gebhart/patrepeval huggingface dataset:
Differential Roles of the <i>Pseudomonas aeruginosa</i> PA14 <i>rpoN</i> Gene in Pathogenicity in Plants, Nematodes, Insects, and Mice (2001)

We cloned the rpoN (ntrA, glnF) gene encoding the alternate sigma factor sigma(54) from the opportunistic multihost pathogen Pseudomonas aeruginosa strain PA14. A marker exchange protocol was used to construct the PA14 rpoN insertional mutation rpoN::Gen(r). PA14 rpoN::Gen(r) synthesized reduced levels of pyocyanin and displayed a variety of phenotypes typical of rpoN mutants, including a lack of motility and the failure to grow on nitrate, glutamate, or histidine as the sole nitrogen source. Compared to wild-type PA14, rpoN::Gen(r) was ca. 100-fold less virulent in a mouse thermal injury model and was significantly impaired in its ability to kill the nematode Caenorhabditis elegans. In an Arabidopsis thaliana leaf infectivity assay, although rpoN::Gen(r) exhibited significantly reduced attachment to trichomes, stomata, and the epidermal cell surface, did not attach perpendicularly to or perforate mesophyll cell walls, and proliferated less rapidly in Arabidopsis leaves, it nevertheless elicited similar disease symptoms to wild-type P. aeruginosa PA14 at later stages of infection. rpoN::Gen(r) was not impaired in virulence in a Galleria mellonella (greater wax moth) pathogenicity model. These data indicate that rpoN does not regulate the expression of any genes that encode virulence factors universally required for P. aeruginosa pathogenicity in diverse hosts.
Directional communication using spatial sound in human-telepresence (2015)

Communication is essential for working effectively with others. We communicate with each other to share their situation and what they are thinking. Especially, using voice is one of the most common ways to communicate. In previous research, we proposed LiveSphere that shares the surrounding environment with a remote person and provides immersive experience to effectively collaborate with each other. This system realizes "human-telepresence" where a person can be in other person and experience the environment. However, the communication in human-telepresence has some problems. In this paper, we propose directional communication with spatial sound to alleviate the problems. We also report on the result of user study.
Phylogeny and evolution of the aspartyl protease family from clinically relevant Candida species (2009)

Aspartyl proteases are a class of enzymes that include the yeast aspartyl proteases and secreted aspartyl protease (Sap) superfamilies. Several Sap superfamily members have been demonstrated or suggested as virulence factors in opportunistic pathogens of the genus Candida. Candida albicans, Candida tropicalis, Candida dubliniensis and Candida parapsilosis harbour 10, four, eight and three SAP genes, respectively. In this work, genome mining and phylogenetic analyses revealed the presence of new members of the Sap superfamily in C. tropicalis (8), Candida guilliermondii (8), C. parapsilosis(11) and Candida lusitaniae (3). A total of 12 Sap families, containing proteins with at least 50% similarity, were discovered in opportunistic, pathogenic Candida spp. In several Sap families, at least two subfamilies or orthologous groups were identified, each defined by > 90% sequence similitude, functional similarity and synteny among its members. No new members of previously described Sap families were found in a Candida spp. clinical strain collection; however, the universality of SAPT gene distribution among C. tropicalis strains was demonstrated. In addition, several features of opportunistic pathogenic Candida species, such as gene duplications and inversions, similitude, synteny, putative transcription factor binding sites and genome traits of SAP gene superfamily were described in a molecular evolutionary context.
A novel multicomponent regulatory system mediates H <sub>2</sub> sensing in <i>Alcaligenes eutrophus</i> (1998)

Oxidation of molecular hydrogen catalyzed by [NiFe] hydrogenases is a widespread mechanism of energy generation among prokaryotes. Biosynthesis of the H2-oxidizing enzymes is a complex process subject to positive control by H2 and negative control by organic energy sources. In this report we describe a novel signal transduction system regulating hydrogenase gene (hox) expression in the proteobacterium Alcaligenes eutrophus. This multicomponent system consists of the proteins HoxB, HoxC, HoxJ*, and HoxA. HoxB and HoxC share characteristic features of dimeric [NiFe] hydrogenases and form the putative H2 receptor that interacts directly or indirectly with the histidine protein kinase HoxJ*. A single amino acid substitution (HoxJ*G422S) in a conserved C-terminal glycine-rich motif of HoxJ* resulted in a loss of H2-dependent signal transduction and a concomitant block in autophosphorylating activity, suggesting that autokinase activity is essential for the response to H2. Whereas deletions in hoxB or hoxC abolished hydrogenase synthesis almost completely, the autokinase-deficient strain maintained high-level hox gene expression, indicating that the active sensor kinase exerts a negative effect on hox gene expression in the absence of H2. Substitutions of the conserved phosphoryl acceptor residue Asp55 in the response regulator HoxA (HoxAD55E and HoxAD55N) disrupted the H2 signal-transduction chain. Unlike other NtrC-like regulators, the altered HoxA proteins still allowed high-level transcriptional activation. The data presented here suggest a model in which the nonphosphorylated form of HoxA stimulates transcription in concert with a yet unknown global energy-responsive factor.
Trypsin-alpha 1-protease inhibitor complexes in serum and clinical course of acute pancreatitis. (1984)

The levels of amylase, trypsinogen, and trypsin-alpha 1-protease inhibitor complexes, both in serum and in peritoneal fluid, were correlated to the severity and clinical course in 27 attacks of acute pancreatitis. Serum levels of trypsin-alpha 1-protease inhibitor complexes on admission correlated well with the severity and clinical course of the disease, whereas serum levels of amylase and trypsinogen did not. This may be of clinical importance in differentiating severe acute pancreatitis from milder and self-limiting forms of the disease.
Activation of the receptor EphB4 by its specific ligand ephrin B2 in human osteoarthritic subchondral bone osteoblasts (2008)

This study is the first to provide evidence that EphB4 receptor activation by ephrin B2 in OA subchondral bone could affect abnormal metabolism in this tissue by inhibiting resorption factors and their activities. Ephrin B2 could be targeted as a specific therapeutic approach in the development of a disease-modifying OA drug.
Simulation methods used to analyze the performance of the GE PG6541B gas turbine utilizing low heating value fuels (1994)

The ability to model the behavior of gas turbine engines is critical in economic, thermal and condition monitoring studies. This is especially true for applications involving alternative fuels, such as biomass and coal derived fuels, where the engine operates far from its ISO performance ratings found in publications such as Gas Turbine World. This paper presents an approach taken for modeling a Frame 6 engine and its control system given a fairly limited set of available data. The approach and model are tested against vendor cycle deck data for both natural gas and a low-Btu biogas fuel. The model is then used to predict behavior of the Frame 6 engine fired by another biomass-derived fuel over a range of ambient and loading conditions. Issues relevant to this fuel/turbine combination and limitations of the modeling method are discussed. The engine model was developed using the individual turbomachinery component modules in the GateCycle analysis software package. The model is based on pressure and flow matching of the turbomachinery components. It includes a compressor map, a relationship to simulate a turbine `map`, and cooling flow calculations. Regardless of the accuracy of the modeling methods, it is always advisable to verify calculations based onmore » aftermarket sources with manufacturer`s values before using the predictions for commercial decisions.« less
Mammalian cell survival and processing in supercritical CO <sub>2</sub> (2006)

We demonstrate that mammalian cells can survive for 5 min within high-pressure CO(2)(.) Cell survival was investigated by exposing a range of mammalian cell types to supercritical CO(2) (scCO(2)) (35 degrees C, 74 bar; 1 bar = 100 kPa) for increasing exposure and depressurization times. The myoblastic C2C12 cell line, 3T3 fibroblasts, chondrocytes, and hepatocytes all displayed appreciable but varying metabolic activity with exposure times up to 1 min. With depressurization times of 4 min, cell population metabolic activity was >/=70% of the control population. Based on survival data, we developed a single-step scCO(2) technique for the rapid production of biodegradable poly(dl-lactic acid) scaffolds containing mammalian cells. By using optimum cell-survival conditions, scCO(2) was used to process poly(dl-lactic acid) containing a cell suspension, and, upon pressure release, a polymer sponge containing viable mammalian cells was formed. Cell functionality was demonstrated by retention of an osteogenic response to bone morphogenetic protein-2 in C2C12 cells. A gene microarray analysis showed no statistically significant changes in gene expression across 4,418 genes by a single-class t test. A significance analysis of microarrays revealed only eight genes that were down-regulated based on a delta value of 1.0125 and a false detection rate of 0.
Fluorescence Excitation Spectrum of Bilirubin in Blood: A Model for the Action Spectrum for Phototherapy of Neonatal Jaundice (2013)

A recent report (Lamola et al. 2013 Pediatric Research, 74, 54-60) presents a semiempirical model for facile calculation of an action spectrum for bilirubin photochemistry in vivo using the most current knowledge of the optics of neonatal skin. The calculations indicate that competition for phototherapy light by hemoglobin in the skin is the predominant factor that defines the spectrum of light absorbed by bilirubin. If the latter is correct, a valid physical analog of the calculated spectrum is the excitation spectrum of bilirubin in blood. The fluorescence excitation spectrum was recorded and, indeed, found to be very similar to the calculated spectrum. Both spectra exhibit maxima near 476 nm and widths at half height of about 50 nm. This result supports the conclusion that light between 460 and 490 nm is most effective for phototherapy of neonatal jaundice.
Age-associated telomere shortening in mouse oocytes (2013)

Long-term adverse effects of low telomerase activity and increased ROS exposure are likely associated with telomere shortening in oocytes from reproductively-aged female mice.
Ineffectiveness of postexposure prophylaxis of rhinovirus infection with low-dose intranasal alpha 2b interferon in families (1989)

Past studies conducted in Australian and American families have demonstrated that alpha 2b interferon (IFN) is effective in preventing rhinovirus-associated illnesses in exposed family members. IFN had been used by intranasal application for 7 days after exposure (5 x 10(6) IU/day). We used the same approach but with only 5 days of spraying (5 x 10(6) IU on day 1 and 2.5 x 10(6) IU on each subsequent day). This amount has been effective in studies involving seasonal prophylaxis. During the study period, a total of 178 rhinoviruses were isolated from the 199 enrolled families in Tecumseh, Mich. There were 434 courses of IFN use and 434 courses of placebo use. Although rhinoviruses were less frequently isolated from those using IFN than those using the placebo, no differences favoring IFN treatment could be found in any of the symptomatic episodes. In fact, more episodes were observed in IFN recipients than in placebo recipients, although the differences were not statistically significant. Additionally, there was no evidence of modification of the severity of episodes of illness. It was concluded that prevention of rhinovirus illness episodes postexposure required a dosage of at least 5 x 10(6) IU of IFN-alpha 2b.
A reinforcement learning fuzzy controller for set-point regulator problems (2002)

Intelligent control refers to controllers that can analyze their performance and make necessary changes to their behavior in order to satisfy certain predefined control goals. This paper describes a self-learning controller model that can efficiently learn the control law for complex systems through reinforcement learning techniques and dynamic programming-like algorithms. The controller is applied to a class of problems called general set-point regulator problems in which the objective is to drive the system to the set-point while optimizing some performance objective function, making no a priori assumptions about the dynamics of the plant or its optimal trajectory. The relevant tasks for a self-learning controller are discussed. Learning is accomplished via incremental, online dynamic programming-like algorithms. Both temporal differences and Q-learning are used in the learning algorithm. Experimental results with both are reported on the inverted pendulum balancing problem, the power system stabilization problem, and the tethered satellite system retrieval problem.
Okadaic acid, a serine/threonine phosphatase inhibitor, induces tyrosine dephosphorylation/inactivation of protein kinase FA/GSK-3 alpha in A431 cells. (1994)

The signal transduction mechanism of protein kinase FA/GSK-3 alpha by tyrosine phosphorylation in A431 cells was investigated. Kinase FA/GSK-3 alpha was found to exist in a highly tyrosine-phosphorylated/activated state in resting cells but could be tyrosine-dephosphorylated and inactivated down to less than 15% of control values in a concentration-dependent manner by 50-400 nM okadaic acid (a specific inhibitor of protein phosphatase types 1 and 2A), as demonstrated by metabolic 32P labeling the cells, followed by immunoprecipitation and two-dimensional phosphoamino acid analysis and by immunodetection in an anti-kinase FA/GSK-3 alpha immunoprecipitate kinase assay. Taken together, the results provide initial evidence that serine/threonine phosphatase(s) may play a role involved in the modulation of kinase FA/GSK-3 alpha activity in cells, suggesting an involvement of serine/threonine dephosphorylation in the modulation of tyrosine phosphorylation and activation of protein kinase FA/GSK-3 alpha, representing a new mode of signal transduction pathway for the regulation of this multisubstrate protein kinase in cells.
Control of brain fatty acids. (1990)

Saturated and monounsaturated fatty acids are mainly synthetized in the brain, but some of them could originate from the diet; in contrast polyunsaturated fatty acids are derived from dietary linoleic and linolenic acid. Saturated fatty acid biosynthesis occurs via three main pathways in mammalian cells. One is de novo synthesis of fatty acids from acetyl-CoA via malonyl-CoA; this system has been isolated in soluble form (the soluble system) from various animal tissues including brain. The second and third pathways involve elongation: in the mitochondrial system, acetyl CoA is the principal substrate in extracts from all organs, even brain; in the microsomal system, however, malonyl-CoA acts as donor of the 2 carbon fragments. In vivo studies in brain have shown that very long chain fatty acids are synthesized by elongation rather than by a than by a de novo mechanism. Feeding animals with oils that have a low n-3 acid content (linolenic series) results in all brain cells and organelles reduced amounts of 22:6 n-3 which is compensated for by an increase in 22:5 n-6. The speed of recuperation from these anomalies is extremely slow for brain cells, organelles and microvessels, in contrast with other organs. Essential fatty acids for the brain could be those with very long chains as shown with cell culture. They are probably synthesized in the liver from linolenic acid. They can also be supplied directly by food. During the period of cerebral development there is a linear relation between the n-3 acid content of the brain and that of food until linolenic acid represents approx. 200 mg per 100 g of food (for 1200 mg linoleic acid). A decrease in acids of the linolenic series in the membranes results in a 40% reduction of Na-K-ATPase in nerve terminals and a 20% reduction in 5'-nucleotidase in whole brain homogenate. A diet low in linolenic acid leads to anomalies in the electroretinogram which disappear partially with age, it seriously affects learning tasks. The presence of linolenic acid in the diet confers a greater resistance to certain neurotoxic agents.
<b>Antidepressant effect of femoxetine and desipramine and relationship to the concentration of amine metabolites in cerebrospinal fluid</b> (1982)

The antidepressant and biochemical effects of femoxetine, a selective serotonin uptake inhibitor, and desipramine, a selective nor-adrenaline uptake inhibitor, have been compared in a double-blind study in 42 outpatients with depressive illness. The patients were allocated at random to treatment with either 600 mg femoxetine or 150 mg desipramine daily for 6 weeks. The total depression score showed a significant decrease in both groups, indicating an overall improvement in depressive symptoms. The patients treated with femoxetine reported significantly less severe anticholinergic effects during the whole treatment period than the desipramine patients. Both drugs, decreased the level of 5-HIAA in CSF, whereas no consistent changes were found in the MHPG and HVA levels. The pretreatment level of the metabolites had no predictive value for the outcome of the treatment with either drug. No significant correlation was found between therapeutic effect and the plasma concentration of the active compounds.
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics (2015)

Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
A horizon-recursive form for predictors and their computation (1990)

Concerns the design of self-tuning controllers using output predictors. A simple, horizon-recursive expression for output predictors is obtained for both SISO and MIMO systems described by ARMAX models. This expression reveals that the predictors for the different prediction horizons are recursively related by a key parameter vector. Thus, by recursively computing this key parameter vector, an efficient algorithm for generating predictors is obtained. It shows certain advantages over methods involving recursive solving of Diophantine equations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CRT colorimetry. part I: Theory and practice (1993)

Abstract The relationship was derived for computer‐controlled color CRT displays between spectral radiant exitance emitted and digital counts. The derivation was historical and could be traced to pioneering work in photographic sensitometry, vacuum tube physics, and broadcast television. By performing radiometric measurements relative to a display's maximum exitance, the model simplified to a two‐stage model. The first stage was a nonlinear transformation relating normalized digital‐to‐analog converter values to device‐dependent monitor tristimulus values using model parameters of gain, offset, and γ. The second stage was a linear transformation where the device‐dependent monitor tristimulus values were transformed to device‐independent CIE tristimulus values. By using the model, colorimetric characterization accuracy of better than 0.5 CIELAB color‐difference units for 125 colors sampling the display color gamut was achieved by measuring the CIE tristimulus values of only eight colors. The model had equivalent performance to methods using extensive measurements and table lookup. © 1993 John Wiley & Sons, Inc.
Semi-classical estimates for resolvents and asymptotics for total scattering cross-sections (1987)

We study the semi-classical asymptotic behavior as h→0 of total scattering cross-sections for Schrodinger operators −(1/2)h 2 Δ+V, when energies are fixed in non-trapping energy ranges. The proof is based on the semi-classical estimates for resolvents and the argument applies to the asymptotics for forward scattering amplitudes On etudie le comportement asymptotique semi-classique quand h→0 de la section efficace totale pour l'operateur de Schrodinger −(1/2)h 2 Δ+V, pour des energies dans des regions sans trajectoires piegees. Les demonstrations sont basees sur des estimations semi-classiques de resolvantes, et les arguments s'appliquent au comportement asymptotique de l'amplitude de diffusion vers l'avant
Hepatitis B Vaccination in Diabetic Patients: Randomized trial comparing recombinant vaccines containing and not containing pre-S2 antigen (1997)

A large majority of diabetic patients can be efficiently vaccinated against the hepatitis B virus using a booster dose at month 4. The choice of the vaccine (with or without pre-S2 antigen) appears to have little influence, if any, on the response rate.