gebhart/patrepeval huggingface dataset:
A <i>Pseudomonas aeruginosa</i> quorum‐sensing molecule influences <i>Candida albicans</i> morphology (2004)

Candida albicans is an opportunistic pathogen that is commonly found as a member of the human microflora. The ability of C. albicans to alter its cellular morphology has been associated with its virulence; yeast cells are more prevalent in commensal interactions whereas filamentous cells appear important in opportunistic infections. C. albicans encounters a multitude of other microbial species in the host environment and it is likely that they impact the C. albicans transition between virulent and non-virulent states. Here, we report that C. albicans morphology is significantly affected by the presence of Pseudomonas aeruginosa, another opportunistic pathogen. In a screen using a C. albicans HWP1-lacZ strain to indicate regions of filamentous growth, we identified P. aeruginosa mutants incapable of inhibiting C. albicans filamentation. Through these studies, we found that 3-oxo-C12 homoserine lactone, a cell-cell signalling molecule produced by P. aeruginosa, was sufficient to inhibit C. albicans filamentation without affecting fungal growth rates. Both microscopic analysis and real-time reverse transcription polymerase chain reaction analysis of morphology-specific markers confirmed that filamentation was suppressed by 200 microM 3-oxo-C12 homoserine lactone. Structurally related compounds with a 12-carbon chain length, e.g. C12-acyl homoserine lactone and dodecanol also affected C. albicans filamentation at similar concentrations. In contrast, other acylated homoserine lactones of different chain lengths did not affect fungal morphology. The activity of 3OC12HSL is compared with that of farnesol, a C. albicans-produced molecule also with a C12-backbone. The effects that bacteria have on the morphology of C. albicans represents one of the ways by which bacteria can influence the behaviour of fungal cells.
In vivo effects of modification of hydroxyapatite/collagen composites with and without chondroitin sulphate on bone remodeling in the sheep tibia (2008)

The addition of chondroitin sulphate (CS) to bone cements with calcium phosphate has lead to an enhancement of bone remodeling and an increase in new bone formation in small animals. The goal of this study was to verify the effect of CS in bone cements in a large animal model simulating a clinically relevant situation of a segmental cortical defect of a critical size on bone-implant interaction and bone remodeling. The influence of adding CS to hydroxyapatite/collagen (HA/Col) composites on host response was assessed in a standard sheep tibia model. A midshaft defect of 3 cm was created in the tibiae of 14 adult female sheep. The defect was filled with a HA/Col cement cylinder in seven animals and with a CS-modified hydroxyapatite/collagen (HA/Col/CS) cement cylinder in seven animals. In all cases the tibia was stabilized with an interlocked universal tibial nail. The animals in each group were analyzed with X-rays, CT scans, histology, immunohistochemistry, and enzymehistochemistry, as well as histomorphometric measurements. The X-ray investigation showed a significantly earlier callus reaction around the HA/Col/CS implants compared to HA/Col alone. The amount of newly formed bone at the end point of the experiment was significantly larger around HA/Col/CS cylinders both in the CT scan and in the histomorphometric analysis. There were still TRAP-positive osteoclasts around the HA/Col implants after 3 months. The number of osteopontin-positive osteoblasts and the direct bone contact were significantly higher around HA/Col/CS implants. We conclude that addition of CS enhances bone remodeling and new bone formation around HA/Col composites.
Nonlinear models of travelling-wave optical amplifiers (1988)

The nonlinear phenomenon in semiconductor travelling wave optical amplifiers has thus far been studied using a pair of coupled partial differential equations, the wave equation and the rate equation. Simple, small- and large-signal nonlinear models of such amplifiers are presented, which, though obtained from the above equations, are much more suitable for computing the output response associated with arbitrary input signals.
PBC 95K, a 95‐kilodalton nuclear autoantigen in primary biliary cirrhosis (1991)

We have identified a novel antinuclear antibody (ANA) in the sera of patients with primary biliary cirrhosis (PBC). Sera from 22 of 50 PBC patients stained the nuclei of HEp-2 cells in a pattern of 5-20 discrete dots, on indirect immunofluorescence. Typically, the titers were higher than 1:1,280. This staining pattern was seen in only 4 of 1,240 ANA-positive samples from patients with other connective tissue diseases, and in none of the ANA-positive sera from 49 patients with other liver diseases. Sera which stained the nuclear dots bound a 95-kd polypeptide in immunoblots of HeLa nuclei and in immunoprecipitates of 35S-methionine-labeled HeLa extracts. Affinity-purified antibodies from the 95-kd protein reproduced the nuclear dot immunofluorescence staining pattern, demonstrating that this polypeptide is located in the nuclear dots. ANA of this type, therefore, occur in 44% of patients with PBC, and they appear to be specific for PBC. These antibodies bind a 95-kd protein that is discrete and is scattered throughout the nucleus.
Efficient Metal-Ion Catalyzed Template-Directed Oligonucleotide Synthesis (1980)

The Pb2+ and Zn2+ ions are efficient catalysts for the polycytidylic acid-directed polymerization of an activated guanylic acid derivative, guanosine 5'-phosphorimidazolide. The products include oligomers of 30 to 40 units in length. The nucleotide residues are predominantly 2'-5' linked when Pb2+ is the catalyst, and predominantly 3'-5' linked in the presence of Zn2+. The significance of these results in the context of the prebiotic evolution of RNA polymerase is discussed.
Mixture designs to assess composition–structure–property relationships in SiO<sub>2</sub>–CaO–ZnO–La<sub>2</sub>O<sub>3</sub>–TiO<sub>2</sub>–MgO–SrO–Na<sub>2</sub>O glasses: Potential materials for embolization (2012)

Embolization with micron-sized particulates is widely applied to treat uterine fibroids. The objective of this work was to develop mixture designs to predict materials composition-structure-property relationships for the SiO₂-CaO-ZnO-La₂O₃-TiO₂-MgO-SrO-Na₂O glass system and compare its fundamental materials properties (density and cytocompatibility), against a state-of-the-art embolic agent (contour polyvinyl alcohol) to assess the potential of these materials for embolization therapies. The glass structures were evaluated using ²⁹Si MAS NMR to identify chemical shift and line width; the particulate densities were determined using helium pycnometry and the cell viabilities were assessed via MTT assay. ²⁹Si MAS NMR results indicated peak maxima for each glass in the range of -82.3 ppm to -89.9 ppm; associated with Q² to Q³ units in silicate glasses. All experimental embolic compositions showed enhanced in vitro compatibility in comparison to Contour PVA with the exceptions of ORP9 and ORP11 (containing no TiO₂). In this study, optimal compositions for cell viability were obtained for the following compositional ranges: 0.095-0.188 mole fraction ZnO; 0.068-0.159 mole fraction La₂O₃; 0.545-0.562 mole fraction SiO₂ and 0.042-0.050 mole fraction TiO₂. To ensure ease of producibility in obtaining good melts, a maximum loading of 0.068 mole fraction La₂O₃ is required. This is confirmed by the desirability approach, for which the only experimental composition (ORP5) of the materials evaluated was presented as an optimum composition; combining high cell viability with ease of production (0.188 mole fraction ZnO; 0.068 mole fraction La₂O₃; 0.562 mole fraction SiO₂ and 0.042 mole fraction TiO₂).
PEGylated Polyplex Micelles from Triblock Catiomers with Spatially Ordered Layering of Condensed pDNA and Buffering Units for Enhanced Intracellular Gene Delivery (2005)

An A-B-C type triblock copolymer, tandemly aligning two types of polycations with different pKa values in a single polymer strand, was developed for the construction of novel polyplex micelles, satisfying a high DNA condensing ability as well as a proton buffering activity directed to elevating gene transfection. The micelle might feature the distinctive three-layered structure, where an inner polyplex layer of condensed pDNA with poly(l-lysine) (pKa approximately 9.4) as the C segment is successively wrapped with an intermediate layer of poly[(3-morpholinopropyl)aspartamide] (B segment) with a comparatively low pKa of approximately 6.2, to provide a buffering effect, and an outer PEG layer (A segment) as a biocompatible palisade.
Modelling of Cloud Computing Centers Using M/G/m Queues (2011)

Cloud computing is a new computing paradigm, whereby shared resources such as infrastructure, hardware platform, and software applications are provided to users on-demand over the internet (Cloud) as services. Successful provision of infrastructure-as-a-service (IaaS) and, consequently, widespread adoption of cloud computing necessitates accurate performance evaluation that allows service providers to dimension their resources in order to fulfil the service level agreements with their customers. In this paper, we describe an analytical model for performance evaluation of cloud server farms, and demonstrate the manner in which important performance indicators such as request response time and number of tasks in the system may be assessed with sufficient accuracy.
NHS Health & Symptom Checker app NHS Health & Symptom Checker app Free (2013)

WHAT STARTED out as an app that was prone to crashing is now available in a much improved version 2.0.3. Developed by NHS Direct, it is targeted at users in England.
Vacuum protection system using an interlocked fast-closing valve for a high-power wiggler beam line (1990)

The finite-element method was used to calculate a rise in temperature at a fast-closing valve (FCV) blade during exposure to intense synchrotron radiation from a 53-pole wiggler at the 2.5-GeV Photon Factory storage ring. The results indicate a possible meltdown of the titanium-alloy blade within 0.1 s at a maximum beam current of 500 mA, making the vacuum protection function of the FCV ineffective for an instantaneous vacuum failure downstream of the wiggler beam line. In order to prevent the blade from melting, the FCV control system has been interlocked with RF klystrons so as to initiate blade closure after dumping the electron beam by turning off the RF power. Performance tests have shown that the system could dump the electron beam within 95 mu s and then close the blade within 12.4 ms after being triggered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Solid-State Proton NMR Characterization of Ethylene Oxide and Propylene Oxide Random and Block Copolymer Composites with Poly(methyl silsesquioxanes) (2001)

Solid-state proton NMR with fast magic-angle sample spinning has been used to study the structure and dynamics of block and random ethylene oxide/propylene oxide copolymers in the bulk and as 30 wt % composites with poly(methyl silsesquioxane) which are precursors to nanoporous ultralow dielectric constant films. The NMR results for the bulk diblock copolymer show that the propylene oxide block is relatively mobile and the proton line widths are effectively narrowed with 12 kHz magic-angle sample spinning, while most of the signals for the semicrystalline ethylene oxide block are too broad to be observed under these conditions. Both the ethylene oxide and propylene oxide signals are observed in the 30 wt % composite, demonstrating that the formation of crystalline domains in the ethylene oxide block is inhibited in the composite. Dipolar filter NMR experiments show that the propylene oxide is less mobile than the ethylene oxide in the block copolymer composites, suggesting that the propylene oxide is near the methyl silsesquioxane interface. The results from proton spin diffusion studies show that the polymer domain sizes in the composites are on the order of 5−7 nm, the size range of most interest for the formation of ultralow dielectric constant materials.
High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface (2011)

Microorganisms colonize a variety of extreme environments, and based on cultivation studies and analyses of PCR-amplified 16S rDNA sequences, microbial life appears to extend deep into the earth crust. However, none of these studies involved comprehensive characterizations of total DNA. Here we report results of a high-coverage DNA pyrosequencing of an apparently representative and uncontaminated sample from a deep sea oil reservoir located 2.5 km subsurface, attributing a pressure and temperature of 250 bars and 85°C respectively. Bioinformatic analyses of the DNA sequences indicate that the reservoir harbours a rich microbial community dominated by a smaller number of taxa. Comparison of the metagenome with sequences in databases indicated that there may have been contact between the oil reservoir and surface communities late in the sequence of geological events leading to oil reservoir formation. One specific gene, encoding a putative enolase, was synthesized and expressed in Escherichia coli. Enolase activity was confirmed and was found to be much more thermotolerant than for a corresponding E. coli enzyme, consistent with the conditions in the oil reservoir.
Inactivation of glycerol dehydrogenase of Klebsiella pneumoniae and the role of divalent cations (1985)

Anaerobically induced NAD-linked glycerol dehydrogenase of Klebsiella pneumoniae for fermentative glycerol utilization was reported previously to be inactivated in the cell during oxidative metabolism. In vitro inactivation was observed in this study by incubating the purified enzyme in the presence of O2, Fe2+, and ascorbate or dihydroxyfumarate. It appears that O2 and the reducing agent formed H2O2 and that H2O2 reacted with Fe2+ to generate an activated species of oxygen which attacked the enzyme. The in vitro-oxidized enzyme, like the in vivo-inactivated enzyme, showed an increased Km for NAD (but not glycerol) and could no longer be activated by Mn2+ which increased the Vmax of the native enzyme but decreased its apparent affinity for NAD. Ethanol dehydrogenase and 1,3-propanediol oxidoreductase, two enzymes with anaerobic function, also lost activity when the cells were incubated aerobically with glucose. However, glucose 6-phosphate dehydrogenase (NADP-linked), isocitrate dehydrogenase, and malate dehydrogenase, expected to function both aerobically and anaerobically, were not inactivated. Thus, oxidative modification of proteins in vivo might provide a mechanism for regulating the activities of some anaerobic enzymes.
Electrogastrography: a document prepared by the gastric section of the American Motility Society Clinical GI Motility Testing Task Force (2003)

The objective of this document is to present the consensus opinion of the American Motility Society Clinical GI Motility Testing Task Force on the performance and clinical utility of electrogastrography (EGG). EGG is a non-invasive means of recording human gastric myoelectrical activity or slow waves from cutaneous leads placed over the stomach. In healthy volunteers, EGG tracings exhibit sinusoidal waveforms with a predominant frequency of 3 cycles per minute (cpm). Clinical studies have shown good correlation of these cutaneous recordings with those acquired from serosally implanted electrodes. The amplitude of the EGG waveform increases with ingestion of caloric or non-caloric meals. Some patients with nausea, vomiting, or other dyspeptic symptoms exhibit EGG rhythm disturbances or blunting of meal-evoked EGG signal amplitude increases. These abnormalities correlate to some degree with delayed gastric emptying of solids. In selected patients, EGG may be complementary to gastric emptying testing. To date, no therapies have convincingly demonstrated in controlled studies that correcting abnormalities detected by EGG improves upper gastrointestinal symptoms. Proposed clinical indications for performance of EGG in patients with unexplained nausea, vomiting and dyspeptic symptoms must be validated by prospective controlled investigations.
Genes and Molecules of Lactobacilli Supporting Probiotic Action (2008)

Lactobacilli have been crucial for the production of fermented products for centuries. They are also members of the mutualistic microbiota present in the human gastrointestinal and urogenital tract. Recently, increasing attention has been given to their probiotic, health-promoting capacities. Many human intervention studies demonstrating health effects have been published. However, as not all studies resulted in positive outcomes, scientific interest arose regarding the precise mechanisms of action of probiotics. Many reported mechanistic studies have addressed mainly the host responses, with less attention being focused on the specificities of the bacterial partners, notwithstanding the completion of Lactobacillus genome sequencing projects, and increasing possibilities of genomics-based and dedicated mutant analyses. In this emerging and highly interdisciplinary field, microbiologists are facing the challenge of molecular characterization of probiotic traits. This review addresses the advances in the understanding of the probiotic-host interaction with a focus on the molecular microbiology of lactobacilli. Insight into the molecules and genes involved should contribute to a more judicious application of probiotic lactobacilli and to improved screening of novel potential probiotics.
Recent Progress in Diaryl Ether Synthesis (2006)

Diaryl ethers form an important class of organic compounds, both in life sciences and in the polymer industry. In general, diaryl ethers can be synthesized by means of copper-catalyzed Ullmann diaryl ether coupling, palladium-catalysed Buchwald-Hartwig reaction, nucleophilic aromatic substitution, arylboronic acid diaryl ether coupling, oxidative coupling, and nucleophilic aromatic addition to metal-arene complexes. This review covers the progress in diaryl ether synthesis since 1999, with literature coverage through September 2005.
Disentangling in vivo the effects of iron content and atrophy on the ageing human brain (2014)

Evidence from magnetic resonance imaging (MRI) studies shows that healthy aging is associated with profound changes in cortical and subcortical brain structures. The reliable delineation of cortex and basal ganglia using automated computational anatomy methods based on T1-weighted images remains challenging, which results in controversies in the literature. In this study we use quantitative MRI (qMRI) to gain an insight into the microstructural mechanisms underlying tissue ageing and look for potential interactions between ageing and brain tissue properties to assess their impact on automated tissue classification. To this end we acquired maps of longitudinal relaxation rate R1, effective transverse relaxation rate R2* and magnetization transfer - MT, from healthy subjects (n=96, aged 21-88 years) using a well-established multi-parameter mapping qMRI protocol. Within the framework of voxel-based quantification we find higher grey matter volume in basal ganglia, cerebellar dentate and prefrontal cortex when tissue classification is based on MT maps compared with T1 maps. These discrepancies between grey matter volume estimates can be attributed to R2* - a surrogate marker of iron concentration, and further modulation by an interaction between R2* and age, both in cortical and subcortical areas. We interpret our findings as direct evidence for the impact of ageing-related brain tissue property changes on automated tissue classification of brain structures using SPM12. Computational anatomy studies of ageing and neurodegeneration should acknowledge these effects, particularly when inferring about underlying pathophysiology from regional cortex and basal ganglia volume changes.
Antioxidant Activity of a Dihydroquercetin Isolated from Larix gmelinii (Rupr.) Rupr. Wood (1996)

We have demonstrated that dihydroquercetin is an antioxidant and possesses the properties of protecting capillaries, which is consistent with its action as an antiinflammatory agent, gastro- and hepatoprotecting agent, and its diuretic and hypolipidaemic activity. As a capillary protector, dihydroquercetin is 3.4 times more effective at a dose of 100 mg/kg and 4.9 times at a dose of 300 mg/kg than the well known bioflavonoid, quercetin. Dihydroquercetin shows a dose dependent suppression of lipid peroxidation in the rat liver. The hypolipidaemic activity of dihydroquercetin at 250 mg/kg is comparable to that of polysponin.
Improved acquisition and tracking performance of PLLs through signal injection (2002)

In the communication we consider the use of signal injection to improve the acquisition and tracking performance of PLLs (PLLI). A dynamic model describing the PLLI behaviour is derived. Based on this model we show that by a proper design the injected signal can be used to improve the acquisition capabilities of conventional PLLs without changing the loop response. Experimental measurements of a PLLI, with a Colpitts VCO designed to allow current injection, are presented which show that this type of loop has wider locking range and a reduced acquisition time relatively to the conventional PLL. With this experimental set-up we also confirm that with low signal injection power the loop response remains identical if injection is made in quadrature.
Si-micromachining in MM-wave circuits (2002)

Despite the excellent characteristics and results in all MMIC implementations, high power has remained a challenge. The low-power output of solid state sources along with their low-impedance, further hindered by conventional transmission line characteristics, results in even lower efficiencies. From a device performance point of view, it is obvious that traditional planar line techniques introduce high losses due to the excitation of substrate wave modes. While parasitic radiation is inherent to microstrip and cannot be suppressed, ground connections can be achieved by use of via hole technology. Via holes, however, result in high parasitic inductance and parasitic radiation leading to a substantial device gain degradation which has a detrimental impact on circuit operation at millimeter-wave frequencies. Conventional coplanar technology also provides limited solutions to some of these problems by bringing the ground plane to the proximity of the active devices at the cost of additional parasitic effects such as the excitation of parallel plate and microstrip modes, thus resulting in increased fabrication complexity. All solutions which have been proposed to eliminate parasitic modes have been proven quite ineffective, thus making conventional microstrip and coplanar transmission line approaches less attractive for use in millimeter wave MMICs. In an effort to increase generated power, reduce loss and design cycle, a new generation of MMICs is needed. RF Si micromachining is an excellent approach that provides solutions to the above problems.
Computer-aided design of microwave frequency doublers using a new circuit structure (1993)

A circuit structure for microwave frequency doublers is presented. It has been used in the design of a MMIC (monolithic microwave integrated circuit) doubler. Its major advantages are effective suppression of the unwanted odd-order harmonics and conversion gain to the desired second harmonic. These advantages have been demonstrated by computer simulation and further verified by measured results for the MMIC circuit. The circuit can be used in both balanced and unbalanced output configurations, without requiring baluns or transformers. The fundamental frequency suppression was found to be over 50 dB, while better than 3 dB conversion gain was achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>