gebhart/patrepeval huggingface dataset:
Computational Studies of Transition Metal Selectivity of Octapeptide Repeat Region of Prion Protein (PrP) (2009)

We have presented a detailed theoretical (density functional theory and ONIOM) study on the structure and M-PrP (prion protein) interaction on various prion models, M(PrP) systems (where PrP = HGG, HGGGW x 3H(2)O, and PrP(61-84), and M = Zn, Cu, Ni, Co, Fe, Mn). It was shown that the geometry of the complex [Mn(HGGGW)(H(2)O)] x 2H(2)O is quite different for M = Mn(III) and Mn(II), and partial unfolding occurs only for the M = Mn(III). In [Zn{PrP(61-84)}], Zn(II) forms a bond with carbonyl oxygen of the Pro(84) residue in the axial position. The coordination of transition metal ions to PrP(61-84) induces the significant geometrical changes in the PrP(61-68) and Prp(69-76) octapeptide repeat regions. The Trp(65) and Trp(73) residues come closer to each other. The glutamines Gln(67) and Gln(75) also come closer to one another and result in the formation of a hydrogen bond between the carbonyl carbon of Gln(67) and one of the NH(2) hydrogens of Gln(75). A specific aggregatory effect is found for Co(II) and Mn(II). The relative binding ability of the metal ions increases in the order Zn(II) < Mn(II) < Cu(II) < Fe(II) < Co(II) < Ni(II). The PrP is most distorted upon binding to Co(II) and least distorted upon binding to Zn(II).
DUAL-ANNULAR SLOT PHASE-SHIFTING CELL LOADED WITH MEMS SWITCHES FOR RECONFIGURABLE REFLECTARRAYS (2013)

Reconfigurable reflectarrays require low-loss and lowdispersion active cells in order to achieve efficient beam scanning or beam shaping on a large bandwidth. The low-loss constraint is the more stringent as the introduction of tunable components (such as MEMS) in resonant phase-shifting cells may dramatically decrease their quality factor. In this paper, a comprehensive review of recent developments at IETR and TAS is carried out with the objective to dynamically control complementary resonant modes in a reconfigurable phase-shifting cell. The new topology consists of a dualannular slot loaded with 8 MEMS switches. It operates around 12 GHz and can provide four equidistributed phase states with low dispersion and low losses. 2.
Figure S1 from UGT2B17 Expedites Progression of Castration-Resistant Prostate Cancers by Promoting Ligand-Independent AR Signaling (2023)

&lt;p&gt;Figure S1: Construction of PCa cell lines using the lentiviral approach&lt;/p&gt;
Cross-Reactive, Cell-Mediated Immunity and Protection of Chickens from Lethal H5N1 Influenza Virus Infection in Hong Kong Poultry Markets (2001)

In 1997, avian H5N1 influenza virus transmitted from chickens to humans resulted in 18 confirmed infections. Despite harboring lethal H5N1 influenza viruses, most chickens in the Hong Kong poultry markets showed no disease signs. At this time, H9N2 influenza viruses were cocirculating in the markets. We investigated the role of H9N2 influenza viruses in protecting chickens from lethal H5N1 influenza virus infections. Sera from chickens infected with an H9N2 influenza virus did not cross-react with an H5N1 influenza virus in neutralization or hemagglutination inhibition assays. Most chickens primed with an H9N2 influenza virus 3 to 70 days earlier survived the lethal challenge of an H5N1 influenza virus, but infected birds shed H5N1 influenza virus in their feces. Adoptive transfer of T lymphocytes or CD8(+) T cells from inbred chickens (B(2)/B(2)) infected with an H9N2 influenza virus to naive inbred chickens (B(2)/B(2)) protected them from lethal H5N1 influenza virus. In vitro cytotoxicity assays showed that T lymphocytes or CD8(+) T cells from chickens infected with an H9N2 influenza virus recognized target cells infected with either an H5N1 or H9N2 influenza virus in a dose-dependent manner. Our findings indicate that cross-reactive cellular immunity induced by H9N2 influenza viruses protected chickens from lethal infection with H5N1 influenza viruses in the Hong Kong markets in 1997 but permitted virus shedding in the feces. Our findings are the first to suggest that cross-reactive cellular immunity can change the outcome of avian influenza virus infection in birds in live markets and create a situation for the perpetuation of H5N1 influenza viruses.
Total Ionizing Dose Effects in FDSOI Compact Model for IC Design (2019)

The total ionizing dose (TID) is a well-known reliability issue for integrated circuits (ICs). It consists in changes of MOSFETs dc characteristics following the irradiation of devices in a given radiative environment, such as space environment. TID effects have been investigated from an experimental and theoretical standpoint, and the compact modeling of TID effects has been included into BULK transistor compact models using PSP formalism in the case of uniform and nonuniform energetic distributions of interface traps. However, TID effects are still not included in fully depleted SOI (FDSOI) standard models. In this paper, TID effects modeling is proposed and included in Leti-UTSOI compact model for FDSOI MOSFETs. This model takes both uniform and nonuniform energetic distributions of both gate oxide/silicon and silicon/buried oxide (BOX) interface traps into account, as well as the contribution of oxide/BOX-trapped charges. Validation of the model has been done through TCAD simulations, and we used this model to extract TID parameters from the experimental data.
A Coupled Resonator for Highly Tunable and Amplified Mixer/Filter (2017)

We present an H-shaped resonator made of two clamped-clamped microbeams mechanically coupled at the middle with a strong coupler to achieve, in a single device, mechanical amplification of the response signal, filtering, and frequency conversion simultaneously. Using mechanical amplification combined with combination resonances generated from a mixed-frequency excitation, a wideband tunable filter, and a simultaneous frequency up and down convertors at multiple bands is demonstrated. The proposed coupled structure, when combined with the easy-to-implement technique of frequency mixing, is promising for applications in an RF chain.
Analysis of SRAM bit failure at high frequency operation (2003)

Careful analysis on SRAM bit failure at high frequency operation has been described. Using nano-prober technique, MOS characteristics of failure bit in actual memory cell had been measured directly. That confirmed drain current of PMOS was about one order smaller and threshold voltage was about 1 V higher than that of normal bit. Newly developed unique selective etching technique using hydrazine mixture showed these degradations ware caused by local gate depletion. And TEM observation showed PMOS gate poly-Si of failure bit had a huge grain. Minimizing grain size of gate poly-Si is found to be quite effective for improving drain current degradation and suppressing failure mode.
Inverting the Swelling Trends in Modular Self‐Oscillating Gels Crosslinked by Redox‐Active Metal Bipyridine Complexes (2017)

Abstract The developing field of active, stimuli‐responsive materials is in need for new dynamic architectures that may offer unprecedented chemomechanical switching mechanisms. Toward this goal, syntheses of polymerizable bipyridine ligands, bis(4‐vinylbenzyl)[2,2′‐bipyridine]‐4,4′‐dicarboxylate and N4,N4′‐bis(4‐vinylphenyl)‐2,2′‐bipyridine‐4,4′‐dicarboxamide, and a number of redox‐active Ruthenium(II) and Iron(II) complexes with them are reported. Detailed characterizations by NMR, Fourier transform infrared spectroscopy, high‐resolution mass‐spectrometry, X‐ray, and cyclic voltammetry show that the topology of these molecules allows them to serve as both comonomers and crosslinkers in polymerization reactions. Electronic properties of the ligands are tunable by choosing carboxylate‐ or carboxamido‐linkages between the core and the vinylaryl moieties, leading to a library of Ru and Fe complexes with the M(III)/M(II) standard redox potentials suitable for catalyzing self‐oscillating Belousov–Zhabotinskii (BZ) reaction. New poly( N ‐isopropylacrylamide)‐based redox‐responsive functional gels containing hydrophilic comonomers, which have been prepared using representative Ru bpy complexes as both a crosslinker and redox‐active catalyst, exhibit a unique feature: their swelling/contraction mode switches its dependence on the oxidation state of the Ru center, upon changing the ratio of comonomers in the hybrid gel network. The BZ self‐oscillations of such crosslinked hydrogels have been observed and quantified for both supported film and free‐standing gel samples, demonstrating their potential as chemomechanically active modules for new functional materials.
<title>In-situ histochemical analysis of human coronary artery by Raman spectroscopy compared with biochemical assay</title> (1995)

We have developed a method to analyze quantitatively the biochemical composition of human coronary artery in situ using near infrared Raman spectroscopy. Human coronary arteries were obtained from explanted hearts after heart transplantation. Samples of normal intima/media, adventitia, non-calcified and calcified plaque were illuminated with 830 nm light from a CW Ti:Sapphire laser. The Raman scattered light was collected and coupled into a 1/4 meter spectrometer that dispersed the light onto a liquid nitrogen cooled, deep-depletion CCD detector. Raman spectra with sufficiently high S/N for extracting biochemical information could be collected in under one second. The spectra were analyzed using a recently developed model to quantitate the relative weight fractions of cholesterol, cholesterol esters, triacylglycerol, phospholipids, protein, and calcium salts. After spectral examination, the artery samples were biochemically assayed to determine the total lipid weight and the amount of the major lipid categories as a percentage of the total lipid content. The results of the lipid biochemical assay and the Raman spectral model compare favorably, indicating that relative lipid weights can be accurately determined in situ. Protein and calcium salts assays are underway. This in situ biochemical information may be useful in diagnosing atherosclerosis and studying disease progression.
Real-Time Robust Finger Gaits Planning under Object Shape and Dynamics Uncertainties (2017)

Dexterous manipulation has broad applications in assembly lines, warehouses and agriculture. To perform large-scale manipulation tasks for various objects, a multi-fingered robotic hand sometimes has to sequentially adjust its grasping gestures, i.e. the finger gaits, to address the workspace limits and guarantee the object stability. However, realizing finger gaits planning in dexterous manipulation is challenging due to the complicated grasp quality metrics, uncertainties on object shapes and dynamics (mass and moment of inertia), and unexpected slippage under uncertain contact dynamics. In this paper, a dual-stage optimization based planner is proposed to handle these challenges. In the first stage, a velocity-level finger gaits planner is introduced by combining object grasp quality with hand manipulability. The proposed finger gaits planner is computationally efficient and realizes finger gaiting without 3D model of the object. In the second stage, a robust manipulation controller using robust control and force optimization is proposed to address object dynamics uncertainties and external disturbances. The dual-stage planner is able to guarantee stability under unexpected slippage caused by uncertain contact dynamics. Moreover, it does not require velocity measurement or expensive 3D/6D tactile sensors. The proposed dual-stage optimization based planner is verified by simulations on Mujoco.
Homogeneous Time-Resolved Fluorescence Quenching Assay (TruPoint) for Nucleic Acid Detection (2004)

Laboratories performing genetic screening studies need simplified methods that allow automation for nucleic acid analysis. Ideally, a method should have as few handling steps as possible and allow the use of a closed-tube assay format to reduce the risk of PCR contamination. Different homogeneous assay chemistries have been exploited to integrate amplification and detection to allow simple nucleic acid analysis with minimal post-PCR handling (1)(2)(3)(4)(5).

Double-stranded DNA probes consisting of a 5′-terminus-labeled fluorescent strand and a complementary strand labeled on the 3′ terminus with a quencher have been exploited in homogeneous hybridization (2)(6)(7). Fluorescence signal is generated when the fluorophore strand hybridizes with the target. When the quencher strand hybridizes with the fluorophore strand, the signal from the fluorophore is quenched. Morrison et al. (6) used probes consisting of strands of equal length and a competitive hybridization technology, whereas others have exploited probes consisting of strands with different lengths for detection of PCR products (2)(7).

The use of stable and fluorescent lanthanide chelates has enabled the development of homogeneous assay technologies based on time resolution (8). Time-resolved fluorescence-quenching assays (TR-FQAs), based on energy transfer from a lanthanide chelate to a nonfluorescent quencher, have been applied in various assays of hydrolyzing enzymes (9)(10) and are commercialized as TruPoint™. The first homogeneous PCR assays with lanthanide-labeled probes used an environmentally sensitive terbium chelate, the fluorescence intensity of which changes on probe hybridization (3)(11). Subsequently, the technology was further improved by use of additional quencher probes (12). Recently, a combination of quenching and competitive hybridization has been applied for end-point detection of PCR products (13).

The aim of the present study was to compare two homogeneous PCR assay approaches based on a …
ChemInform Abstract: Diethylaluminum Ethoxide Mediated Crossed Aldol Reaction of Enol Esters with Carbonyl Compounds. (2000)

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.
Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity (2018)

The ten-eleven translocation (TET) protein family, consisting of three isoforms (TET1/2/3), have been found in mammalian cells and have a crucial role in 5-methylcytosine demethylation in genomic DNA through the catalysis of oxidation reactions assisted by 2-oxoglutarate (2OG). DNA methylation/demethylation contributes to the regulation of gene expression at the transcriptional level, and recent studies have revealed that TET1 is highly elevated in malignant cells of various diseases and related to malignant alteration. TET1 inhibitors based on a scaffold of thioether macrocyclic peptides, which have been discovered by the random nonstandard peptide integrated discovery (RaPID) system, are reported. The affinity-based selection was performed against the TET1 compact catalytic domain (TET1CCD) to yield thioether macrocyclic peptides. These peptides exhibited inhibitory activity of the TET1 catalytic domain (TET1CD), with an IC<sub>50</sub> value as low as 1.1 μm. One of the peptides, TiP1, was also able to inhibit TET1CD over TET2CD with tenfold selectivity, although it was likely to target the 2OG binding site; this provides a good starting point to develop more selective inhibitors.
Unusual Features of Vaccinia Virus Extracellular Virion Form Neutralization Resistance Revealed in Human Antibody Responses to the Smallpox Vaccine (2012)

The extracellular virion form (EV) of vaccinia virus (VACV) is essential for viral pathogenesis and is difficult to neutralize with antibodies. Why this is the case and how the smallpox vaccine overcomes this challenge remain incompletely understood. We previously showed that high concentrations of anti-B5 antibodies are insufficient to directly neutralize EV (M. R. Benhnia, et al., J. Virol. 83:1201-1215, 2009). This allowed for at least two possible interpretations: covering the EV surface is insufficient for neutralization, or there are insufficient copies of B5 to allow anti-B5 IgG to cover the whole surface of EV and another viral receptor protein remains active. We endeavored to test these possibilities, focusing on the antibody responses elicited by immunization against smallpox. We tested whether human monoclonal antibodies (MAbs) against the three major EV antigens, B5, A33, and A56, could individually or together neutralize EV. While anti-B5 or anti-A33 (but not anti-A56) MAbs of appropriate isotypes were capable of neutralizing EV in the presence of complement, a mixture of anti-B5, anti-A33, and anti-A56 MAbs was incapable of directly neutralizing EV, even at high concentrations. This remained true when neutralizing the IHD-J strain, which lacks a functional version of the fourth and final known EV surface protein, A34. These immunological data are consistent with the possibility that viral proteins may not be the active component of the EV surface for target cell binding and infectivity. We conclude that the protection afforded by the smallpox vaccine anti-EV response is predominantly mediated not by direct neutralization but by isotype-dependent effector functions, such as complement recruitment for antibodies targeting B5 and A33.
Lateral stress evolution in chromium sulfide cermets with varying excess chromium (2016)

The shock response of chromium sulfide-chromium, a cermet of potential interest as a matrix material for ballistic applications, has been investigated at two molar ratios. Using a combustion synthesis technique allowed for control of the molar ratio of the material, which was investigated under near-stoichiometric (cermet) and excess chromium (interpenetrating composite) conditions, representing chromium:sulfur molar ratios of 1.15:1 and 4:1, respectively. The compacts were investigated via the plate-impact technique, which allowed the material to be loaded under a one-dimensional state of strain. Embedded manganin stress gauges were employed to monitor the temporal evolution of longitudinal and lateral components of stress in both materials. Comparison of these two components has allowed assessment of the variation of material shear strength both with impact pressure/strain-rate and time for the two molar ratio conditions. The two materials exhibited identical material strength despite variations in their excess chromium contents.
On the Use of the Power-Law Model for Interpreting Constant-Phase-Element Parameters (2014)

International audience
Supplementary Figure Legends for Table 1 and Figures 1-6 from Combining Histone Deacetylase Inhibitor Vorinostat with Aurora Kinase Inhibitors Enhances Lymphoma Cell Killing with Repression of c-Myc, hTERT, and microRNA Levels (2023)

Supplementary Figure Legends for Table 1 and Figures 1-6 from Combining Histone Deacetylase Inhibitor Vorinostat with Aurora Kinase Inhibitors Enhances Lymphoma Cell Killing with Repression of c-Myc, hTERT, and microRNA Levels
Broadly Applicable Z‐ and Diastereoselective Ring‐Opening/Cross‐Metathesis Catalyzed by a Dithiolate Ru Complex (2014)

Abstract A broadly applicable Ru‐catalyzed protocol for Z ‐selective ring‐opening/cross‐metathesis (ROCM) is disclosed. In addition to reactions relating to terminal alkenes of different sizes, the first examples of Z ‐selective ROCM processes involving heteroaryl olefins, 1,3‐dienes, and O‐ and S‐substituted alkenes as well as allylic and homoallylic alcohols are reported. Z ‐Selective transformations with an α‐substituted allylic alcohol are shown to afford congested Z alkenes with high diastereoselectivity. Transformations are performed in the presence of 2.0–5.0 mol % of a recently disclosed Ru‐based dithiolate complex that can be easily prepared in a single step from commercially available starting materials. Typically, transformations proceed at ambient temperature and are complete within eight hours; products are obtained in up to 97 % yield, &gt;98:2 Z / E , and &gt;98:2 diastereomeric ratio. The present investigations reveal a mechanistically significant attribute of the Ru‐based dithiolates that arises from electrostatic interactions with anionic S‐based ligands.
Bioactive Synthetic Polymer-Based Polyelectrolyte LbL Coating Assembly on Surface Treated AZ31-Mg Alloys (2023)

Polyelectrolyte layer-by-layer (LbL) films on pretreated Mg containing 3 wt.% Al and 1 wt.% Zn (MgAZ31) alloy surfaces were prepared under physiological conditions offering improved bioresponse and corrosive protection. Pretreatments of the model MgAZ31 substrate surfaces were performed by alkaline and fluoride coating methods. The anti-corrosion and cytocompatibility behavior of pretreated substrates were evaluated. The LbL film assembly consisted of an initial layer of polyethyleneimine (PEI), followed by alternate layers of poly (lactic-co-glycolic acid) (PLGA) and poly (allylamine hydrochloride) (PAH), which self-arrange via electrostatic interactions on the pretreated MgAZ31 alloy substrate surface. The physicochemical characterization, surface morphologies, and microstructures of the LbL films were investigated using Fourier-transformed infrared spectroscopy (FTIR), atomic force microscopy (AFM), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The in vitro stability studies related to the LbL coatings confirmed that the surface treatments are imperative to achieve the lasting stability of PLGA/PAH layers. Electrochemical impedance spectroscopy measurements demonstrated that pretreated and LbL multilayered coated substrates enhanced the corrosion resistance of the bare MgAZ31 alloy. Cytocompatibility studies using human mesenchymal stem cells seeded directly over the substrates showed that the pretreated and LbL-generated surfaces were more cytocompatible, displaying reduced cytotoxicity than the bare MgAZ31. The release of bovine serum albumin protein from the LbL films was also studied. The initial data presented cooperatively demonstrate the promise of creating LbL layers on Mg-related bioresorbable scaffolds to obtain improved surface bio-related activity.
A quantum leap in laser emission (1999)

Medium- and long-haul, high-speed fiber communication systems are dominated by the need for low optical loss and low dispersion, and these systems require laser diodes and photodiodes that emit and detect at 1.33 and 1.55 μm. InGaAs/GaAs quantum dots enable 1.3 μm wavelengths in GaAs-based lasers for fiber-optic communication.
A direct assay for each translocase of the hepatic microsomal glucose-6-phosphatase system (1987)

Conference Article| December 01 1987 A direct assay for each translocase of the hepatic microsomal glucose-6-phosphatase system IAN D. WADDELL; IAN D. WADDELL 1Department of Medicine, Ninewells Hospital and Medical School, Dundee DD1 9SY, U.K. Search for other works by this author on: This Site PubMed Google Scholar ANN BURCHELL ANN BURCHELL * *To whom correspondence should be addressed. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1987) 15 (6): 1125–1126. https://doi.org/10.1042/bst0151125 Article history Received: June 06 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation IAN D. WADDELL, ANN BURCHELL; A direct assay for each translocase of the hepatic microsomal glucose-6-phosphatase system. Biochem Soc Trans 1 December 1987; 15 (6): 1125–1126. doi: https://doi.org/10.1042/bst0151125 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: ER, endoplasmic reticulum This content is only available as a PDF. © 1987 Biochemical Society1987 Article PDF first page preview Close Modal You do not currently have access to this content.