gebhart/patrepeval huggingface dataset:
Processing of HIV-1 envelope glycoprotein for class I-restricted recognition: dependence on TAP1/2 and mechanisms for cytosolic localization. (1999)

Processing of viral proteins for recognition by CTL involves degradation of the proteins in the cytosol of an infected cell followed by transport of the resulting peptides into the endoplasmic reticulum (ER) by the TAP1/2 complex. Uncertainty exists over the site of processing of viral envelope (env) proteins since the extracellular domains of env proteins are not present in the cytosol where the class I Ag-processing pathway begins. Rather, the ectodomains of env proteins are cotranslationally translocated into the ER during biosynthesis. To analyze env protein processing, we used the herpes simplex virus protein ICP47 to block peptide transport by TAP1/2 and examined the effects of TAP blockade on the processing of the HIV-1 env protein. For the majority of env-specific CD8+ CTL, the processing pathway required TAP1/2-mediated transport of cytosolic peptides into the ER. To determine how env peptides are generated in the cytosol, we analyzed the processing of two TAP1/2-dependent epitopes containing N-linked glycosylation sites. In each case, processing involved glycosylation-dependent posttranslational modification of asparagine residues to aspartic acid. These results are consistent with cotranslational translocation of env into the ER, where glycosylation occurs. This is followed by export of a fraction of the newly synthesized protein into the cytosol, where it is deglycosylated, with conversion of the asparagines to aspartic acid residues. Following cytoplasmic proteolysis, env peptides are retransported by TAP1/2 into the ER, where association with class I occurs. Thus, the env protein can enter the class I pathway through multiple distinct processing mechanisms.
Ability of recombinant or native proteins to protect monkeys against heterologous challenge with Plasmodium falciparum (1991)

To circumvent problems associated with polymorphic vaccine candidates for Plasmodium falciparum malaria, we evaluated recombinant proteins representing sequences from relatively high conserved regions of the precursor to the major merozoite surface proteins, gp190, for their ability to protect Saimiri monkeys against malaria challenge. Recombinant proteins represented amino acid residues 147 to 321 (p190-1) or 147 to 321 and 1060 to 1195 (p190-3), and their efficacy was compared with that of native gp190 and its processed products. All antigens were derived from P. falciparum K1, a Thai isolate, while the challenge strain was Palo Alto (from Uganda, Africa), which contains, with the exception of the N-terminal 375 amino acids, which are almost identical to the K1 sequence, essentially the MAD-20 allelic form of gp190. By 12 days following challenge, each control monkey required drug treatment. Three monkeys injected with p190-3 required therapy, while one cleared the parasites without therapy. Two monkeys injected with p190-1 received therapy on day 14, while the remaining two cleared the parasites without therapy. Of four animals injected with native gp190, because of health reasons unrelated to malaria, one was not challenged with parasites and one was removed from the study 8 days after challenge when its parasitemia was 1.1% (parasitemias in control animals ranged from 4.3 to 9%); the remaining two cleared the parasites after maximum parasitemias of 0.45 and 0.53%. The highest levels of antiparasite antibody were produced by animals immunized with native gp190. There was a significant correlation between monkeys which did not require drug treatment and antiparasite antibody. These results may suggest that native gp190 and/or its processed products can provide excellent protection against heterologous challenge and that antibody is important for protection. The challenge for vaccine development is to identify the protective sequence(s).
Interaction of sweet proteins with their receptor (2004)

The mechanism of interaction of sweet proteins with the T1R2-T1R3 sweet taste receptor has not yet been elucidated. Low molecular mass sweeteners and sweet proteins interact with the same receptor, the human T1R2-T1R3 receptor. The presence on the surface of the proteins of "sweet fingers", i.e. protruding features with chemical groups similar to those of low molecular mass sweeteners that can probe the active site of the receptor, would be consistent with a single mechanism for the two classes of compounds. We have synthesized three cyclic peptides corresponding to the best potential "sweet fingers" of brazzein, monellin and thaumatin, the sweet proteins whose structures are well characterized. NMR data show that all three peptides have a clear tendency, in aqueous solution, to assume hairpin conformations consistent with the conformation of the same sequences in the parent proteins. The peptide corresponding to the only possible loop of brazzein, c[CFYDEKRNLQC(37-47)], exists in solution in a well ordered hairpin conformation very similar to that of the same sequence in the parent protein. However, none of the peptides has a sweet taste. This finding strongly suggests that sweet proteins recognize a binding site different from the one that binds small molecular mass sweeteners. The data of the present work support an alternative mechanism of interaction, the "wedge model", recently proposed for sweet proteins [Temussi, P. A. (2002) FEBS Lett.526, 1-3.].
Receptor-mediated endocytosis of immunoglobulin-coated colloidal gold particles in cultured mouse peritoneal macrophages. Chloroquine and monensin inhibit transfer of the ligand from endocytic vesicles to lysosomes. (1985)

Earlier studies have shown that immunoglobulin G (IgG)-coated colloidal gold particles bind to specific receptors on the macrophage surface and accumulate in coated pits. They are then internalized via endocytic vesicles and transferred to lysosomes. During this process the plasma membrane is depleted of binding sites for IgG, suggesting that both the receptor and the ligand end up in lysosomes. Here, we have examined the effects of the weak base chloroquine and the Na+-H+ ionophore monensin on endocytosis and intracellular transport of IgG-coated colloidal gold particles in cultured macrophages. The results indicate that chloroquine and monensin do not arrest uptake of IgG-coated particles bound to the cell surface. On the other hand, the drugs strongly inhibit transfer of the particles from endocytic vesicles to lysosomes, the latter marked by prior pulse-chase labeling of the cells with horseradish peroxidase. Since the main effect shared by chloroquine and monensin is to raise pH in acid compartments such as endocytic vesicles and lysosomes, the findings suggest that the transfer of IgG-coated particles into the lysosomes is a pH-dependent process. It remains to be shown whether it is the membrane fusion as such that is controlled by pH or, more specifically, the transfer of receptor-bound ligands into the lysosomes.
A study of the photochemical response of <i>o</i>‐nitrobenzyl cholate derivatives in P(MMA‐MAA) matrices (1983)

Abstract Ortho ‐nitrobenzyl cholate esters have been successfully used as photosensitive components in solution inhibition deep UV photoresists. The photochemical behavior of a variety of substituted o ‐nitrobenzyl cholate derivaties has been examined and resist sensitivity is related to the quantum yield of the reaction. The most efficient system examined is o , o ′‐dinitrobenzyl cholate/P(MMA‐MMA), where the quantum yield of photoreaction is 0.2 and resist sensitivity is ca. 150 mJ/cm 2 for a 1.5 μm film. The mode of resist behaviour on irradiation and development is also reported.
Correction of Lethal Intestinal Defect in a Mouse Model of Cystic Fibrosis by Human <i>CFTR</i> (1994)

Cystic fibrosis (CF) is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). A potential animal model of CF, the CFTR-/- mouse, has had limited utility because most mice die from intestinal obstruction during the first month of life. Human CFTR (hCFTR) was expressed in CFTR-/- mice under the control of the rat intestinal fatty acid-binding protein gene promoter. The mice survived and showed functional correction of ileal goblet cell and crypt cell hyperplasia and cyclic adenosine monophosphate-stimulated chloride secretion. These results support the concept that transfer of the hCFTR gene may be a useful strategy for correcting physiologic defects in patients with CF.
Esophagopericardial Fistula Arising From Barrett's Esophagus (1998)

Esophagopericardial fistula is a rare complication of numerous benign, malignant, and traumatic conditions of the esophagus. Approximately 100 cases of fistulae between the esophagus and heart have been reported. We describe the second reported case of an esophagopericardial fistula secondary to a benign esophageal ulcer within Barrett's mucosa without prior surgery. The radiologic, endoscopic, and surgical management of this case are discussed.
Polyfluorene containing diphenylquinoline pendants and their applications in organic light emitting diodes (2005)

Abstract We present a short, efficient synthetic route for the preparation of a novel polyfluorene copolymer (PF‐Q) containing two electron‐deficient, 2,4‐diphenylquinoline groups functionalized at the C‐9 positions of alternate fluorene units that form a three‐dimensional cardostructure. The presence of the rigid bulky pendent groups leads to a polyfluorene possessing a high glass‐transition temperature (207 °C) and very good thermal stability (5% weight loss observed at 460 °C). A photoluminescence study revealed that the Förster energy transfer from the excited quinoline groups to the polyfluorene backbone is very efficient; it also demonstrated that the commonly observed aggregate/excimer formation in polyfluorenes is suppressed very effectively in this polymer, even after it has been annealed at 150 °C for 20 h. A light emitting diode (LED) device prepared with PF‐Q as the emitting layer exhibits a stable blue emission with a maximum brightness of 1121 cd/m 2 at 12 V and a maximum external quantum efficiency of 0.80% at 250 cd/m 2 . We also used PF‐Q, which contains diphenylquinoline units that behave as electron‐transporting side chains, as a host material and doped it with 2.4 wt % of a red‐emitting phosphorescent dye, Os(fppz), to realize a red electroluminescence with CIE color coordinates of (0.66, 0.34). The doped device exhibits a maximum external quantum efficiency of 6.63% (corresponding a luminance efficiency of 8.71 cd/A) at a current density of 47.8 mA/cm 2 , together with a maximum brightness of 10457 cd/m 2 . © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 859–869, 2005
Development and Validation of Stability Indicating UFLC Method for the Estimation of Anti-spasmodic Drug - Valethamate Bromide (2017)

&lt;p&gt;A stability indicating Ultra-Fast Liquid Chromatography (UFLC) method has been developed to estimate valethamate bromide (V&amp;B) in tablet dosage forms and to separate analyte from other degradants and to carryout forced degradation studies. The chromatographic separation was achieved by using phenomenex kinetex 5 μ C&lt;sub&gt;18&lt;/sub&gt; 100A (250x 4.6 mm) column with a flow rate of 1 mL/min in an isocratic mode with the mobile phase consisting of 0.05 M potassium dihydrogen phosphate buffer pH 7.5 (adjusted with potassium hydroxide) and acetonitrile in the ratio of 50:50. The eluents were monitored with PDA detector at 227 nm. In this developed method valethamate bromide was eluted at a retention time of 4.4 ± 0.1 min. The proposed method is having linearity in the concentration range of 2-12 μg/mL. The present method was successfully validated with respect to system suitability, linearity, precision, accuracy, limit of detection (LOD), limit of quantification (LOQ) and robustness as per international council for harmonization (ICH) guidelines. The drug was subjected to different degradation conditions like acid and alkali hydrolysis, oxidation, thermal and UV radiation etc. Peak purity of the drug was passed in all degradation conditions which demonstrated the specificity of assay method for it in presence of degradation products. The proposed method can be applied for determination of valethamate bromide in pure drug and in pharmaceutical formulation.&lt;/p&gt;
<title>Molecular substitution and nonlinear optical properties of chromophores</title> (1997)

Different factors controlling the linear and nonlinear optical (NLO) properties are discussed for conjugated organic materials having linear chain or ladder structure. It is shown that one-dimensional conjugated molecules reveal similar values of hyperpolarizability as molecules with ladder structures having the same geometric length. After normalizing the value of third order nonlinear response to the number of pi-electrons involved, the chain molecules show significantly higher values. The introduction of heteroatoms into the conjugated part of molecules or linking pendent groups to them are efficient means to tailor not only linear but also nonlinear optical properties. One example of heterosubstitution is the introduction of nitrogen into the conjugated main chain which leads to a change of molecular geometry compared to pure hydrocarbon molecules which is connected with a change of absorption and nonlinear optical properties. So azomethine dyes have a blue shifted absorption and lower NLO susceptibility than stilbene dyes. This can be explained by a non-planar structure of the azomethine molecules reducing the overlap of pi-orbitals. A second important modification of optical properties can be reached by partial fluorination of the molecules or by replacing usual acceptors like nitril- or nitrogroups by a trifluoromethyl group. The second order hyperpolarizabilities beta of different fluorine-containing chromophores were determined by solvatochromic measurements. The investigated fluorine-containing chromophores show beta- values as high as standard NLO-dyes like disperse red I but different linear optical properties.
Optical and structural properties of GaN nanopillar and nanostripe arrays with embedded InGaN∕GaN multi-quantum wells (2006)

GaN nanopillar and nanostripe arrays with embedded InGaN∕GaN multi-quantum wells (MQWs) were fabricated by holographic lithography and subsequent reactive ion etching. Etch related damage of the nanostructures was successfully healed through annealing in NH3∕N2 mixtures under optimized conditions. The nanopatterned samples exhibited enhanced luminescence in comparison to the planar wafers. X-ray reciprocal space maps recorded around the asymmetric (101¯5) reflection revealed that the MQWs in both nanopillars and nanostripes relaxed after nanopatterning and adopted a larger in-plane lattice constant than the underlying GaN layer. The pillar relaxation process had no measurable effect on the Stokes shift typically observed in MQWs on c-plane GaN, as evaluated by excitation power dependent photoluminescence (PL) measurements. Angular-resolved PL measurements revealed the extraction of guided modes from the nanopillar arrays.
A Systematic Review of Cost-Effectiveness Analyses Alongside Randomised Controlled Trials of Acupuncture (2012)

Overall, this review demonstrates the cost-effectiveness of acupuncture. Despite such promising results, any generalisation of these results needs to be made with caution given the diversity of diseases and the different status of acupuncture in the various countries.
A Software Product Model Emphasizing Relationships (2004)

Managing software products during software development is essential. A model is needed to model products and facilitates product management. Important product management functions include: 1) version control. 2) configuration management. 3) product consistency management, 4) reference completeness management, and 5) product reuse support. This paper proposes a product model to facilitate the functions above. Since product relationships play important roles in product management, the proposed model especially emphasizes them.
Current photo-initiators in dental materials (2017)

Light induced reactions are based on the absorption of light that excites the electrons of a molecule and can, under favorable circumstances, lead to dissociation, isomerization, abstraction, electron or energy transfer, and bond formation. The most commonly used initiating system for photopolymerizable dental implants is a Type II PI consisting of camphorquinone (CQ) and ethyl 4-dimethylaminobenzoate (DMAB). However, this bimolecular PI-system exhibits numerous significant drawbacks such as low reactivity and stability, especially in water-based formulations. The demand for an appropriate PI for visible light curing is high for dental restoratives. This paper reviews the options of new photoinitiators for restorative materials.
Preface (2018)

Conference Proceedings, OCG. 2018. “Preface”. Central and Eastern European EDem and EGov Days 325 (February):13-14. https://doi.org/10.24989/ocg.v325.1.
Synthesis and Opioid Receptor Affinity of Morphinan and Benzomorphan Derivatives:  Mixed κ Agonists and μ Agonists/Antagonists as Potential Pharmacotherapeutics for Cocaine Dependence (1999)

This report concerns the synthesis and preliminary pharmacological evaluation of a novel series of kappa agonists related to the morphinan (-)-cyclorphan (3a) and the benzomorphan (-)-cyclazocine (2) as potential agents for the pharmacotherapy of cocaine abuse. Recent evidence suggests that agonists acting at kappa opioid receptors may modulate the activity of dopaminergic neurons and alter the neurochemical and behavioral effects of cocaine. We describe the synthesis and chemical characterization of a series of morphinans 3a-c, structural analogues of cyclorphan [(-)-3-hydroxy-N-cyclopropylmethylmorphinan S(+)-mandelate, 3a], the 10-ketomorphinans 4a,b, and the 8-ketobenzomorphan 1b. Binding experiments demonstrated that the cyclobutyl analogue 3b [(-)-3-hydroxy-N-cyclobutylmethylmorphinan S(+)-mandelate, 3b, MCL-101] of cyclorphan (3a) had a high affinity for mu, delta, and kappa opioid receptors in guinea pig brain membranes. Both 3a,b were approximately 2-fold more selective for the kappa receptor than for the mu receptor. However 3b (the cyclobutyl analogue) was 18-fold more selective for the kappa receptor in comparison to the delta receptor, while cyclorphan (3a) had only 4-fold greater affinity for the kappa receptor in comparison to the delta receptor. These findings were confirmed in the antinociceptive tests (tail-flick and acetic acid writhing) in mice, which demonstrated that cyclorphan (3a) produced antinociception that was mediated by the delta receptor while 3b did not produce agonist or antagonist effects at the delta receptor. Both 3a,b had comparable kappa agonist properties. 3a,b had opposing effects at the mu receptor: 3b was a mu agonist whereas 3a was a mu antagonist.
Spectrogram-Based Automatic Modulation Recognition Using Convolutional Neural Network (2018)

We study a system for classifying modulation types with spectrograms obtained through short-time Fourier transform. AWGN-based carrier modulated signals and their spectrograms are generated. In order to extract features from spectrogram automatically, we learned our convolutional neural network model with the generated data. Even at low SNRs, the performance is fairly good, but additional modulation type applications and comparisons with others in various environments are necessary.
Construction of TNF-binding proteins by grafting hypervariable regions of F10 antibody on human fibronectin domain scaffold (2012)

Tumor necrosis factor (TNF) plays a key role in the pathogenesis of various diseases. To study the possibility of constructing TNF-binding proteins by grafting hypervariable regions of immunoglobulins (CDR), we have replaced amino acid sequences of loops from the tenth type III domain of human fibronectin ((10)Fn3) by amino acid sequences of CDR from the light and heavy chains of the anti-TNF antibody F10. The assessment of TNF-binding properties of the resulting proteins by ELISA has revealed the highest activity of Hd3 containing sequences CDR-H1 and CDR-H2 of the antibody F10 and of Hd2 containing sequences CDR-H1 and CDR-H3. The proteins constructed by us on the fibronectin domain scaffold specifically bound TNF during Western blotting and also weakened its cytotoxic effect on L929 line cells. The highest neutralizing activity was demonstrated by the proteins Hd2 and Hd3, which induced, respectively, 10- and 50-fold increase in the EC(50) of TNF.
A Photoemission Study of Ethylene Decomposition on a Co(0001) Surface: Formation of Different Types of Carbon Species (2012)

We have studied the interaction of ethylene on Co(0001) in detail by X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS). At 130 K, the chemisorption and decomposition of C2H4 were found to depend on the vacant sites available on Co(0001). C2H4 chemisorbs dissociatively at low exposures but both dissociatively and molecularly at large exposures. Upon heating, some C2H4(a) desorbs molecularly from the surface, releasing vacant surface sites that result in the simultaneous decomposition of other C2H4(a). C2H2(a) is the surface intermediate for the decomposition of C2H4(a) on Co(0001). At elevated temperatures, C2H2(a) simultaneously undergoes the direct dehydrogenation and the cyclopolymerization–dehydrogenation to form surface C2 cluster and graphitic carbon on Co(0001). At 500 K, C2H4 directly decomposes on Co(0001), forming surface atomic carbon. These results provide novel information on the chemisorption and decomposition of C2H4 on Co(0001) and the nature of resulted carbon species, greatly deepening our fundamental understanding of the relevant heterogeneous catalytic reactions catalyzed by Co-based catalysts and the growth of graphene on Co surfaces by chemical vapor deposition.
Contribution à la modélisation et à la commande des systèmes électrohydrauliques (2006)

In this manuscript, we gave a new result on the stabilization of the nonlinear systems which are only continuous, it acts of the systems defined by a field of vectors which is not derivable. The application of this result, we carried out it for the stabilization of the electrohydraulic systems by taking account of the dynamics of the servovalves used, this without carrying out any linearization of the model descriptions. Indeed, we treated the case of an electrohydraulic system ordered by one and two servovalves, this by taking account of their dynamics. Simulations carried out show that the results obtained are very satisfactory. In order to carry out a comparison we studied various linear controls, in particular, the control by feedback thus the control by return of exit or by a corrector PID. This type of order proves to give good results. Indeed, they made it possible to answer several criteria, for example the response time, going beyond, etc And they led to good results of simulation. Nevertheless, they present some disadvantages. For example a linearization around a point of equilibrium reveals a local character, and thus this technique becomes inappropriate if one seeks to operate on an operating range. This work could also apply to the stabilization of the electropneumatic actuators.