gebhart/patrepeval huggingface dataset:
Inhibition of the alternative C3 convertase and classical C5 convertase of complement by group A streptococcal M protein (1990)

When Streptococcus pyogenes group A type 3 strain C203 (M+) and its M-protein-lacking derivative, strain C203S (M-), were treated with normal human serum in the presence of magnesium-EGTA [ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid], virulent M+ bacteria bound only 10 to 30% as much C3 and factors B and P as did avirulent M- bacteria. After treatment of M+ bacteria with trypsin, which inactivates M protein, their binding of these substances was similar to that of M- bacteria. Pretreatment of M+ bacteria with the Fab fragment of rabbit immunoglobulin G anti-M antibody also increased their binding of C3 in the absence of Ca2+. Therefore, M protein inhibits the alternative C3 convertase. In contrast, in the presence of Ca2+ and Mg2+, M+ bacteria bound 75% as much C3 as M- bacteria. This binding was mostly mediated by classical pathway activation, because M+ bacteria bound much smaller amounts of factors B and P than did M- bacteria but consumed amounts of C4 and C2 comparable to those consumed by M- bacteria. On the other hand, the amount of C5 bound to M+ bacteria was much less than that bound to M- bacteria, and the consumption of C5 and C8 by M+ bacteria was also much less than that by M- bacteria. Therefore, M protein does not inhibit the classical C3 convertase but does inhibit the classical C5 convertase. When M+ and M- streptococci were incubated with normal human serum containing radiolabeled C3 in the presence of Ca2+ and Mg2+, more than 85% of the C3 bound to either type of streptococcus was extractable by sodium dodecyl sulfate and alkali treatment. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the C3 extracted from both strains showed that it was mostly C3b and iC3b. The proportions of C3b and iC3b, respectively, were 7.5 and 71.9% on M+ bacteria and 18.9 and 58.4% on M- bacteria. These results support and extend previous findings that the antiphagocytic activity of streptococcal M protein may be due to complement inhibition mediated by the binding of factor H.
Experimental hepatocellular carcinoma: MR receptor imaging. (1991)

Relaxation time measurements and magnetic resonance (MR) imaging were performed in three different animal models of hepatocellular carcinoma (HCC). After intravenous administration of asialoglycoprotein-directed arabinogalactan-stabilized ultrasmall superparamagnetic iron oxide (10 mumol Fe/kg receptor agent), T2 of normal liver decreased from 41.6 msec +/- 1.0 to 19.4 msec +/- 1.7 (P less than .05) in rats. T2 of HCC implanted in normal liver or liver with chronic hepatitis was essentially unchanged. These results were similar to those obtained by administration of a reticuloendothelial cell-directed conventional iron oxide; however, the required dose of receptor agent was lower. MR imaging in a woodchuck model of virally induced HCC confirmed the distribution of the hepatocyte-directed agent to regions of functioning and differentiated hepatocytes but not to malignant tumor tissue. The results suggest that MR receptor imaging may play a role in the differentiation between primary liver tumor and functional liver tissue such as that in normal liver hepatitis or regenerating nodules.
Siah-1 N-Terminal RING Domain Is Required for Proteolysis Function, and C-Terminal Sequences Regulate Oligomerization and Binding to Target Proteins (1999)

The Drosophila seven in absentia (sina) gene was initially discovered because its inactivation leads to R7 photoreceptor defects. Recent data indicate that Sina binds to the Sevenless pathway protein Phyllopod, and together they mediate degradation of Tramtrack, a transcriptional repressor of R7 cell fate. Independent studies have shown that Sina and its highly related mammalian homologues Siah-1 and Siah-2 bind to the DCC (deleted in colorectal cancer) protein and promote its proteolysis via the ubiquitin-proteasome pathway. To determine the roles of mammalian Siahs in proteolysis and their interactions with target proteins, we sought to define Siah-1 domains critical for regulation of DCC. Mutant Siah-1 proteins, harboring missense mutations in the carboxy (C)-terminal domain analogous to those present in Drosophila sina loss-of-function alleles, failed to promote DCC degradation. Point mutations and deletion of the amino (N)-terminal RING finger domain of Siah-1 abrogated its ability to promote DCC proteolysis. In the course of defining Siah-1 sequences required for DCC degradation, we found that Siah-1 is itself rapidly degraded via the proteasome pathway, and RING domain mutations stabilized the Siah-1 protein. Siah-1 was found to oligomerize with itself and other Sina and Siah proteins via C-terminal sequences. Finally, evidence that endogenous Siah-1 regulates DCC proteolysis in cells was obtained through studies of an apparent dominant negative mutant of Siah-1, as well as via an antisense approach. The data indicate that the Siah-1 N-terminal RING domain is required for its proteolysis function, while the C-terminal sequences regulate oligomerization and binding to target proteins, such as DCC.
In question answering, two heads are better than one (2003)

Motivated by the success of ensemble methods in machine learning and other areas of natural language processing, we developed a multi-strategy and multi-source approach to question answering which is based on combining the results from different answering agents searching for answers in multiple corpora. The answering agents adopt fundamentally different strategies, one utilizing primarily knowledge-based mechanisms and the other adopting statistical techniques. We present our multi-level answer resolution algorithm that combines results from the answering agents at the question, passage, and/or answer levels. Experiments evaluating the effectiveness of our answer resolution algorithm show a 35.0% relative improvement over our baseline system in the number of questions correctly answered, and a 32.8% improvement according to the average precision metric.
FemABX Family Members Are Novel Nonribosomal Peptidyltransferases and Important Pathogen-specific Drug Targets (2001)

Pathogen-specific antibiotics kill the offending species without inviting the patient's flora to help develop a resistance mechanism. The current scarcity of pathogen-specific antibiotics reflects the rarity of essential genes that are also not widely represented in and conserved among species. The FemX enzyme that initiates the synthesis of the interchain peptide of the peptidoglycan in a subset of bacterial species was purified from Lactobacillus viridescens. Subsequently, the encoding femX gene was cloned and sequenced using reverse genetics. The femX gene is a member of the femAB family, a large family of genes previously implicated in interchain peptide synthesis but with unknown specific functions. Mutagenesis of the femX gene identified the members of the extended FemABX family as novel nonribosomal peptidyltransferases. Determinants of FemX complex substrate recognition and a strong stimulator of FemX activity were also identified. The FemABX family members are ideal candidates for pathogen-specific antibiotic development.
Magnetic RF integrated thin-film inductors (2002)

The magnetic thin film inductor with a 4-turn, 337/spl times/337 /spl mu/m/sup 2/ size spiral coil showed inductance 21% larger than the air core's while its quality factor was lower than the air core's. Keeping the similar quality factor as the air core, the micro patterned magnetic film inductor showed 11% inductance enhancement. The proposed inductor can be made on the passivation of integrated semiconductor devices.
Photoluminescence up-conversion in InAs/GaAs self-assembled quantum dots (2000)

We report up-converted photoluminescence in a structure with InAs quantum dots embedded in GaAs. An efficient emission from the GaAs barrier is observed with resonant excitation of both the dots and the wetting layer. The intensity of the up-converted luminescence is found to increase superlinearly with the excitation density. The results suggest that the observed effect is due to a two-step two-photon absorption process involving quantum dot states.
Fabricating Arrays of Single Protein Molecules on Glass Using Microcontact Printing (2002)

Microcontact printing biomolecules from elastomeric micropatterned stamps onto surfaces is a versatile method to prepare surfaces for diagnostic applications. We show how to create patterns of proteins having a lengthscale lower than 100 nm using high-resolution microcontact printing. The elastomeric stamps used have meshes composed of 100- and 40-nm-wide lines, arrays of 100 × 400 nm2 features, and arrays of 100-nm-wide posts. The spherical geometry of the posts on the stamps contributes to reduce the printed areas below the effective size of the molded features. Proteins adsorb onto the hydrophobic surface of the stamp during the inking step, and by varying the concentration of the protein solutions, it is possible to adsorb a single or a few protein molecules, such as antibodies (fluorescently labeled) or green fluorescence proteins, on each of the elements forming the high-resolution pattern of the stamp. The transfer of the proteins from the stamp to a hydrophilic glass surface occurs during the printing step. Characterization of the printed patterns using atomic force microscopy and fluorescence confocal microscopy reveals sites unoccupied or occupied by one or more protein molecules that are located within 50 nm of the expected printed locations. The placement of a small number of protein molecules on a surface at precise locations is the key to localizing and identifying single proteins and might constitute a method of choice to study single protein molecules on surfaces.
Design of Hydrophilic Metal Organic Framework Water Adsorbents for Heat Reallocation (2015)

A new hydrothermally stable Al polycarboxylate metal-organic framework (MOF) based on a heteroatom bio-derived aromatic spacer is designed through a template-free green synthesis process. It appears that in some test conditions this MOF outperforms the heat reallocation performances of commercial SAPO-34.
In Depth Analysis on the Unusual Multistep Aggregation Process of Oligo(ethylene glycol) Methacrylate-Based Polymers in Water (2014)

Dynamic thermal phase transition behavior of a thermoresponsive copolymer P(MEO2MA-co-PEGMA2080) synthesized by ATRP random copolymerization of 2-(2-methoxyethoxy)ethyl methacrylate(MEO2MA, Mn = 188 g/mol) and poly(ethylene glycol) methyl ether methacrylate (PEGMA, Mn= 2080 g/mol) in D2O was studied by means of infrared spectroscopy in combination with two-dimensional correlation analysis (2Dcos). Because of the absence of strong intermolecular hydrogen bonding interactions between polymer chains and the amphiphilic property of PEGMA2080 with long ethylene glycol segments, this copolymer exhibited an unusual thermally induced multistep aggregation process. In general, the change of hydrophilic side chain takes place before carbonyl groups and backbones during the whole process and thus the driving force of this phase transition process of P(MEO2MA-co-PEGMA2080) should be hydration changes of side chains. 2Dcos was finally employed to discern the sequence order of all the group motions during heating process in different temperature regions. It is concluded that during the phase transition P(MEO2MA-co-PEGMA2080) chains successively experience “unimers–clusters–micelles– aggregates” four consecutive conformation changes.
Broad spectrum of cytokine abnormalities in panic disorder and posttraumatic stress disorder (2009)

These findings suggest that a generalized inflammatory state may be present in individuals with PD or PTSD.
Fluorinated Amphiphiles Control the Insertion of α-Hemolysin Pores into Lipid Bilayers (2011)

The insertion of fully folded and assembled ion channels and pores into planar lipid bilayers for electrical recording has been facilitated by the use of conventional detergents at a final concentration below the critical micelle concentration (CMC). After the desired number of channels or pores (often one) has been incorporated into a bilayer, it is important to prevent further insertion events, which is often done by awkward techniques such as perfusion. Here, we show that the addition of single-chain fluorinated amphiphiles (F-amphiphiles) with zwitterionic, simple neutral, and neutral oligomeric headgroups at a concentration above the CMC prevents the further insertion of staphylococcal α-hemolysin pores, MspA pores, and Kcv potassium channels into lipid bilayers. We found the commercially available F(6)FC (fluorinated fos-choline with a C(6)F(13)C(2)H(4) chain) to be the least perturbing and most effective agent for this purpose. Bilayers are known to be resistant to F-amphiphiles, which in this case we suppose sequester the pores and channels within amphiphile aggregates. We suggest that F-amphiphiles might be useful in the fabrication of bilayer arrays for nanopore sensor devices and the rapid screening of membrane proteins.
Second Simulation of the Satellite Signal in the Solar Spectrum, 6S: an overview (1997)

Remote sensing from satellite or airborne platforms of land or sea surfaces in the visible and near infrared is strongly affected by the presence of the atmosphere along the path from Sun to target (surface) to sensor. This paper presents 6S (Second Simulation of the Satellite Signal in the Solar Spectrum), a computer code which can accurately simulate the above problems. The 6S code is an improved version of 5S (Simulation of the Satellite Signal in the Solar Spectrum), developed by the Laboratoire d'Optique Atmospherique ten years ago. The new version now permits calculations of near-nadir (down-looking) aircraft observations, accounting for target elevation, non lambertian surface conditions, and new absorbing species (CH/sub 4/, N/sub 2/O, CO). The computational accuracy for Rayleigh and aerosol scattering effects has been improved by the use of state-of-the-art approximations and implementation of the successive order of scattering (SOS) algorithm. The step size (resolution) used for spectral integration has been improved to 2.5 nm. The goal of this paper is not to provide a complete description of the methods used as that information is detailed in the 6S manual, but rather to illustrate the impact of the improvements between 5S and 6S by examining some typical remote sensing situations. Nevertheless, the 6S code has still limitations. It cannot handle spherical atmosphere and as a result, it cannot be used for limb observations. In addition, the decoupling the authors are using for absorption and scattering effects does not allow to use the code in presence of strong absorption bands.
Low Dose Oral Combination Chemoprophylaxis with Oseltamivir and Amantadine for Influenza a Virus Infections in Mice (2007)

In the present study, the effect of combining anti-influenza drugs active at different steps of the influenza virus replication cycle, oseltamivir as a neuraminidase (NA) inhibitor and amantadine targeting M2 protein, was investigated in vivo by oral administration in a mouse model of aerosol influenza virus infection and in vitro in MDCK cells. In mice, doses of oseltamivir and amantadine providing 50-60% survival against A/Hongkong/1/68 (H3N2) or A/PR/8/34 (H1N1) were capable of conferring complete protection when used simultaneously, suggesting that increased inhibition of influenza virus replication by combining oseltamivir and amantadine in vitro translates into protection from lethal infection of mice. The combination of amantadine with oseltamivir required 15-fold less oseltamivir than monotherapy to confer complete protection against lethal aerosol influenza virus infection. Remarkably, amantadine-based combination chemoprophylaxis was even effective against amantadine-resistant A/PR/8/34 influenza virus. Thus, combination chemotherapy may be more efficacious than monotherapy against newly emerging Influenza A subtypes.
Historical overview of the use of polynucleotides in cancer. (1985)

A search for effective inducers of interferon lead to the discovery of polyinosinic-polycytidylic acid [poly(I,C)], which was effective in rodents but not primates. Stabilization of poly(I,C) with poly-L-lysine and carboxymethyl-cellulose produced a derivative that is much more effective as an inducer in humans, but also more toxic. The ability of modified poly(I,C) to induce interferon in primates appears to be at least partly related to its ability to resist hydrolysis by nucleases. As the ability to induce interferon in primates increases, so does the toxicity. Several investigations have emphasized increasing the ease of hydrolysis in order to minimize toxicity. The inducers should not be considered just as a readily available source of interferon, as there are a number of differences between the biologic effects of the inducers and exogenous interferon.
Hepatic processing of recombinant human renin: mechanisms of uptake and degradation (1991)

Biologically active 125I-Bolton-Hunter-labeled recombinant human renin (BH-renin) was used to study hepatic processing of renin both in vivo in bile fistula rats and in vitro in isolated perfused rat livers. BH-renin was composed mainly (80%) of a form that bound to concanavalin A-agarose (CB-renin). Twenty minutes after femoral venous injection of CB-renin in vivo, 47% of injected radiolabel was present in liver. Hepatic uptake of CB-renin was inhibited in a dose-dependent manner by mannosylated bovine serum albumin (MBSA) and mannan, but was unaffected by asialofetuin and mannose 6-phosphate. MBSA also significantly inhibited the plasma disappearance of endogenous renin in kidney-ligated rats. Cell separation techniques and light microscopic autoradiography showed that CB-renin was preferentially cleared by hepatic nonparenchymal cells via the mannose receptor, but was also cleared by hepatocytes via an unidentified mechanism. Tissue fractionation demonstrated that after injection of CB-renin, radiolabel was concentrated in lysosome-enriched liver fractions. In the liver, CB-renin was rapidly degraded to trichloroacetic acid-soluble fragments, which accumulated in urine and bile. Leupeptin, an inhibitor of lysosomal proteases, decreased degradation of CB-renin by 60%; vinblastine and colchicine, microtubule binding agents, each inhibited CB-renin degradation by 40%. Our results show that the liver plays a major role in the regulation of plasma renin levels via clearance by the mannose receptor on nonparenchymal cells and subsequent degradation in lysosomes.
Region 2 of the Escherichia coli K5 capsule gene cluster encoding proteins for the biosynthesis of the K5 polysaccharide (1995)

The nucleotide sequence of region 2 of the Escherichia coli K5 capsule gene cluster has been determined. This region, essential for the biosynthesis of the K5 polysaccharide, contained four genes, termed kfiA-D. The G + C ratio was 33.4%, which was lower than the typical G + C ratio for E. coli and that of the flanking regions 1 and 3 in the K5 capsule gene cluster. Three major RNA transcripts were detected within region 2 by Northern blotting and three promoters located by transcript mapping. Promoter activity was confirmed by promoter-probe analysis. The predicted amino acid sequence of KfiC had homology to a number of glycosyl transferase enzymes and overexpression of the KfiC gene resulted in increased K5 transferase activity. The predicted amino acid sequence of KfiD had homology to a number of NAD-dependent dehydrogenase enzymes and was demonstrated to be a UDP-glucose dehydrogenase that catalyses the information of UDP-glucuronic acid from UDP-glucose.
Photosensitization of the lens by 8-methoxypsoralen. (1977)

During the past decade, ambient ultraviolet radiation has been implicated in the age-related increase in fluorescence and pigmentation of the human lens nucleus. 8-Methoxypsoralen (8-MOP) (currently in vogue for the treatment of psoriasis) is a well-known photosensitizing agent. This drug lar fluorescence (360/440 nm.) and a change in receiving a single intraperitoneal dose (4 to 8 mg./kg.) of 8-MOP. When such rats are subjected to ambient light or ultraviolet (UV) radiation in vivo, there is an enhancement of lenticular fluorescence (360/440 nm.) and a change in their phosphorescence spectra. In vitro studies on lenses derived from rats given 8-MOP and exposed to monochromatic UV radiation show effects similar to those of the in vivo experiments. The foregoing studies demonstrate that 8-methoxypsoralen enters the lens and can be affected by ambient light as well as UV radiation, resulting in a photosensitized enhancement of lenticular fluorescence and a binding of this photosensitizing agent to macromolecules within the lens.
Tributylstibine‐mediated olefination of carbonyl compounds with bromomalonic ester and with dibromomalonic ester—A possible pathway through a stibonium ylide via halophilic initiation by tertiary stibines (1990)

Abstract Tributylstibine can mediate the olefination of carbonyl compounds with bromomalonic ester and with dibromomalonic ester. An initial halophilic attack of tributylstibine on the bromine of bromomalonic or dibromomalonic ester forming an ion pair of bromotributylstibonium cation and malonic (A) or bromomalonic ester carbanion (B) , respectively, is proposed. These ion pairs react with carbonyl compounds to achieve subsequent olefination. Alternatively, 2 equiv of A collapse, with elimination of malonic ester, to form stiborane D , and the ion pair B reacts with another equivalent of tributylstibine to form stiborane D. This last undergoes a Wittig‐type reaction with carbonyl compound to achieve olefination.
First-principles investigation of lattice constants and bowing parameters in wurtzite AlxGa1 xN, InxGa1 xN and InxAl1 xN alloys (2003)

First-principles calculations, by means of the full-potential augmented plane wave method using the local density approximation, were carried out for the structural and electronic properties of the AlxGa1−xN, InxGa1−xN and InxAl1−xN alloys in the wurtzite structure. We have investigated the lattice parameters and band gap energies. The lattice constants a and c are found to change linearly for the AlxGa1−xN alloy, while for both InxGa1−xN and InxAl1−xN alloys the lattice parameters, a, exhibit an upward bowing. The calculated band gap variation for the three alloys exhibit a downward bowing of 0.71 eV, 1.7 eV and 4.09 eV for AlxGa1−xN, InxGa1−xN and InxAl1−xN, respectively.
Calcium Action in Synaptic Transmitter Release (1987)

In this review we are concerned with the mechanisms by which the electrical potential across the membrane of presynaptic nerve terminals regulates the release of neurotransmitter substances into the synaptic cleft . ions play a central role in this process: Release occurs when a voltage-depen­ dent channel in the presynaptic membrane opens, thus permitting an influx of ions and diffusion of in cytoplasm, followed by binding of at some cytoplasmic site that triggers the exocytotic release of quanta of neurotransmitter. These concepts, introduced mainly by the work of Katz and associates (Katz 1 969), comprise the Ca of trans­ mitter release, a hypothesis now widely accepted. Although the general role of as a presynaptic messenger is well supported, many important specifics of its action remain to be resolved. We review progress with these details in three parts, corresponding to