gebhart/patrepeval huggingface dataset:
Using Implicit Feedback for User Modeling in Internet and Intranet Searching ϕ (2000)

Powerize Server 1.0, developed by Powerize.com, is a content-based information filtering and retrieval system that presently uses a manually constructed user model known as a search profile. User modeling captures a user’s information needs. A user model can be constructed explicitly by the user or implicitly by exploiting feedback from the user about which documents are relevant. Implicit feedback can be inferred from user behavior without any additional work on the part of the user. The study reported in this paper investigates a way of implementing the implicit feedback technique of user modeling for the Powerize Server 1.0. Previous studies on Internet discussion groups (USENET news) have shown reading time to be a useful source of implicit feedback for predicting a user’s preferences. In this study, we examined: 1) whether reading time is useful for predicting a user’s preferences for academic or professional journal articles, and 2) whether printing behavior adds anything to what we already know from reading time. Two experiments were conducted with undergraduate students using professional articles from the telecommunications and pharmaceutical industries. The results of the experiments showed that reading time could be used to predict the relevancy of documents, although the threshold on reading time required to detect relevant documents would be higher than for USENET news articles. The experiments also showed that printing behavior adds to what can be inferred from reading time. All the documents that were printed in the experiments were relevant, but the reading time for many of these documents was below the mean reading time for all documents read. This result implies that the use of printing behavior with reading time could increase the precision and recall ratios for detecting relevant documents. Suggestions for incorporating the results of the study into the Powerize Server were made in conclusion. This paper also reports detailed technical descriptions of the experiment design, including research problem, experimental system, and data collection.
Improved Method for Determining Food Protein Degree of Hydrolysis (2001)

ABSTRACT When producing hydrolyzed proteins, it is important to determine the degree of hydrolysis (DH). The trinitro‐benzene‐sulfonic acid (TNBS) method is well established with regard to enzymatic hydrolysis. However, this method is laborious, cannot be used to follow a hydrolysis reaction continuously, and includes hazardous and unstable chemicals. This paper describes a method based on the reaction of primary amino groups with o‐phthaldialdehyde (OPA). The conclusion is that the OPA method of analyzing the DH of protein hydrolyses is more accurate, is easier and faster to carry out, has a broader application range, and is environmentally safer than the TNBS method.
Enhancement of the Aquaporin Adipose Gene Expression by a Peroxisome Proliferator-activated Receptor γ (2001)

The current study demonstrates that aquaporin adipose (AQPap), an adipose-specific glycerol channel (Kishida, K., Kuriyama, H., Funahashi, T., Shimomura, I., Kihara, S., Ouchi, N., Nishida, M., Nishizawa, H., Matsuda, M., Takahashi, M., Hotta, K., Nakamura, T., Yamashita, S., Tochino, Y., and Matsuzawa, Y. (2000) J. Biol. Chem. 275, 20896-20902), is a target gene of peroxisome proliferator-activated receptor (PPAR) gamma. The AQPap mRNA amounts increased following the induction of PPARgamma in the differentiation of 3T3-L1 adipocytes. The AQPap mRNA in the adipose tissue increased when mice were treated with pioglitazone (PGZ), a synthetic PPARgamma ligand, and decreased in PPARgamma(+/-) heterozygous knockout mice. In 3T3-L1 adipocytes, PGZ augmented the AQPap mRNA expression and its promoter activity. Serial deletion of the promoter revealed the putative peroxisome proliferator-activated receptor response element (PPRE) at -93/-77. In 3T3-L1 preadipocytes, the expression of PPARgamma by transfection and PGZ activated the luciferase activity of the promoter containing the PPRE, whereas the PPRE-deleted mutant was not affected. The gel mobility shift assay showed the direct binding of PPARgamma-retinoid X receptor alpha complex to the PPRE. DeltaPPARgamma, which we generated as the dominant negative PPARgamma lacking the activation function-2 domain, suppressed the promoter activity in 3T3-L1 cells, dose-dependently. We conclude that AQPap is a novel adipose-specific target gene of PPARgamma through the binding of PPARgamma-retinoid X receptor complex to the PPRE region in its promoter.
Molecular characterization of the B′ regulatory subunit gene family ofArabidopsisprotein phosphatase 2A (1999)

Type 2A serine/threonine protein phosphatases (PP2A) have been implicated as important mediators of a diverse array of reversible protein phosphorylation events in plants. We have identified a novel Arabidopsis gene (AtB' delta) which encodes a 55-kDa B' type regulatory subunit of PP2A. The protein encoded by this gene is 57-63% identical and 69-74% similar to the previously identified AtB' genes. The AtB' delta gene appears to be expressed in all Arabidopsis organs indicating its protein product has a basic housekeeping function in plant cells. Unlike certain mRNAs derived from the AtB' gamma gene, AtB' delta mRNAs do not fluctuate significantly in response to heat stress. Further analysis of cDNA sequences derived from the AtB' genes identified an alternatively spliced cDNA derived from AtB' gamma. This cDNA differs from the previously identified AtB' gamma cDNA by the absence of a 133-bp region in its 5' untranslated region. The missing 133-bp region appears to constitute an unspliced intron and its presence in the AtB' gamma gene was confirmed by PCR using Arabidopsis genomic DNA as a template. AtB' gamma mRNA containing the 133-bp intron accumulate in all Arabidopsis organs and their levels fluctuate differentially in response to heat stress. The 133-bp insert contains two short open reading frames and hence might serve as a translational control mechanism affecting AtB' gamma protein synthesis. Finally we show, using both the yeast two hybrid system and in vitro binding assays, that the B' subunit of Arabidopsis PP2A is able to associate with other PP2A subunits, supporting the notion that the B' protein serves as a regulator of PP2A activity in plants.
Soluble interferon‐α receptor molecules are present in body fluids (1992)

Soluble forms of the interferon-alpha receptor (sIFN-alpha R) were identified in human serum and urine by Western blotting with monoclonal antibodies (MAb) directed against IFN-alpha R, and by immunoprecipitation (Iptn) of a covalently cross-linked complex of IFN-alpha R and [125I]IFN-alpha with anti IFN-alpha MAb. Elevated levels of sIFN-alpha R were found in sera of hairy cell leukemia patients. The soluble receptor from serum migrated as a 55 kDa protein in SDS-PAGE, and, as expected, the cross-linked product migrated as a 75 kDa protein. The soluble receptor from urine was found to be a protein of mol. wt. 45 kDa and its cross-linked complex migrated as a 65 kDa protein. The calculated mol. wt. of the entire extracellular domain of the IFN-alpha R prior to post-translational modifications is 47,000. Since there are 12 potential glycosylation points in this extracellular domain, its actual mol. wt. may be as high as 70,000 Da. It is therefore concluded that sIFN-alpha R molecules, corresponding to truncated forms of the extracellular domain of the cell surface IFN-alpha R, are present in human serum and in normal human urine.
Macrophage activation: priming activity from a T-cell hybridoma is attributable to interferon-gamma. (1983)

Antiviral and macrophage-priming activities in the supernatant medium of a subclone of a concanavalin A-stimulated mouse T-cell hybridoma were investigated. The two activities were associated with a molecular weight of approximately 50,000 and could not be separated by various approaches. Both activities were eliminated by a highly specific neutralizing antibody against mouse interferon-gamma, but not by antibody against interferon-alpha and -beta. The ratio of priming to antiviral activity in the hybridoma culture supernate was indistinguishable from the ratio obtained with mouse interferon-gamma prepared by recombinant DNA technology. It was concluded from these data that the priming activity in hybridoma culture supernates was attributable to interferon-gamma and that this mediator is one form of the lymphokine macrophage-activating factor. Interferon-gamma was greater than 800 times more efficient at priming mouse macrophages for tumor cell killing than was a mixture of interferon-alpha and -beta. This finding contributes to growing awareness that type II interferon may have greater immunoregulatory potential than type I interferons.
Effects of Curing and Fertilization on Nitrosamine Formation in Bright and Burley Tobacco (1992)

Abstract A bright and a Burley tobacco were grown at four fertilization rates and each tobacco was then both flue-cured and air-cured. Levels of alkaloids and nitrosamines were found to increase with increasing fertilization levels. Levels of alkaloids, N-nitrosonornicotine (NNN), and other tobacco-specific nitrosamines (TSNA) were consistently higher in the Burley tobacco than in the bright tobacco, regardless of curing method. In comparing the effects of curing, it was found that NNN and total TSNA levels were higher in the midrib than in the lamina of the air-cured samples, while just the opposite was found for the flue-cured samples. Flue-curing bright tobacco produced three times the level of TSNA vs air-curing the same tobacco. On the other hand, flue-curing Burley tobacco reduced the alkaloids, but greatly increased the TSNA in the lamina. As midribs from the air-cured Burley leaves had three times the TSNA concentration of the lamina, the use of air-cured midribs in tobacco products should be avoided. It was concluded that lower fertilization levels and careful manipulations of curing parameters could lower nitrosamine levels in cured tobacco.
Preparation and properties of plasma-deposited films with surface energies varying over a wide range (1986)

Polymer surfaces have been modified by chemical reaction or thin film deposition using a capacitatively coupled plasma RF-discharge system. This has allowed the production of a graded, reproducible series of surfaces with surface energies ranging from low to high. Three gases, hexafluoroethane (C2F6), perfluoropropane (C3F8), and hexafluoropropene (CF3CFCF2), were used to prepare the low-energy surfaces. Ethylene oxide (C2H4O) was used to prepare the higher energy surfaces. Intermediate values of surface energy were obtained by using gas mixtures of perfluoropropane and ethylene oxide. The plasma-deposited films were characterized by ESCA and contact-angle studies. In the low-energy range, the critical surface tension (γc) values of the films prepared were found to be lower than those for Teflon. For the higher energy surfaces, values up to about 45 dyn/cm were obtained. Addition of oxygen to the plasma permitted the production of films with still higher γc values. ESCA studies indicate that, under the reaction conditions used, C3F8 and CF3CFCF2 form a fluoropolymer deposit on glass that is at least 100 Å thick. For the same reaction parameters, C2F6 resulted in more etching and deposition of a much thinner film.
Nanoparticles for Radiation Therapy Enhancement: the Key Parameters (2015)

This review focuses on the radiosensitization strategies that use high-Z nanoparticles. It does not establish an exhaustive list of the works in this field but rather propose constructive criticisms pointing out critical factors that could improve the nano-radiation therapy. Whereas most reviews show the chemists and/or biologists points of view, the present analysis is also seen through the prism of the medical physicist. In particular, we described and evaluated the influence of X-rays energy spectra using a numerical analysis. We observed a lack of standardization in preclinical studies that could partially explain the low number of translation to clinical applications for this innovative therapeutic strategy. Pointing out the critical parameters of high-Z nanoparticles radiosensitization, this review is expected to contribute to a larger preclinical and clinical development.
Predicting Coiled Coils from Protein Sequences (1991)

The probability that a residue in a protein is part of a coiled-coil structure was assessed by comparison of its flanking sequences with sequences of known coiled-coil proteins. This method was used to delineate coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin. More than 200 proteins that probably have coiled-coil domains were identified in GenBank, including alpha- and beta-tubulins, flagellins, G protein beta subunits, some bacterial transfer RNA synthetases, and members of the heat shock protein (Hsp70) family.
Series elastic actuators (2002)

It is traditional to make the interface between an actuator and its load as stiff as possible. Despite this tradition, reducing interface stiffness offers a number of advantages, including greater shock tolerance, lower reflected inertia, more accurate and stable force control, less inadvertent damage to the environment, and the capacity for energy storage. As a trade-off, reducing interface stiffness also lowers zero motion force bandwidth. In this paper, the authors propose that for natural tasks, zero motion force bandwidth isn't everything, and incorporating series elasticity as a purposeful element within the actuator is a good idea. The authors use the term elasticity instead of compliance to indicate the presence of a passive mechanical spring in the actuator. After a discussion of the trade-offs inherent in series elastic actuators, the authors present a control system for their use under general force or impedance control. The authors conclude with test results from a revolute series-elastic actuator meant for the arms of the MIT humanoid robot Cog and for a small planetary rover.
Biomimetically Triggered Inorganic Crystal Transformation by Biomolecules: A New Understanding of Biomineralization (2009)

Phase transformation is an important strategy in biomineralization. However, the role of biomolecules in the mineral transition is poorly understood despite the fact that the biomineralization society greatly highlights the organic controls in the formation of the inorganic phase. Here, we report an induced biomimetic phase transformation from brushite (a widely used calcium phosphate precursor in biological cement) to hydroxyapatite (main inorganic composition of skeletal mineral) by citrate (a rich organic component in bone tissue). The transformation in the absence of the organic additive cannot be spontaneously initiated in an aqueous solution with a pH of 8.45 (no phase transition is detected in 4 days), which is explained by a high interfacial energy barrier between brushite-solution and hydroxyapatite-solution interfaces. Citrate can oppositely regulate these two interfaces, which decreases and increases the stabilities of brushite and hydroxyapatite surfaces in the solution, respectively. Thus, the interfacial energy barrier can be greatly reduced in the presence of citrate and the reaction is triggered; e.g., at 1 mM citrate, the total transformation from brushite to hydroxyapatite can be completed within 3 days. The relationship between the transition kinetics and citrate concentration is also studied. The work reveals how the organic components direct solid-solid phase transformation, which can be understood by an energetic control of the interfacial barrier. It is emphasized that the terms of interfacial energy must be taken into account in the studies of phase transformation. We suggest that this biomimetic approach may provide an in-depth understanding of biomineralization.
Characterization of murine CD70, the ligand of the TNF receptor family member CD27 (1997)

Human CD70 (CD27 ligand) is a type II transmembrane glycoprotein belonging to the TNF family. The protein is not expressed on resting lymphocytes, but is rapidly induced on these cells after cellular activation. Importantly, interaction of CD70 with its receptor CD27 gives a costimulatory signal for lymphocyte activation. Whereas CD27 has been molecularly characterized in the mouse, murine CD70 (mCD70) was undefined until now. Here, we describe the cDNA cloning and initial characterization of mCD70 and the determination of its gene structure. mCD70 is a polypeptide of 195 amino acids that has 62% homology with its human counterpart. In analogy to human CD70, mCD70 transcript levels are strongly but transiently up-regulated during lymphocyte activation, which is in line with a role for the CD27-CD70 receptor pair early in the immune response. In accordance with the comitogenic activity of mCD27-specific mAb, recombinant mCD70 potently costimulates T cell proliferation. Finally, the mCD70 gene consists of three exons spanning approximately 4 kb of DNA and is localized on chromosome 17.
A normally masked nuclear matrix antigen that appears at mitosis on cytoskeleton filaments adjoining chromosomes, centrioles, and midbodies. (1992)

mAbs were generated against HeLa nuclear matrix proteins and one, HIB2, which selectively stained mitotic cells, was selected for further study. Western blot analysis showed H1B2 antibody detected a protein of 240 kD in the nuclear matrix fractions. The H1B2 antigen was completely masked in immunofluorescently stained interphase cells. However, removing chromatin with DNase I digestion and 0.25 M ammonium sulfate extraction exposed the protein epitope. The resulting fluorescence pattern was bright, highly punctate, and entirely nuclear. Further extraction of the nuclear matrix with 2 M NaCl uncovers an underlying, anastomosing network of 9-13 nm core filaments. Most of the H1B2 antigen was retained in the fibrogranular masses enmeshed in the core filament network and not in the filaments themselves. The H1B2 antigen showed remarkable behavior at mitosis. As cells approached prophase the antigen became unmasked to immunofluorescent staining without the removal of chromatin. First appearing as a bright spot, the antibody staining spread through the nucleus finally concentrating in the region around the condensed chromosomes. The antibody also brightly stained the spindle poles and, more weakly, in a punctate pattern in the cytoskeleton around the spindle. As the chromosomes separated at anaphase, H1B2 remained with the separating daughter sets of chromosomes. The H1B2 antigen returned to the reforming nucleus at telophase, but left a bright staining region in the midbody. Immunoelectron microscopy of resinless sections showed that, in the mitotic cell, the H1B2 antibody did not stain chromosomes and centrioles themselves, but decorated a fibrogranular network surrounding and connected to the chromosomes and a fibrogranular structure surrounding the centriole.
Controlled alignment of carbon nanofibers in a large-scale synthesis process (2002)

Controlled alignment of catalytically grown carbon nanofibers (CNFs) at a variable angle to the substrate during a plasma-enhanced chemical vapor deposition process is achieved. The CNF alignment is controlled by the direction of the electric field lines during the synthesis process. Off normal CNF orientations are achieved by positioning the sample in the vicinity of geometrical features of the sample holder, where bending of the electric field lines occurs. The controlled growth of kinked CNFs that consist of two parts aligned at different angles to the substrate normal also is demonstrated.
Deep Residual Learning for Image Recognition (2016)

Deeper neural networks are more difficult to train. We present a residual learning framework to ease the training of networks that are substantially deeper than those used previously. We explicitly reformulate the layers as learning residual functions with reference to the layer inputs, instead of learning unreferenced functions. We provide comprehensive empirical evidence showing that these residual networks are easier to optimize, and can gain accuracy from considerably increased depth. On the ImageNet dataset we evaluate residual nets with a depth of up to 152 layers - 8× deeper than VGG nets [40] but still having lower complexity. An ensemble of these residual nets achieves 3.57% error on the ImageNet test set. This result won the 1st place on the ILSVRC 2015 classification task. We also present analysis on CIFAR-10 with 100 and 1000 layers. The depth of representations is of central importance for many visual recognition tasks. Solely due to our extremely deep representations, we obtain a 28% relative improvement on the COCO object detection dataset. Deep residual nets are foundations of our submissions to ILSVRC & COCO 2015 competitions1, where we also won the 1st places on the tasks of ImageNet detection, ImageNet localization, COCO detection, and COCO segmentation.
Microbial degradation of acenaphthene and naphthalene under denitrification conditions in soil-water systems (1988)

This study examined the microbial degradation of acenaphthene and naphthalene under denitrification conditions at soil-to-water ratios of 1:25 and 1:50 with soil containing approximately 10(5) denitrifying organisms per g of soil. Under nitrate-excess conditions, both acenaphthene and naphthalene were degraded from initial aqueous-phase concentrations of about 1 and several mg/liter respectively, to nondetectable levels (less than 0.01 mg/liter) in less than 9 weeks. Acclimation periods of 12 to 36 days were observed prior to the onset of microbial degradation in tests with soil not previously exposed to polycyclic aromatic hydrocarbon (PAH) compounds, whereas acclimation periods were absent in tests with soil reserved from prior PAH degradation tests. It was judged that the apparent acclimation period resulted from the time required for a small population of organisms capable of PAH degradation to attain sufficient densities to exhibit detectable PAH reduction, rather than being a result of enzyme induction, mutation, or use of preferential substrate. About 0.9% of the naturally occurring soil organic carbon could be mineralized under denitrification conditions, and this accounted for the greater proportion of the nitrate depletion. Mineralization of the labile fraction of the soil organic carbon via microbial denitrification occurred without an observed acclimation period and was rapid compared with PAH degradation. Under nitrate-limiting conditions the PAH compounds were stable owing to the depletion of nitrate via the more rapid process of soil organic carbon mineralization. Soil sorption tests showed at the initiation of a test that the total mass of PAH compound was divided in comparable proportions between solute in the aqueous phase and solute sorbed on the solid phase. The microbial degradation of the PAH compound depends on the interrelationships between (i) the desorption kinetics and the reversibility of desorption of sorbed compound from the soil, (ii) the concentration of PAH-degrading microorganisms, and (iii) the competing reaction for nitrate utilization via mineralization of the labile fraction of naturally occurring soil organic carbon.