gebhart/patrepeval huggingface dataset:
Instability of Natural Antibody Repertoires in Systemic Lupus Erythematosus Patients, Revealed by Multiparametric Analysis of Serum Antibody Reactivities (1997)

Recent views on autoimmune diseases invoke generalized but specific perturbations in antibody repertoires, rather than the clonally restricted or non-specific polyclonal alterations proposed thus far. The present experiments analyse serum antibody reactivities in 24 systemic lupus erythematosus (SLE) patients and 17 healthy controls, using a method that quantitatively scores a large number of antibody reactivities and allows for multiparametric statistical analyses. The results show global but relatively specific perturbations in SLE antibody repertoires, and identify novel disease-associated reactivity patterns. Furthermore, a time series analysis of serum antibodies over 3 months demonstrates instability of natural antibody repertoires in individual SLE patients, contrasting with their remarkable conservation in healthy donors. Moreover, the method used clusters controls and patients independently, and might prove of diagnostic value, once large data bases are established.
Room-Temperature Soft Magnetic Iron Oxide Nanocrystals: Synthesis, Characterization, and Size-Dependent Magnetic Properties (2008)

Monodisperse faceted and cubic magnetite nanoparticles were synthesized by the reduction of iron (III) acetylacetonate (Fe(acac)3) with N-methylpyrrole or pyrrole in the presence of the surfactants oleic acid and oleylamine in air. Particle size control can be attained by careful adjustment of the concentrations of the reactants and the surfactants. We also obtained monodisperse maghemite nanoparticles by the oxidation of the as-prepared Fe3O4 nanoparticles. The magnetic studies exhibit that increasing the size of iron oxides nanoparticles leads to the enhanced magnetic properties. In particular, the iron oxides nanoparticles with size more than 5 nm are soft ferromagnetic at room temperature.
Formation of SiN Films by Plazma-Enhanced Chemical Vapor Deposition Using [(CH3)2N]3SiN3 (1994)

An organic source gas, tris-dimethyl-amino-silyl-azide (TDSA, [(CH 3 ) 2 N] 3 SiN 3 ), was newly synthesized and utilized for the deposition of a passivation film of sub-half-micrometer devices. Deposition temperature dependence of the film formed by plasma-enhanced chemical vapor deposition (PECVD) using TDSA was investigated and step coverage of the TDSA film was examined. As a result, it was clarified that hydrocarbon content in the film decreased with increasing deposition temperature. The bottom step coverage of the films formed using TDSA was greatly improved compared to that of the conventional silicon nitride film.
Secondary structure and orientation of the surfactant protein SP-B in a lipid environment. A Fourier transform infrared spectroscopy study (1992)

Attenuated total reflection Fourier transform infrared spectroscopy was used to investigate the secondary structure of the surfactant protein SP-B. Nearly half of the polypeptide chain is folded in an alpha-helical conformation. No significant change of the secondary structure content was observed when the protein is associated to a lipid bilayer of dipalmitoylphosphatidylcholine (DPPC)/phosphatidylglycerol (PG) or of dipalmitoylphosphatidylglycerol (DPPG). The parameters related to the gamma w(CH2) vibration of the saturated acyl chains reveal no modification of the conformation or orientation of the lipids in the presence of SP-B. A model of orientation of the protein at the lipid/water interface is proposed. In this model, electrostatic interactions between charged residues of SP-B and polar headgroups of PG, and the presence of small hydrophobic alpha-helical peptide stretches slightly inside the bilayers, would maintain SP-B at the membrane surface.
ER-α36, a novel isoform of ER-α66, is commonly over-expressed in apocrine and adenoid cystic carcinomas of the breast (2010)

ER-α36, a novel isoform of ER-α66, is frequently over-expressed in apocrine and adenoid cystic carcinomas of the breast. These results indicate a potential for a novel targeted treatment in these cancers.
Urinary excretion of glucosyl‐galactosyl pyridinoline: a specific biochemical marker of synovium degradation (2001)

Glc-Gal-PYD may be useful for the clinical investigation of patients with joint disease.
Comparison of the absorption of two protein hydrolysates and their effects on water and electrolyte movements in the human jejunum. (1980)

Because of the generally more rapid amino acid absorption and lower osmotic pressure of small peptides compared with free amino acids, it has been suggested that 'elemental' diets should contain both small peptides and free amino acids as the nitrogen source. While studying protein hydrolysates intended for use in such diets we observed surprising differences in the absorption of amino acids, water, and Na+ during jejunal perfusion of partial enzymic hydrolysates of two proteins (lactalbumin and fish) which contained high and approximately equal amounts of their constituent amino acids in the form of small peptides. Total alpha amino nitrogen (alpha NH2N) absorption from the lactalbumin hydrolysate was greater, and individual amino acid absorption more even, than from equinitrogenous solutions of the fish protein hydrolysate, or from mixture of free amino acids simulating either hydrolysate. Net water and Na+ absorption occurred during perfusion of the lactalbumin hydrolysate, whereas net water and Na+ secretion occurred during perfusion of the fish protein hydrolysate. These differences were significant (P < 0.05 or less). As the differences between the hydrolysates are so marked, we conclude that it is unwise to assume that all protein hydrolysates are equally suitable for use in patients.
A Short Survey of Document Structure Similarity Algorithms (2004)

This paper provides a brief survey of document structural similarity algorithms, including the optimal Tree Edit Distance algorithm and various approximation algorithms. The approximation algorithms include the simple weighted tag similarity algorithm, Fourier transforms of the structure, and a new application of the shingle technique to structural similarity. We show three surprising results. First, the Fourier transform technique proves to be the least accurate of any of approximation algorithms, while also being slowest. Second, optimal Tree Edit Distance algorithms may not be the best technique for clustering pages from different sites. Third, the simplest approximation to structure may be the most effective and efficient mechanism for many applications.
Cloning and Sequence Analysis of the Saccharomyces cerevisiae RAD9 Gene and Further Evidence that Its Product Is Required for Cell Cycle Arrest Induced by DNA Damage (1989)

Procaryotic and eucaryotic cells possess mechanisms for arresting cell division in response to DNA damage. Eucaryotic cells arrest division in the G2 stage of the cell cycle, and various observations suggest that this arrest is necessary to ensure the completion of repair of damaged DNA before the entry of cells into mitosis. Here, we provide evidence that the Saccharomyces cerevisiae RAD9 gene, mutations of which confer sensitivity to DNA-damaging agents, is necessary for the cell cycle arrest phenomenon. Our studies with the rad9 delta mutation show that RAD9 plays a role in the cell cycle arrest of methyl methanesulfonate-treated cells and is absolutely required for the cell cycle arrest in the temperature-sensitive cdc9 mutant, which is defective in DNA ligase. At the restrictive temperature, cell cycle progression of cdc9 cells is blocked sometime after the DNA chain elongation step, whereas cdc9 rad9 delta cells do not arrest at this point and undergo one or two additional divisions. Upon transfer from the restrictive to the permissive temperature, a larger proportion of the cdc9 cells than of the cdc9 rad9 delta cells forms viable colonies, indicating that RAD9-mediated cell cycle arrest allows for proper ligation of DNA breaks before the entry of cells into mitosis. The rad9 delta mutation does not affect the frequency of spontaneous or UV-induced mutation and recombination, suggesting that RAD9 is not directly involved in mutagenic or recombinational repair processes. The RAD9 gene encodes a transcript of approximately 4.2 kilobases and a protein of 1,309 amino acids of Mr 148,412. We suggest that RAD9 may be involved in regulating the expression of genes required for the transition from G2 to mitosis.
On the effect of surface roughness height, wettability, and nanoporosity on Leidenfrost phenomena (2011)

In recent quenching heat transfer studies of nanofluids, it was found that deposition of nanoparticles on a surface raises its Leidenfrost point (LFP) considerably [Kim et al., Int. J. Multiphase Flow 35, 427 (2009) and Kim et al., Int. J. Heat Mass Transfer 53, 1542 (2010)]. To probe the physical mechanism underlying this observation, the effects of surface properties on LFP of water droplets were studied, using custom-fabricated surfaces for which roughness height, wettability, and porosity were controlled at the nanoscale. This approach reveals that nanoporosity is the crucial feature in efficiently increasing the LFP by initiating heterogeneous nucleation of bubbles during short-lived solid-liquid contacts, which results in disruption of the vapor film.
Fully Electronic $E$-Band Personnel Imager of 2 m$^2$ Aperture Based on a Multistatic Architecture (2012)

The demand on advanced personnel screening systems led to the development of several active and passive imagers. Among them, active multistatic imaging ensures high image quality and allows fully electronic screening. An active <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</i> -band imager is presented in this paper, which measures in real-time and delivers images of 30-dB dynamic range. Imaging of humans is achieved by optimizing the acquisition time using a dedicated digital signal processing solution. This paper introduces the system hardware, the calibration procedure, and several measurement results demonstrating high quality imaging capabilities.
Aggregation of Lipid Rafts Accompanies Signaling via the T Cell Antigen Receptor (1999)

The role of lipid rafts in T cell antigen receptor (TCR) signaling was investigated using fluorescence microscopy. Lipid rafts labeled with cholera toxin B subunit (CT-B) and cross-linked into patches displayed characteristics of rafts isolated biochemically, including detergent resistance and colocalization with raft-associated proteins. LCK, LAT, and the TCR all colocalized with lipid patches, although TCR association was sensitive to nonionic detergent. Aggregation of the TCR by anti-CD3 mAb cross-linking also caused coaggregation of raft-associated proteins. However, the protein tyrosine phosphatase CD45 did not colocalize to either CT-B or CD3 patches. Cross-linking of either CD3 or CT-B strongly induced tyrosine phosphorylation and recruitment of a ZAP-70(SH2)(2)-green fluorescent protein (GFP) fusion protein to the lipid patches. Also, CT-B patching induced signaling events analagous to TCR stimulation, with the same dependence on expression of key TCR signaling molecules. Targeting of LCK to rafts was necessary for these events, as a nonraft- associated transmembrane LCK chimera, which did not colocalize with TCR patches, could not reconstitute CT-B-induced signaling. Thus, our results indicate a mechanism whereby TCR engagement promotes aggregation of lipid rafts, which facilitates colocalization of LCK, LAT, and the TCR whilst excluding CD45, thereby triggering protein tyrosine phosphorylation.
Cardiovascular and Pulmonary Effects of Aerosolized Prostacyclin Administration in Severe Respiratory Failure Using a Ventilator Nebulization System (1996)

We investigated the effects of aerosolized prostacyclin (PGI2) administration on hemodynamics and pulmonary gas exchange in 8 patients with severe respiratory failure and acute pulmonary hypertension. Nebulization of epoprostenol (5 ng/kg body weight for 15 min) decreased mean pulmonary blood pressure from 41.2 +/- 6.7 mm Hg (mean +/- SD, before administration) to 36.1 +/- 6 mm Hg < or = 15 min (p < 0.05). The effect was reversed 10 min after discontinuation of PGI2 (40.9 +/- 6.3 mm Hg). Pulmonary vascular resistance index (339 +/- 138 dynes.s.cm-5.m2, before administration) was significantly (p < 0.05) reduced < or = 15 min (260 +/- 89 dynes.s.cm-5.m2) and increased again after discontinuation of PGI2 (341 +/- 142 dynes.s.cm-5.m2). The ratio of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2) increased from 119 +/- 34 mm Hg (before administration) to 163 +/- 76 mm Hg (15 min after initiation of administration p < 0.05) and was reduced after PGI2 discontinuation (116 +/- 35 mm Hg). Heart rate, mean blood pressure, central venous pressure, and pulmonary arterial wedge pressure remained unchanged, whereas cardiac index was slightly reduced. We assume that PGI2 aerosolization is a beneficial technique, applied with a ventilator nebulization system. The beneficial effect might be caused by selective pulmonary vasodilatation in well-ventilated areas of the lung.
T Cell Costimulation with Anti-CD137 Monoclonal Antibodies Is Mediated by K63–Polyubiquitin-Dependent Signals from Endosomes (2013)

Agonist anti-CD137 (4-1BB) mAbs enhance CD8-mediated antitumor immunity. Agonist anti-human CD137 mAbs binding to four distinct epitopes on the CD137 glycoprotein costimulated T cell activation irrespective of the engaged epitope or its interference with CD137L binding. CD137 perturbation with all these agonist mAbs resulted in Ag and Ab internalization toward an endosomal vesicular compartment. Internalization was observed in activated T lymphocytes from humans and mice, not only in culture but also in Ab-injected living animals. These in vivo experiments were carried out upon systemic i.v. injections with anti-CD137 mAbs and showed CD137 internalization in tumor-infiltrating lymphocytes and in activated human T cells transferred to immunodeficient mice. Efficient CD137 internalization required K63 polyubiquitination and endocytosed CD137-containing vesicles recruited TNFR-associated factor (TRAF) 2 and were decorated with K63 polyubiquitins. CD137 stimulation activates NF-κB through a K63-linked polyubiquitination-dependent route, and CD137-associated TRAF2 becomes K63 polyubiquitinated. Consistent with a role for TRAF2 in CD137 signaling, transgenic mice functionally deficient in TRAF2 showed delayed immunotherapeutic activity of anti-CD137 mAbs. As a whole, these findings advance our knowledge of the mechanisms of action of anti-CD137 immunostimulatory mAbs such as those currently undergoing clinical trials in cancer patients.
p300, and p300-associated proteins, are components of TATA-binding protein (TBP) complexes. (1993)

The transforming proteins encoded by the adenovirus E1A gene bind to a 300-kDa cellular product, p300, via the N-terminal E1A sequences. Residues important for p300 binding are required for the transformation function of E1A and for other E1A-mediated gene-regulating functions, including activation of cell cycle-regulated products and repression of tissue-specific enhancer activity. Recent evidence indicates that p300 is a DNA-binding protein with specific affinity for known enhancer motifs, suggesting that p300 may be a component of transcription factor complexes. The possibility that upstream element-binding factors might interact with basal transcription factors led us to investigate whether p300 interacts, directly or indirectly, with the TATA-binding protein (TBP). We report here that TBP-specific immunoprecipitations show a 300-kDa protein co-precipitating with TBP. This protein is lost from the precipitated material if the lysates are boiled in sodium dodecyl sulfate prior to immunoprecipitation, implying that its presence does not result from non-specific antibody cross-reactivity, but is dependent on specific association with TBP. The TBP-associated 300-kDa protein and p300 originally defined by E1A association show indistinguishable partial proteolytic digest patterns, indicating that these are identical or closely related species. Moreover, p300-specific complexes and TBP-specific complexes include at least two additional common polypeptide species, phosphoproteins of 64 and 59 kDa. These results suggest that p300 interacts with TBP, possibly through intermediate protein-protein associations. They thus provide additional biochemical evidence for postulated protein-protein interactions between upstream regulatory factors and the basal transcriptional machinery.
Viral inactivation in blood and red cell concentrates with benzoporphyrin derivative. (1992)

Using both the vesicular stomatitis virus (VSV) and feline leukemia virus (FeLV) as models we have shown that the photosensitizer benzoporphyrin derivative ring A (BPD), when activated with red light (600-700 nm), is effective in eliminating both free virus and virally infected cells from spiked blood products and whole blood drawn from viremic cats experimentally infected with FeLV, under conditions which appear to share red blood cells. The effect of photodynamic therapy on infected lymphocytes, as visualized by scanning electron microscopy, initially appeared as a limited area of tiny holes in the membrane. These holes were subsequently seen to increase in size until the membrane appeared completely decomposed. The red cell membranes however, seem to be undamaged by such photodynamic treatment.
A 60-GHz CMOS Receiver Front-End (2005)

The unlicensed band around 60 GHz can be utilized for wireless communications at data rates of several gigabits per second. This paper describes a receiver front-end that incorporates a folded microstrip geometry to create resonance at 60 GHz in a common-gate LNA and active mixers. Realized in 0.13-/spl mu/m CMOS technology, the receiver front-end provides a voltage gain of 28 dB with a noise figure of 12.5 dB while consuming 9 mW from a 1.2-V supply.
Bioactive Saponins and Glycosides. III. Horse Chestnut. (1): The Structures, Inhibitory Effects on Ethanol Absorption, and Hypoglycemic Activity of Escins Ia, Ib, IIa, IIb, and IIIa from the Seeds of Aesculus hippocastanum L. (1996)

Five bioactive triterpene oligoglycosides named escins, Ia, Ib, IIa, IIb, and IIIa were isolated from the seeds of horse chestnut tree, Aesculus hippocastanum L. (Hippocastanaceae). The chemical structures of escins Ia, Ib, IIa, IIb, and IIIa were determine on the basis of chemical and physicochemical evidence, which included selective cleavage of the glucuronide linkage using photochemical reaction and lead tetraacetate decarboxylation reaction. Escins Ia, Ib, IIa, and IIb were found to exhibit an ethanol absorption-inhibitory effect and hypoglycemic activity in the oral glucose tolerance test in rats. Some structure-activity relationships are reported.
An in planta biolistic method for stable wheat transformation (2017)

The currently favoured method for wheat (Triticum aestivum L.) transformation is inapplicable to many elite cultivars because it requires callus culture and regeneration. Here, we developed a simple, reproducible, in planta wheat transformation method using biolistic DNA delivery without callus culture or regeneration. Shoot apical meristems (SAMs) grown from dry imbibed seeds were exposed under a microscope and subjected to bombardment with different-sized gold particles coated with the GFP gene construct, introducing DNA into the L2 cell layer. Bombarded embryos were grown to mature, stably transformed T<sub>0</sub> plants and integration of the GFP gene into the genome was determined at the fifth leaf. Use of 0.6-µm particles and 1350-psi pressure resulted in dramatically increased maximum ratios of transient GFP expression in SAMs and transgene integration in the fifth leaf. The transgene was integrated into the germ cells of 62% of transformants, and was therefore inherited in the next generation. We successfully transformed the model wheat cultivar 'Fielder', as well as the recalcitrant Japanese elite cultivar 'Haruyokoi'. Our method could potentially be used to generate stable transgenic lines for a wide range of commercial wheat cultivars.
Characterization and distribution of natriuretic peptide receptors in the rat uterus (1995)

Atrial natriuretic peptide (ANP) receptors were characterized in rat uterus. The binding of [125I]ANP to uterine membranes was completely competed for by increasing concentrations of unlabeled ANP (Kd = 0.39 nM) and brain natriuretic peptide (Kd = 1.24 nM) and partially by C-type natriuretic peptide (CNP; Kd = 80.4 nM), but not by C-ANF. Also, [125I]Tyr-CNP bound to uterine membranes was completely competed by unlabeled CNP (Kd = 1.12 nM). Cross-linking of [125I]ANP to uterine membranes revealed the presence of one band of 130 kilodaltons, corresponding to the guanylyl cyclase (GC-A and/or GC-B) subtypes of natriuretic peptide receptors. The presence of messenger RNA coding for genes of both GC-A and GC-B receptors was shown by quantitative reverse transcriptase polymerase chain reaction. Furthermore, ANP and, to a lesser degree, CNP stimulated the production of cGMP in rat uterus. Autoradiographic studies localized the highest binding of [125I]ANP in the endometrium, whereas [125I]Tyr-CNP binding was distributed in the endometrium as well as in the myometrium. These results demonstrate that rat uterine ANP receptors are of the guanylyl cyclase-coupled subtypes. The uterus is a target of natriuretic peptides where ANP induces its biological effects through the production of cGMP.
First Artificial Receptors and Chemosensors toward Phosphorylated Peptide in Aqueous Solution (2002)

The first fluorescent chemosensors toward a native phosphorylated peptide are successfully synthesized. Dinuclear zinc(II)-dipicolylamine-based anthracene (1, 2) can selectively recognize and sense phosphorylated species with an increase in the fluorescence intensity. We also demonstrated that these artificial receptors fluorometrically detect a phosphorylated peptide with high affinity (>107 M-1) in aqueous solution.
Distinct Structural Changes in a G Protein-coupled Receptor Caused by Different Classes of Agonist Ligands (2007)

The activity of G protein-coupled receptors can be modulated by different classes of ligands, including agonists that promote receptor signaling and inverse agonists that reduce basal receptor activity. The conformational changes in receptor structure induced by different agonist ligands are not well understood at present. In this study, we employed an in situ disulfide cross-linking strategy to monitor ligand-induced conformational changes in a series of cysteine-substituted mutant M(3) muscarinic acetylcholine receptors. The observed disulfide cross-linking patterns indicated that muscarinic agonists trigger a separation of the N-terminal segment of the cytoplasmic tail (helix 8) from the cytoplasmic end of transmembrane domain I. In contrast, inverse muscarinic agonists were found to increase the proximity between these two receptor regions. These findings provide a structural basis for the opposing biological effects of muscarinic agonists and inverse agonists. This study also provides the first piece of direct structural information as to how the conformations induced by these two functionally different classes of ligands differ at the molecular level. Given the high degree of structural homology found among most G protein-coupled receptors, our findings should be of broad general relevance.