gebhart/patrepeval huggingface dataset:
A plant cell factor induces <i>Agrobacterium tumefaciens vir</i> gene expression (1986)

The virulence genes of Agrobacterium are required for this organism to genetically transform plant cells. We show that vir gene expression is specifically induced by a small (<1000 Da) diffusible plant cell metabolite present in limiting quantities in the exudates of a variety of plant cell cultures. Active plant cell metabolism is required for the synthesis of the vir-inducing factor, and the presence of bacteria does not stimulate this production. vir-inducing factor is (i) heat and cold stable; (ii) pH stable, although vir induction with the factor is sensitive above pH 6.0; and (iii) partially hydrophobic. Induction of vir gene expression was assayed by monitoring beta-galactosidase activity in Agrobacterium strains that carry gene fusions between each of the vir loci and the lacZ gene of Escherichia coli. vir-inducing factor (partially purified on a C-18 column) induces both the expression in Agrobacterium of six distinct loci and the production of T-DNA circular molecules, which are thought to be involved in the transformation process. vir-inducing factor potentially represents the signal that Agrobacterium recognizes in nature as a plant cell susceptible to transformation.
[In vitro study of radiation sensitizing effect of hydroxycamptothecin]. (2000)

HCPT has been shown a radiosensitizing effect in vitro on gastric and nasopharyngeal cancer cells.
Superconducting bearings (2000)

The physics and technology of superconducting bearings is reviewed. Particular attention is given to the use of high-temperature superconductors (HTSs) in rotating bearings. The basic phenomenology of levitational forces is presented, followed by a brief discussion of the theoretical models that can be used for conceptual understanding and calculations. The merits of various HTS bearing designs are presented, and the behaviour of HTS bearings in typical situations is discussed. The article concludes with a brief survey of various proposed applications for HTS bearings.
Confinement losses in microstructured optical fibers (2001)

We describe a multipole formulation that can be used for high-accuracy calculations of the full complex propagation constant of a microstructured optical fiber with a finite number of holes. We show how the imaginary part of the microstructure, which describes confinement losses not associated with absorption, varies with hole size, the number of rings of holes, and wavelength, and give the minimum number of rings of holes required for a specific loss for given parameters.
Derivation and efficient implementation of the fast multipole method (1994)

The fast multipole method (FMM) of Greengard evaluates Coulomb interactions of point charges with computational requirements that increase linearly with the number of particles. In this work, the central transformations of the FMM are obtained in a very compact manner from simple algebraic manipulations of two addition theorems. The intermediate multipole and Taylor expansions are defined differently from previous work to yield simplified and more efficient transformations. Error estimates are obtained due to the effect of multipole truncation and the use of the multipole to Taylor transformation operator. Efficient implementation of the FMM for potential and forces is discussed, and calculations are presented that probe the accuracy and performance of the method.
Algorithms for Spectral Analysis of Irregularly Sampled Time Series (2004)

In this paper, we present a spectral analysis method based upon least square approximation. Our method deals with nonuniform sampling. It provides meaningful phase information that varies in a predictable way as the samples are shifted in time. We compare least square approximations of real and complex series, analyze their properties for sample count towards infinity as well as estimator behaviour, and show the equivalence to the discrete Fourier transform applied onto uniformly sampled data as a special case. We propose a way to deal with the undesirable side effects of nonuniform sampling in the presence of constant offsets. By using weighted least square approximation, we introduce an analogue to the Morlet wavelet transform for nonuniformly sampled data. Asymptotically fast divide-and-conquer schemes for the computation of the variants of the proposed method are presented. The usefulness is demonstrated in some relevant applications.
Ecological consequences of artificial night lighting (2006)

One of the less obvious effects of population growth is that a vastly increased proportion of the Earth is now illuminated at night, with increasingly powerful lights. This book will provide the first reference on the profound effects that these lights have on plants, animals, and whole ecosystems. The best-known research on this topic has focused on birds and sea turtles. But artificial lighting also affects other species in ways that are less well-known: foraging behavior of amphibians is altered, lights affect the dispersal patterns young cougars, and fireflies may be inhibited from finding mates. Because of the tremendous prevalence of night lights, and because of the intricate (and often poorly understood) interactions of different life forms, these impacts are far-reaching, affecting not only survival of various species, but also influencing adaptations and evolution. These are important issues for people who are researching and working to protect biodiversity. To date, research on the impacts of artificial light has been isolated within taxonomic specialties, with no synthesis of overall effects of the loss of natural darkness on ecological communities. This volume will help to remedy the information need.
Glutathione in Parkinson's disease: A link between oxidative stress and mitochondrial damage? (1992)

Several links exist between the two mechanisms of neuronal degeneration (i.e., oxygen radical production and mitochondrial damage) proposed to have a role in Parkinson's disease. Indeed, mitochondria are critical targets for the toxic injury induced by oxygen radicals, and experimental evidence suggests that mitochondrial damage may cause an increased generation of oxygen radicals. A potentially important link between these two mechanisms of neurodegeneration is glutathione. Because of the scavenging activity of glutathione against accumulation of oxygen radicals, its decrease in the brains of parkinsonian patients has been interpreted as a sign of oxidative stress; however, this change may also result from or lead to mitochondrial damage. It is conceivable therefore that regardless of whether oxidative stress or mitochondrial damage represents the initial insult, these toxic mechanisms may both contribute to neuronal degeneration via changes in glutathione levels.
Three-dimensional culture of hepatocytes for prediction of drug-induced hepatotoxicity (2010)

Hepatocytes in 3D cultures, although in need of further standardization required by the throughput operation, show great potential in attempts to ensure the efficacy on prediction of drug hepatotoxicity.
Nanoscale Intermolecular Interactions between Human Serum Albumin and Low Grafting Density Surfaces of Poly(ethylene oxide) (2003)

The net nanoscale interaction between a probe tip covalently bound with the blood plasma protein human serum albumin (HSA) and a surface of end-grafted poly(ethylene oxide) (PEO) mushrooms (Mn ∼ 50K, Flory radius RF ∼ 9 nm, contour length Lcontour ∼ 393 nm) was measured directly on approach (loading) and retract (unloading) in aqueous buffer solution using the technique of high-resolution force spectroscopy (HRFS). On approach of the HSA probe tip to the PEO surface, a monotonic nonlinear repulsive net force was observed for tip−sample separation distances of <30 nm, the magnitude of which is much larger than that predicted by either electrostatic double layer or steric theories based on configurational entropy. Attractive contacts between the PEO and HSA are formed during experimentation, enabling the tethering and extension of individual PEO chains on retraction. The mean binding force of the HSA probe tip to individual PEO chains was determined to be 〈Fadh〉 = 0.06 ± 0.10 nN or 〈Fadh/Radius〉 = 0.9 ± 1.6 mN/m (where Radius is the end radius of the probe tip as measured by scanning electron microscopy). By combining the results of HRFS experiments with theoretical approaches, we have shown that this technique is a valuable tool for understanding biocompatibility at the nanoscale and can provide valuable information that may be used as a guideline for the design of improved synthetic macromolecular systems for future biomedical applications.
Direct detection of activated protein C in blood from human subjects (1992)

Abstract The antithrombotic enzyme, activated protein C (APC) was measured in blood using an enzyme capture assay (ECA). The ECA involved (1) collection of blood into anticoagulant containing a reversible inhibitor of the enzyme, (2) specific affinity capture of the enzyme by an immobilized antibody that does not inhibit the enzyme, (3) removal of the reversible inhibitor by washing, and (4) direct assay of the captured enzyme's amidolytic activity. The ECA for APC used benzamidine for inhibition, anti-PC light-chain murine monoclonal antibody for capture, and the oligopeptide substrate S-2366 for enzyme assay. The sensitivity of this assay was 5 pmol/L (0.3 ng/mL) APC. The APC activity in normal pooled plasma corresponded to the amidolytic activity of 38 pmol/L (2.26 +/- 0.2 ng/mL) purified human plasma- derived APC in the ECA. APC levels in 41 normal donors ranged from 64% to 143%, averaging 104.9% +/- 19.6% (SD). Thus, APC is a measurable and normal component of circulating human blood, and this ECA may be useful for identifying APC deficiency. Moreover, similar ECAs for other enzymes in the circulation may be useful.
Phylogenetic Relationships among Highly Virulent Newcastle Disease Virus Isolates Obtained from Exotic Birds and Poultry from 1989 to 1996 (1998)

Newcastle disease virus [NDV (avian paramyxovirus type 1 [APMV1])] isolates were recovered from imported exotic birds confiscated following importation into the United States, from waterbirds in the United States, and from poultry. The exotic birds probably originated from Central and South America, Asia, and Africa. The NDV isolates were initially characterized as highly virulent because of a short mean death time in embryonated chicken eggs. The isolates were typed as neurotropic or viscerotropic velogenic by intracloacal inoculation of adult chickens. Intracerebral pathogenicity index values for the virulent NDV isolates ranged from 1.54 to 1.90, compared to a possible maximum value of 2.0. These isolates had a dibasic amino acid motif in the fusion protein cleavage site sequence required for host systemic replication. Sequence differences were detected surrounding the fusion protein cleavage site and the matrix protein nuclear localization signal, indicating evolution of highly virulent NDV. Phylogenetically, these isolates were categorized with other highly virulent NDV strains that caused outbreaks in southern California poultry during 1972 and in cormorants in the north central United States and southern Canada during 1990 and 1992. These isolates are related to NDV that may have the APMV1 strain chicken/Australia/AV/32 or a related virus as a possible progenitor. Recent virulent NDV isolates and those recovered during disease outbreaks since the 1970s are phylogenetically distinct from current vaccine viruses and standard challenge strains.
Effect of ion beam mixing on microstructure and magnetic properties of Gd-Co multilayer films (1996)

This work investigated the effect of ion beam mixing on the magnetic and structural characteristics of Gd-Co multilayer films. Multilayer films with bilayer periods (BP) from 10 to 300 Å were mixed by 150 to 300 keV Ar+ ion doses of 1016 cm−2. The magnetizations of the as-deposited multilayers were dominated by oxidation, and by the asymmetric redistribution of Co atoms. Ion beam mixing eliminated much of these effects, but the degree was strongly dependent on the layer thickness. The small BP films were completely mixed, with amorphous nanoparticles, but the large BP films contained small, microcrystals in an amorphous matrix due to incomplete mixing. The magnetic moment of ion beam mixed films were strongly dependent on the ion beam energy and the layer thickness.
CLASSIFICATION OF BROADLEAF AND GRASS WEEDS USING GABOR WAVELETS AND AN ARTIFICIAL NEURAL NETWORK (2003)

A texturebased weed classification method was developed. The method consisted of a lowlevel Gaborwaveletsbased feature extraction algorithm and a highlevel neural networkbased pattern recognition algorithm. Thisclassification method was specifically developed to explore the feasibility of classifying weed images into broadleaf and grasscategories for spatially selective weed control. In this research, three species of broadleaf weeds (common cocklebur,velvetleaf, and ivyleaf morning glory) and two grasses (giant foxtail and crabgrass) that are common in Illinois were studied.After processing 40 sample images with 20 samples from each class, the results showed that the method was capable ofclassifying all the samples correctly with high computational efficiency, demonstrating its potential for practicalimplementation under realtime constraints.
A Survey on Robust Model Predictive Control from 1999-2006 (2006)

This paper provides an overview of methods on robust model predictive control (RMPC) from 1999- 2006. First, some optimization problems in model predictive control (MPC) have been reviewed. Then, the methods based on model uncertainty and the methods, which are using disturbance uncertainties, based on optimization problem are considered. Finally, applied and simulated methods of proposed problem are stated.
DNA-dependent protein kinase stimulates an independently active, nonhomologous, end-joining apparatus. (2000)

Double-strand breaks (DSBs) can be efficiently removed from the DNA of higher eukaryotes by nonhomologous end-joining (NHEJ). Genetic studies implicate the DNA-dependent protein kinase (DNA-PK) in NHEJ, but the exact function of this protein complex in the rejoining reaction remains to be elucidated. We compared rejoining of DNA DSBs in a human glioma cell line, M059-J, lacking the catalytic subunit of DNA-PK (DNA-PKcs), and their isogenic but DNA-PK-proficient counterpart, M059-K. In both cell lines, rejoining of DNA DSBs was biphasic, with a fast and a slow component operating with a half-life of approximately 22 min and 12 h, respectively. Deficiency in DNA-PK activity did not alter the half-times of either of these components of rejoining but increased from 17 to 72% the proportion of DNA DSB rejoining with slow kinetics. DNA DSB rejoining was nearly complete in both cell lines, and there was only a small increase in the number of unrejoined breaks in M059-J as compared with M059-K cells after 30 h of incubation. Wortmannin radiosensitized to killing M059-K cells and strongly inhibited DNA DSB rejoining. Wortmannin did not affect the radiosensitivity to killing and produced only a modest inhibition in DNA DSB rejoining in M059-J cells, suggesting that, for these end points, DNA-PK is the principal target of the drug. These observations demonstrate that DNA-PK deficiency profoundly decreases the proportion of DNA DSB rejoining with fast kinetics but has only a small effect on the fraction remaining unrejoined. We propose that in higher eukaryotes, an evolutionarily conserved, independently active, but inherently slow NHEJ pathway is stimulated 30-fold by DNA-PKcs to rapidly remove DNA DSBs from the genome. The stimulation is expected to be of local nature and the presence of DNA-PKcs in the vicinity of the DNA DSB determines whether rejoining will follow fast or slow kinetics. Structural and regulatory functions of DNA-PKcs may mediate this impressive acceleration of DNA DSB rejoining, and regions of chromatin within a certain range from this large protein may benefit from these activities. We propose the term DNA-PK surveillance domains to describe these regions.
Pixel Recursive Super Resolution (2017)

Super resolution is the problem of artificially enlarging a low resolution photograph to recover a plausible high resolution version. In the regime of high magnification factors, the problem is dramatically underspecified and many plausible, high resolution images may match a given low resolution image. In particular, traditional super resolution techniques fail in this regime due to the multimodality of the problem and strong prior information that must be imposed on image synthesis to produce plausible high resolution images. In this work we propose a new probabilistic deep network architecture, a pixel recursive super resolution model, that is an extension of PixelCNNs to address this problem. We demonstrate that this model produces a diversity of plausible high resolution images at large magnification factors. Furthermore, in human evaluation studies we demonstrate how previous methods fail to fool human observers. However, high resolution images sampled from this probabilistic deep network do fool a naive human observer a significant fraction of the time.
Cancer markers in patients receiving chemotherapy for colorectal cancer: A preliminary report (1977)

Abstract The combination of CEA, hepatic function marker enzymes, and four acute phase reactant proteins (haptoglobin, α 1 antitrypsin, α 1 acid glycoprotein, and prealbumin) has been used to monitor patients with colorectal cancer receiving chemotherapy. In 18 patients with advanced lesions who survived at least 3 months treatment the markers predicted progression in 92% of 25 incidents of progression; the mean lead time was 2.8 months. A rising CEA was only present in 28%, but in these patients it gave a mean lead time of 4 months. In the group of 14 patients with minimal residual disease progression to clinically detectable disease has occurred in 9 of them. In these cases the markers predicted progression with a mean lead time of 6 months; in a further six patients the markers have indicated progression, but as yet their disease is not detectable, the mean lead time being at least 8.6 months. CEA and the liver enzyme markers are the most sensitive indicators of progression of the minimal residual disease group.
BaTiO<sub>3</sub> Thin Films from Atomic Layer Deposition: A Superlattice Approach (2017)

A superlattice approach for the atomic layer deposition of polycrystalline BaTiO3 thin films is presented as an example for an effective route to produce high-quality complex oxide films with excellent thickness and compositional control. This method effectively mitigates any undesirable reactions between the different precursors and allows an individual optimization of the reaction conditions for the Ba–O and the Ti–O subcycles. By growth of nanometer thick alternating Ba(OH)2 and TiO2 layers, the advantages of binary oxide atomic layer deposition are transferred into the synthesis of ternary compounds, permitting extremely high control of the cation ratio and superior uniformity. Whereas the Ba(OH)2 layers are partially crystalline after the deposition, the TiO2 layers remain mostly amorphous. The layers react to polycrystalline, polymorph BaTiO3 above 500 °C, releasing H2O. This solid-state reaction is accompanied by an abrupt decrease in film thickness. Transmission electron microscopy and Raman spectroscopy reveal the presence of hexagonal BaTiO3 in addition to the perovskite phase in the annealed films. The microstructure with relatively small grains of ∼70 Å and different phases is a direct consequence of the abrupt formation reaction. The electrical properties transition from the initially highly insulating dielectric semiamorphous superlattice into a polycrystalline BaTiO3 thin film with a dielectric constant of 117 and a dielectric loss of 0.001 at 1 MHz after annealing at 600 °C in air, which, together with the suppression of ferroelectricity at room temperature, are very appealing properties for voltage tunable devices.
Efficient encoding for dual-diagonal structured LDPC codes based on parity bit prediction and correction (2008)

In this paper, an efficient encoding scheme for dual-diagonal structured LDPC codes is proposed. Our encoding algorithm employs parity bit prediction and correction to break up the data dependency within the encoding process. The encoder can achieve higher level of parallelism and better hardware utilization. The number of required clock cycles for encoding one codeword can be reduced to achieve higher throughput performance. The proposed scheme can be directly applied to IEEE 802.11n and 802.16e dual-diagonal codes without any matrix modification. A low-complexity encoder architecture is proposed and implemented to verify these characteristics. Results show that the proposed architecture outperforms conventional works in terms of throughput and throughput/area ratio.
Controlled Cluster Size in Patterned Particle Arrays via Directed Adsorption on Confined Surfaces (2002)

Regular arrays of single colloidal particles on confined regions of patterned polyelectrolyte templates are fabricated based on alternating charged docking sites and neutral deposition resists on the surface. The diameter ratio between surface patterns and the colloid controls the size and spatial arrangement of the clusters. The Figure shows an optical image of up to seven-membered clusters of colloidal beads 4.3 μm in diameter (see also cover).