gebhart/patrepeval huggingface dataset:
The Posttranscriptional Regulator RsmA Plays a Role in the Interaction between <i>Pseudomonas aeruginosa</i> and Human Airway Epithelial Cells by Positively Regulating the Type III Secretion System (2006)

Posttranscriptional regulation of certain virulence-related genes in Pseudomonas aeruginosa is brought about by RsmA, a small RNA-binding protein. During interaction with airway epithelial cells, RsmA promoted actin depolymerization, cytotoxicity, and anti-internalization of P. aeruginosa by positively regulating the virulence-associated type III secretion system.
Context‐Dependence of the Contribution of Disulfide Bonds to β‐Hairpin Stability (2007)

Incorporation of disulfide bonds to stabilize protein and peptide structures is not always a successful strategy. To advance current knowledge on the contribution of disulfide bonds to beta-hairpin stability, a previously reported beta-hairpin-forming peptide was taken as a template to design a series of Cys-containing peptides. The conformational behavior of these peptides in their oxidized, disulfide-cyclized peptides, and reduced, linear peptides, was investigated on the basis of NMR parameters: NOEs, and 1H and 13C chemical shifts. We found that the effect of disulfide bonds on beta-hairpin stability depends on its location within the beta-hairpin structure, being very small or even destabilizing when connecting two hydrogen-bonded facing residues. When the disulfide bond is linking non-hydrogen-bonded facing residues, we estimated that its contribution to the free-energy change of beta-hairpin folding is approximately -1.0 kcal mol(-1). This value is larger than those reported for most beta-hairpin-stabilizing cross-strand side-chain-side-chain interactions, except for some aromatic-aromatic interactions, in particular the Trp-Trp one, and the cation-pi interaction between Trp and the non-natural methylated Arg/Lys. As disulfide bonds are frequently used to stabilize peptide conformations, our conclusions can be useful for peptide, peptidomimetic, and protein design, and may even extend to other chemical cross-links.
Inhibition of Pathogenic Bacterial Adhesion by Acidic Polysaccharide from Green Tea (<i>Camellia sinensis</i>) (2006)

An acidic polysaccharide CS-F2 from Camellia sinensis was examined to characterize its anti-adhesive effects against pathogenic bacteria, most notably Helicobacter pylori, Propionibacterium acnes, and Staphylococcus aureus. CS-F2 showed marked inhibitory activity against the pathogen-mediated hemagglutination with a minimum inhibitory concentration (MIC) between 0.01 and 0.1 mg/mL, which is lower than the previously reported MIC values for Panax ginseng and Artemisia capillaris. The inhibitory effects of CS-F2 on the adhesion of H. pylori to AGS adenocarcinoma gastric epithelial cells, or P. acnes and S. aureus to NIH 3T3 fibroblast cells, were further assessed resulting in MIC values between 0.063 and 0.13 mg/mL. Importantly, CS-F2 showed no inhibitory effects against Lactobacillus acidophilus, Escherichia coli, or Staphylococcus epidermidis. Our results suggest that CS-F2, which is a pectin-type polysaccharide with a molecular weight of approximately 8.0 x 10(4) Da, may exert a selective anti-adhesive effect against certain pathogenic bacteria, while exerting no effects against beneficial and commensal bacteria.
The Centre for Image Information: the shape of things to come (1993)

Since its transfer to De Montfort University at Leicester, Britain’s National Art Slide Library, formerly at the Victoria and Albert Museum, has become the catalyst for a new Centre for Image Information. The Centre will provide a clearing house for information, a research centre, and an image bank, and will concern itself with images in all formats with an emphasis on new technology. Whether moving images are to be included will depend on the availability of funding. A major component of the Centre’s initial strategy will be the development of a high resolution database of images capable of being delivered as medium resolution databases, optical discs, slides, or on paper. Although the Centre has been conceived primarily as a national service, institutions in other countries in addition to those in the UK are invited to join as Associates, and the Centre is eager to exchange information across national boundaries.
Insulin-like growth factor 1 alters feto-placental protein and carbohydrate metabolism in fetal sheep. (1994)

Insulin-like growth factor 1 (IGF-1) is an anabolic hormone in postnatal life and may be an important endocrine regulator of fetal growth. However, its effects on fetal metabolism in vivo have not previously been determined. We studied the effect of 50 micrograms/h.kg IGF-1 infusion in 12 chronically catheterized fetal sheep. Fetal blood amino nitrogen concentrations fell 10% and maternal 7%, consistent with a rise in feto-placental amino acid uptake. Fetal amino acid oxidation, measured by fetal urea production fell by 30% (44.4 +/- 10.5 to 30.9 +/- 8.0 mumol/min). Fetal and maternal blood glucose concentrations both fell by 0.1 mM, consistent with increased feto-placental glucose uptake. Placental lactate production fell 30% (114 +/- 15 to 78 +/- 11 mumol/min), as did fetal and uterine lactate uptake. There was no change in umbilical or uterine blood flows, nor in placental transfer by simple or facilitated diffusion. We conclude that IGF-1 has anabolic effects on feto-placental protein and carbohydrate metabolism. Circulating IGF-1 may in part mediate the regulation of fetal growth in response to fetal nutrient supply.
<i>Pax6</i>regulates granule cell polarization during parallel fiber formation in the developing cerebellum (2001)

The molecular mechanisms that govern the coordinated programs of axonogenesis and cell body migration of the cerebellar granule cell are not well understood. In Pax6 mutant rats (rSey2/rSey2), granule cells in the external germinal layer (EGL) fail to form parallel fiber axons and to migrate tangentially along these fibers despite normal expression of differentiation markers. In culture, mutant cells sprout multiple neurites with enlarged growth cones, suggesting that the absence of Pax6 function perturbs cytoskeletal organization. Some of these alterations are cell-autonomous and rescuable by ectopic expression of Pax6 but not by co-culture with wild-type EGL cells. Cell-autonomous control of cytoskeletal dynamics by Pax6 is independent of the ROCK-mediated Rho small GTPase pathway. We propose that in addition to its roles during early patterning of the CNS, Pax6 is involved in a novel regulatory step of cytoskeletal organization during polarization and migration of CNS neurons.
Organocatalyzed Asymmetric α-Oxidation, α-Aminoxylation and α-Amination of Carbonyl Compounds (2010)

Organocatalytic asymmetric alpha-oxidation and amination reactions of carbonyl compounds are highly useful synthetic methodologies, especially in generating chiral building blocks that previously have not been easily accessible by traditional methods. The concept is relatively new and therefore the list of new catalysts, oxidizing and aminating reagents, as well as new substrates, are expanding at an amazing rate. The scope of this review includes new reactions and catalysts, mechanistic aspects and synthetic applications of alpha-oxidation, hydroxylation, aminoxylation, amination, hydrazination, hydroxyamination and related alpha-heteroatom functionalization of aldehydes, ketones and related active methylene compounds published during 2005-2009.
Probabilistic Constellation Shaping for Optical Fiber Communications (2019)

We review probabilistic constellation shaping (PCS), which has been a key enabler for several recent record-setting optical fiber communications experiments. PCS provides both fine-grained rate adaptability and energy efficiency (sensitivity) gains. We discuss the reasons for the fundamentally better performance of PCS over other constellation shaping techniques that also achieve rate adaptability, such as time-division hybrid modulation, and examine in detail the impact of sub-optimum shaping and forward error correction (FEC) on PCS systems. As performance metrics for systems with PCS, we compare information-theoretic measures such as mutual information (MI), generalized MI (GMI), and normalized GMI, which enable optimization and quantification of the information rate (IR) that can be achieved by PCS and FEC. We derive the optimal parameters of PCS and FEC that maximize the IR for both ideal and non-ideal PCS and FEC. To avoid plausible pitfalls in practice, we carefully revisit key assumptions that are typically made for ideal PCS and FEC systems.
Selective message distribution with people-tagging in user-collaborative environments (2009)

Oftentimes, we would like to distribute call-for-participation messages by email to people who are potentially interested in the topics of the corresponding events. Meanwhile, people either broadcast such messages to everyone in their organizations or maintain a number of mailing lists for different topics. But both approaches have drawbacks.
Neutrophil Elastase Induces <i>MUC</i> 5AC Gene Expression in Airway Epithelium via a Pathway Involving Reactive Oxygen Species (2002)

Neutrophil-predominant airway inflammation and mucus obstruction of the airways are major pathologic features of chronic airway diseases, including cystic fibrosis and chronic bronchitis. Neutrophils release elastase, a serine protease that impairs mucociliary clearance and stimulates goblet cell metaplasia and mucin production. We previously reported that neutrophil elastase increases expression of a major respiratory mucin gene, MUC5AC, by enhancing mRNA stability. However, the molecular mechanisms of elastase-regulated MUC5AC expression are not known. We hypothesized that reactive oxygen species, generated by elastase treatment, mediate MUC5AC gene expression. To test this hypothesis, A549, a respiratory epithelial cell line, was treated with elastase in the presence or absence of the oxygen radical scavenger, dimethylthiourea, or the iron chelator, desferrioxamine. MUC5AC mRNA levels were assessed by Northern analysis. Both antioxidants significantly inhibited elastase-induced MUC5AC gene expression. Dimethylthiourea also inhibited the neutrophil elastase (NE)-induced increase in MUC5AC expression in normal human bronchial epithelial cells. To determine whether elastase treatment generated reactive oxygen species, A549 and normal human bronchial epithelial cells were loaded with dichlorodihydrofluorescein, a fluorescent indicator of oxidative stress. NE treatment increased cellular fluorescence in both cell types, indicating generation of intracellular reactive oxygen species. We conclude that NE treatment increases MUC5AC gene expression by an oxidant-dependent mechanism.
Quantum Dot‐Based Mortalin Staining as a Visual Assay for Detection of Induced Senescence in Cancer Cells (2007)

Quantum dots (QDs) are fluorescent nanocrystals that are emerging as fine alternatives to the conventional organic dyes. They have several advantages including greater photostability and a wider range of excitation-emission wavelengths. By using mortalin staining as a model, we initially demonstrated that the QDs are more stable and provide better resolution in protein imaging in fixed cells. With the help of an internalizing antibody, we generated internalizing QD (i-QD) and demonstrated its inertness to cell replication, structure, and viability. Based on the superior resolution, stability and inertness, we propose the use of QD staining of mortalin as a cell-based visual assay to screen for senescence-inducing drugs, proteins, and siRNAs.
Synthetic Capabilities of Plasmolyzed Cells and Spheroplasts of <i>Escherichia coli</i> (1970)

Effects of plasmolysis and spheroplast formation on deoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, and phospholipid synthesis by Escherichia coli strain THU were studied. RNA and protein synthesis were severely diminished. DNA and phospholipid synthesis were inhibited, but less so; they could be partly restored. DNA synthesis could be restored by replacing thymine in the medium with thymidine, and phospholipid synthesis, by adding back small quantities of soluble cell extract. Plasmolysis effected marked reductions in rates of growth and macro-molecule synthesis, and temporarily reduced culture viability. Plasmolysis also caused an anomalous stimulation of phospholipid synthesis. Spheroplasts and plasmolyzed cells synthesized small amounts of ribosomal RNA that sedimented normally. However, this ribosomal RNA was very inefficiently packaged to ribosome subunits. Spheroplasts were unable to carry out induced synthesis of beta-galactosidase, and plasmolyzed cells were delayed in this function. Radioautographs examined in an electron microscope showed that DNA synthesis in plasmolyzed cells and spheroplasts was performed by a substantial fraction of the culture populations. That DNA and membrane were associated in the spheroplasts used in this study was suggested by formation of M-bands containing membrane and most of the cell's DNA. The results are discussed in terms of alterations of membrane structure and conformation attending plasmolysis and spheroplasting.
Enhanced annealing of the Z1∕2 defect in 4H–SiC epilayers (2008)

The authors investigated the application of the carbon-implantation/annealing method for the annealing of the main lifetime limiting defect Z1∕2 in thick 4H–SiC epilayers. Examination of different implantation doses and annealing temperatures showed that finding the optimum conditions is crucial for obtaining thick layers with carrier trap concentration below 1011cm−3 in the whole 100μm epilayer. The carrier lifetime increased from less than 200ns to over 1μs at room temperature in the samples annealed with the carbon-implanted layer. The thick 4H–SiC epilayers after the application of the carbon-implantation/annealing were confirmed to be applicable for fabrication of high-voltage bipolar devices and resulted in improved conductivity modulation. Possible annealing mechanisms are discussed in detail making a comparison between annealing of as-grown material and irradiated material.
Total dose and frequency of administration critically affect success of nasal mucosal tolerance induction (2001)

These results indicate that both dose and frequency of intranasal antigen administration are pivotal to tolerance induction and subsequent suppression of T cell mediated autoimmune disease.
VP3, a Structural Protein of Infectious Pancreatic Necrosis Virus, Interacts with RNA-Dependent RNA Polymerase VP1 and with Double-Stranded RNA (2007)

Infectious pancreatic necrosis virus (IPNV) is a bisegmented, double-stranded RNA (dsRNA) virus of the Birnaviridae family that causes widespread disease in salmonids. Its two genomic segments are encapsulated together with the viral RNA-dependent RNA polymerase, VP1, and the assumed internal protein, VP3, in a single-shell capsid composed of VP2. Major aspects of the molecular biology of IPNV, such as particle assembly and interference with host macromolecules, are as yet poorly understood. To understand the infection process, analysis of viral protein interactions is of crucial importance. In this study, we focus on the interaction properties of VP3, the suggested key organizer of particle assembly in birnaviruses. By applying the yeast two-hybrid system in combination with coimmunoprecipitation, VP3 was proven to bind to VP1 and to self-associate strongly. In addition, VP3 was shown to specifically bind to dsRNA in a sequence-independent manner by in vitro pull-down experiments. The binding between VP3 and VP1 was not dependent on the presence of dsRNA. Deletion analyses mapped the VP3 self-interaction domain within the 101 N-terminal amino acids and the VP1 interaction domain within the 62 C-terminal amino acids of VP3. The C-terminal end was also crucial but not sufficient for the dsRNA binding capacity of VP3. For VP1, the 90 C-terminal amino acids constituted the only dispensable part for maintaining VP3-binding ability. Kinetic analysis revealed the presence of VP1-VP3 complexes prior to the formation of mature virions in IPNV-infected CHSE-214 cells, which indicates a role in promoting the assembly process.
Cross-linking of U2 snRNA using nitrogen mustard. Evidence for higher order structure. (1992)

Nuclear mRNA precursors are spliced by a large macromolecular complex called the spliceosome which contains, in most eucaryotes, five small nuclear RNAs (snRNAs) each in the form of a small ribonucleoprotein particle (the U1, U2, U5, and U4/U6 snRNPs). Although secondary structures have been derived for all five spliceosomal snRNAs based on phylogenetic, biochemical, and genetic data, little tertiary structure information is available. Here we use the general cross-linking reagent nitrogen mustard [bis-(2-chloroethyl)methylamine] to detect tertiary interactions within U2 snRNA. After the cross-linking of deproteinized HeLa nuclear extract, two intramolecularly cross-linked U2 species with anomalous electrophoretic mobility can be detected (X-U2#1 and X-U2#2). The 3' and 5' boundaries of each cross-link were determined by rapid enzymatic RNA sequencing of end-labeled RNA. X-U2#1 is cross-linked between the region U41-U55 and G105 or G106, X-U2#2 between U53 and G97 or G98. We then tested the ability of the two cross-linked species to bind snRNP proteins in vitro (in nuclear extract or S100) and in vivo (in Xenopus oocytes). X-U2#2 reconstituted efficiently both in vitro and in vivo but X-U2#1 did not, as judged by immunoprecipitation with antibodies specific for Sm- and U2-specific proteins. Since the cross-link in X-U2#2 involves the Sm binding site but does not block snRNP assembly, our data strongly suggest that the Sm binding site lies on the surface of the native snRNP.
Inhibition of premixed carbon monoxide-hydrogen-oxygen-nitrogen flames by iron pentacarbonyl (1999)

This paper presents measurements of the burning velocity of premixed CO-H2-O2-N2 flames with and without the inhibitor Fe(CO)5 over a range of initial H2 and O2 mole fractions. A numerical model is used to simulate the flame inhibition using a gas-phase chemical mechanism. For the uninhibited flames, predictions of burning velocity are excellent and for the inhibited flames, the qualitative agreement is good. The agreement depends strongly on the rate of the CO+OHCO2+H reaction and the rates of several key iron reactions in catalytic H-and O-atom scavenging cycles. Most of the chemical inhibition occurs through a catalytic cycle that converts O atoms into O2 molecules. This O-atom cycle is not important in methane flames. The H-atom cycle that causes most of the radical scavenging in the methane flames is also active in CO-H2 flames, but is of secondary importance. To vary the role of the H-and O-atom radical pools, the experiments and calculations are performed over a range of oxygen and hydrogen mole fraction. The degree of inhibition is shown to be related to the fraction of the net H-and O-atom destruction through the iron species catalytic cycles. The Oatom cycle saturates at a relatively low inhibitor mole fraction (~100 ppm), while the Hatom cycle saturates at a much higher inhibitor mole fraction (~400 ppm). The calculations reinforce the previously suggested idea that catalytic cycle saturation effects may limit the achievable degree of chemical inhibition.
Wide-span optical frequency comb generator for accurate optical frequency difference measurement (1993)

An optical frequency comb (OFC) generator was realized for accurate optical frequency difference measurement of 1.5 mu m wavelength semiconductor lasers by using a high frequency LiNbO/sub 3/ electrooptic phase modulator which was installed in a Fabry-Perot cavity. It was confirmed that the span of the OFC was wider than 4 THz. By using semiconductor lasers whose spectrum linewidths were narrowed to 1 kHz and a sensitive optical balanced-mixer-receiver for measuring beat signal between the sideband of the comb and the laser, we demonstrated a frequency difference measurement up to 0.5 THz with a signal-to-noise ratio higher than 61 dB, and a heterodyne optical phase locking with a heterodyne frequency of 0.5 THz in which the residual phase error variance was less than 0.01 rad/sup 2/. The maximum measurable frequency difference, which was defined as the sideband frequency with the signal-to-noise ratio of 0 dB, was estimated to be 4 THz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Combined linkage maps and QTLs in sugar beet (<i>Beta vulgaris</i> L.) from different populations (1999)

Abstract The construction of genetic maps is an expensive and time‐consuming process. The breeder is therefore interested in using maps developed from other mapping populations but this is only possible if the genetic structure is similar for the chromosomal regions of interest. In this paper, maps of three populations of sugar beet ( Beta vulgaris L.) with common polymorphic marker loci are compared. Maps were constructed with MAPMAKER 3.0 and JOINMAP 2.0. Both mapping programs gave, in general, the same order for common markers. However, the number of common markers was too low to construct a combined map for all chromosomes. For one population, in contrast to the other two, the map constructed with MAPMAKER 3.0 was much longer than that constructed with JOINMAP 2.0. For two of these populations yield traits were also available from different environments. For quantitative trait loci (QTL) analysis of the yield data, the packages MAPMAKER/QTL 1.1 and PLABQTL were used. No QTL common for the two populations could be detected. The program and the version used strongly influenced the estimated positions of QTLs. There was also a strong interaction with environments.
Preparation and Properties of Alginate/Water‐Soluble Chitin Blend Fibers (2005)

Water‐soluble chitin (half‐deacetylated chitin) was prepared from chitosan by N‐acetylation with acetic anhydride. Alginate/water‐soluble chitin blend fibers were prepared by spinning their mixture solution through a viscose‐type spinneret into a coagulating bath containing aqueous CaCl2 and ethanol. The structure and properties of the blend fibers were studied with the aids of infrared spectra (IR), X‐ray diffraction (XRD) and scanning electron microscopy (SEM). structure analysis indicated good miscibility existed between alginate and water‐soluble chitin, due to the strong interaction from the intermolecular hydrogen bonds and electrostatic interactions. Best values for the dry tensile strength and breaking elongation were obtained when the water‐soluble chitin content was 30 wt%. The wet tensile strength and breaking elongation decreased with the increase of water‐soluble chitin content. The introduction of water‐soluble chitin in the blend fiber can improve the water‐retention properties of the blend fiber compared to pure alginate fiber. The fibers treated with aqueous solution of silver nitrate have good antibacterial activity to Staphylococcus aureus.
Maxwell–Wagner Effect in Multi-Layered Dielectrics: Interfacial Charge Measurement and Modelling (2017)

The development of high voltage direct current (HVDC) technologies generates new paradigms in research. In particular and contrary to the AC case, investigation of electrical conduction is not only needed for understanding the dielectric breakdown but also to describe the field distribution inside the insulation. Here, we revisit the so-called Maxwell–Wagner effect in multi-layered dielectrics by considering on the one hand a non-linear field dependent model of conductivity and on the other hand by performing space charge measurements giving access to the interfacial charge accumulated between different dielectrics. We show that space charge measurements give access to the amount of interfacial charge built-up by the Maxwell–Wagner effect between two dielectrics of different natures. Measurements also demonstrate that the field distribution undergoes a transition from a capacitive distribution to a resistive one, under long lasting stress.