information systems based on spatiotemporal proximity in social contexts. The approach is motivated by a survey of festival visitors confirming that similarities of interests extend beyond events defining specific social contexts. We show how opportunistic information sharing in mobile ad hoc networks can be used to realize decentralized collaborative filtering appropriate for mobile environments and show its equivalence to existing centralized approaches.
Interscan registration using navigator echoes (2004)

A common problem in clinical MRI is anatomic misalignment of imaging slices across successive examinations. This unnecessarily complicates the radiologic assessment of anatomic change over time on serial MRI studies. To address this problem, spherical navigator echoes, which can detect rigid body motion in all six degrees of freedom, were used to guide spatial location and orientation adjustments to an exam prescription to match the reference frame of images acquired in an earlier exam. An initial linear navigator echo is also necessary to effect coarse Z translation adjustments prior to fine six degrees of freedom adjustment with a spherical navigator echo. Results of this technique are presented for head image volumes of five volunteers. Each volunteer was imaged on two scanners. In all cases, the reference frame adjustments provided by the navigator echoes substantially improved the alignment of the latter exam and performed well compared to retrospective image-based registration.