gebhart/patrepeval huggingface dataset:
New Insights into<i>Prevotella</i>Diversity and Medical Microbiology (2010)

In light of recent studies based on cultivation-independent methods, it appears that the diversity of Prevotella in human microbiota is greater than was previously assumed from cultivation-based studies, and that the implication of these bacteria in several human diseases was unrecognized. While some Prevotella taxa were found during opportunistic infections, changes in Prevotella abundance and diversity were discovered during dysbiosis-associated diseases. As member of the microbiota, Prevotella may also be considered as a reservoir for resistance genes. Greater knowledge on Prevotella diversity, as well as new insights into its pathogenic potential and implication in dysbiosis are expected from the use of human microbe identification microarrays, from whole-genome sequence analyse, and from the NIH Human Microbiome Project data. New approaches, including molecular-based methods, could contribute to improve the diagnosis of Prevotella infections.
Generation of the <i>Brucella melitensis</i> ORFeome Version 1.1: Figure 1 (2004)

The bacteria of the Brucella genus are responsible for a worldwide zoonosis called brucellosis. They belong to the alpha-proteobacteria group, as many other bacteria that live in close association with a eukaryotic host. Importantly, the Brucellae are mainly intracellular pathogens, and the molecular mechanisms of their virulence are still poorly understood. Using the complete genome sequence of Brucella melitensis, we generated a database of protein-coding open reading frames (ORFs) and constructed an ORFeome library of 3091 Gateway Entry clones, each containing a defined ORF. This first version of the Brucella ORFeome (v1.1) provides the coding sequences in a user-friendly format amenable to high-throughput functional genomic and proteomic experiments, as the ORFs are conveniently transferable from the Entry clones to various Expression vectors by recombinational cloning. The cloning of the Brucella ORFeome v1.1 should help to provide a better understanding of the molecular mechanisms of virulence, including the identification of bacterial protein-protein interactions, but also interactions between bacterial effectors and their host's targets.
Biotechnological Advances in Resveratrol Production and its Chemical Diversity (2019)

The very well-known bioactive natural product, resveratrol (3,5,4'-trihydroxystilbene), is a highly studied secondary metabolite produced by several plants, particularly grapes, passion fruit, white tea, and berries. It is in high demand not only because of its wide range of biological activities against various kinds of cardiovascular and nerve-related diseases, but also as important ingredients in pharmaceuticals and nutritional supplements. Due to its very low content in plants, multi-step isolation and purification processes, and environmental and chemical hazards issues, resveratrol extraction from plants is difficult, time consuming, impracticable, and unsustainable. Therefore, microbial hosts, such as <i>Escherichia coli</i>, <i>Saccharomyces cerevisiae</i>, and <i>Corynebacterium glutamicum</i>, are commonly used as an alternative production source by improvising resveratrol biosynthetic genes in them. The biosynthesis genes are rewired applying combinatorial biosynthetic systems, including metabolic engineering and synthetic biology, while optimizing the various production processes. The native biosynthesis of resveratrol is not present in microbes, which are easy to manipulate genetically, so the use of microbial hosts is increasing these days. This review will mainly focus on the recent biotechnological advances for the production of resveratrol, including the various strategies used to produce its chemically diverse derivatives.
Serine hydroxymethyltransferase: mechanism of the racemization and transamination of D- and L-alanine (1988)

The reaction specificity and stereochemical control of Escherichia coli serine hydroxymethyltransferase were investigated with D- and L-alanine as substrates. An active-site H228N mutant enzyme binds both D- and L-alanine with Kd values of 5 mM as compared to 30 and 10 mM, respectively, for the wild-type enzyme. Both wild-type and H228N enzymes form quinonoid complexes absorbing at 505 nm by catalyzing the loss of the alpha-proton from both D- and L-alanine. Racemization and transamination reactions were observed to occur with both alanine isomers as substrates. The relative rates of these reactions are quinonoid formation greater than alpha-proton solvent exchange greater than racemization greater than transamination. The observation that the rate of quinonoid formation with either alanine isomer is an order of magnitude faster than solvent exchange suggests that the alpha-protons from both D- and L-alanine are transferred to base(s) on the enzyme. The rate of racemization is 2 orders of magnitude slower than the formation of the quinonoid complexes. This latter difference in rate suggests that the quinonoid complexes formed from D- and L-alanine are not identical. The difference in structure of the two quinonoid complexes is proposed to be the active-site location of the alpha-protons lost from the two alanine isomers, rather than two orientations of the pyridoxal phosphate ring. The results are consistent with a two-base mechanism for racemization.
Influence of phenylacetic acid on poly-β-hydroxybutyrate (PHB) polymerization and cell elongation in <i>Azotobacter chroococcum</i> Beij. (1972)

The influence of phenylacetic acid on the polymerization of β-hydroxybutyrate and cell elongation in Azotobacter chroococcum has been investigated.The polymer was extracted by a new method. Its molecular weight, calculated by intrinsic viscosity and light-scattering, was about 300 000 for control cells and increased to 330 000 for cells treated with phenylacetic acid. The dispersivity of the polymer was clearly influenced by phenylacetic acid.As shown by electron microscopy, the existence of a membrane surrounding the granules of poly-β-hydroxybutyrate (PHB) was confirmed; cell wall structures, cell membrane, and mesosomes appeared not to be damaged by the treatment with phenylacetic acid, and also the formation of the septa was not influenced; on the contrary, the cells growing in the presence of phenylacetic acid were more lengthened than the control ones (average length of 7.1 μ against 2.7 μ).
Responsive Vesicles from Dynamic Covalent Surfactants (2011)

Breaking bilayers: Incorporation of dynamic covalent bonds in vesicle-forming surfactants leads to the formation of responsive vesicles, which can be switched back and forth between the bilayer state and the isotropic solution using either dilution or a change in the pH value as external stimuli.
Analysis and compensation of nonlinearity mismatches in time-interleaved ADC arrays (2004)

Time-interleaved ADCs (TIADCs) are used to achieve high sampling rates. The drawback of such an architecture are mismatch effects, which decrease the signal-to-noise and distortion ratio (SINAD) and the spurious-free dynamic range (SFDR). Many papers have investigated the problem of mismatches but very few have considered he problem of nonlinearity mismatches. We present a mathematical framework for nonlinearity mismatches, describe their main characteristics, and show an effective compensation method to increase the SFDR.
Androgen hydroxylation catalysed by a cell line (SD1) that stably expresses rat hepatic cytochrome <i>P</i>-450 PB-4 (IIB1) (1989)

Androgen hydroxylation catalysed by Chinese hamster fibroblast SD1 cells, which stably express cytochrome P-450 form PB-4, the rat P450IIB1 gene product, was assessed and compared to that catalysed by purified cytochrome P-450 PB-4 isolated from rat liver. SD1 cell homogenates catalysed the NADPH-dependent hydroxylation of androstenedione and testosterone with a regioselectivity very similar to that purified by P-450 PB-4 (16 beta-hydroxylation/16 alpha-hydroxylation = 6.0-6.8 for androstenedione; 16 beta/16 alpha = 0.9 for testosterone). Homogenates prepared from the parental cell line V79, which does not express detectable levels of P-450 PB-4 or any other cytochrome P-450, exhibited no androgen 16 beta- or 16 alpha-hydroxylase activity. The hydroxylase activities catalysed by the SD1 cell homogenate were selectively and quantitatively inhibited (greater than 90%) by a monoclonal antibody to P-450 PB-4 at a level of antibody (40 pmol of antibody binding sites/mg of SD1 homogenate) that closely corresponds to the P-450 PB-4 content of the cells (48 pmol of PB-4/mg of SD1 homogenate). Fractionation of cell homogenates into cytosol and microsomes revealed that the P-450 PB-4-mediated activities are associated with the membrane fraction. Although the P-450 PB-4-specific content of the SD1 microsomes was 15% of that present in phenobarbital-induced rat liver microsomes, the P-450 PB-4-dependent androstenedione 16 beta-hydroxylase activity of the SD1 membrane fraction was only 2-3% of that present in the liver microsomes. This activity could be stimulated several-fold, however, by supplementation of SD1 microsomes with purified rat NADPH P-450 reductase. These studies establish that a single P-450 gene product (IIB1) can account for the hydroxylation of androgen substrates at multiple sites, and suggest that SD1 cells can be used to assess the catalytic specificity of P-450 PB-4 with other substrates as well.
Reeled Pipe Technology for Deepwater Drilling Utilizing a Dual Gradient Mud System (2000)

Abstract The search for hydrocarbons is constantly moving into deeper and deeper waters. This introduces new challenges to the drilling industry as production demands requires that large, high volume completions are placed in these wells. In addition, narrow pore pressure and fracture pressure margins increase the number and subsequently size of casings to be set. The use of a "Dual Gradient" drilling system provides an answer to these challenges. The use of large diameter "Reeled Pipe" further facilitates the dual gradient drilling process. The DeepVision project has developed and tested several critical components of such a system. The system includes a subsea centrifugal pump system, large diameter reeled pipe up to 5.5", bottom hole assembly components, and a new injector head concept for the reeled pipe. The project is ready to be advanced into prototype field testing and commercialization.
Utilization of similar mechanisms by Legionella pneumophila to parasitize two evolutionarily distant host cells, mammalian macrophages and protozoa (1997)

The Legionnaires' disease bacterium, Legionella pneumophila, is an intracellular pathogen of humans that is amplified in the environment by intracellular multiplication within protozoa. Within both evolutionarily distant hosts, the bacterium multiplies in a rough endoplasmic reticulum-surrounded phagosome that is retarded from maturation through the endosomal-lysosomal degradation pathway. To gain an understanding of the mechanisms utilized by L. pneumophila to invade and replicate within two evolutionarily distant hosts, we isolated a collection of 89 mini-Tn10::kan insertion mutants that exhibited defects in cytotoxicity, intracellular survival, and replication within both U937 macrophage-like cells and Acanthamoeba polyphaga. Interestingly, the patterns of defects in intracellular survival and replication of the mutants within both host cells were highly similar, and thus we designated the defective loci in these mutants pmi (for protozoan and macrophage infectivity loci). On the basis of their ability to attach to host cells and their growth kinetics during the intracellular infection, the mutants were grouped into five groups. Groups 1 and 2 included 41 mutants that were severely defective in intracellular survival and were completely or substantially killed during the first 4 h of infection in both host cells. Three members of group 1 were severely defective in attachment to both U937 cells and A. polyphaga, and another four mutants of group 1 exhibited severe defects in attachment to A. polyphaga but only a mild reduction in their attachment to U937 cells. Four members of groups 1 and 2 were serum sensitive. Intracellular replication of mutants of the other three groups was less defective than that of mutants of groups 1 and 2, and their growth kinetics within both host cells were similar. The mutants were tested for several other phenotypes in vitro, revealing that 14 of the pmi mutants were resistant to NaCl, 3 had insertions in dot or icm, 3 were aflagellar, 12 were highly intolerant to a hyperosmotic medium, and one failed to grow in a minimal medium. Our data indicated that similar mechanisms are utilized by L. pneumophila to replicate within two evolutionarily distant hosts. Although some mechanisms of attachment to both host cells were similar, other distinct mechanisms were utilized by L. pneumophila to attach to A. polyphaga. Our data supported the hypothesis that preadaptation of L. pneumophila to infection of protozoa may play a major role in its ability to replicate within mammalian cells and cause Legionnaires' disease.
Conducting a Marketing Audit: A Service Organization Illustration (1996)

ABSTRACT WRDC Television Station, an NBC affiliate television station, is subjected to a preliminary marketing audit after recently being purchased and changing its “call” letters. Even under the new call letters, it is having some difficulty repositioning itself in the minds of viewers because of the reputation of the old station. Under its UHF license, WRDC's signal is not as powerful as the three VHF licensed stations in WRDC's geographical market area. The strength of the signal affects the station's “Reach” which affects such things as: (1) the advertising rate the station can charge and still be competitive, (2) the programming, (3) the ratings and, ultimately, market share. An analysis was conducted on the Marketing Environment; Systems and Strategies; Resources, Information Services, Planning and Control, and Tools and Tactics in an attempt to develop, among others, the recommendations that management should: conduct a marketing-effectiveness rating review, take time to write out a formal marketing plan, set up specific review processes for sales personnel and develop a process for stabilizing prices.
Impact of Molecular Hydrogen on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon <i>Metallosphaera sedula</i> (2010)

Hydrogen served as a competitive inorganic energy source, impacting the CuFeS(2) bioleaching efficiency of the extremely thermoacidophilic archaeon Metallosphaera sedula. Open reading frames encoding key terminal oxidase and electron transport chain components were triggered by CuFeS(2). Evidence of heterotrophic metabolism was noted after extended periods of bioleaching, presumably related to cell lysis.
Synthesis of Polynuclear Aromatic Compounds Incorporating a Fused Thiophene Ring (2005)

The present review gives an account of the various synthetic routes to polynuclear heteroaromatic compounds incorporating a fused thiophene ring which include analogs of several biologically active compounds.These compounds are synthesized using a suitably functionalised benzo[b]thiophene as the core and applying various annulation reactions.Directed metalation was extensively used both for functionalisation and in annulation reactions.intramolecular nucleophilic attack in one pot to afford the cyclic imines (8 and 9) (R = CN, CO 2 Et, CONH 2 and CSNH 2 ) respectively.The crude imines upon heating with 2M hydrochloric acid on a boiling water bath for 30 min afforded the thienocoumarines (2 and 3) in yields ranging from 40 to 75%.
Unipotential electrostatic lenses: Paraxial properties and aberrations of focal length and focal point (1985)

An experimental study of electrostatic electron lenses as a function of geometrical and electrical parameters is described. The lenses are of the symmetrical three-electrode unipotential type. The parameters are the thickness of the center electrode and the interelectrode spacing, both relative to the center electrode aperture diameter, and the ratio of lens voltage to cathode voltage. The lens properties are characterized in terms of the focal length and focal distance, and the spherical and chromatic aberrations of these quantities. In general, the principal surfaces of a lens are not plane, and the aberrations of focal length and focal distance are not the same. Expressions are derived relating the focal length and focal distance aberrations to the spherical and chromatic imaging aberration coefficients Cs and Cc, and the magnification aberrations. The advantages of formulating the lens properties in terms of focal length and focal distance and their aberrations, and the usefulness of the data presented here, are illustrated with several examples.
Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR (2016)

Cystic fibrosis is a fatal genetic disease, most frequently caused by the retention of the CFTR (cystic fibrosis transmembrane conductance regulator) mutant protein in the endoplasmic reticulum (ER). The binding of the 14-3-3 protein to the CFTR regulatory (R) domain has been found to enhance CFTR trafficking to the plasma membrane. To define the mechanism of action of this protein-protein interaction, we have examined the interaction in vitro. The disordered multiphosphorylated R domain contains nine different 14-3-3 binding motifs. Furthermore, the 14-3-3 protein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated motifs. This results in a number of possible binding mechanisms between these two proteins. Using multiple biochemical assays and crystal structures, we show that the interaction between them is governed by two binding sites: The key binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary binding site occupies the other binding groove. We show that fusicoccin-A, a natural-product tool compound used in studies of 14-3-3 biology, can stabilize the interaction between 14-3-3 and CFTR by selectively interacting with a secondary binding motif of CFTR (pS753). The stabilization of this interaction stimulates the trafficking of mutant CFTR to the plasma membrane. This definition of the druggability of the 14-3-3-CFTR interface might offer an approach for cystic fibrosis therapeutics.
Influence of Fineness of Fly Ashes on Their Hydraulic Activity (1989)

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Roles of glycerol and glycerol-3-phosphate dehydrogenase (NAD+) in acquired osmotolerance of Saccharomyces cerevisiae (1989)

In a cell culture of Saccharomyces cerevisiae exponentially growing in basal medium, only 0.02% of the cells were osmotolerant, i.e., survived transfer to medium containing 1.4 M NaCl. Short-time conditioning in 0.7 M NaCl medium transformed the whole population into an osmotolerance phenotype. During this conditioning, the rate of formation of glycerol, the main compatible solute in S. cerevisiae, increased threefold and the specific activity of glycerol-3-phosphate dehydrogenase (NAD+) (GPDH) (EC 1.1.1.8) was enhanced sixfold. The apparent flux control coefficient for GPDH in the formation of glycerol was estimated to be 0.6. Glycerol production was also favored by regulated activities of alcohol dehydrogenase (EC 1.1.1.1) and aldehyde dehydrogenase [NAD(P)]+ (EC 1.2.1.5). About 50% of the total glycerol produced during conditioning in 0.7 M NaCl was retained intracellularly, and the increased glycerol accumulation was shown to be not merely a result of enhanced production rate but also of increased retention of glycerol. Washing the cells with solutions of lower salinities resulted in loss of glycerol, with retained levels proportional to the concentration of NaCl in the washing solution. Cycloheximide addition inhibited the development of acquired osmotolerance and conditioned cells washed free of glycerol retained a high degree of osmotolerance, which indicate that protein synthesis was required to establish the osmotolerance state.
Protection against Experimental Allergic Encephalomyelitis with Peptides Derived from Myelin Basic Protein: Presence of Intact Encephalitogenic Site Is Essential (1976)

Abstract Experimental allergic encephalomyelitis (EAE) is a cell-mediated autoimmune response directed toward a component of central nervous system (CNS) tissue, myelin basic protein (BP). Injection of animals with either whole CNS tissue or purified BP in complete Freund's adjuvant (CFA) induces severe and usually fatal disease. Preimmunization of animals with BP in incomplete Freund's adjuvant (IFA) prevents EAE. We have examined the relative abilities of whole guinea pig BP and its fragments to protect guinea pigs from subsequent EAE induction. The data suggest that the presence of the intact encephalitogenic site (residues 113–121) in the molecules used for preimmunization is necessary but may not be sufficient for complete protection against EAE induction.
Bur Abscission in Japanese Chestnut(Castanea crenata Sieb. et Zucc.)as Related to Degeneration of Ovules. (1991)

Bur abscission in Japanese chestnut (Castanea crenata Sieb. et Zucc.) 'Yamato-Wase' was investigated in relation to development and degeneration of ovules.
Neuroprotective Effects of Trigeminal Nerve Stimulation in Severe Traumatic Brain Injury (2017)

Following traumatic brain injury (TBI), ischemia and hypoxia play a major role in further worsening of the damage, a process referred to as 'secondary injury'. Protecting neurons from causative factors of secondary injury has been the guiding principle of modern TBI management. Stimulation of trigeminal nerve induces pressor response and improves cerebral blood flow (CBF) by activating the rostral ventrolateral medulla. Moreover, it causes cerebrovasodilation through the trigemino-cerebrovascular system and trigemino-parasympathetic reflex. These effects are capable of increasing cerebral perfusion, making trigeminal nerve stimulation (TNS) a promising strategy for TBI management. Here, we investigated the use of electrical TNS for improving CBF and brain oxygen tension (PbrO<sub>2</sub>), with the goal of decreasing secondary injury. Severe TBI was produced using controlled cortical impact (CCI) in a rat model, and TNS treatment was delivered for the first hour after CCI. In comparison to TBI group, TBI animals with TNS treatment demonstrated significantly increased systemic blood pressure, CBF and PbrO<sub>2</sub> at the hyperacute phase of TBI. Furthermore, rats in TNS-treatment group showed significantly reduced brain edema, blood-brain barrier disruption, lesion volume, and brain cortical levels of TNF-α and IL-6. These data provide strong early evidence that TNS could be an effective neuroprotective strategy.