gebhart/patrepeval huggingface dataset:
Magnetic noise spectroscopy as a probe of local electronic correlations in two-dimensional systems (2017)

We develop the theoretical framework for calculating magnetic noise from conducting two-dimensional (2D) materials. We describe how local measurements of this noise can directly probe the wave-vector dependent transport properties of the material over a broad range of length scales, thus providing new insight into a range of correlated phenomena in 2D electronic systems. As an example, we demonstrate how transport in the hydrodynamic regime in an electronic system exhibits a unique signature in the magnetic noise profile that distinguishes it from diffusive and ballistic transport and how it can be used to measure the viscosity of the electronic fluid. We employ a Boltzmann approach in a two-time relaxation-time approximation to compute the conductivity of graphene and quantitatively illustrate these transport regimes and the experimental feasibility of observing them. Next, we discuss signatures of isolated impurities lodged inside the conducting 2D material. The noise near an impurity is found to be suppressed compared to the background by an amount that is directly proportional to the cross-section of electrons/holes scattering off of the impurity. We use these results to outline an experimental proposal to measure the temperature dependent level shift and linewidth of the resonance associated with an Anderson impurity.
The Novel Combination of Nitroxoline and PD-1 Blockade, Exerts a Potent Antitumor Effect in a Mouse Model of Prostate Cancer (2019)

Programmed cell death protein 1 (PD-1) blockade is a promising therapeutic strategy against prostate cancer. Nitroxoline has been found to have effective anticancer properties in several cancer types. We investigated the efficacy of a combination therapy involving nitroxoline and PD-1 blockade in a prostate cancer mouse model. In our <i>in vitro</i> analysis<i>,</i> we found that nitroxoline inhibited the viability and proliferation of the mouse prostate cancer cell line RM9-Luc-PSA. Additionally, nitroxoline downregulated the expressions of phospho-PI3 kinase, phospho-Akt (Thr308), phospho-Akt (Ser473), phospho-GSK-3β, Bcl-2, and Bcl-xL. Nitroxoline also downregulated programmed death-ligand 1 (PD-L1) expression levels in prostate cancer cell line and tumor tissue. In our murine prostate cancer orthotopic model, nitroxoline plus PD-1 blockade synergistically suppressed tumor growth when compared with nitroxoline or PD-1 blockade alone, leading to reductions in tumor weight, bioluminescence tumor signals, and serum prostate-specific antigen levels. Furthermore, fluorescence-activated cell sorting analysis showed that the combination strategy significantly enhanced antitumor immunity by increasing CD44<sup>+</sup>CD62L<sup>+</sup>CD8<sup>+</sup> memory T cell numbers and reducing myeloid-derived suppressor cell numbers in peripheral blood. In conclusion, our findings suggest that nitroxoline plus PD-1 blockade may be a promising treatment strategy in patients with prostate cancer.
Hematite (α-Fe<sub>2</sub>O<sub>3</sub>) with Various Morphologies: Ionic Liquid-Assisted Synthesis, Formation Mechanism, and Properties (2009)

The alpha-Fe(2)O(3) with various morphologies has been successfully synthesized via an ionic liquid-assisted hydrothermal synthetic method. The samples are characterized by X-ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscope (FE-SEM), transmission electron microscopy, and high-resolution transmission electron microscopy. The results indicate that the as-prepared samples are alpha-Fe(2)O(3) nanoparticles, mesoporous hollow microspheres, microcubes, and porous nanorods. The effects of the ionic liquid 1-n-butyl-3-methylimidazolium chloride ([bmim][Cl]) on the formation of the alpha-Fe(2)O(3) with various morphologies have been investigated systematically. The proposed formation mechanisms have also been investigated on the basis of a series of FE-SEM studies of the products obtained at different durations. Because of the unique porous structure, the potential application in water treatment of the alpha-Fe(2)O(3) porous nanorods was investigated. The UV-vis measurements suggest that the as-synthesized pure alpha-Fe(2)O(3) with various morphologies possess different optical properties depending on the shape and size of the samples. The magnetic hysteresis measurements indicate the interesting magnetic property evolution in the as-prepared alpha-Fe(2)O(3) samples, which is attributed to the superstructure or the shape anisotropy of the samples. This method is expected to be a useful technique for controlling the diverse shapes of crystalline inorganic materials for a variety of applications, such as sensors, gas and heavy metal ion adsorbents, catalytic fields, hydrogen and Li ion storage, and controlled drug delivery, etc.
Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo (1998)

Article Free Access Share on Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo Authors: Jae K. Lee Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CA Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CAView Profile , Vlado Dančík Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CA Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CAView Profile , Michael S. Waterman Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CA Department of Mathematics, University of Southern California, 1042 W. 36th Place, DRB 155, Los Angeles, CAView Profile Authors Info & Claims RECOMB '98: Proceedings of the second annual international conference on Computational molecular biologyMarch 1998 Pages 147–152https://doi.org/10.1145/279069.279108Online:01 March 1998Publication History 3citation228DownloadsMetricsTotal Citations3Total Downloads228Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Three‐dimensional P and S wave velocity structures of southern Peru and their tectonic implications (1986)

In 1981 an 18‐station regional array was operated in southern Peru above the area where the dip of the subducted Nazca plate changes from virtually horizontal in the northwest to about 30° in the southeast. Arrival times of compressional (P) and shear (S) waves from microearthquakes recorded by this array are used in this paper to investigate the three‐dimensional velocity structure of the crust and upper mantle in the region between the coast and the Cordillera Occidental. The results suggest a crustal thickness of about 40 km beneath the coast, increasing to about 70 km beneath the Cordillera Occidental. This change in thickness occurs abruptly in the northwest but is gradual in the southeast. The inverse correlation between the dip of the Moho and the dip of the slab suggests a broad‐scale, causal relation between the two. At the same time, free‐air gravity anomalies suggest that the steepening of the Moho in the northwest may occur only in the region under the array. Because the crust is thicker in the southeast than originally surmised, a suite of earthquakes previously thought to occur in the mantle now appears to be confined to the crust. The association of these earthquakes with a shallow dipping Moho is suggestive of ongoing crustal deformation to the west of the Andes. However, other seismological and geological observations make the role of these earthquakes in crustal deformation unclear. S wave velocities in the mantle between 70‐ and 130‐km depth above the 30° dipping slab are low, suggesting the presence of partially melted asthenosphere that may be responsible for the magmatic activity observed in southern Peru.
Traction of a Model Pneumatic Tyre on a Rigid Surface (1978)

The paper describes an experimental program aimed at accounting for the typical slip/pull characteristics of a deformable wheel (pneumatic tyre) on arigid surface. A wheel and tyre 200 mm diameter by 50 mm wide were run at laboratory scales of speed, load and torque, on a short suspended track of any desired surface. The traction developed in the track was measured by a proving ring that restrained its longitudinal motion. On a track of plate glass, it was possible to observe the wheel's contact patch and changes of shape and movement within it, under normal and tangential load. The mechanics of the tangential deformation of the tyre and of its sliding at the contact patch are discussed. The typical slip/pull characteristics appear to consist of:- (a) a low-slip regime where slip is due to the tangential deformation of the tyre, and (b) a high-slip regime under increasing traction where the whole area of contact is sliding towards stall, and slip is due both to tangential deformation and to sliding.
Editorial Notes: Our Persian Gulf Veterans (1991)

Two veterinary students and one professor from the ISU College of Veterinary Medicine were called to active duty in November of 1990, during the Middle East crisis. David Oelberg and Jennifer Noblett were both well into the first semester of their junior year, while Dr. Kenneth Platt was in Bangkok, Thailand working on aU.N. sponsored proposal, when they received notification that their units had been alerted. Their assignments were as follows.
BER computation of generalized QAM constellations (2002)

Based on a Karnaugh map style Gray coding of constellations, we derive a recursive algorithm for the exact bit error rate computation of generalized hierarchical M-ary pulse amplitude modulations (PAM) over additive white Gaussian noise (AWGN) and fading channels. We also show how this algorithm can be extended to generalized hierarchical quadrature amplitude modulation constellations (square and rectangular). For the AWGN case, these expressions are in the form of a weighted sum of complementary error functions and are solely dependent on the constellation size M, the carrier-to-noise ratio, and a constellation parameter which controls the relative message importance.
High-Speed and Stable Operation of Highly Unidirectional III-V/Silicon Microring Lasers for On-chip Optical Interconnects (2015)

We demonstrated high-speed, stable and unidirectional microring III-V laser diodes with in-cavity feedback silicon waveguide, and the integration with III-V photodetector on a silicon-on-insulator platform to achieve on-chip data transmission with a data rate of 12.5 Gb/s.
Sensitivity to propofol in the elderly (1986)

Two studies were carried out on 609 fit, unpremedicated patients to assess the influence of patient age on the response to the rapidly-acting hindered phenol, propofol, which is being evaluated for induction of anaesthesia. In the first study, 1.25 mg/kg was injected over 20 seconds followed by 10-mg increments every 15 seconds until loss of verbal contact. This showed a great individual variation in response to the drug. A reduction in the 'induction' dose was found in elderly patients, which became marked around 60 years. In the second (340), doses ranging from 1.5-3.0 mg/kg in patients under 60 years and 1.25-2.25 mg/kg in those over 60 years were injected as a bolus over 20 seconds. Doses of 2.25-2.5 mg/kg were required to induce anaesthesia in patients under 60 years, whilst 1.5-1.75 mg/kg was adequate in those over 60 years. Side effects were more marked with the rapid injection and doses in excess of 1.75 mg/kg caused significant hypotension and apnoea in the elderly. These studies reveal marked sensitivity to propofol in the elderly with respect to both induction dose and acute toxicity.
Resolution of interferometric angular velocity measurements (2011)

An analysis of the resolution of a new method of interferometric angular velocity measurement is presented. The angular velocity of a moving object is proportional to the frequency of the interferometer response produced when the object passes through the interferometer beam pattern. The technique allows measurement of the angular velocity without complex processing or narrow beamwidth. A derivation of the resolution is presented for a general system, and it is shown that the frequency resolution is dependent on the system antenna pattern, as well as the system bandwidth. Increasing the beamwidth is shown to result in better frequency resolution. A specific example is given for a system designed to measure the velocity of a moving human. Simulated results of a moving point source are shown, as well as simulated and experimental data from a moving human.
Secreted phospholipases A2, a new class of HIV inhibitors that block virus entry into host cells (1999)

Mammalian and venom secreted phospholipases A(2) (sPLA(2)s) have been associated with a variety of biological effects. Here we show that several sPLA(2)s protect human primary blood leukocytes from the replication of various macrophage and T cell-tropic HIV-1 strains. Inhibition by sPLA(2)s results neither from a virucidal effect nor from a cytotoxic effect on host cells, but it involves a more specific mechanism. sPLA(2)s have no effect on virus binding to cells nor on syncytia formation, but they prevent the intracellular release of the viral capsid protein, suggesting that sPLA(2)s block viral entry into cells before virion uncoating and independently of the coreceptor usage. Various inhibitors and catalytic products of sPLA(2) have no effect on HIV-1 infection, suggesting that sPLA(2) catalytic activity is not involved in the antiviral effect. Instead, the antiviral activity appears to involve a specific interaction of sPLA(2)s to host cells. Indeed, of 11 sPLA(2)s from venom and mammalian tissues assayed, 4 venom sPLA(2)s were found to be very potent HIV-1 inhibitors (ID(50) < 1 nM) and also to bind specifically to host cells with high affinities (K(0.5) < 1 nM). Although mammalian pancreatic group IB and inflammatory-type group IIA sPLA(2)s were inactive against HIV-1 replication, our results could be of physiological interest, as novel sPLA(2)s are being characterized in humans.
Effect of low nucleotide concentrations on abortive elongation catalysed by wheat-germ RNA polymerase II (1987)

A kinetic study of the effect of elongating nucleotide concentration on the reactions of abortive elongation catalysed by wheat-germ RNA polymerase II on a poly[d(A-T)] template suggests that the shift from abortive to productive elongation may involve the participation of at least two nucleotides, according to a mechanism very similar to that reported for Escherichia coli RNA polymerase. Experiments performed with non-complementary nucleotides with respect to the DNA template, and with substrate derivatives, allow an analysis of the substrate specificity during these reactions. Similar experiments performed with poly[d(A-A-T)].poly[d(T-T-A)] as template provide a starting point for a better understanding of the effect of DNA sequence on the rates of abortive and productive elongation catalysed by the plant enzyme.
THE LABORATORY DETERMINATION OF DISPERSANT EFFECTIVENESS: METHOD DEVELOPMENT AND RESULTS (1981)

ABSTRACT A research project is described in which a previously devised effectiveness test for chemical oil spill dispersants was further developed and standardized. The principle of the test is that known volumes of dispersant and crude oil are contacted on the surface of seawater in a laboratory-scale vessel in which there is a circulating air current that imparts a swirling wave action to the water. This flow geometry is believed to simulate ocean surface conditions better than tests that involve shaking, stirring, or pumping as turbulence-generating mechanisms. From the results of a series of tests at various dispersant-to-oil ratios, the ratios that affect the dispersion of 50 and 75 percent of the original amount of oil added to the water surface are calculated and used as an indication of dispersant effectiveness. The corresponding percent of the oil that remains dispersed after settling is also deduced. The results of a series of tests using two crude oils, Murban (light) and La Rosa (heavy), and 17 dispersants are presented. These results show a wide range in the dispersant-to-oil ratio necessary to achieve 50- to 75-percent dispersion. Five products failed to achieve 50-percent dispersion of both crude oils at a dispersant-to-oil ratio of 0.2, which is regarded as the practical upper limit of dispersant dosage. There was a group of highly effective dispersants requiring a dispersant-to-oil ratio of only 0.005 to 0.007 to accomplish 50-percent dispersion. The test method can discriminate between two dispersant products with effectivenesses which differ by approximately 10 percent. The implications of these experimental results are discussed.
The radiative properties of electrically-small antennas (2002)

The radiative properties of electrically-small antennas are examined using the theory given by Wheeler, Chu, and Harrington. This theory predicts fundamental limitations on the bandwidth of such antennas. Some approximations are made in the theory; these approximations are examined. Several electrically-small antenna designs are evaluated in terms of how close they come to attaining the predicted fundamental limit of bandwidth. Also, the ideas upon which these designs are based are discussed. Finally, a technique for the measurement of the radiation and and the radiation efficiency of electrically-small antennas is reviewed and discussed with emphasis on the accurate separation of conduction and radiation losses.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Lactate monooxygenase. II. Site-directed mutagenesis of the postulated active site base histidine 290. (1994)

Lactate monooxygenase catalyzes the oxidation of L-lactate with molecular oxygen to acetate, CO2, and water. Histidine 290 has been proposed to be the active site base in lactate monooxygenase (Giegel, D. A., Williams, C. H., Jr., and Massey, V. (1990) J. Biol. Chem. 265, 6626-6632) and was mutated to a glutamine (H290Q). The mutant enzyme shows properties that support strongly the postulated function of the histidine. The ability of L-lactate to reduce the enzyme flavin is essentially abolished, whereas reoxidation of reduced enzyme with oxygen proceeds at 1.4 x 10(4) M-1 s-1, a rate essentially like that found in the wild type enzyme. The substrate, L-lactate, is bound with a Kd equal to 2.0 x 10(-2) M, and D-lactate, a competitive inhibitor with a Kd of 3.1 x 10(-3) M. Both values are similar to binding measured in the wild type enzyme. Unlike the situation with wild type enzyme, where the transition state analog oxalate is bound tightly in a two-step reaction involving proton uptake from solution (Ghisla, S., and Massey, V. (1977) J. Biol. Chem. 252, 6729-6735), the mutant enzyme binds oxalate weakly, in a single step reaction, with a Kd in the order of 0.1 M. No effect was observed upon varying the pH, indicating that binding does not include a protonation step. Replacing the histidine also has a significant effect on the ability of the enzyme to stabilize the flavin N(5)-sulfite adduct. Sulfite is bound at least 1000-fold weaker than it is in the wild type enzyme.
Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana (2015)

As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.
Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host (2018)

Throughout history, the yeast <i>Saccharomyces cerevisiae</i> has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, <i>S. cerevisiae</i> has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast <i>Kluyveromyces marxianus</i> to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of <i>K. marxianus</i> can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered <i>K. marxianus</i> strains, we combined three complex traits-thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross <i>K. marxianus</i> strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of <i>K. marxianus</i> isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish <i>K. marxianus</i> as a synthetic biology platform comparable to <i>S. cerevisiae</i>, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.<b>IMPORTANCE</b> The yeast <i>Kluyveromyces marxianus</i> grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast <i>Saccharomyces cerevisiae</i> in industrial applications. Here, we describe genetic tools for genome editing and breeding <i>K. marxianus</i> strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using <i>K. marxianus</i> as a versatile synthetic biology platform organism for industrial applications.