gebhart/patrepeval huggingface dataset:
The <i>Chlamydia trachomatis</i> Plasmid Is a Transcriptional Regulator of Chromosomal Genes and a Virulence Factor (2008)

Chlamydia trachomatis possesses a cryptic 7.5-kb plasmid of unknown function. Here, we describe a comprehensive molecular and biological characterization of the naturally occurring plasmidless human C. trachomatis strain L2(25667R). We found that despite minimal chromosomal polymorphisms, the LGV strain L2(25667R) was indistinguishable from plasmid-positive strain L2(434) with regard to its in vitro infectivity characteristics such as growth kinetics, plaquing efficiency, and plaque size. The only in vitro phenotypic differences between L2(434) and L2(25667R) were the accumulation of glycogen granules in the inclusion matrix and the lack of the typical intrainclusion Brownian-like movement characteristic of C. trachomatis strains. Conversely, we observed a marked difference between the two strains in their abilities to colonize and infect the female mouse genital tract. The 50% infective dose of plasmidless strain L2(25667R) was 400-fold greater (4 x 10(6) inclusion-forming units [IFU]) than that of plasmid-bearing strain L2(434) (1 x 10(4) IFU). Transcriptome analysis of the two strains demonstrated a decrease in the transcript levels of a subset of chromosomal genes for strain L2(25667R). Among those genes was glgA, encoding glycogen synthase, a finding consistent with the failure of L2(25667R) to accumulate glycogen granules. These findings support a primary role for the plasmid in in vivo infectivity and suggest that virulence is controlled, at least in part, by the plasmid's ability to regulate the expression of chromosomal genes. Our findings have important implications in understanding a role for the plasmid in the pathogenesis of human infection and disease.
<i>In Vivo</i> Nuclear Magnetic Resonance Imaging of Lithium (1985)

Magnetic resonance imaging techniques have previously been applied to 1H, 23Na, 31P, and 19F nuclei. This is the first report of application of these techniques to 7Li. Lithium images of both aqueous phantoms and a rat abdomen are presented. Applications of this technique to humans are discussed.
Alternative Design of a Unity-Gain Follower with Buffer (1978)

The design of a unity-gain buffer amplifier in which an extremely low input capacity is achieved by bootstrapping the entire input stage, including the power sources, which was published in 1973 and further discussed in 1976, needs redesigning in order to make it less critical with respect to the choice of components. The new design is stili very simple and based on commercially available operational amplifiers without any matching requirements.
Vaccines against malaria (2011)

There is no licenced vaccine against any human parasitic disease and Plasmodium falciparum malaria, a major cause of infectious mortality, presents a great challenge to vaccine developers. This has led to the assessment of a wide variety of approaches to malaria vaccine design and development, assisted by the availability of a safe challenge model for small-scale efficacy testing of vaccine candidates. Malaria vaccine development has been at the forefront of assessing many new vaccine technologies including novel adjuvants, vectored prime-boost regimes and the concept of community vaccination to block malaria transmission. Most current vaccine candidates target a single stage of the parasite's life cycle and vaccines against the early pre-erythrocytic stages have shown most success. A protein in adjuvant vaccine, working through antibodies against sporozoites, and viral vector vaccines targeting the intracellular liver-stage parasite with cellular immunity show partial efficacy in humans, and the anti-sporozoite vaccine is currently in phase III trials. However, a more effective malaria vaccine suitable for widespread cost-effective deployment is likely to require a multi-component vaccine targeting more than one life cycle stage. The most attractive near-term approach to develop such a product is to combine existing partially effective pre-erythrocytic vaccine candidates.
Alirocumab for the treatment of hypercholesterolaemia (2017)

Prescription of statins for low-density lipoprotein cholesterol (LDL-C) reduction is the standard of care in primary and secondary prevention of cardiovascular disease; nevertheless, a large number of patients treated with statins are unable to reach the recommended LDL-C targets. Therefore, there is need for safe and effective novel therapies for the pharmacological management of hypercholesterolaemia, in addition or as alternative to lipid-lowering therapies (LLT) currently in use. Areas covered: In 2015, the Food and Drug Administration and the European Medicines Agency approved alirocumab (Praluent®; Sanofi), a fully human monoclonal antibody against proprotein convertase subtilisin/kexin type 9 (PCSK9), for the treatment of hypercholesterolaemic patients unable to meet LDL-C targets, as an adjunct to diet in addition/alternative to LLT. The authors review the pharmacological features, clinical efficacy, and safety of alirocumab in lowering LDL-C, and discuss its therapeutic perspectives based on the most recent clinical trials. Expert commentary: Alirocumab causes a marked reduction in LDL-C, presents good safety and tolerability, and represents a promising approach for LDL-C lowering, particularly in patients with intolerance to statin or elevated LDL-C despite maximal statin therapy; nevertheless, further long-term data on safety and efficacy are necessary, such as data on the improvement of cardiovascular outcomes.
Effect of Genetically Modifying the Lactococcal Proteolytic System on Ripening and Flavor Development in Cheddar Cheese (1994)

THREE BATCHES OF SIX CHEDDAR CHEESES WERE MANUFACTURED BY USING THE FOLLOWING LACTOCOCCAL STRAINS: (i) UC317 as a control; (ii) JL3601, a proteinase-negative derivative of UC317 transformed with high-copy-number plasmid pCI3601 containing the cloned proteinase gene complex from UC317; (iii) AM312, a proteinase-negative derivative of UC317 transformed with plasmid pMG36enpr containing the neutral proteinase gene from Bacillus subtilis; (iv) AC322, JL3601 transformed with pMG36enpr; (v) AC311, UC317 transformed with plasmid pNZ1120, which contains the aminopeptidase N (pepN) gene from Lactococcus lactis subsp. lactis MG1363; and (vi) AC321, JL3601 transformed with pNZ1120. Organoleptic and chemical analyses indicated that (i) the control cheeses, which were made with UC317, were of the highest quality; (ii) cheeses made with strains harboring pCI3601 in addition to either pMG36enpr (AC322) or pNZ1120 (AC321) did not ripen in a significantly different manner than cheeses made with AM312 (containing only pMG36enpr) or AC311 (containing only pNZ1120), respectively; (iii) cheeses made with strains that overproduce pepN did not have improved body, texture, and flavor characteristics; and (iv) cheeses made with strains harboring the neutral proteinase from B. subtilis (AM312 and AC322) underwent greatly accelerated proteolysis.
Detection and Characterization of Plasmids in <i>Pseudomonas aeruginosa</i> Strain PAO (1973)

Using a variety of techniques, it has been established that the sex factor FP2 has a density of 1.717 g/cm(3) (corresponding to a guanine plus cytosine [G + C] content of 58%) and a mean circular contour length of 28.5 +/- 0.6 mum (corresponding to a molecular weight of 59 x 10(6)). Another sex factor FP39 has a density of 1.719 g/cm(3) (corresponding to a G + C content of 60%) and a mean circular contour length of 26.5 +/- 0.5 mum (corresponding to a molecular weight of 55 x 10(6)). It appears that all, or nearly all, of the FP sex factor deoxyribonucleic acid occurs as covalent circular molecules under the conditions employed. In addition, these procedures have been used to demonstrate that strain PAO, a naturally occurring female (i.e., FP(-)) strain of Pseudomonas aeruginosa, harbors a number of cryptic plasmids having similar densities to the bulk of the cell deoxyribonucleic acid (1.726 g/cm(3)) and occurring as covalent circular molecules.
Upside-down Quakes: Displaying 3D Seismicity with Google Earth (2009)

Research Article| May 01, 2009 Upside-down Quakes: Displaying 3D Seismicity with Google Earth Duncan Carr Agnew Duncan Carr Agnew Institute of Geophysical and Planetary Physics Scripps Institution of Oceanorgraphy University of California, San Diego IGPP 0225 9500 Gilman Drive La Jolla, California 92093-0225 U.S.A. Search for other works by this author on: GSW Google Scholar Author and Article Information Duncan Carr Agnew Institute of Geophysical and Planetary Physics Scripps Institution of Oceanorgraphy University of California, San Diego IGPP 0225 9500 Gilman Drive La Jolla, California 92093-0225 U.S.A. Publisher: Seismological Society of America First Online: 09 Mar 2017 Online ISSN: 1938-2057 Print ISSN: 0895-0695 © 2009 by the Seismological Society of America Seismological Research Letters (2009) 80 (3): 499–505. https://doi.org/10.1785/gssrl.80.3.499 Article history First Online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Duncan Carr Agnew; Upside-down Quakes: Displaying 3D Seismicity with Google Earth. Seismological Research Letters 2009;; 80 (3): 499–505. doi: https://doi.org/10.1785/gssrl.80.3.499 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietySeismological Research Letters Search Advanced Search Seismologists have long struggled with how to display their data effectively, since earthquakes, like other geological processes, occur in three spatial dimensions and time. Seismicity has additional dimensions: there is the obvious variable of earthquake size, which itself becomes multidimensional once we extend this to the tensor-valued quantity (the moment tensor) that is the simplest description of the earthquake source. Given the human ability to see patterns, visualization is a powerful tool for investigating earthquake behavior; although it can be perilous if the patterns seen are not statistically checked, it is better to have seen and abandoned a pattern than... You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Urethral catheter insertion forces: a comparison of experience and training (2009)

We propose the maximum force that should be utilized during urethral catheter insertion is 5 Newtons. This force deserves validation in a larger population and should be considered when designing urethral catheters or creating catheter simulators. Understanding urethral catheter insertion forces may also aid in establishing competency parameters for health care professionals in training.
A virtual platform environment for exploring power, thermal and reliability management control strategies in high-performance multicores (2010)

The use of high-end multicore processors today can incur high power density with significant variability in spatial and temporal usage of resources by workloads. This situation leads to power and temperature hotspots, which in turn may lead to non-uniform ageing and accelerated chip failure. These drawbacks can be mitigated by online tuning of system performance and adopting closed-loop thermal and reliability management policies. The development and evaluation of these policies cannot be performed solely on real hardware - due to observability and flexibility limitations or just by relying on trace-driven simulation, due to dependencies present among power, thermal effects, reliability and performance. We present a complete and virtual platform to develop, simulate and evaluate power, temperature and reliability management control strategies for high-performance multicores. The accuracy and effectiveness of our solution are ensured by integrating a established system simulator (Simics) with models for power consumption, temperature distribution and aging. The models are based on characterization on real hardware. Control strategies exploration and design are carried out in the MATLAB/Simulink framework allowing the use of control theory tools. Fast prototyping is achieved by developing a suitable interface between Simics and MATLAB/Simulink, enabling co-simulation of hardware platforms and controllers.
Quantum Noise of Actively Mode-Locked Lasers With Dispersion and Amplitude/Phase Modulation (2004)

A quantum theory for the noise of optical pulses in actively mode-locked lasers is presented. In the presence of phase modulation and/or group velocity dispersion, the linear operator that governs the time evolution of the pulse fluctuations inside the laser cavity is not Hermitian (or normal) and the eigenmodes of this operator are not orthogonal. As a result, the eigenmodes have excess noise and the noise in different eigenmodes is highly correlated. We construct quantum operators for the pulse photon number, phase, timing, and frequency fluctuations. The nonorthogonality of the eigenmodes results in excess noise in the pulse photon number, phase, timing, and frequency. The excess noise depends on the frequency chirp of the pulse and is present only at low frequencies in the spectral densities of the pulse noise operators.
Nanostructure design of amorphous FePO<sub>4</sub>facilitated by a virus for 3 V lithium ion battery cathodes (2010)

Amorphous iron phosphate nanowires with diameters of 10 to 20 nm were synthesized using genetically engineered M13 virus for lithium ion battery cathodes. Hydrolysis of Fe3+ ions has been effectively suppressed by forming conjugates with the virus and synthesizing at low temperature, 4 °C. The M13 virus biological template facilitated elaborate nanostructure design and environmentally benign, low temperature synthesis. By implementing heterostructures with silver, we demonstrated experimentally that uniformly distributed Ag nanoparticles throughout the whole structure appeared more advantageous than locally limited network formation by Ag nanowires in enhancing overall electronic conductivity of the entire system, thereby improving battery performances. Electrochemical properties were further improved by dehydration of structural waters. The synergetic use of biological template and synthetic chemistry could enable the synthesis of anhydrous a-FePO4 without thermal treatment via low-temperature and eco-efficient chemistry. The first discharge capacity at a discharge rate of C/10 and 1C was 165 mA h g−1 (93% of the theoretical value) and 110 mA h g−1, respectively. These electrochemical properties are comparable to the best reported values for a-FePO4 synthesized at high temperature. In this study, we set the important step for the practical applications of biological approaches in designing and fabricating energy devices, which may be a promising alternative to the traditional processing techniques that consume energy and are costly.
Extragenic suppressors of yeast glucose derepression mutants leading to constitutive synthesis of several glucose-repressible enzymes (1991)

Saccharomyces cerevisiae regulatory genes CAT1 and CAT3 constitute a positive control circuit necessary for derepression of gluconeogenic and disaccharide-utilizing enzymes. Mutations within these genes are epistatic to hxk2 and hex2, which cause defects in glucose repression. cat1 and cat3 mutants are unable to grow in the presence of nonfermentable carbon sources or maltose. Stable gene disruptions were constructed inside these genes, and the resulting growth deficiencies were used for selecting epistatic mutations. The revertants obtained were tested for glucose repression, and those showing altered regulatory properties were further investigated. Most revertants belonged to a single complementation group called cat4. This recessive mutation caused a defect in glucose repression of invertase, maltase, and iso-1-cytochrome c. Additionally, hexokinase activity was increased. Gluconeogenic enzymes are still normally repressible in cat4 mutants. The occurrence of recombination of cat1::HIS3 and cat3::LEU2 with some cat4 alleles allowed significant growth in the presence of ethanol, which could be attributed to a partial derepression of gluconeogenic enzymes. The cat4 complementation group was tested for allelism with hxk2, hex2, cat80, cid1, cyc8, and tup1 mutations, which were previously described as affecting glucose repression. Allelism tests and tetrad analysis clearly proved that the cat4 complementation group is a new class of mutant alleles affecting carbon source-dependent gene expression.
Design of Periodic Antenna Arrays With the Excitation Phases Synthesized for Optimum Near-Field Patterns via Steepest Descent Method (2011)

We present the design and realization of a microstrip patch array antenna, which is operated at 24 GHz band, and can be used in the applications of vital-sign detection with a higher resolution. The design uses the steepest descent method (SDM) to synthesize the excitation phases of the array such that the radiation has an optimum near-field pattern in the desired area. Both theoretical development of SDM formulations and experimental validations over the antenna prototype are presented.
In Situ X-Ray Observation on the Intercalation of Weak Interaction Molecules into Perovskite-Type Layered Crystals (C9H19NH3)2PbI4 and (C10H21NH3)2CdCl4 (1986)

Abstract The intercalation-deintercalation process of weak interaction organic molecules such as 1-chloronaphthalene and o-dichlorobenzene into highly oriented polycrystalline (C10H21NH3)2CdCl4 films and hexane into (C9H19NH3)2Pbl4 single crystals has been observed in situ by using X-ray technique. The process is highly reversible. Increasing of interlayer spacing is in reasonable agreement with the size of the intercalated molecules and corresponds to the parallel orientation of aromatic ring planes or hexane chains in between two paraffin layers of the host crystals.
High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot (2000)

Little is known about the nature of recombination hotspots in the human genome and the relationship between crossover activity and patterns of linkage disequilibrium. We have therefore used both haplotype analysis and direct detection of crossovers in sperm to characterize a putative recombination hotspot in the TAP2 gene within the class II region of the MHC. Haplotype diversity provided evidence for a localized hotspot within intron 2 of this gene. Sperm DNA typing using allele-specific PCR primers to selectively amplify recombinant TAP2 molecules revealed a highly localized meiotic crossover hotspot approximately 1.2 kb long, unusually abundant in sequence polymorphisms and flanked by DNA much less active in recombination. Sperm crossover appeared to be fully reciprocal, and almost all crossover products were simple, involving a single exchange between adjacent heterozygous markers. This hotspot appears to be much more active in female than male meiosis. No primary sequence similarities could be found between any of the very few well defined crossover hotspots in the human genome, all of which show recombinationally active domains 1-2 kb long. Direct comparison of recombination frequency and haplotype diversity in TAP2 showed that linkage disequilibrium measures were a poor predictor of crossover frequency in this region, with non-recombining markers sometimes in free association and with examples of pairs of markers spanning the recombination hotspot showing substantial or even absolute linkage disequilibrium.
Adaptive friction compensation for bi-directional low-velocity position tracking (2005)

A comparative investigation of friction-compensating control strategies designed to improve low-velocity reversals for servomechanisms is presented. The methods considered include adaptive control and estimation-based control. The various controller designs incorporate different friction models ranging from classical friction and Stribeck friction to the less popular Dahl friction model. The control strategies are compared in an extensive test program involving sinusoidal position trajectory tracking experiments on a direct-drive DC motor. The results show that the adaptive and estimation-based controllers outperform more traditional linear controllers. It is also shown that the Dahl model, typically ignored in the literature, is significant for the friction-compensating control problem with repeated zero-velocity crossings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Evaluation of an Electronic Flight Bag with Integrated Routing and Runway Incursion Detection Functions (2006)

An electronic flight bag showing an ownship referenced airport map, supports the pilot in knowing where the aircraft is with respect to the taxiway and runway structure. However, since the desired route is still implicit, communication errors (e.g. due to misinterpretation) and memorization errors continue to lead to possible navigation error. By integrating the planned route information into the airport map context, the pilot would be supported in knowing where the aircraft is and also where it would have to be. Furthermore, the information can be used by a route conformance monitoring function, to alert the pilot in case of a route deviation, violation of a hold-short instruction, etc. This paper describes the design and initial evaluation of an electronic flight bag with integrated routing, conformance monitoring and runway incursion detection functions.
Plasmon-induced optical switching of electrical conductivity in porous anodic aluminum oxide films encapsulated with silver nanoparticle arrays (2010)

We report on plasmon induced optical switching of electrical conductivity in two-dimensional (2D) arrays of silver (Ag) nanoparticles encapsulated inside nanochannels of porous anodic aluminum oxide (AAO) films. The reversible switching of photoconductivity greatly enhanced by an array of closely spaced Ag nanoparticles which are isolated from each other and from the ambient by thin aluminum oxide barrier layers are attributed to the improved electron transport due to the localized surface plasmon resonance and coupling among Ag nanoparticles. The photoconductivity is proportional to the power, and strongly dependent on the wavelength of light illumination. With Ag nanoparticles being isolated from the ambient environments by a thin layer of aluminum oxide barrier layer of controlled thickness in nanometers to tens of nanometers, deterioration of silver nanoparticles caused by environments is minimized. The electrochemically fabricated nanostructured Ag/AAO is inexpensive and promising for applications to integrated plasmonic circuits and sensors.