gebhart/patrepeval huggingface dataset:
When Does the IC<sub>50</sub> Accurately Assess the Blocking Potency of a Drug? (2020)

Preclinical assessment of drug-induced proarrhythmicity is typically evaluated by the potency of the drug to block the potassium human ether-à-go-go-related gene (hERG) channels, which is currently quantified by the IC<sub>50</sub>. However, channel block depends on the experimental conditions. Our aim is to improve the evaluation of the blocking potency of drugs by designing experimental stimulation protocols to measure the IC<sub>50</sub> that will help to decide whether the IC<sub>50</sub> is representative enough. We used the state-of-the-art mathematical models of the cardiac electrophysiological activity to design three stimulation protocols that enhance the differences in the probabilities to occupy a certain conformational state of the channel and, therefore, the potential differences in the blocking effects of a compound. We simulated an extensive set of 144 in silico <i>I</i><sub>Kr</sub> blockers with different kinetics and affinities to conformational states of the channel and we also experimentally validated our key predictions. Our results show that the IC<sub>50</sub> protocol dependency relied on the tested compounds. Some of them showed no differences or small differences on the IC<sub>50</sub> value, which suggests that the IC<sub>50</sub> could be a good indicator of the blocking potency in these cases. However, others provided highly protocol dependent IC<sub>50</sub> values, which could differ by even 2 orders of magnitude. Moreover, the protocols yielding the maximum IC<sub>50</sub> and minimum IC<sub>50</sub> depended on the drug, which complicates the definition of a "standard" protocol to minimize the influence of the stimulation protocol on the IC<sub>50</sub> measurement in safety pharmacology. As a conclusion, we propose the adoption of our three-protocol IC<sub>50</sub> assay to estimate the potency to block hERG in vitro. If the IC<sub>50</sub> values obtained for a compound are similar, then the IC<sub>50</sub> could be used as an indicator of its blocking potency, otherwise kinetics and state-dependent binding properties should be accounted.
Spectral dynamics in the B800 band of LH2 from Rhodospirillum molischianum: a single-molecule study (2004)

The BChl a absorptions in the B800 spectrum of individual LH2 complexes from Rhodospirillum molischianum show sudden, reversible spectral jumps between a finite number of spectral positions. From our data, we conclude that these fluctuations result from conformational changes of the protein backbone in close vicinity of the chromophores which provides a sensitive tool to monitor local modulations of the pigment–protein interaction.
Macrophage Accumulation Associated With Rat Cardiac Allograft Rejection Detected by Magnetic Resonance Imaging With Ultrasmall Superparamagnetic Iron Oxide Particles (2001)

This MRI method offers promise as a noninvasive method for detecting transplant allograft rejection.
Antigen-Decorated Shell Cross-Linked Nanoparticles:  Synthesis, Characterization, and Antibody Interactions (2005)

Antigen-decorated shell cross-linked knedel-like nanoparticles (SCKs) were synthesized and studied as multivalent nanoscale surfaces from which antibody-binding units were presented in a manner that was designed to approach virus particle surfaces. The SCK nanostructures were fabricated with control over the number of antigenic groups, from mixed micellization of amphiphilic diblock copolymer building blocks that contained either an antigen (2,4-dinitrophenyl) or an ethylpropionate group at the hydrophilic alpha-chain terminus. Amphiphilic diblock copolymers were synthesized by atom transfer radical polymerization of tert-butyl acrylate and methyl acrylate sequentially from either a 2,4-dinitrophenyl-functionalized initiator or ethyl 2-bromopropionate, followed by selective removal of the tert-butyl groups to afford 2,4-dinitrophenyl-poly(acrylic acid)60-b-poly(methyl acrylate)60 (DNP-PAA(60)-b-PMA60) and poly(acrylic acid)70-b-poly(methyl acrylate) (PAA70-b-PMA70). Micelles were assembled via addition of water to THF solutions of the polymers in 0:1, 1:1, and 1:0 molar ratios of DNP-PAA60-b-PMA60 to PAA70-b-PMA70, followed by dialysis against water. The acrylic acid groups of the micelle coronas were partially cross-linked (nominally 50%) with 2,2'-(ethylenedioxy)bis(ethylamine), in the presence of 1-(3'-dimethylaminopropyl)-3-ethylcarbodiimide methiodide. Following extensive dialysis against water, the 0%, 50%, and 100% dinitrophenylated shell cross-linked nanoparticles (DNP-SCKs) were characterized with dynamic light scattering (DLS), transmission electron microscopy (TEM), atomic force microscopy (AFM), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), infrared and UV-vis spectroscopies, and analytical ultracentrifugation (AU). The surface accessibility and bioavailability of the DNP units upon the DNP-SCKs were investigated by performing quenching titrations of fluorescein-labeled IgE antibody in solution and degranulation of IgE sensitized RBL-2H3 cells. The DNP antigens proved to be surface-available and able to form multivalent bonds with IgE antibodies, causing degranulation.
Production of ligninolytic enzymes by Pleurotus sp. and Dichomitus squalens in soil and lignocellulose substrate as influenced by soil microorganisms (1998)

The activities of the extracellular enzymes laccase and manganese peroxidase (MnP) of the white rot fungi Pleurotus sp. and Dichomitus squalens were measured in the straw substrate and soil layers of solid state cultures. Cultures with sterile soil were compared to cultures with nonsterile soil. For both organisms, enzyme activities in sterile soil were approximately the same as in straw when calculated to the base of the liquid phases (water content) in the straw or soil material. The growth rate and enzyme activities of Pleurotus sp. were not significantly influenced by the presence of soil microorganisms. In contrast, D. squalens did not penetrate the nonsterile soil, and no enzyme activities could be detected in nonsterile soil. Laccase and MnP activities in the straw declined to zero. From this point of view, highly competitive strains like Pleurotus sp. seem to be more suitable for the application in soil remediation than weak competitors (D. squalens) which are not able to maintain appropriate levels of enzyme activities in nonsterile soil.
Enhanced pseudorandom number generator based on Blum-Blum-Shub and elliptic curves (2018)

Blum-Blum-Shub (BBS) is a less complex pseudorandom number generator (PRNG) that requires very large modulus and a squaring operation for the generation of each bit, which makes it computationally heavy and slow. On the other hand, the concept of elliptic curve (EC) point operations has been extended to PRNGs that prove to have good randomness properties and reduced latency, but exhibit dependence on the secrecy of point P. Given these pros and cons, this paper proposes a new BBS-ECPRNG approach such that the modulus is the product of two elliptic curve points, both primes of length, and the number of bits extracted per iteration is by binary fraction. We evaluate the algorithm performance by generating 1000 distinct sequences of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> bits each. The results were analyzed based on the overall performance of the sequences using the NIST standard statistical test suite. The average performance of the sequences was observed to be above the minimum confidence level of 99.7 percent and successfully passed all the statistical properties of randomness tests.
The Economic Feasibility of Tree Fruit Integrated Pest Management in the Northeast (1982)

A pilot tree fruit pest management program in Wayne County, New York was evaluated. Thirty-three blocks of fruit were matched for 26 participants in the pilot program and for 23 nonparticipants. Participants reduced pesticide costs and total pest management costs in comparison to nonparticipants. Factors which will affect the adoption of Integrated Pest Management in other locations include the attitudes of growers, farm size, and the density of fruit production. Integrated Pest Management programs are economically feasible for several other areas of high tree fruit density in the Northeast.
Capillary Isoelectric Focusing without Carrier Ampholytes (2000)

A novel capillary isoelectric focusing (CIEF) separation of proteins in pure water was investigated using the whole-column imaging detection technique. Protons and hydroxyl ions are produced by the electrolysis of water, and the pH gradient is created by the electromigration of protons and hydroxyl ions into the separation capillary. The addition of acids to the anodic solution and bases to the cathodic solution enhances the formation of the gradients. Fast CIEF separation of proteins by electrolysis of water is demonstrated.
Studies in Vertical and Horizontal Well-Flow Behavior in Cases of Permeability Anisotropy (2001)

Abstract Modified 2-phase analytical equation solutions to vertical well behavior match simulated results quite well for fluid flow in both isotropic and highly anisotropic permeability cases above and below the bubble point. Also no matter what the contrast in kx and ky, if the geometric mean permeability was held constant, the simulated rate vs. pressure results were essentially identical to each other. This confirmed the often-used geometric mean permeability approximation. In contrast, analytical solutions to horizontal well flow generally follow simulated solutions in isotropic media but do not match simulated horizontal results very well in horizontally anisotropic permeability conditions. Also horizontal simulations diverge markedly from one another as the permeability contrast increases despite keeping the geometric mean identical. The mismatch is especially pronounced as the x and y directional permeability contrast increases, in cases of pressure above the bubble point and in cases where the well length is large compared to the reservoir dimensions. This behavior is not predicted from standard analytical equations utilizing geometric mean permeabilities. Extensive simulation experiments allowed construction of graphical relationships that present the effect of increasing degrees of reservoir permeability anisotropy on horizontal well fluid flow as a function of dimensionless well length, reservoir dimension ratios, grid block size and density, reservoir pressure and severities of anisotropy. Despite a constant geometric mean permeability, the flow rate deviation from the isotropic case increases as the degree permeability contrast becomes more severe in the principal x and y directions. The deviation from the isotropic case also increases as the well length increases for any given reservoir dimension. The deviation is also more apparent as reservoir pressure increases above the bubble point. The number of grid blocks used did not seem to have any appreciable effect on the results.
Implementation of coarse-grain coherence tracking support in ring-based multiprocessors (2007)

As the number of processors in multiprocessor system-on-chip devices continues to in-crease, the complexity required for full cache coherence support is often unwarranted for application-specific designs. Bus-based interconnects are no longer suitable for larger-scale systems, and the logic and storage overhead associated with the use of a complex packet-switched network and directory-based cache coherence may be undesirable in single-chip systems. Unidirectional rings are a suitable alternative because they offer many properties favorable to both on-chip implementation and to supporting cache coherence. Reducing the overhead of cache coherence traffic is, however, a concern for these systems. This thesis adapts two filter structures that are based on principles of coarse-grained coherence tracking, and applies them to a ring-based multiprocessor. The first structure tracks the total number of blocks of remote data cached by all processors in a node for a set of regions, where a region is a large area of memory referenced by the upper bits of an address. The second structure records regions of local data whose contents are not cached by any remote node. When used together to filter incoming or outgoing requests,
Some New Derivatives of Harmaline Series of Bases (1986)

Abstract In the course of pharmaco-chemical studies in the structure and activity relationship in harmaline series of β-carboline bases, a number of new derivatives of harmaline have been obtained and characterized through chemical and spectral studies. Pharmacological screening carried out on one of these (9) shows that it has mild physiological activity without any toxicity.
Specialized transduction of the ilvD-thyB-ilvA region mediated by Bacillus subtilis bacteriophage SP beta (1982)

Specialized transducing SP beta particles were found that carried the Bacillus subtilis genes lying to the left of the prophage attachment site. Three classes of transducing particles were differentiated, depending upon whether they carried ilvA only, thyB and ilvA, or ilvD, thyB, and ilvA. Lysates prepared by the induction of strains that carried both a transducing phage and a plaque-forming phage contained the two particles in a ratio of about 1:3,000. When the transducing particles were used to transduce a phage-sensitive auxotrophic strain to prototrophy, some of the transductants carried only the transducing phage genomes which, by themselves, were defective. One putative nondefective transducing phage (for ilvA only) is also described. SP beta can mediate specialized transduction even in the absence of the major (recE) bacterial recombination system.
Word identification for Mandarin Chinese sentences (1992)

Chinese sentences are composed with string of characters without blanks to mark words. However the basic unit for sentence parsing and understanding is word. Therefore the first step of processing Chinese sentences is to identify the words. The difficulties of identifying words include (1) the identification of complex words, such as Determinative-Measure, reduplications, derived words etc., (2) the identification of proper names, (3) resolving the ambiguous segmentations. In this paper, we propose the possible solutions for the above difficulties. We adopt a matching algorithm with 6 different heuristic rules to resolve the ambiguities and achieve an 99.77% of the success rate. The statistical data supports that the maximal matching algorithm is the most effective heuristics.
A Revised Implementation of the Reverse Search Vertex Enumeration Algorithm (2000)

This paper describes an improved implementation of the reverse search vertex enumeration/convex hull algorithm for d-dimensional convex polyhedra. The implementation uses a lexicographic ratio test to resolve degeneracy, works on bounded or unbounded polyhedra and uses exact arithmetic with all integer pivoting. It can also be used to compute the volume of the convex hull of a set of points. For a polyhedron with m inequalities indvariables and known extreme point, it finds all bases in time O(md) 2 per basis. This implementation can handle problems of quite large size, especially for simple polyhedra (where each basis corresponds to a vertex and the complexity reduces to O (md) per vertex). Computational experience is included in the paper, including a comparison with an earlier implementation.
Localized Mobility Management for SDN-Integrated LTE Backhaul Networks (2015)

Small cell (SCell) and Software Define Network (SDN) are two key enablers to meet the evolutional requirements of future telecommunication networks, but still on the initial study stage with lots of challenges faced. In this paper, the problem of mobility management in SDN-integrated LTE (Long Term Evolution) mobile backhaul network is investigated. An 802.1ad double tagging scheme is designed for traffic forwarding between Serving Gateway (S-GW) and SCell with QoS (Quality of Service) differentiation support. In addition, a dynamic localized forwarding scheme is proposed for packet delivery of the ongoing traffic session to facilitate the mobility of UE within a dense SCell network. With this proposal, the data packets of an ongoing session can be forwarded from the source SCell to the target SCell instead of switching the whole forwarding path, which can drastically save the path-switch signalling cost in this SDN network. Numerical results show that compared with traditional path switch policy, more than 50% signalling cost can be reduced, even considering the impact on the forwarding path deletion when session ceases. The performance of data delivery is also analysed, which demonstrates the introduced extra delivery cost is acceptable and even negligible in case of short forwarding chain or large backhaul latency.
Incompressible Paired Hall State, Stripe Order, and the Composite Fermion Liquid Phase in Half-Filled Landau Levels (2000)

We consider the two lowest Landau levels at half filling. In the higher Landau level (nu = 5/2), we find a first-order phase transition separating a compressible striped phase from a paired quantum Hall state, which is identified as the Moore-Read state. The critical point is very near the Coulomb potential and the transition can be driven by increasing the width of the electron layer. We find a much weaker transition (either second-order or a crossover) from pairing to the composite fermion Fermi-liquid behavior. A very similar picture is obtained for the lowest Landau level, but the transition point is not near the Coulomb potential.
Improvements in snap-shot nuclear magnetic resonance imaging (1988)

New variants of the ultra-high-speed echo-planar imaging technique have been used to obtain snap-shot images of adult patients and volunteers at 0.1 T. Modified pulsed-gradient sequences together with non-linear signal sampling and activity screened gradients have greatly improved the image quality obtainable by single-shot methods. A particular variant, modulus blipped echo-planar single-pulse technique (MBEST), although slightly slower than the blipped echo-planar single-pulse technique (BEST), is experimentally more robust and incorporates intrinsic T2 weighting. An account of these improvements together with some experimental results is presented.
The Equity Accounting Saga in Australia: Cyclical Standard Setting (1996)

Equity accounting in Australia has had a long, chequered history. This article examines that history by reference to a succession of six Exposure Drafts, one Statement of Accounting Practice and two Standards issued between 1968 and 1995. We adapt Nobes' (1991, 1992a. 1992b) cycle model of regulation to explain variation in ‘standardization’ across these documents. Nobes defined ‘standardization’ to mean the restriction of choice in accounting methods but we modify the concept to allow for measurement rule ‘improvements’ and changes in required disclosure levels. Nobes' cycle model has four stages: a starting point of varied practice: energy inputs, often crises, drawing attention to the issue at hand: forces opposing and forces in favour of standardization. A cycle‐ like pattern of variation in standardization emerges in the present context. Potential shortcomings of the cycle model are addressed, including Skerratt and Whittington's (1992) criticisms of Nobes' cycle model. The article extends the literature with respect to a cyclical explanation of the standard setting process. The cycle pattern evident here reflects a slow and incomplete resolution of various conceptual and legal difficulties in regulating equity accounting in Australia.
Characteristics of the Gene That Encodes Acetyl‐CoA Carboxylase in the Diatom <i>Cyclotella cryptica<sup>a</sup></i> (1994)

Efforts are currently under way in several laboratories to develop renewable fuels from biological sources. Our group conducts research involving the production of lipid-derived "biodiesel" fuel from microscopic algae. Lipid accumulation in algae typically occurs during periods of environmental stress, including growth under nutrient-deficient conditions. Biochemical studies have suggested that acetyl-CoA carboxylase (ACCase), a biotin-containing enzyme that catalyzes an early step in fatty acid biosynthesis, may be involved in the control of this lipid accumulation process. Therefore, it may be possible to enhance lipid production rates by increasing the activity of this enzyme via genetic engineering. As a first step toward this objective, we have cloned the gene that encodes ACCase from the eukaryotic alga Cyclotella cryptica. This is the first time that this gene has been isolated from a photosynthetic organism. The amino acid sequence of ACCase deduced from this gene exhibits a high degree of similarity to the sequences of animal and yeast ACCases in the biotin carboxylase and carboxyltransferase domains, but less similarity exists in the biotin carboxyl carrier protein domain. Comparison of the genomic nucleotide sequence to the sequences of cDNA clones has revealed the presence of two introns in the gene. We are currently constructing expression vectors containing this gene and developing algal transformation protocols to enable overexpression of ACCase in C. cryptica and other algal species.
Sphingolipid base metabolism. Partial purification and properties of sphinganine kinase of brain. (1976)

The presence of sphinganine kinase in bovine brain has been demonstrated. The product of the action of the brain enzyme on sphinganine has been characterized as sphingamine 1-phosphate by a combination of chemical, enzymatic, and chromatographic techniques. The bovine brain enzyme has been partially purified and appears to exist in multiple forms. The molecular weight of the most highly purified preparation of the enzyme was estimated to be 190,000 by gel filtration. The purified form of the enzyme showed highest activity with ATP but was also active with other purine nucleoside triphosphates. UTP and CTP did not serve as substrates for the enzyme.
The Nature of the Interaction Between Polyaniline and 2,5-Dimercapto-1,3,4-thiadiazole in Electrochemical Redox Processes (2002)

The interaction between polyaniline (PAn) and 2,5-dimercapto-1,3,4-thiadiazole (DMcT) was investigated by means of cyclic voltammetry and UV-visible spectroscopy. The results show that the polymerization-depolymerization reaction of DMcT or its dilithium salt is a kinetically quasi-reversible process. PAn exhibits very weak electrochemical activity in neutral propylene carbonate. After doping with protonic acid, such as hydrochloric acid or maleic acid etc., however, it shows an extensively enhanced electroactivity. For the complex system, PAn-DMcT or polyaniline has no catalytic activity for the electrochemical polymerization-depolymerization reaction of DMcT or Instead, the enhancement of the electrochemical redox activity of PAn-DMcT system compared with that of PAn, DMcT, and comes from the protonic doping of PAn by DMcT. © 2002 The Electrochemical Society. All rights reserved.
Dynamic Exchange Coupling in Magnetic Bilayers (2003)

A long-range dynamic interaction between ferromagnetic films separated by normal-metal spacers is reported, which is communicated by nonequilibrium spin currents. It is measured by ferromagnetic resonance and explained by an adiabatic spin-pump theory. In such a resonance the spin-pump mechanism of spatially separated magnetic moments leads to an appreciable increase in the resonant linewidth when the resonance fields are well apart, and results in a dramatic linewidth narrowing when the resonant fields approach each other.