gebhart/patrepeval huggingface dataset:
The effect of calcium chelators on microsomal pyridine nucleotide-linked dehydrogenases of sugarbeet cells (1994)

Cell suspension cultures of Beta vulgaris L., treated with calcium chelators or untreated, were used to characterize pyndine nucleotide-dependent diaphorases of microsomes. The microsomal activity of NADH-dependent duroquinone reductase from cultures treated with 10 mM Na2EGTA for 24 h increased by a factor of 1.8 with respect to control microsomes, and was mainly associated with particles of d=1.17g ml−1. NADPH-duroquinone reductase and NADH-ferricyanide reductase activities showed smaller increases. Bacterial protein-lipopolysaccharide complexes (prLPS) also promoted the increase of microsomal diaphorases; CaEGTA was Ineffective. EGTA effects on enzymes of supernatant and mitochondria were negligible, although Na2EGTA treatment induced cell aggregation and strong acidification of the medium. When microsomes from control cultures were solubilized with 1% LPC and fractionated in high-efficiency gel permeation columns (FPLC) the diaphorase activities were found associated to three major proteins: (i) NADH-specific quinone reductase (NADH-QR) of 340 kDa; (ii) pyndine nucleotide-nonspecific quinone reductase (NAD(P)H-QR) of 85 kDa also having ferricyanide reductase activity; (iii) NADH-specific ferricyanide reductase (NADH-FCR) of 38 kDa. The microsomes from EGTA-treated cells also showed a highly active NADH-QR having a larger molecular mass (440 kDa) than in control cells. NAD(P)H-QR also showed increased activity. We conclude that external Ca2+ chelation induces changes in dehydrogenase components in microsomes. Furthermore, prLPS probably exert part of their effect on plants through Ca2+ chelation.
Magnetic plasmonic metamaterials in actively pumped host medium and plasmonic nanolaser (2006)

We consider plasmonic nanoantennas immersed in active host medium. Specifically shaped metal nanoantennas can exhibit strong magnetic properties in the optical spectral range due to the excitation of Magnetic Plasmon Resonance (MPR). A case when a metamaterial comprising such nanoantennas can demonstrate both "left-handiness" and negative permeability in the optical range is considered. We show that high losses predicted for optical "left- handed" materials can be compensated in the gain medium. Gains required to achieve local generation in such magnetic active metamaterials are calculated for real metals. We propose plasmonic nanolaser, where the metal nanoantenna operates like a resonator. The size of the proposed plasmonic laser is much smaller than the wavelength. Therefore, it can serve as a very compact source of EM radiation.
Cumulated gain-based evaluation of IR techniques (2002)

Modern large retrieval environments tend to overwhelm their users by their large output. Since all documents are not of equal relevance to their users, highly relevant documents should be identified and ranked first for presentation. In order to develop IR techniques in this direction, it is necessary to develop evaluation approaches and methods that credit IR methods for their ability to retrieve highly relevant documents. This can be done by extending traditional evaluation methods, that is, recall and precision based on binary relevance judgments, to graded relevance judgments. Alternatively, novel measures based on graded relevance judgments may be developed. This article proposes several novel measures that compute the cumulative gain the user obtains by examining the retrieval result up to a given ranked position. The first one accumulates the relevance scores of retrieved documents along the ranked result list. The second one is similar but applies a discount factor to the relevance scores in order to devaluate late-retrieved documents. The third one computes the relative-to-the-ideal performance of IR techniques, based on the cumulative gain they are able to yield. These novel measures are defined and discussed and their use is demonstrated in a case study using TREC data: sample system run results for 20 queries in TREC-7. As a relevance base we used novel graded relevance judgments on a four-point scale. The test results indicate that the proposed measures credit IR methods for their ability to retrieve highly relevant documents and allow testing of statistical significance of effectiveness differences. The graphs based on the measures also provide insight into the performance IR techniques and allow interpretation, for example, from the user point of view.
Selective distribution of saturated fatty acids into the monoglyceride fraction during enzymatic glycerolysis (1992)

Four triglyceride fats and oils (beef tallow, lard, rapeseed oil and soybean oil) were reacted with glycerol while using lipase as the catalyst. For all fats examined, at reaction temperatures above the critical temperature (T c ), the fatty acid compositions of the monoglyceride (MG) and diglyceride (DG) fractions and of the original fat were similar. A relatively low yield of MG was obtained (20–30 wt%). When the reaction was carried out with beef tallow or lard at a temperature below the T c (40°C), the concentration of saturated fatty acids in the MG fraction was 2 to 4 times greater than that in the DG fraction. Correspondingly, the concentration of unsaturated fatty acids in the DG fraction was more than two times greater than that in the MG fraction. At 5°C, a similar trend was observed for rapeseed oil and soybean oil. Direct analysis of partial glycerides during glycerolysis by high‐temperature gas‐liquid chromatography showed that below T c the content of C16 MG increased relatively more than C18 MG. C36 DG and C54 TG were apparently resistant to glycerolysis. Preferential distribution of saturated fatty acids into the MG fraction was accompanied by a high yield of monoglyceride (45–70 wt%) and solidification of the reaction mixture. It is concluded that during glycerolysis below T c , preferential crystallization occurs for MGs that contain a saturated fatty acid.
2-methoxyestradiol-induced growth suppression and lethality in estrogen-responsive MCF-7 cells may be mediated by down regulation of p34cdc2 and cyclin B1 expression. (1999)

MCF-7 breast cancer cells increase their rate of proliferation, as indicated by incorporation of tritiated thymidine into DNA, when exposed to estrogen. In confirmation of other studies, 10 nM 17beta-estradiol (E2) increased proliferation by 2.8-fold after 6 days of exposure. As indicated by trypan blue exclusion and TUNEL assays, cell survival was increased and apoptosis decreased by the presence of E2. The estradiol metabolite 2-methoxyestradiol (2-ME) when present in the culture medium in concentrations greater than 1 microM for three days, dose-dependently reduced the effectiveness of E2 on cell proliferation by increasing the rate of apoptosis. To examine a mechanism for the increase in apoptosis, expression of p34cdc2 and cyclin B1 protein levels were monitored by examination of immunoblots of their proteins. E2 increased p34cdc2 and cyclin B1 protein levels significantly after 6 days of exposure. This effect was inhibited significantly by the presence of 2-ME. The results indicate that up-regulation of p34cdc2 and cyclin B1 is closely associated with increased survivability and lack of apoptosis in estrogen-induced proliferation of MCF-7 cells. Further, anti-estrogenic effects of 2-ME in these cells can be accounted for by its activation of apoptotic functions, which are correlated with reductions in expression of p34cdc2 and cyclin B1 genes.
Nanorice:  A Hybrid Plasmonic Nanostructure (2006)

We have designed and fabricated a new hybrid nanoparticle that combines the intense local fields of nanorods with the highly tunable plasmon resonances of nanoshells. This dielectric core-metallic shell prolate spheroid nanoparticle bears a remarkable resemblance to a grain of rice, inspiring the name "nanorice". This geometry possesses far greater structural tunability than either a nanorod or a nanoshell, along with much larger local field intensity enhancements and far greater sensitivity as a surface plasmon resonance (SPR) nanosensor than any dielectric-metal nanostructures reported previously. Invoking the plasmon hybridization picture allows us to understand the plasmon resonances of this geometry, as arising from a hybridization of the primitive plasmons of a solid spheroid and an ellipsoidal cavity inside a continuous metal.
Large Deformation Diffeomorphic Metric Mapping And Fast-Multipole Boundary Element Method Provide New Insights For Binaural Acoustics (2014)

This paper describes how Large Deformation Diffeomorphic Metric Mapping (LDDMM) can be coupled with a Fast Multipole (FM) Boundary Element Method (BEM) to investigate the relationship between morphological changes in the head, torso, and outer ears and their acoustic filtering (described by Head Related Transfer Functions, HRTFs). The LDDMM technique provides the ability to study and implement morphological changes in ear, head and torso shapes. The FM-BEM technique provides numerical simulations of the acoustic properties of an individual's head, torso, and outer ears. This paper describes the first application of LDDMM to the study of the relationship between a listener's morphology and a listener's HRTFs. To demonstrate some of the new capabilities provided by the coupling of these powerful tools, we examine the classical question of what it means to ``listen through another individual's outer ears.'' This work utilizes the data provided by the Sydney York Morphological and Acoustic Recordings of Ears (SYMARE) database.
Simulation of wrinkled surfaces (1978)

Computer generated shaded images have reached an impressive degree of realism with the current state of the art. They are not so realistic, however, that they would fool many people into believing they are real. One problem is that the surfaces tend to look artificial due to their extreme smoothness. What is needed is a means of simulating the surface irregularities that are on real surfaces. In 1973 Ed Catmull introduced the idea of using the parameter values of parametrically defined surfaces to index into a texture definition function which scales the intensity of the reflected light. By tying the texture pattern to the parameter values, the texture is guaranteed to rotate and move with the object. This is good for showing patterns painted on the surface, but attempts to simulate rough surfaces in this way are unconvincing. This paper presents a method of using a texturing function to perform a small perturbation on the direction of the surface normal before using it in the intensity calculations. This process yields images with realistic looking surface wrinkles without the need to model each wrinkle as a separate surface element. Several samples of images made with this technique are included.
Developmental Abnormalities in Mice Transgenic for Bovine Oncostatin M (1995)

Oncostatin M belongs to the subfamily of hematopoietin cytokines that binds a receptor complex containing gp130. To date, only the human form of oncostatin M has been identified, and its evolutionary conservation is unresolved. We have isolated a bovine gene whose open reading frame encodes a precursor protein that is 58% identical to human oncostatin M. A comparison of the bovine and human amino acid sequences predicts significant similarity, including the four-alpha-helical-bundle structure and the placement of disulfide bridges. As with the human protein, bovine oncostatin M binds specific receptors on human H2981 cells and inhibits the proliferation of human A375 tumor cells and mouse M1 leukemia cells. To identify activities regulated in vivo, we injected bovine oncostatin M fusion genes containing various tissue-specific promoters into mouse embryos. The frequencies of transgenic mice were reduced significantly, suggesting that overexpression of the bovine cytokine is detrimental to normal mouse development. In addition to deaths associated with expression in neurons and keratinized epithelia, bovine oncostatin M caused abnormalities in bone growth and spermatogenesis, stimulated fibrosis surrounding islets in the pancreas, and disrupted normal lymphoid tissue development. This work establishes the existence of a nonprimate oncostatin M gene and provides the first demonstration that this cytokine can function in a pleiotropic manner in vivo. Information regarding bovine oncostatin M may help characterize the structure and function of this cytokine in other vertebrate species.
Prevention of homocysteine thiolactone induced atherogenesis in rats. (2002)

Thioretinamide was conjugated to coenzyme B12 to produce thioretinaco. Thioretinamide, thioretinaco, and coenzyme B12 were injected weekly into Rattus rattus that were also given atherogenic doses of homocysteine thiolactone. The presence or absence of lesions in aorta-intercostal artery junctions was examined. Control rats injected with homocysteine thiolactone (CON-Hcy) had 56.6 +/- 5.8% lesions when compared to 34.8 +/- 3.4% in control rats injected with saline (CON-Sal). Rats that received homocysteine thiolactone injection with thioretinamide (NHTR-Hcy), thioretinaco ((NHTR)2B12-Hcy), and coenzyme B12 (B12-Hcy) had 30.1 +/- 4.2%, 27.5 +/- 3.5%, and 22.8 +/- 3.0% lesions, respectively. These lesion rates were not different from those of rats receiving thioretinamide (NHTR-Sal), thioretinaco ((NHTR)2B12-Sal), and coenzyme B12 (B12-Sal) which were 31.3 +/- 1.8%, 29.8 +/- 3.9%, and 32.0 +/- 4.6%, respectively. In this study the percentage of intercostal artery lesions in rats receiving thioretinamide and homocysteine (NHTR-Hcy), coenzyme B12 and homocysteine (B12-Hcy), and thioretinaco and homocysteine ((NHTR)2/B12-Hcy) were significantly lower, 53.2%, 48.6%, and 40.3% respectively, compared to than that of the control group receiving homocysteine (CON-Hcy). Thioretinaco, thioretinamide, and coenzyme B12 provided protective effects against the atherogen homocysteine thiolactone. A new method for the synthesis of the N-substituted derivative of homocysteine thiolactone, thioretinamide, was also reported.
Decision-Theoretic Planning: Structural Assumptions and Computational Leverage (1999)

Planning under uncertainty is a central problem in the study of automated sequential decision making, and has been addressed by researchers in many different fields, including AI planning, decision analysis, operations research, control theory and economics. While the assumptions and perspectives adopted in these areas often differ in substantial ways, many planning problems of interest to researchers in these fields can be modeled as Markov decision processes (MDPs) and analyzed using the techniques of decision theory. This paper presents an overview and synthesis of MDP-related methods, showing how they provide a unifying framework for modeling many classes of planning problems studied in AI. It also describes structural properties of MDPs that, when exhibited by particular classes of problems, can be exploited in the construction of optimal or approximately optimal policies or plans. Planning problems commonly possess structure in the reward and value functions used to describe performance criteria, in the functions used to describe state transitions and observations, and in the relationships among features used to describe states, actions, rewards, and observations. Specialized representations, and algorithms employing these representations, can achieve computational leverage by exploiting these various forms of structure. Certain AI techniques -- in particular those based on the use of structured, intensional representations -- can be viewed in this way. This paper surveys several types of representations for both classical and decision-theoretic planning problems, and planning algorithms that exploit these representations in a number of different ways to ease the computational burden of constructing policies or plans. It focuses primarily on abstraction, aggregation and decomposition techniques based on AI-style representations.
DOCK2 associates with CrkL and regulates Rac1 in human leukemia cell lines (2002)

The CDM (ced-5 of Caenorhabditis elegans, DOCK180 [downstream of Crk with molecular weight of 180 kDa] of humans, and myoblast city of Drosophila melanogaster) family of proteins has been shown to play a pivotal role in the integrin-mediated signaling pathway under the regulation of an adaptor molecule c-CT10-related kinase II (c-Crk-II) in adherent cells. Recently, hematopoietic cell-specific CDM protein DOCK2 has been shown to be indispensable for lymphocyte migration. However, the regulatory mechanism for DOCK2 is still unknown because DOCK2 lacks a c-Crk-II binding consensus motif. In this study, we demonstrated that DOCK2 bound to CrkL, which is present exclusively in hematopoietic cells both in vivo and in vitro, and we also found that 2 separate regions of DOCK2 contributed to its binding to Src homology 3 (SH3) domain of CrkL. Colocalization of DOCK2 with Crk-like (CrkL) and F-actin was shown by immunocytochemical analysis with the use of Jurkat cells. We also found that CrkL-induced activation of small guanine triphosphatase (GTPase) Rac1 was significantly inhibited by the DOCK2-dCS mutant in 293T cells. Furthermore, the association of DOCK2 and Vav, the guanine-nucleotide exchanging factor (GEF) for Rac1, was demonstrated in Jurkat cells. Finally, the stable expression of DOCK2-dCS mutant in Jurkat cells was shown to reduce cell attachment. These data suggest the presence of a novel protein complex of CrkL, DOCK2, and Vav to regulate Rac1 in leukemia cell lines.
GALα(1,3)GAL IS THE MAJOR XENOEPITOPE EXPRESSED ON PIG ENDOTHELIAL CELLS RECOGNIZED BY NATURALLY OCCURRING CYTOTOXIC HUMAN ANTIBODIES (1994)

Hyperacute rejection, mediated by natural antibody, is the major barrier to xenotransplantation. The studies reported herein were aimed at evaluating antibody-mediated cytotoxicity and the role of the Gal alpha(1,3)Gal epitope, which we had previously demonstrated was the major epitope of pig cells detected by naturally occurring human antibodies. Also, we had shown that this epitope could be induced in non-expressing cells by the transfection of a cDNA clone encoding alpha(1,3)galactosyl transferase, the enzyme that produces this epitope. The importance of the Gal alpha(1,3)Gal epitope was supported by (1) sugar inhibition studies; (2) complete absorption of cytotoxic antibodies by melibiose-sepharose columns; and (3) the ability of normal human serum to lyse COS cells after transfection with a cDNA clone encoding alpha(1,3)galactosyl transferase. These findings strongly suggest that the majority of cytotoxic human antibodies that would recognize a xenogeneic graft are directed to the Gal alpha(1,3)Gal epitope.
Joule heating in electrokinetic flow (2007)

Electrokinetic flow is an efficient means to manipulate liquids and samples in lab-on-a-chip devices. It has a number of significant advantages over conventional pressure-driven flow. However, there exists inevitable Joule heating in electrokinetic flow, which is known to cause temperature variations in liquids and draw disturbances to electric, flow and concentration fields via temperature-dependent material properties. Therefore, both the throughput and the resolution of analytic studies performed in microfluidic devices are affected. This article reviews the recent progress on the topic of Joule heating and its effect in electrokinetic flow, particularly the theoretical and experimental accomplishments from the aspects of fluid mechanics and heat/mass transfer. The primary focus is placed on the temperature-induced flow variations and the accompanying phenomena at the whole channel or chip level.
Bioremediation of soils contaminated with the herbicide 2-sec-butyl-4,6-dinitrophenol (dinoseb) (1992)

A novel soil treatment method for achieving the removal of dinoseb (2-sec-butyl-4,6-dinitrophenol) from contaminated soils was investigated. One soil contained dinoseb as the major contaminant, although several other hazardous compounds were also present. A second soil was highly contaminated with dinoseb. Dinoseb was not degraded in these soils under the aerobic conditions at each site. Pretreatment of the soils by the addition of a starchy potato-processing by-product and flooding with phosphate buffer stimulated the consumption of oxygen and nitrate from the soils, thereby lowering the redox potential and creating anaerobic conditions. Anaerobiosis (Eh less than -200 mV) promoted the establishment of an anaerobic microbial consortium that degraded dinoseb completely, without the formation of the polymerization products seen under aerobic or microaerophilic conditions. When dinoseb was present at low concentrations in a chronically contaminated soil, the natural microflora was capable of establishing anaerobic conditions and degrading dinoseb as a result of starch degradation. Inoculation of this soil with an aerobic starch-degrading microorganism and then an acclimated, anaerobic, dinoseb-degrading consortium did not improve dinoseb degradation. In a second acutely contaminated soil, these inoculations improved dinoseb degradation rates over those of uninoculated controls.
Scheduling Algorithms for Grid Computing: State of the Art and Open Problems (2006)

Thanks to advances in wide-area network technologies and the low cost of computing resources, Grid computing came into being and is currently an active research area. One motivation of Grid computing is to aggregate the power of widely distributed resources, and provide non-trivial services to users. To achieve this goal, an efficient Grid scheduling system is an essential part of the Grid. Rather than covering the whole Grid scheduling area, this survey provides a review of the subject mainly from the perspective of scheduling algorithms. In this review, the challenges for Grid scheduling are identified. First, the architecture of components involved in scheduling is briefly introduced to provide an intuitive image of the Grid scheduling process. Then various Grid scheduling algorithms are discussed from different points of view, such as static vs. dynamic policies, objective functions, applications models, adaptation, QoS constraints, strategies dealing with dynamic behavior of resources, and so on. Based on a comprehensive understanding of the challenges and the state of the art of current research, some general issues worthy of further exploration are proposed.
Quantum Coherence with a Single Cooper Pair (1998)

A metallic electrode connected to electron reservoirs by tunnel junctions has a series of charge states corresponding to the number of excess electrons in the electrode. In contrast with the charge state of an atomic or molecular ion, the charge states of such an "island" involve a macroscopic number of conduction electrons of the island. Island charge states bear some resemblance with the photon number states of the cavity in cavity QED, the phase conjugate to the number of electrons being analogous to the phase of the field in the cavity. For a normal island, charge states decay irreversibly into charge states of lower energies. However, the ground state of a superconducting island connected to superconducting reservoirs can be a coherent superposition of charge states differing by two electrons (i.e. a Cooper pair). We describe an experiment in which this Josephson effect involving only one Cooper pair is measured.
Spectral-Domain Optical Coherence Tomography as an Indicator of Fluorescein Angiography Leakage from Choroidal Neovascularization (2011)

The evidence of fluid on SD-OCT is sensitive but nonspecific in identifying FA leaky CNV. The assessment of neurosensory detachment as well as other ultrastructural elements may increase the specificity of analysis.