gebhart/patrepeval huggingface dataset:
Immune responses of systemic and mucosal lymphoid organs to Pnu-Imune vaccine as a function of age and the efficacy of monophosphoryl lipid A as an adjuvant (1992)

A murine model system was established to study immune responses to the Pnu-Imune vaccine, which is made up of 23 different pneumococcal capsular polysaccharides. In this animal model, antibody-forming cell responses to 21 of 23 individual polysaccharides in the vaccine were detected. The Pnu-Imune vaccine elicited good antibody responses from the spleens and mesenteric lymph nodes (MLN) of young mice, whereas a variety of other peripheral lymph nodes were unresponsive. The immunoglobulin M plaque-forming cell (PFC) response in the spleen to the Pnu-Imune vaccine (given intraperitoneally or subcutaneously) decreased dramatically with increasing age. However, the spleen and MLN differed in their susceptibility to an age-associated decline in immune function. While the PFC responses in the spleen declined with age, the PFC response in the mucosa-associated MLN did not decline with age but instead remained constant over the entire age span of 4 to 28 months studied. These studies showed that the spleen, peripheral lymph nodes, and MLN did not demonstrate parallel age-associated defects in antibody responses to pneumococcal polysaccharides when the antigen was administered systematically. Also, the deficient splenic antibody response to Pnu-Imune vaccine in aged mice could be enhanced by injecting a combination of Pnu-Imune vaccine and the nontoxic adjuvant monophosphoryl lipid A. Moreover, an immunoglobulin G response was induced when the immunogen was a mixture of vaccine and adjuvant.
An information theoretic foundation of synchronized detection (2001)

The constrained capacity of a coherent coded modulation (CM) digital communication system with data-aided channel estimation and a discrete, equiprobable symbol alphabet is derived under the assumption that the system operates on a flat fading channel and uses an interleaver to combat the bursty nature of the channel. It is shown that linear minimum mean square error channel estimation directly follows from the derivation and links average mutual information to the channel dynamics. Based on the assumption that known training symbols are transmitted, the achievable rate of the system is optimized with respect to the amount of training information needed. Furthermore, the results are compared to the additive white Gaussian noise channel, and the case when ideal channel state information is available at the receiver.
Frontiers in multiple sclerosis : clinical research and therapy (1997)

Classification, genetics and epidemiology basic immunology mechanisms of demyelination and remyelination cytokines and growth factors clinical studies the future.
Mitogen‐activated protein kinases in chronic intestinal inflammation — targeting ancient pathways to treat modern diseases (2003)

Conventional treatment of chronic inflammatory disorders, including inflammatory bowel diseases, employs broad-range anti-inflammatory drugs. In order to reduce the side-effects and increase the efficacy of treatment, several strategies have been developed in the last decade to interfere with intercellular and intracellular inflammatory signalling processes. The highly conserved mitogen-activated protein kinase pathways regulate most cellular processes, particularly defence mechanisms such as stress reactions and inflammation. In this review, we provide an overview of the current knowledge of the specificity and interconnection of mitogen-activated protein kinase pathways, their functions in the gut immune system and published and ongoing studies on the role of mitogen-activated protein kinases in inflammatory bowel disease. The development of mitogen-activated protein kinase inhibitors and their use for the therapy of inflammatory disorders is a paradigm of the successful bridging of the gap between basic research and clinical practice.
Recent Advances in Molecular Approaches to Gut Microbiota in Inflammatory Bowel Disease (2009)

Inflammatory bowel diseases [IBD], ulcerative colitis [UC] and Crohn ’ s disease [CD], are chronic intestinal disorders of unknown etiology. UC and CD are heterogeneous diseases characterized by various genetic abnormalities that lead to overly aggressive T-cell responses to a subset of commensal enteric bacteria in genetically susceptible individuals. As one of critical factors involved in pathogenesis of IBD, relative imbalance of aggressive and protective bacterial species, termed dysbiosis, has been reported by various literatures. Since early days of microbiology, representatives of microbial species [over 400 species] have been isolated from human gastrointestinal tract, and analyses of dysbiosis in IBD were mainly dependent on culture techniques. However, recent molecular ecological studies based on ribosomal RNA [rRNA] sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. These techniques enable characterization and quantification of the microbiota. Clone libraries enable identification of the composition of the microbiota. Microbial community structure can be analyzed via fingerprinting techniques, and dot blot hybridization or fluorescent in situ hybridization can analyze abundance of particular taxa. Recent report shows a systematic framework of the microbial diversity in the human gut of more than 1000 different species-level phylogenetic types [phylotypes]. This review focuses on recent advances in the molecular ecological approaches for studying the gut microbiota in IBD.
Three-dimensional solution structure of a curaremimetic toxin from Naja nigricollis venom: a proton NMR and molecular modeling study (1992)

The solution conformation of toxin alpha from Naja nigricollis (61 amino acids and four disulfides), a snake toxin which specifically blocks the activity of the nicotinic acetylcholine receptor (AcChoR), has been determined using nuclear magnetic resonance spectroscopy and molecular modeling. The solution structures were calculated using 409 distance and 73 dihedral angle restraints. The average atomic rms deviation between the eight refined structures and the mean structure is approximately 0.5 A for the backbone atoms. The overall folding of toxin alpha consists of three major loops which are stabilized by three disulfide bridges and one short C terminal loop stabilized by a fourth disulfide bridge. All the disulfides are grouped in the same region of the molecule, forming a highly constrained structure from which the loops protrude. As predicted, this structure appears to be very similar to the 1.4-A resolution crystal structure of another snake neurotoxin, namely, erabutoxin b from Laticauda semifasciata. The atomic rms deviation for the backbone atoms between the solution and crystal structures is approximately 1.7 A. The minor differences which are observed between the two structures are partly related to the deletion of one residue from the chain of toxin alpha. It is notable that, although the two toxins differ from each other by 16 amino acid substitutions, their side chains have an essentially similar spatial organization. However, most of the side chains which constitute the presumed AcChoR binding site for the curaremimetic toxins are poorly resolved in toxin alpha.(ABSTRACT TRUNCATED AT 250 WORDS)
Treating Bupivacaine Arrhythmias: Preliminary Report (1981)

Nodal and ventricular arrhythmias, along with intraventricular conduction defects, appeared in 34 of 36 cats after approximately 70% of a convulsant dose of bupivacaine was infused at a rate of 1 mg/kg/min. Five minutes after completing double the convulsant dose of bupivacaine (11.8 ± 2.2 mg/kg), a benzodiazepine was given intravenously to arrest convulsions. In 28 cats, the cardiac rhythm converted spontaneously to sinus in the next 20 minutes. In the six cats with persistent arrhythmias, one had ventricular tachycardia following diazepam 2 mg/kg; the rhythm converted to sinus when lidocaine 2.5 mg/kg was given 10 minutes later. The other five cats were given lidocaine 2.5 mg/kg 30 minutes after the benzodiazepine. In four of the five, the rhythm converted to sinus after 1 or 2 lidocaine boluses. The fifth cat had sinus flurries that reverted to nodal rhythm after each of four lidocaine boluses. Lidocaine did not precipitate hypotension or induce fresh convulsions.
Apolipoprotein A-containing lipoprotein particles: physiological role, quantification, and clinical significance. (1992)

High-density lipoprotein (HDL) particles are made up of two major populations of particles, differing in composition and metabolism. Both contain apolipoprotein (apo) A-I but only one contains apo A-II. Lipoprotein particles that contain only apo A-I (LpA-I particles) can increase cellular cholesterol efflux from cultured cells in vitro. LpA-I:A-II particles, however, do not increase cholesterol efflux. LpA-I:A-II can be determined directly with an enzyme-linked differential antibody immunosorbent assay. LpA-I is determined by differential electroimmunoassay: in the presence of a large excess of anti-apo A-II, LpA-I:A-II particles are retained in one peak, whereas LpA-I migrates grates as a second peak. Both lipoprotein forms of apo A-I-containing particles are present mainly in HDL, but the relative proportion of LpA-I is greater in HDL2 than in HDL3. Concentrations of LpA-I in plasma samples from normolipemic subjects average approximately 10% higher in women than in men. The lower apo A-I concentrations in patients with significant coronary artery disease reflect a decrease in the LpA-I particles. Data obtained in octogenarians also support the possibility that LpA-I might represent the anti-atherogenic fraction of HDL. Moreover, the concentration of LpA-I in children of parents with premature coronary heart disease was lower than that of a control group without any family history of this disease. Nutrients and hypolipidemic drugs seem to affect the two kinds of particles differently.
Degradation mechanism in carbon-doped GaAs minority-carrier injection devices (1996)

Hydrogen incorporated in GaAs-based minority-carrier injection devices can cause degradation, i.e., an increase in injection leakage current at low bias voltage. "Isolated" hydrogen donors (H/sup +/) induce rapid degradation, and even carbon-hydrogen complexes which are believed to be electrically neutral induce slow degradation. The decomposition of the carbon-hydrogen complexes is enhanced by minority-carrier injection producing electrically active isolated hydrogen donors (H/sup +/). The kinetics of the leakage current increase are well explained by the decomposition kinetics of the carbon-hydrogen complexes. Under minority-carrier injection, isolated hydrogen donors (H/sup +/) change to hydrogen acceptors (H/sup -/) by capturing two electrons. Hydrogen donors (H/sup +/) and hydrogen acceptors (H/sup -/) combine and become a molecular hydrogen which is thought to form {111} platelets. We infer that the degradation mechanism is closely related to the leakage through the {111} platelets.
Direct visualization of ligand‐protein interactions using atomic force microscopy (2002)

1. Streptavidin is a 60-kDa tetramer which binds four molecules of biotin with extremely high affinity (K(A) approximately 10(14) M(-1)). We have used atomic force microscopy (AFM) to visualize this ligand-protein interaction directly. 2. Biotin was tagged with a short (152-basepair; 50-nm) DNA rod and incubated with streptavidin. The resulting complexes were then imaged by AFM. The molecular volume of streptavidin calculated from the dimensions of the protein particles (105+/-3 nm(3)) was in close agreement with the value calculated from its molecular mass (114 nm(3)). Biotinylation increased the apparent size of streptavidin (to 133+/-2 nm(3)), concomitant with an increase in the thermal stability of the tetramer. 3. Images of streptavidin with one to four molecules of DNA-biotin bound were obtained. When two ligands were bound, the angle between the DNA rods was either acute or obtuse, as expected from the relative orientations of the biotin binding sites. The ratio of acute : obtuse angles (1 : 3) was lower than the expected value (1 : 2), indicating a degree of steric hindrance in the binding of the DNA-biotin. The slight under-representation of higher occupancy states supported this idea. 4. Streptavidin with a single molecule of DNA-biotin bound was used to tag biotinylated beta-galactosidase, a model multimeric enzyme. 5. The ability to image directly the binding of a ligand to its protein target by AFM provides useful information about the nature of the interaction, and about the effect of complex formation on the structure of the protein. Furthermore, the use of DNA-biotin/streptavidin tags could potentially shed light on the architecture of multi-subunit proteins.
R: A Language for Data Analysis and Graphics (1996)

Abstract In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing computer languages. We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping.
Hypertension induced by recombinant human erythropoietin (rHU-EPO) can be prevented by indomethacin. Pathogenetic role of cytosolic calcium. (1997)

Hypertension complicating the therapy of renal anemia with rHU-EPO is characterized by an increase in total peripheral vascular resistance, but the mechanisms underlying arteriolar vasoconstriction remain unclear. To assess the role of altered cellular calcium metabolism, resting platelet cytosolic calcium was measured in 12 previously normotensive patients with end-stage renal disease before and after 12 weeks of EPO-therapy, after 12 weeks of combined antihypertensive pharmacotherapy of EPO-induced hypertension, and after 12 weeks of concurrent administration of EPO and indomethacin. Patients with EPO-induced hypertension showed a significant raise in platelet calcium by comparison with calcium levels prior to EPO (179 +/- 15 vs 120 +/- 8 nmol/l), and there was a positive correlation between their blood pressure and platelet calcium levels (r = 0.9, p < 0.001). Antihypertensive therapy of EPO-induced hypertension resulted in a reduction of blood pressure and a reduction of platelet calcium to near normal levels (128 +/- 6 nmol/l). The non-steroidal antiinflammatory drug indomethacin prevented EPO-induced hypertension and EPO-associated alterations in platelet calcium. The results of the present study suggest that EPO-induced hypertension might be related to altered cellular calcium homeostasis. If EPO therapy induces alterations in calcium metabolism not only in platelets but also in vascular smooth muscle cells, these changes in calcium influx may contribute to arteriolar vasoconstriction during EPO therapy.
Reduction of radiated electromagnetic fields by removing power planes (2004)

The noise voltage in the reference or ground of a printed circuit board is often the cause of unwanted radiated emission. Power supply planes attribute to the noise voltage. By replacing the power supply planes by tracks, the noise voltage in the reference or ground can be considerably reduced, which leads to a dramatic reduction of the radiated electromagnetic fields. This has been shown using transmission line equations for a general two-conductor line. Simulation and measurements results confirm the beneficial effect of removing power planes. A reduction of 50 dB in radiated electromagnetic field strength was obtained.
Isolation and Characterization of a Monomeric Cationic Titanium Hydride (2004)

Methyl cations 1-Cp and 1-Cp*, stabilized by the tri-tert-butylphophinimine ligand and either C5H5 or C5Me5, were generated from the neutral dimethyl precursors and [Ph3C]+[B(C6F5)4]-. Reaction of these compounds with H2 resulted in contrasting reactions. For 1-Cp, hydrogenolysis of the Ti-CH3 group led to rapid reduction to Ti(III) and production of a cationic Ti(III) dimer, 2, presumably formed upon loss of H2 from a transiently generated Ti(IV) hydride. Compound 2 was characterized crystallographically and via its cleavage with donor solvents such as THF to form the monomeric [Cp(L)Ti(THF)2]+[B(C6F5)4]-, 3. In contrast, 1-Cp* reacted rapidly with H2 to form a cationic Ti(IV) hydride species, 4, which was resistant to reduction. While only moderately stable in solution under H2, a stable, isolable THF adduct preciptitated upon addition of THF, giving 4.THF, which was fully characterized, including via X-ray crystallography. Naked hydride 4 was very reactive toward haloarene solvents such as bromobenzene, giving the cationic bromide [Cp*(L)TiBr]+[B(C6F5)4]-, 5, which was fully characterized as its THF adduct 5.THF. The contrasting behavior of 1-Cp and 1-Cp* is a result of the greater steric protection and electron donation provided by the Cp* ligand relative to the Cp donor.
Low-dislocation-density, nonplanar GaN templates for buried heterostructure lasers grown by lateral epitaxial overgrowth (2005)

We report here the formation of nonplanar GaN templates, which consist of low-dislocation-density, naturally grown GaN ridge mesas, as a mean to facilitate the fabrication of buried heterostructure lasers. Defect reduction is realized by introducing a two-step lateral epitaxial overgrowth procedure that utilizes dislocation bending in the formation of pyramidal mesas to eradicate the threading dislocations that originate from a planar buffer layer. Transmission electron microscopy and atomic force microscopy indicate a mesa top facet having low defect density (∼8×107cm−2), atomic flatness (∼0.29nm mean roughness). Our demonstration has opened the possibility of forming buried heterostructure lasers on nonplanar GaN templates.
Characterization of the spectrum of insecticidal activity of a double-stranded RNA with targeted activity against Western Corn Rootworm (Diabrotica virgifera virgifera LeConte) (2013)

The sequence specificity of the endogenous RNA interference pathway allows targeted suppression of genes essential for insect survival and enables the development of durable and efficacious insecticidal products having a low likelihood to adversely impact non-target organisms. The spectrum of insecticidal activity of a 240 nucleotide (nt) dsRNA targeting the Snf7 ortholog in Western Corn Rootworm (WCR; Diabrotica virgifera virgifera) was characterized by selecting and testing insects based upon their phylogenetic relatedness to WCR. Insect species, representing 10 families and 4 Orders, were evaluated in subchronic or chronic diet bioassays that measured potential lethal and sublethal effects. When a specific species could not be tested in diet bioassays, the ortholog to the WCR Snf7 gene (DvSnf7) was cloned and corresponding dsRNAs were tested against WCR and Colorado potato beetle (Leptinotarsa decemlineata); model systems known to be sensitive to ingested dsRNA. Bioassay results demonstrate that the spectrum of activity for DvSnf7 is narrow and activity is only evident in a subset of beetles within the Galerucinae subfamily of Chrysomelidae (>90% identity with WCR Snf7 240 nt). This approach allowed for evaluating the relationship between minimum shared nt sequence length and activity. A shared sequence length of ≥ 21 nt was required for efficacy against WCR (containing 221 potential 21-nt matches) and all active orthologs contained at least three 21 nt matches. These results also suggest that WCR resistance to DvSnf7 dsRNA due to single nucleotide polymorphisms in the target sequence of 240 nt is highly unlikely.
Optical Performance of Extreme Ultraviolet Lithography Mask with an Indium Tin Oxide Absorber (2012)

In this study, we propose a new extreme ultraviolet (EUV) binary mask with an indium tin oxide (ITO) absorber. The optical constant of ITO film at 13.5 nm wavelength in the EUV regime was determined by means of X-ray reflectivity measurements and the chemical composition was determined using Rutherford backscattering spectrometry. The reflectance of a binary mask with an ITO absorber layer at various thicknesses was also measured to investigate the optical performance in the EUV regime. It was found that the extinction coefficient of ITO film is higher than that of a typical absorber layer, TaN, and that the reflectance of the ITO absorber in the binary mask at a wavelength of 13.5 nm is reduced to 0.62% at a thickness of 45 nm. Therefore, it is expected that the ITO film can be employed as a thin absorber of a binary mask to reduce the geometrical shadow effect in extreme ultraviolet lithography.
Extracellular matrix mineralization is regulated locally; different roles of two gla-containing proteins (2004)

Extracellular matrix mineralization (ECMM) is a physiologic process in the skeleton and in teeth and a pathologic one in other organs. The molecular mechanisms controlling ECMM are poorly understood. Inactivation of Matrix gla protein (Mgp) revealed that MGP is an inhibitor of ECMM. The fact that MGP is present in the general circulation raises the question of whether ECMM is regulated locally and/or systemically. Here, we show that restoration of Mgp expression in arteries rescues the arterial mineralization phenotype of Mgp-/- mice, whereas its expression in osteoblasts prevents bone mineralization. In contrast, raising the serum level of MGP does not affect mineralization of any ECM. In vivo mutagenesis experiments show that the anti-ECMM function of MGP requires four amino acids which are gamma-carboxylated (gla residues). Surprisingly, another gla protein specific to bone and teeth (osteocalcin) does not display the anti-ECMM function of MGP. These results indicate that ECMM is regulated locally in animals and uncover a striking disparity of function between proteins sharing identical structural motifs.
Ascorbic Acid Reduces Noise‐Induced Nitric Oxide Production in the Guinea Pig Ear (2008)

Abstract Objectives: Noise‐induced hearing loss can be caused, among other causes, by increased nitric oxide (NO) production in the inner ear leading to nitroactive stress and cell destruction. Some studies in the literature suggest that the degree of hearing loss (HL) could be reduced in an animal model through ascorbic acid supplementation. To identify the effect of ascorbic acid on tissue‐dependent NO content in the inner ear of the guinea pig, we determined the local NO production in the organ of Corti and the lateral wall separately 6 hours after noise exposure. Study Design: Prospective animal study in guinea pigs. Methods: Over a period of 7 days, male guinea pigs were supplied with minimum (25 mg/kg body weight/day) and maximum (525 mg/kg body weight/day) ascorbic acid doses, and afterwards exposed to noise (90 dB sound pressure level for 1 hour). The acoustic‐evoked potentials were recorded before and after noise exposure. The organ of Corti and the lateral wall were incubated differently for 6 hours in culture medium, and the degree of NO production was determined by chemiluminescence. Results: Ascorbic acid treatment reduced the hearing threshold shift after noise exposure depending on concentration. When the maximum ascorbic acid dose was substituted, NO production was significantly reduced in the lateral wall after noise exposure and slightly reduced in the organ of Corti. Conclusions: Oral supplementation of the natural radical scavenger ascorbic acid reduces the NO‐production rate in the inner ear in noisy conditions. This finding supports the concept of inner ear protection by ascorbic acid supplementation.