gebhart/patrepeval huggingface dataset:
The Wavy Mechanical Face Seal Theoretical and Experimental Results (1980)

In this report the results of theoretical and experimental investigations on the effects of waviness on mechanical face seal performance are presented. In previous work it was shown how waviness imposed on a seal face leads to reduced friction and wear while creating only a small leakage in a water seal. It was also shown that the waviness must be moved slowly around the seal ring in order that the effect of waviness remain indefinitely. A test apparatus for measuring the effects of waviness is described. A computer based system is used to record the data and monitor the test. A test procedure is outlined. Results from wavy seal experiments show that waviness reduces seal wear compared to a flat face seal a factor of four to forty and reduces torque a factor of four. Long term tests show that by moving the wave the effect remains indefinitely. As the amount of waviness is increased, friction torque decreases and leakage increases. Wear profiles show that the seal faces have a tilt in addition to waviness. This alters the pressure distribution significantly when compared to the radially parallel wavy faces analyzed previously. Tests using a converging radially tapered seal show that the taper wears away with time.
RAGE: A Single Receptor for Several Ligands and Different Cellular Responses: The Case of Certain S100 Proteins (2007)

The S100 protein family comprises at least 25 members which, with the exception of S100G, act as Ca2+-sensor proteins that participate in Ca2+ signal transduction by interacting with target proteins thereby modifying their activities. S100 proteins are expressed in vertebrates exclusively, display a cell-specific distribution, and regulate a large variety of intracellular activities. Some S100 proteins are released by a non-classical pathway and exert regulatory effects on several cell types. The receptor for advanced glycation end products (RAGE) has been shown to transduce extracellular effects of S100B, S100A4, S100A6, S100A11, S100A12, S100A13 and S100P. However, some S100 proteins can signal by engaging RAGE as well as non-RAGE receptors. Immune cells (i.e., monocytes/macrophages/microglia, neutrophils and lymphocytes), activated endothelial and vascular smooth muscle cells, neurons, astrocytes, chondrocytes and pancreatic tumor cells are the cell types reported to respond to certain S100 proteins via RAGE engagement. In general, relatively high concentrations of S100 proteins are required for activation of RAGE in responsive cells. S100B is unique in that it can engage RAGE in neurons at low and high concentrations with trophic and toxic effects, respectively, and S100A4 stimulates matrix metalloproteinase 13 release from chondrocytes at nanomolar doses in a RAGE-mediated manner. Oligomerization of S100 proteins under the non-reducing, high-Ca2+ conditions found extracellularly appears to play a relevant role in RAGE activation, and binding of at least S100A12 and S100B results in RAGE oligomerization. Thus, S100/RAGE interactions might have important consequences during development and in tissue homeostasis as well as in inflammatory, degenerative and tumor processes.
Cytotoxic T Lymphocyte Responses to Transgene Product, Not Adeno-Associated Viral Capsid Protein, Limit Transgene Expression in Mice (2009)

The use of adeno-associated viral (AAV) vectors for gene replacement therapy is currently being explored in several clinical indications. However, reports have suggested that input capsid proteins from AAV-2 vector particles may result in the stimulation of cytotoxic T lymphocyte (CTL) responses that can result in a loss of transduced cells. To explore the impact of anti-AAV CTLs on AAV-mediated transgene expression, both immunocompetent C57BL=6 mice and B cell-deficient muMT mice were immunized against the AAV2 capsid protein (Cap) and were injected intravenously with an AAV-2 vector encoding alpha-galactosidase (alpha-Gal). C57BL=6 mice, which developed both CTL and neutralizing antibody responses against Cap, failed to show any detectable alpha-Gal expression. In contrast, serum alpha-Gal levels comparable to those of naive mice were observed in muMT mice despite the presence of robust CTL activity against Cap, indicating that preexisting Cap-specific CTLs did not have any effect on the magnitude and duration of transgene expression. The same strategy was used to assess the impact of CTLs against the alpha-Gal transgene product on AAV-mediated gene delivery and persistence of transgene expression. Preimmunization of muMT mice with an Ad=alpha-Gal vector induced a robust CTL response to alpha-Gal. When these mice were injected with AAV2=alpha-Gal vector, initial levels of alpha-Gal expression were reduced by more than 1 log and became undetectable by 2 weeks postinjection. Overall, our results indicate that CTLs against the transgene product as opposed to AAV capsid protein are more likely to interfere with AAV transgene expression.
Ignition target design and robustness studies for the National Ignition Facility (1996)

Recent results are presented from two-dimensional LASNEX [G. B. Zimmerman and W. L. Kruer, Comments Plasmas Phys. Controlled Thermonucl. Fusion 2, 51 (1975)] calculations of the indirectly driven hohlraum and ignition capsules proposed for the National Ignition Facility (NIF). The calculations concentrate on two capsule designs, the baseline design that has a bromine-doped plastic ablator, and the beryllium design that has a copper-doped beryllium ablator. Both capsules have a cryogenic fuel layer. Primary emphasis in these calculations is placed upon robustness studies detailing various sensitivities. Because of computer modeling limitations these studies fall into two categories: those performed with integrated modeling where the capsule, hohlraum, and laser rays all are modeled simultaneously with the laser power levels as the only energy input; and those performed in a capsule-only mode where an externally imposed radiative flux is applied to the exterior of the capsule, and only the capsule performance is modeled. Integrated modeling calculations address sensitivities to, e.g., the laser pointing; among other things, capsule-only calculations address yield degradation due to the growth of hydrodynamic instabilities seeded by initial surface roughnesses on the capsules. Limitations of the calculational models and directions for future research are discussed. The results of the robustness studies performed to date enhance the authors’ confidence that the NIF can achieve ignition and produce 10–15 MJ of capsule yield with one or more capsule designs.
Single-Walled Carbon Nanotube Pillars: A Superhydrophobic Surface (2009)

A series of SWNT arrays have been constructed by disproportionation of carbon monoxide on Co−Mo catalyst films deposited on flat Si wafer substrates. The arrays include a two-dimensional SWNT thin film prepared by spraying a SWNT suspension, as well as random SWNT networks, and vertically aligned SWNT. In addition, a novel SWNT array has been developed and termed SWNT “pillars”. These pillars are prepared by controlled synthesis of SWNT over a templated substrate. When water droplets are deposited on these surfaces, it is observed that the static contact angle changes dramatically with the type of SWNT array. The higher is the degree of surface roughness (at the nano and microscales) of these structures, the higher is the contact angle. The novel SWNT pillars exhibit superhydrophobicity (i.e., contact angle ∼ 160°). To quantify the effect of surface roughness, two simple models have been employed. The Wenzel model can be used to quantify the behavior of the SWNT thin films while the Cassie−Baxter model is used for the SWNT arrays with three-dimensional structure (grass, forest, and pillars).
[Compact structure of random copolymers of hydrophobic and hydrophilic amino acid residues]. (1980)

Studies are made of the pH-induced intramolecular structuring of such random copolymers as glutamic acid with leucine. It is shown that these copolymers, consisting of hydrophobic and hydrophilic residues, contain large amounts of fractions capable of acquiring non-aggregating compact structures in aqueous medium. These fractions have an approximately similar amino acid composition which does not almost depend on the composition of the initial copolymers. A decrease in the degree of ionization of side groups of glutamic acid promotes a formation of helical regions in the molecules of these fractions. At a further deionization, the helical regions collapse into compact structures stabilized by hydrophobic interactions of side groups of leucine. The compactness of the obtained structures is close to that of protein globules.
Cooperative diversity with opportunistic relaying (2006)

In this paper, we present single-selection-opportunistic-relaying with decode-and-forward (DaF) and amplify-and-forward (AaF) protocols under an aggregate power constraint. We show that opportunistic DaF relaying is equivalent to the outage bound of the optimal DaF strategy using all potential relays. We further show that opportunistic AaF relaying is outage-optimal with single-relay selection and significantly outperforms an AaF strategy with multiple-relay (MR) transmissions, in the presence of limited channel knowledge. These findings reveal that cooperative diversity benefits (under an aggregate power constraint) are useful even when cooperative relays choose not to transmit but rather choose to cooperatively listen; they act as passive relays and give priority to the transmission of a single opportunistic relay
Selection of Antibodies Against Biotinylated Antigens (2003)

Phage antibody (Ab) library selections on peptides or proteins are usually carried out using antigens (Ags) directly coated onto a plastic surface (e.g., Petri dishes, microtiter plate wells, and immunotubes). This straightforward method is easy to perform and has been shown to be successful for a diverse set of Ags (for review, see ref. 1). However, phage Ab selections on some proteins and especially on peptides are not always successful, which is often caused by immobilization-associated features. The main problem observed for selection on peptides is the poor coating efficiency of some peptides and the altered availability of epitopes on plastic-coated peptides. The direct coating of proteins on plastic is usually more efficient, but may also be problematic because the passive adsorption on plastic at pH 9.6 is a mechanism of protein denaturation. Under these conditions, 95% of adsorbed proteins are nonfunctional (,) This problem is not important for a classical enzyme-linked immunosorbant assay (ELISA) mostly because a small fraction of proteins having a native conformation are still detectable. However, this phenomenon can be troublesome for phage Ab library selections because phage Abs binding to epitopes, only present in denatured molecules may be selected.
Hierarchical Question-Image Co-Attention for Visual Question Answering (2016)

A number of recent works have proposed attention models for Visual Question Answering (VQA) that generate spatial maps highlighting image regions relevant to answering the question. In this paper, we argue that in addition to modeling "where to look" or visual attention, it is equally important to model "what words to listen to" or question attention. We present a novel co-attention model for VQA that jointly reasons about image and question attention. In addition, our model reasons about the question (and consequently the image via the co-attention mechanism) in a hierarchical fashion via a novel 1-dimensional convolution neural networks (CNN). Our model improves the state-of-the-art on the VQA dataset from 60.3% to 60.5%, and from 61.6% to 63.3% on the COCO-QA dataset. By using ResNet, the performance is further improved to 62.1% for VQA and 65.4% for COCO-QA.
Metabolism of linoleic acid in the cat (1979)

Cats fed a diet containing linoleate as the only polyunsaturated fatty acid showed extremely low levels of arachidonate in the plasma lipids, as well as an increase in linoleate, eicosadienoate and an unknown fatty acid. Administration of [1-14C]linoleic acid and [2-14C]eicosa-8,11,14-trienoic acid to cats showed that in the liver there was no conversion of the [1-14C] 18:2 to arachidonate, whereas there was significant metabolism of [2-14C] 20:3 to arachidonate. It was found when methyl-gamma-linolenate was fed to cats that the level of 20:3 omega 6 and 20:4 omega 6 in the erythrocytes increased significantly. These results show that there is no significant delta 6 desaturase activity in the cat, whereas chain elongation and delta 5 desaturase enzymes are operative. The unknown fatty acid was isolated from the liver lipids and shown to be a 20-carbon fatty acid with 3 double bonds and which by gas liquid chromatography could be separated from 20:3 omega 9 and 20:3 omega 6. The presence of the delta 5-desaturase activity and the results of the ozonolysis studies indicated that this unknown fatty acid was eicosa-5,11,14-trienoic acid.
“Click Chemistry” Inspired Synthesis of pseudo-Oligosaccharides and Amino Acid Glycoconjugates (2005)

[reaction: see text] Various pseudo-oligosacchardies and amino acid glycoconjugates were synthesized via an intermolecular 1,3-dipolar cycloaddition ("click") reaction using easily accessible carbohydrate and amino acid derived azides and alkynes as building blocks. It is pertinent to mention that the conjugation reaction is highly regioselective and high yielding and can be carried out under mild reaction conditions.
Crystal Structure of the Broadly Cross-Reactive HIV-1-Neutralizing Fab X5 and Fine Mapping of Its Epitope, (2004)

The human monoclonal antibody Fab X5 neutralizes a broad range of HIV-1 primary isolates. The crystal structure of X5 has been determined at 1.9 A resolution. There are two crystallographically independent Fab fragments in the asymmetric unit. The crystallographic R value for the final model is 0.22. The antibody-combining site features a long (22 amino acid residues) CDR H3 with a protruding hook-shaped motif. The X5 structure and site-directed mutagenesis data suggest that X5 amino acid residues W100 and Y100F in the CDR H3 motif may be critical for the binding of Fab X5 to gp120. X5 bound to a complex of a CD4 mimetic and gp120 with approximately the same kinetics and affinity as to a CD4-gp120 complex, suggesting that specific interactions between CD4 and X5 are unlikely to contribute to the binding of X5 to gp120-CD4 complexes. Binding of X5 to alanine scanning mutants of gp120JR-CSF complexed with CD4 suggested a critical role of the highly conserved amino acid residues at positions 423 and 432. The X5 structure and fine mapping of its epitope may assist in the elucidation of the mechanisms of viral entry and neutralization, and the development of HIV-1 inhibitors and vaccines.
COLLAGEN ARTHRITIS—WHAT CAN IT TEACH US? (1994)

Collagen-induced arthritis is an arthritic disease that can be induced in rodents and primates. It is used widely as a model of disease processes and potential therapies. The immunology of collagen arthritis has some compelling parallels with human disease and these have been exploited recently in several novel ways to analyse the nature of autoreactivity against joint antigens and to test new therapies. Antibodies against lymphocyte surface markers, such as CD4, CD40L and MHC Class II, have been shown to suppress disease progression. Manipulation of cytokines, notably TNF-alpha, IL-1 and IL-2, has been extensively studied using the cytokines themselves, antibodies against cytokines and other antagonists with varied, but promising results. The search for antigen-specific immunosuppression has gained new impetus through manipulation of collagen arthritis by mucosal delivery of collagen to induce tolerance that suppresses disease. This review examines the salient features of collagen arthritis that are relevant to human disease and discusses the meaning and potential application of experimental therapies to the control of human arthritis.
Nanopore sequencing of polynucleotides assisted by a rotating electric field (2003)

The translocation kinetics of a polynucleotide chain through a nanopore is studied using Monte-Carlo simulations for both lattice and off-lattice models, by which we demonstrate a method in sequencing polynucleotides assisted by a rotating electric field. At low frequencies of the rotating field, the translocation time of the chain is inversely proportional to the rotating field frequency. More specifically, in these cases, the translocation time of each nucleotide is nearly quantized, and thus it greatly improves the resolution of blockade-current time series obtained from nanopore sequencing experiments. The polynucleotide sequences can be accurately determined from analyzing several time series of current variation through the nanopore.
Spectroscopic investigations of ferric cytochrome P-450-CAM ligand complexes. Identification of the ligand trans to cysteinate in the native enzyme. (1982)

An extensive series of ligand complexes of ferric cytochrome P-450-CAM has been examined by UV-visible absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopy in an attempt to identify the ligand trans to cysteinate in the six-coordinate resting state of the enzyme. Thus, the ligands used have been chosen to serve as models for coordination by potential endogenous amino acids and include alcohol, amide and carboxylate oxygen donors, amine, imidazole and indole nitrogen donors and disulfide, thioether, thiol, and thiolate sulfur donors. As this investigation has been by nature an empirical one, the conclusions are strengthened by the concurrent use of three different spectroscopic techniques. All of the complexes formed except those resulting from thiolate addition display spectroscopic properties that are broadly similar to those of low spin, six-coordinate P-450. Of the sulfur donor adducts, disulfide and thioether-bound P-450 have properties that are different enough in detail to distinguish them from native P-450. While the spectral features of the thiol-bound species and of low spin ferric P-450 are alike, the former are pH dependent due to interconversion to bound thiolate, whereas the latter display essentially no spectral changes with pH. Of the oxygen donor complexes, all but carboxylate have spectra that very closely match those of the resting enzyme. Adducts formed with most nitrogenous ligands, including several imidazole derivatives, exhibit spectra that are sufficiently different from native P-450 to exclude them as candidates for the sixth ligand. Interestingly, the spectral properties of a complex formed with an imidazole derivative having a bulky electron-withdrawing substituent in the alpha position are comparable to those native P-450 except for the line shape of the EPR spectrum. Previously published theoretical work suggests that the spectral differences seen between this imidazole derivative and the other examined are electronic and not steric in origin. As no similar electronic mechanism exists for the protein to reduce the electron-donating ability or histidine, it is felt that coordination of histidine in the sixth position of P-450 can be ruled out. In conclusion, close examination of all spectral data reveals that amino acid analog adducts of P-450-CAM with amides and, in particular, alcohols, produce spectra that almost exactly duplicate those of native P-450 and suggests that the ligand trans to cysteinate in the six-coordinate ferric enzyme has an oxygen donor atom.
Gene expression profiling of human endometrial receptivity on days LH+2 versus LH+7 by microarray technology (2003)

In humans, embryonic implantation and reproduction depends on the interaction of the embryo with the receptive endometrium. To gain a global molecular understanding of human endometrial receptivity, we compared gene expression profiles of pre-receptive (day LH+2) versus receptive (LH+7) endometria obtained from the same fertile woman (n = 5) in the same menstrual cycle in five independent experiments. Biopsies were analysed using the Affymetrix HG-U95A array, a DNA chip containing approximately 12,000 genes. Using the pre-defined criteria of a fold change >/=3 in at least four out of five women, we identified 211 regulated genes. Of these, 153 were up-regulated at LH+7 versus LH+2, whereas 58 were down-regulated. Amongst these 211 regulated genes, we identified genes that were known to play a role in the development of a receptive endometrium, and genes for which a role in endometrial receptivity, or even endometrial expression, has not been previously described. Validation of array data was accomplished by mRNA quantification by real time quantitative fluorescent PCR (Q-PCR) of three up-regulated [glutathione peroxidase 3 (GPx-3), claudin 4 (claudin-4) and solute carrier family 1 member 1 (SLC1A1)] genes in independent LH+2 versus LH+7 endometrial samples from fertile women (n = 3) and the three up-regulated genes throughout the menstrual cycle (n = 15). Human claudin-4 peaks specifically during the implantation window, whereas GPx-3 and SLC1A1 showed highest expression in the late secretory phase. In-situ hybridization (ISH) experiments showed that GPx-3 and SLC1A1 expression was restricted to glandular and luminal epithelial cells during the mid- and late luteal phase. The present work adds new and important data in this field, and highlights the complexity of studying endometrial receptivity even using global gene-expression analysis.
Altered Levels of Scavenging Enzymes in Embryos Subjected to a Diabetic Environment (1996)

Maternal diabetes during pregnancy is associated with an increased rate of congenital malformations in the offspring. The exact molecular etiology of the disturbed embryogenesis is unknown, but an involvement of radical oxygen species in the teratological process has been suggested. Oxidative damage presupposes an imbalance between the activity of the free oxygen radicals and the antioxidant defence mechanisms on the cellular level. The aim of the present study was to investigate if maternal diabetes in vivo, or high glucose in vitro alters the expression of the free oxygen radical scavenging enzymes superoxide dismutase (CuZnSOD and MnSOD), catalase and glutathione peroxidase in rat embryos during late organogenesis. We studied offspring of normal and diabetic rats on gestational days 11 and 12, and also evaluated day-11 embryos after a 48 hour culture period in 10 mM or 50 mM glucose concentration. Both maternal diabetes and high glucose culture caused growth retardation and increased rate of congenital malformations in the embryos. The CuZnSOD and MnSOD enzymes were expressed on gestational day 11 and both CuZnSOD, MnSOD and catalase were expressed on day 12 with increased concentrations of MnSOD transcripts when challenged by a diabetic milieu. There was a good correlation between mRNA, protein, and activity levels, suggesting that the regulation of these enzymes occurs primarily at the pretranslational level. Maternal diabetes in vivo and high glucose concentration in vitro induced increased MnSOD expression, concomitant with increased total SOD activity, and a tentative decrease in catalase expression and activity in the embryos. These findings support the notion of enhanced oxidative stress in the embryo as an etiologic agent in diabetic teratogenesis.