gebhart/patrepeval huggingface dataset:
Plasmon-Enhanced Ultraviolet Photoluminescence from Hybrid Structures of Graphene/ZnO Films (2010)

We report substantially enhanced photoluminescence (PL) from hybrid structures of graphene/ZnO films at a band gap energy of ZnO (∼3.3 eV/376 nm). Despite the well-known constant optical conductivity of graphene in the visible-frequency regime, its abnormally strong absorption in the violet-frequency region has recently been reported. In this Letter, we demonstrate that the resonant excitation of graphene plasmon is responsible for such absorption and eventually contributes to enhanced photoemission from structures of graphene/ZnO films when the corrugation of the ZnO surface modulates photons emitted from ZnO to fulfill the dispersion relation of graphene plasmon. These arguments are strongly supported by PL enhancements depending on the spacer thickness, measurement temperature, and annealing temperature, and the micro-PL mapping images obtained from separate graphene layers on ZnO films.
NAD(P)H Oxidase (2000)

Reactive oxygen species have emerged as important molecules in cardiovascular function. Recent work has shown that NAD(P)H oxidases are major sources of superoxide in vascular cells and myocytes. The biochemical characterization, activation paradigms, structure, and function of this enzyme are now partly understood. Vascular NAD(P)H oxidases share some, but not all, characteristics of the neutrophil enzyme. In response to growth factors and cytokines, they produce superoxide, which is metabolized to hydrogen peroxide, and both of these reactive oxygen species serve as second messengers to activate multiple intracellular signaling pathways. The vascular NAD(P)H oxidases have been found to be essential in the physiological response of vascular cells, including growth, migration, and modification of the extracellular matrix. They have also been linked to hypertension and to pathological states associated with uncontrolled growth and inflammation, such as atherosclerosis.
Prevention and treatment of cytomegalovirus infection after marrow transplantation. (1988)

Based on the known epidemiology of cytomegalovirus (CMV) infection, primary infection among seronegative patients is preventable by use of seronegative blood products including marrow. A potential alternative is use of leukocyte-depleted blood products. Efficacy of passive immunoprophylaxis remains uncertain, and this modality cannot be recommended until additional studies are available. Antiviral agents can be used to suppress or delay CMV infection among seropositive patients who develop active infection from reactivation of latent virus. Intravenous acyclovir significantly reduced the probability of CMV infection and disease among seropositive patients in a controlled trial. The new antiviral agents ganciclovir and foscarnet may provide better results, although the marrow toxicity of ganciclovir may limit its utility. For treatment of CMV pneumonia the combination of ganciclovir and CMV immunoglobulin has shown promise in initial trials.
An Engineered DNA‐Binding Protein Self‐assembles Metallic Nanostructures (2010)

The golden age of DNA: We describe a strategy for engineering bifunctional proteins that simultaneously associate with metals and DNA to create self-assembled nanostructures. A DNA binding protein engineered with a gold binding peptide arranges colloidal gold particles along a DNA guide by virtue of its introduced peptide motif. These self-assembled complexes represent a step toward constructing nanoarchitectures with potential in nanoelectronic and photonic devices.
Using Probiotics in Gastrointestinal Disorders (2012)

Accumulating data have strongly linked gut microbes to human health. Accordingly, manipulating intestinal microbiota holds promise as a potential treatment for restoring health. Although antibiotics have been the primary clinical choice for achieving this objective, supplementing the gastrointestinal microbiota with probiotics—or encouraging their growth with prebiotics—is now widely used as an alternative approach. Among gastrointestinal disorders, data of varying quality support the use of probiotics in preventing and treating diarrhea, inflammatory bowel disease (particularly pouchitis), irritable bowel syndrome, and liver disease. Although some data are indeed promising, the profusion of probiotic products and the fact that species, strain, and formulation all clearly influence efficacy have led to significant confusion regarding the best choice for different indications. Although sufficient evidence is not currently available to provide a clear guidance on the best probiotic for a particular clinical indication, key scientific concepts are now emerging. Building on these concepts, this review will provide practical information on the use of these products in clinical practice.
Structural Color in Porous, Superhydrophilic, and Self‐Cleaning SiO2/TiO2 Bragg Stacks (2007)

Thin-film Bragg stacks exhibiting structural color have been fabricated by a layer-by-layer (LbL) deposition process involving the sequential adsorption of nanoparticles and polymers. High- and low-refractive-index regions of quarter-wave stacks were generated by calcining LbL-assembled multilayers containing TiO(2) and SiO(2) nanoparticles, respectively. The physical attributes of each region were characterized by a recently developed ellipsometric method. The structural color characteristics of the resultant nanoporous Bragg stacks could be precisely tuned in the visible region by varying the number of stacks and the thickness of the high- and low-refractive-index stacks. These Bragg stacks also exhibited potentially useful superhydrophilicity and self-cleaning properties.
CHD5 is down-regulated through promoter hypermethylation in gastric cancer (2009)

CHD5 was a TSG epigenetically down-regulated in gastric cancer.
Mechanisms of Protease-activated Receptor-4 Actions in Cardiomyocytes (2003)

Protease-activated receptor (PAR)-4 is a low affinity thrombin receptor with slow activation and desensitization kinetics relative to PAR-1. This study provides novel evidence that cardiomyocytes express functional PAR-4 whose signaling phenotype is distinct from PAR-1 in cardiomyocytes. AYPGKF, a modified PAR-4 agonist with increased potency at PAR-4, activates p38-mitogen-activated protein kinase but is a weak activator of phospholipase C, extracellular signal-regulated kinase, and cardiomyocyte hypertrophy; AYPGKF and thrombin, but not the PAR-1 agonist SFLLRN, activate Src. The observation that AYPGKF and thrombin activate Src in cardiomyocytes cultured from PAR-1(-/-) mice establishes that Src activation is via PAR-4 (and not PAR-1) in cardiomyocytes. Further studies implicate Src and epidermal growth factor receptor (EGFR) kinase activity in the PAR-4-dependent p38-mitogen-activated protein kinase signaling pathway. Thrombin phosphorylates EGFRs and ErbB2 via a PP1-sensitive pathway in PAR-1(-/-) cells that stably overexpress PAR-4; the Src-mediated pathway for EGFR/ErbB2 transactivation underlies the protracted phases of thrombin-dependent extracellular signal-regulated kinase activation in PAR-1(-/-) cells that overexpress PAR-4 and in cardiomyocytes. These studies identify a unique signaling phenotype for PAR-4 (relative to other cardiomyocyte G protein-coupled receptors) that is predicted to contribute to cardiac remodeling and influence the functional outcome at sites of cardiac inflammation.
A trans-acting regulatory mutation that causes overproduction of phosphatidylserine synthase in Escherichia coli. (1983)

We have isolated three mutants of Escherichia coli which have elevated levels of the phospholipid synthetic enzyme phosphatidylserine synthase. One of these strains carries a mutation, designated pssR1, which maps near minute 84 of the chromosome, distinct from the synthase structural gene (pss) at minute 56. The pssR1 mutation causes selective overproduction of phosphatidylserine synthase, since the levels of six other lipid synthetic enzymes are unaltered. The specific activity of the synthase in crude cell extracts of mutants harboring pssR1 is about five times greater than wild type. The synthase can also be overproduced 10-fold in wild type strains with hybrid ColE1 plasmids carrying the synthase structural gene (pss). A pssR1 mutant harboring such a pss plasmid overproduces the synthase about 50-fold. This multiplicative interaction of pssR1 and cloned pss demonstrates that pssR1 is trans-acting. The synthase has been purified in parallel from pssR1 and pssR+ strains. The pssR1 mutant yields more total synthase protein than pssR+, but the pure enzyme has the same specific activity in both cases. Therefore, pssR1 acts by increasing the amount of the normal protein, not by activating the enzyme. The discovery of pssR shows that there are regulatory loci which control the production of enzymes involved in membrane lipid synthesis.
Identification of New Races and Deviating Strains of the Spinach Downy Mildew Pathogen Peronospora farinosa f. sp. spinaciae (2013)

Spinach downy mildew disease, caused by the obligate pathogen Peronospora farinosa f. sp. spinaciae, is the most economically important spinach (Spinacia oleracea) disease. New races of this pathogen have been emerging at a rapid rate over the last 15 years. This is likely due to production changes, particularly in California, such as high-density plantings and year-round spinach production. As of 2004, 10 races of P. farinosa f. sp. spinaciae had been identified, and the spinach resistance locus RPF2 provided resistance to races 1 to 10. Based on disease reactions on a set of spinach differentials containing six hypothesized resistance loci (RPF1-RPF6), races 11, 12, 13, and 14 of P. farinosa f. sp. spinaciae were characterized based on samples collected in the past 5 years as part of this study. Race 11, identified in 2008, could overcome the resistance of spinach cultivars resistant to races 1 to 10. Spinach resistance loci RPF1, RPF3, and RPF6 provided resistance to race 11. Race 12 was identified in 2009 and could overcome the resistances of the RPF1 and RPF2 loci. The RPF3 locus was effective against race 12. Race 13 was identified in 2010 and could overcome the resistance imparted by the RPF2 and RPF3 loci, whereas the RPF1 locus was effective against race 13. Race 14 was similar to race 12 and caused identical disease responses on the standard differentials but could be distinguished from race 12 by its ability to cause disease on a number of newly released cultivars, including 'Pigeon', 'Cello', and 'Celesta'. Five novel strains of P. farinosa f. sp. spinaciae were also identified. For example, isolate UA4711 of the pathogen, collected from Spain in 2011, was able to overcome the resistance imparted by the RPF1 and RPF3 loci, while RPF2 and RPF4 were effective against this strain. A total of 116 spinach cultivars, including 103 commercial lines and 13 differential cultivars, were evaluated for resistance to race 10 and the newly designated races 11, 12, 13, and 14.
Succinyl-CoA:( R )-Benzylsuccinate CoA-Transferase: an Enzyme of the Anaerobic Toluene Catabolic Pathway in Denitrifying Bacteria (2001)

Anaerobic microbial toluene catabolism is initiated by addition of fumarate to the methyl group of toluene, yielding (R)-benzylsuccinate as first intermediate, which is further metabolized via beta-oxidation to benzoyl-coenzyme A (CoA) and succinyl-CoA. A specific succinyl-CoA:(R)-benzylsuccinate CoA-transferase activating (R)-benzylsuccinate to the CoA-thioester was purified and characterized from Thauera aromatica. The enzyme is fully reversible and forms exclusively the 2-(R)-benzylsuccinyl-CoA isomer. Only some close chemical analogs of the substrates are accepted by the enzyme: succinate was partially replaced by maleate or methylsuccinate, and (R)-benzylsuccinate was replaced by methylsuccinate, benzylmalonate, or phenylsuccinate. In contrast to all other known CoA-transferases, the enzyme consists of two subunits of similar amino acid sequences and similar sizes (44 and 45 kDa) in an alpha(2)beta(2) conformation. Identity of the subunits with the products of the previously identified toluene-induced bbsEF genes was confirmed by determination of the exact masses via electrospray-mass spectrometry. The deduced amino acid sequences resemble those of only two other characterized CoA-transferases, oxalyl-CoA:formate CoA-transferase and (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase, which represent a new family of CoA-transferases. As suggested by kinetic analysis, the reaction mechanism of enzymes of this family apparently involves formation of a ternary complex between the enzyme and the two substrates.
Cigarette Smoke‐Induced Oxidative Stress and TGF‐β1Increase p21waf1/cip1Expression in Alveolar Epithelial Cells (2002)

Sustained oxidative stress caused by cigarette smoking induces a chronic inflammatory response, resulting in the destruction of the alveolar cell wall characteristic of emphysema. The loss of tissue may involve the progressive depletion of epithelial cells through inhibition of proliferation leading to cell death. The cell cycle regulator p21(waf1/cip1) acts as a G(1)/S and G(2)/M phase checkpoint regulator. We hypothesize that cigarette smoke-induced oxidative stress and transforming growth factor beta 1 (TGF-beta(1)) may inhibit cellular proliferation by p21(waf1/cip1) in type II alveolar epithelial cells (A549). A significant increase was observed in p21(waf1/cip1) mRNA expression in A549 cells by cigarette smoke condensate, H(2)O(2), and TGF-beta(1). In conclusion, cigarette smoke-induced oxidative stress and TGF-beta(1) modulate expression of the cell cycle inhibitor p21(waf1/cip1). This may be important in the growth arrest and cell survival of alveolar type II cells in the G(1) phase.
Spinal Cord Stimulation-induced Analgesia (2010)

These results suggest a potential cellular mechanism underlying spinal cord stimulation-induced pain relief. This in vivo model allows the neurophysiologic basis for spinal cord stimulation-induced analgesia to be studied.
Analysis of Sequences and Loci of p44 Homologs Expressed by Anaplasma phagocytophila in Acutely Infected Patients (2002)

Anaplasma phagocytophila is an obligatory intragranulocytic bacterium that causes human granulocytic ehrlichiosis. Immunodominant 44-kDa outer membrane proteins of A. phagocytophila are encoded by a p44 multigene family. In the present study, expression profiles of p44 genes in the blood of acutely infected patients in the year 2000 were characterized. A single p44 gene was predominantly expressed in peripheral blood leukocytes from one patient, while up to 17 different p44 genes were transcribed without a single majority in the other two patients. The cDNA sequences of the central hypervariable region of several p44 genes were identical among the isolates from the three patients and a 1995 A. phagocytophila isolate. A. phagocytophila was isolated by cell culture from all of the three 2000 patients. Genomic Southern blot analysis of the three 2000 and two 1995 A. phagocytophila isolates with probes specific to the most dominant p44 transcript in each patient showed that the p44 loci in the A. phagocytophila genome were conserved. Analysis of the predicted amino acid sequences of 43 different p44 genes including 19 new sequences found in the present study, revealed that five amino acids were absolutely conserved. The hypervariable region was subdivided into five domains, including three extremely hypervariable central domains. These results suggest that variations in the sequences of p44 are not random but are restricted. Furthermore, several p44 genes are not hypermutatable in nature, based on the conservation of gene sequences and loci among isolates obtained 5 years apart.
Strain-Controlled Switching of Hierarchically Wrinkled Surfaces between Superhydrophobicity and Superhydrophilicity (2011)

Recent years have witnessed intense interest in multifunctional surfaces that can be designed to switch between different functional states with various external stimuli including electric field, light, pH value, and mechanical strain. The present paper is aimed to explore whether and how a surface can be designed to switch between superhydrophobicity and superhydrophilicity by an applied strain. Based on well-established theories of structure buckling and solid-liquid contact, we show that this objective may be achieved through a hierarchically wrinkled surface. We derive general recursive relations for the apparent contact angle at different levels of the hierarchical surface and investigate the thermodynamic stability of different contact states. Our study may provide useful guidelines for the development of multifunctional surfaces for many technological applications.
Emission characteristics and stability of a helium field ion source (1988)

The emission characteristics and stability of a helium field ion source were studied. Detailed measurements of current emitted from the (111) plane of a tungsten emitter revealed a sharp peak in I–V characteristics that shifted toward a higher voltage when the helium pressure increased or the emitter temperature rose. Measurements of the pressure dependence of the ion current showed a decrease in current above the critical pressure, ∼1.3 Pa. To determine why the current decreased, we varied the helium flow rate and the distance between the emitter tip and aperture. The measured characteristics indicated that the decrease in current was not caused by a large flow of warm helium or by a charge exchange of emitted He+ ions with neutral He atoms inside the ion source, so we had to assume the cause lies elsewhere. We recorded ion current versus time characteristics to determine emission stability, which could be improved to ±10% within 60 min by reducing impurities in the helium gas.
NspS, a Predicted Polyamine Sensor, Mediates Activation of Vibrio cholerae Biofilm Formation by Norspermidine (2005)

Vibrio cholerae is both an environmental bacterium and a human intestinal pathogen. The attachment of bacteria to surfaces in biofilms is thought to be an important feature of the survival of this bacterium both in the environment and within the human host. Biofilm formation occurs when cell-surface and cell-cell contacts are formed to make a three-dimensional structure characterized by pillars of bacteria interspersed with water channels. In monosaccharide-rich conditions, the formation of the V. cholerae biofilm requires synthesis of the VPS exopolysaccharide. MbaA (locus VC0703), an integral membrane protein containing a periplasmic domain as well as cytoplasmic GGDEF and EAL domains, has been previously identified as a repressor of V. cholerae biofilm formation. In this work, we have studied the role of the protein NspS (locus VC0704) in V. cholerae biofilm development. This protein is homologous to PotD, a periplasmic spermidine-binding protein of Escherichia coli. We show that the deletion of nspS decreases biofilm development and transcription of exopolysaccharide synthesis genes. Furthermore, we demonstrate that the polyamine norspermidine activates V. cholerae biofilm formation in an MbaA- and NspS-dependent manner. Based on these results, we propose that the interaction of the norspermidine-NspS complex with the periplasmic portion of MbaA diminishes the ability of MbaA to inhibit V. cholerae biofilm formation. Norspermidine has been detected in bacteria, archaea, plants, and bivalves. We suggest that norspermidine serves as an intercellular signaling molecule that mediates the attachment of V. cholerae to the biotic surfaces presented by one or more of these organisms.
The specific JNK inhibitor SP600125 targets tumour necrosis factor‐α production and epithelial cell apoptosis in acute murine colitis (2006)

Stress-activated protein kinases (SAPKs) are activated in human inflammatory bowel disease (IBD). Recently it has been demonstrated that p38MAPK (mitogen-activated protein kinase) inhibition using SB203580 is effective in reducing disease in both dextran sulphate sodium (DSS)-induced and 2,4,6-trinitrobenzenesulphonic acid (TNBS)-induced murine colitides, underscoring the importance of this pathway in gastrointestinal inflammation. However, the contribution of c-Jun N-terminal kinase (JNK) in intestinal inflammation is unknown. Based on the known involvement of JNK in tumour necrosis factor-alpha (TNF-alpha) expression and in mediating the effects of oxidant stress, we hypothesized that JNK inhibition would also affect colitis. Our studies in mice with DSS-induced colitis treated with the JNK inhibitor SP600125, indicate that there is a significant reduction in wasting as well as a significant reduction in histological damage scores. Both total colonic and mesenteric lymphocyte CD3/CD28-stimulated TNF-alpha levels were dramatically reduced under the same circumstances. This was associated with a reduction in JNK protein expression and activity, as well as a reduction in AP-1 DNA binding with SP600125. Interestingly, there were no apparent changes in either p38MAPK or p42/44ERKs. Immunofluorescence of the colon for the active form of JNK revealed a prominent signal arising from the infiltrating inflammatory cells. SP600125 reduced this as well as, specifically, macrophage infiltration. Strikingly, we also demonstrate reduced epithelial cell apoptosis in response to treatment with SP600125. We conclude that specific inhibition of JNK is beneficial in the DSS model of colitis, and may be of value in human IBD.
The Development of New High Speed Paper Machine Series. (2002)

A new Mitsubishi high-speed paper machine development project has started in 1999 and concluded with product offering to the market in October 2001. The new product is known as MJ series and is designed to complement the current MH series Mitsubishi paper machines.The goal of MJ series paper machine is to produce quality paper at 2, 000 m/min operation speed while being an operator friendly product. The MJ series has been developed in the course of the intensive elementary study, program simulation, model test, and final verification on our pilot paper machine in Mitsubishi R&D center of Mihara, Japan.This paper presents the concept and features of the MJ series paper machine.
Synchronisation in the carrier recovery of a satellite link using Turbo-Codes with the help of tentative decisions (1999)

The paper demonstrates how the use of tentative decisions can improve the carrier recovery over a satellite link under severe conditions with a C/N that can quickly decrease under 3 dB when using a turbo-code. We demonstrate how we overcome the synchronisation errors, especially carrier phase errors in the tracking mode for transmission in a continuous mode. We present simulation results such as improvements on the S-curve of a phase detector, reduction of the cycle slip rate and the global system performance. (7 pages)
Inhibitory Effect of α2-Macroglobulin on Vibrio vulnificus Protease (1989)

Vibrio vulnificus, an etiologic agent of wound infections and septicemia in humans, elaborates a metalloprotease which is known to be an important virulence factor of the Vibrio. The proteolytic activity of V. vulnificus metalloprotease (VVP) toward casein and elastin was inhibited by alpha 2-macroglobulin (alpha 2 M) at the molar ratio of 1:1, although partial activity was maintained. Permeability-enhancing and hemorrhagic activities were also inhibited, but the peptidase activity toward Z-Gly-Phe-NH2 was not reduced, even by an excess amount of alpha 2 M. VVP formed a complex with alpha 2 M through cleavage of the bait regions of all four alpha 2 M subunits and elicitation of conformational change of the alpha 2 M molecule, which resulted in entrapment of VVP in the alpha 2 M molecule. The peptidase activity of alpha 2 M-VVP complex was inhibited by low-molecular-weight inhibitors such as phosphoramidon, but IgG antibody against VVP failed to neutralize its peptidase activity. Of human plasma proteins, alpha 2 M was the only inhibitor for VVP. These findings indicate that VVP produced during V. vulnificus infection is inactivated by plasma alpha 2 M that leaks from the vascular system.