gebhart/patrepeval huggingface dataset:
A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. (1986)

Proteins encoded by oncogenes such as v-fps/fes, v-src, v-yes, v-abl, and v-fgr are cytoplasmic protein tyrosine kinases which, unlike transmembrane receptors, are localized to the inside of the cell. These proteins possess two contiguous regions of sequence identity: a C-terminal catalytic domain of 260 residues with homology to other tyrosine-specific and serine-threonine-specific protein kinases, and a unique domain of approximately 100 residues which is located N terminal to the kinase region and is absent from kinases that span the plasma membrane. In-frame linker insertion mutations in Fujinami avian sarcoma virus which introduced dipeptide insertions into the most stringently conserved segment of this N-terminal domain in P130gag-fps impaired the ability of Fujinami avian sarcoma virus to transform rat-2 cells. The P130gag-fps proteins encoded by these transformation-defective mutants were deficient in protein-tyrosine kinase activity in rat cells. However v-fps polypeptides derived from the mutant Fujinami avian sarcoma virus genomes and expressed in Escherichia coli as trpE-v-fps fusion proteins displayed essentially wild-type enzymatic activity, even though they contained the mutated sites. Deletion of the N-terminal domain from wild-type and mutant v-fps bacterial proteins had little effect on autophosphorylating activity. The conserved N-terminal domain of P130gag-fps is therefore not required for catalytic activity, but can profoundly influence the adjacent kinase region. The presence of this noncatalytic domain in all known cytoplasmic tyrosine kinases of higher and lower eucaryotes argues for an important biological function. The relative inactivity of the mutant proteins in rat-2 cells compared with bacteria suggests that the noncatalytic domain may direct specific interactions of the enzymatic region with cellular components that regulate or mediate tyrosine kinase function.
Reciprocal-space solvent flattening (1999)

Solvent flattening is a powerful tool for improving crystallographic phases for macromolecular structures obtained at moderate resolution, but uncertainties in the optimal weighting of experimental phases and modified phases make it difficult to extract all the phase information possible. Solvent flattening is essentially an iterative method for maximizing a likelihood function which consists of (i) experimental phase information and (ii) information on the likelihood of various arrangements of electron density in a map, but the likelihood function is generally not explicitly defined. In this work, a procedure is described for reciprocal-space maximization of a likelihood function based on experimental phases and characteristics of the electron-density map. The procedure can readily be applied to phase improvement based on solvent flattening and can potentially incorporate information on a wide variety of other characteristics of the electron-density map.
Star‐Polymer‐Catalyzed Living Radical Polymerization: Microgel‐Core Reaction Vessel by Tandem Catalyst Interchange (2011)

A star is born: Star polymer catalysts that carry a versatile microgel-core reaction vessel were obtained from catalyst interchange, coupled with ruthenium-catalyzed living radical polymerization, in situ hydrogenation, and removal and introduction of metals (see picture). Thanks to the catalyst encapsulation in the unique environment, the star catalysts show high activity, versatility, functionality tolerance, and recyclability in living radical polymerization.
xia2: an expert system for macromolecular crystallography data reduction (2009)

An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes. This can automatically identify multi-wedge, multi-pass and multiwavelength data sets and includes explicit procedures to test for crystallographic special cases. With the push towards high-thoughput crystallography at synchrotron beamlines and automation of structure solution, the ability to reduce data with no user input fills an important gap in the pipeline.
Hybridization of Mismatched or Partially Matched DNA at Surfaces (2002)

We investigate how probe density influences hybridization for unlabeled target oligonucleotides that contain mismatched sequences or targets that access different binding locations on the immobilized probe. We find strong probe density effects influencing not only the efficiency of hybridization but also the kinetics of capture. Probe surfaces are used repeatedly, and the potentially large contributions of sample-to-sample variations in surface heterogeneity and nonspecific adsorption are addressed. Results of kinetic, equilibrium, and temperature-dependent studies, obtained using in-situ surface plasmon resonance (SPR) spectroscopy, show that hybridization for surface immobilized DNA is quite different from the well-studied solution-phase reaction. Surface hybridization depends strongly on the target sequence and probe density. Much of the data can be explained by the presence of steric crowding at high probe density; however, the behavior of mismatched sequences cannot be understood using standard models of hybridization even at the lowest density studied. In addition to unusual capture kinetics observed for the mismatched targets, we find that the binding isotherms can be fit only if a heterogeneous model is used. For mismatched targets, the Sips model adequately describes probe-target binding isotherms; for perfectly matched targets, the Langmuir model can be used.
reCAPTCHA: Human-Based Character Recognition via Web Security Measures (2008)

CAPTCHAs (Completely Automated Public Turing test to tell Computers and Humans Apart) are widespread security measures on the World Wide Web that prevent automated programs from abusing online services. They do so by asking humans to perform a task that computers cannot yet perform, such as deciphering distorted characters. Our research explored whether such human effort can be channeled into a useful purpose: helping to digitize old printed material by asking users to decipher scanned words from books that computerized optical character recognition failed to recognize. We showed that this method can transcribe text with a word accuracy exceeding 99%, matching the guarantee of professional human transcribers. Our apparatus is deployed in more than 40,000 Web sites and has transcribed over 440 million words.
An information theoretic similarity-based learning method for databases (2002)

Similarity-based learning has been widely and successfully used in some domains. Despite these successes, most similarity measures used in the current literature are defined on limited feature types. Therefore, these similarity measures cannot be applied to the database environment due to the variety of data types that exist. In this paper, we propose a new method of similarity-based learning for databases using information theory. The current similarity measures are improved in several ways. Similarity is defined on every attribute type in the database, and each attribute is assigned a weight depending on its importance with respect to the target attribute. Besides, our nearest neighbor algorithm gives different weights to the selected instances. Our system is implemented and tested on some typical machine learning databases. Our experiments show that the classification accuracy of our system is, in general, superior to that of other learning methods. >
Abundant expression of translation initiation factor EIF-4E in post-meiotic germ cells of the rat testis. (1995)

Full activity of EIF-4E in translation requires the phosphorylation of the protein on a specific serine residue. Thus the elevated level of EIF-4E observed in the adult rat testis should be reflected in increase of the functional activity of EIF-4E. Based on the results of in situ hybridization analysis and characterization of EIF-4E, it was concluded that abundant EIF-4E in the testis may play an important role in spermatogenesis through translational regulation of stage-specific mRNAs during germ cell development.
When the brain changes its mind: Interocular grouping during binocular rivalry (1996)

The prevalent view of binocular rivalry holds that it is a competition between the two eyes mediated by reciprocal inhibition among monocular neurons. This view is largely due to the nature of conventional rivalry-inducing stimuli, which are pairs of dissimilar images with coherent patterns within each eye's image. Is it the eye of origin or the coherency of patterns that determines perceptual alternations between coherent percepts in binocular rivalry? We break the coherency of conventional stimuli and replace them by complementary patchworks of intermingled rivalrous images. Can the brain unscramble the pieces of the patchwork arriving from different eyes to obtain coherent percepts? We find that pattern coherency in itself can drive perceptual alternations, and the patchworks are reassembled into coherent forms by most observers. This result is in agreement with recent neurophysiological and psychophysical evidence demonstrating that there is more to binocular rivalry than mere eye competition.
Dll4-containing exosomes induce capillary sprout retraction in a 3D microenvironment (2014)

Delta-like 4 (Dll4), a membrane-bound Notch ligand, plays a fundamental role in vascular development and angiogenesis. Dll4 is highly expressed in capillary endothelial tip cells and is involved in suppressing neighboring stalk cells to become tip cells during angiogenesis. Dll4-Notch signaling is mediated either by direct cell-cell contact or by Dll4-containing exosomes from a distance. However, whether Dll4-containing exosomes influence tip cells of existing capillaries is unknown. Using a 3D microfluidic device and time-lapse confocal microscopy, we show here for the first time that Dll4-containing exosomes causes tip cells to lose their filopodia and trigger capillary sprout retraction in collagen matrix. We demonstrate that Dll4 exosomes can freely travel through 3D collagen matrix and transfer Dll4 protein to distant tip cells. Upon reaching endothelial sprout, it causes filopodia and tip cell retraction. Continuous application of Dll4 exosomes from a distance lead to significant reduction of sprout formation. This effect correlates with Notch signaling activation upon Dll4-containing exosome interaction with recipient endothelial cells. Furthermore, we show that Dll4-containing exosomes increase endothelial cell motility while suppressing their proliferation. These data revealed novel functions of Dll4 in angiogenesis through exosomes.
Influence of Input Multiplicity of Infection on the Antiviral Activity of Interferon (1980)

The antiviral activity of interferon was shown to be dependent on the input m.o.i. Cells could not be protected against the cytopathogenic effect of vaccinia, herpes, Echo or vesicular stomatitis virus at m.o.i. greater than 1. At a m.o.i. of less than or equal to 1, cells could be protected but the amount of interferon necessary to yield protection was inversely related to the m.o.i. When protection was afforded, it was only transient. The duration of the antiviral effect of interferon was also inversely related to the m.o.i. The dependence of the antiviral effect on the m.o.i. could not be explained by assuming the viruses to be mixtures of subtypes with different interferon sensitivity. Also, selection by interferon treatment of interferon-insensitive subtypes could not be shown. The greater antiviral effect of interferon at low m.o.i. was probably not caused by induction of interferon by the infecting virus. A direct inactivation by the virus of the antiviral effect of interferon could not be demonstrated. These results indicate that when interferon-treated cells are infected, they will not survive the infection. The only result of the interferon treatment will be to inhibit virus replication to some extent, leading only to a delay in cell death.
Respiratory syncytial virus vaccine development (2011)

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract viral disease in infants and young children. Presently, there are no explicit recommendations for RSV treatment apart from supportive care. The virus is therefore responsible for an estimated 160,000 deaths per year worldwide. Despite half a century of dedicated research, there remains no licensed vaccine product. Herein are described past and current efforts to harness innate and adaptive immune potentials to combat RSV. A plethora of candidate vaccine products and strategies are reviewed. The development of a successful RSV vaccine may ultimately stem from attention to historical lessons, in concert with an integral partnering of immunology and virology research fields.
Antiviral Activity of Prostaglandin A on Encephalomyocarditis Virus-infected Cells: A Unique Effect Unrelated to Interferon (1985)

Antiviral effects of prostaglandins of the A series (PGAs) on Sendai, vaccinia and vesicular stomatitis viruses have previously been reported and a relationship between the antiviral actions of PGAs and interferons has been suggested. We have investigated the antiviral activity of PGAs on encephalomyocarditis (EMC) virus. Using single-cycle assays of virus replication our results indicate that PGAs only inhibit when present in the culture medium after the cells are infected, and that they are most effective during incubation periods including from 3 to 5 h post-infection. Furthermore, viral RNA synthesis is blocked in infected cells treated with PGA and, as a result, viral antigens are greatly reduced in the cytoplasm of the cells 5 h post-infection. Since the antiviral effect of PGAs is unperturbed by actinomycin D, when cellular RNA synthesis is greatly reduced, it appears unlikely that induction of new cellular proteins is the reason for the antiviral activity of PGAs. In separate experiments we were unable to demonstrate directly the induction of interferon, or of the two dsRNA-dependent enzymes, 2',5'-oligoadenylate synthetase and protein kinase, which are greatly increased in interferon-treated cells. Thus, we conclude that the antiviral activity of PGAs is unrelated to the antiviral action of interferons and involves a unique mechanism independent of cellular protein synthesis.
Discrete dipole approximation for calculating extinction and Raman intensities for small particles with arbitrary shapes (1995)

We present a discrete dipole approximation (DDA) method to determine extinction and Raman intensities for small metal particles of arbitrary shape. The Raman intensity calculation involves evaluation of surface electromagnetic fields, and thus is relevant to surface enhanced Raman scattering (SERS) intensities. We demonstrate convergence of the method by considering light absorption and scattering from an isolated spheroid, from an isolated tetrahedron, from two coupled spheroids, and from a spheroid on a flat surface. We also examine comparisons with traditional T-matrix methods. Extensions and simplifications of the method in studies of clusters and arrays of particles are presented.
Computation of optical flow using a neural network (1988)

A method for computing optical flow using a neural network is presented. Usually, the measurement primitives used for computing optical flow from successive image frames are the image-intensity values and their spatial and temporal derivatives, and tokens such as edges, corners, and linear features. Conventional methods based on such primitives suffer from edge sparsity, noise distortion, or sensitivity to rotation. The authors first fit a 2-D polynomial to find a smooth continuous image-intensity function in a window and estimate the subpixel intensity values and their principal curvatures. Under the local rigidity assumption and smoothness constraints, a neural network is then used to implement the computing procedure based on the estimated intensity values and their principal curvatures. Owing to the dense measured primitives, a dense optical flow with subpixel accuracy is obtained with only a few iterations. Since intensity values and their principle curvatures are rotation-invariant, this method can detect both rotating and translating objects in the scene. Experimental results using synthetic image sequences demonstrate the efficacy of the method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ultracomputers: a teraflop before its time (1992)

article Free Access Share on Ultracomputers: a teraflop before its time Author: Gordon Bell 450 Old Oak Court, Los Altos, CA 450 Old Oak Court, Los Altos, CAView Profile Authors Info & Claims Communications of the ACMVolume 35Issue 8Aug. 1992pp 26–47https://doi.org/10.1145/135226.135227Published:01 August 1992Publication History 98citation843DownloadsMetricsTotal Citations98Total Downloads843Last 12 Months75Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
A Heterologous Helper T-Cell Epitope Enhances the Immunogenicity of a Multiple-Antigenic-Peptide Vaccine Targeting the Cryptic Loop-Neutralizing Determinant ofBacillus anthracisProtective Antigen (2009)

We previously showed that a multiple antigenic peptide (MAP) displaying amino acids (aa) 305 to 319 from the 2beta2-2beta3 loop of protective antigen (PA) can elicit high-titered antibody that neutralizes lethal toxin (LeTx) in vitro and that this loop-neutralizing determinant (LND) specificity is absent in PA-immune rabbits. Some immune rabbits were, however, nonresponders to the MAP. We hypothesized that the immunogen elicited suboptimal major histocompatibility complex (MHC) class II-restricted T-cell help and that introduction of a functional helper T-cell epitope would increase MHC-restricted responsiveness and the magnitude and affinity of the antibody responses. In the current study, we characterized the T- and B-cell responses to LND peptides in mice, then designed second-generation MAP immunogens for eliciting LND-specific immunity, and tested them in rabbits. The 305-319 sequence was devoid of helper T-cell epitopes in three strains of mice; however, a T-B peptide comprising aa 305 to 319, colinearly synthesized with the P30 helper epitope of tetanus toxin, elicited robust LeTx-neutralizing immunity in mice. T-B MAPs displaying B-cell epitopes 304 to 319 (MAP304) or 305 to 319 (MAP305) elicited high-titer, durable antibody responses in rabbits which exhibited potent neutralization of LeTx in vitro. All MAP304-immune rabbits demonstrated neutralization titers exceeding that of hyperimmune sera of rabbits immunized with PA in Freund's adjuvant, with peak neutralization titers 23-, 6-, and 3-fold higher than that of the PA antiserum. Overall, immunization with MAPs containing the P30 epitope elicited higher antibody and toxin neutralization titers and peptide-specific affinity than immunization with an LND MAP lacking a helper epitope. P30-containing MAP304 represents a promising LND-specific vaccine for anthrax.
Zoomable User Interfaces as a Medium for Slide Show Presentations (2002)

In this paper, the authors propose Zoomable User Interfaces as an alternative presentation medium to address several common presentation problems. Zoomable User Interfaces offer new techniques for managing multiple versions of a presentation, providing interactive presentation navigation, and distinguishing levels of detail. These zoomable presentations may also offer several cognitive benefits over their commercial slide show counterparts. The authors also introduce CounterPoint, a tool to simplify the creation and delivery of zoomable presentations, discuss the techniques they have used to make authoring and navigation manageable in the multidimensional space. Lastly, some of the visualization principles compiled by the authors for designing these types of presentations are presented.
Transparent, Conductive, and Flexible Carbon Nanotube Films and Their Application in Organic Light-Emitting Diodes (2006)

We have carried out comparative studies on transparent conductive thin films made with two kinds of commercial carbon nanotubes: HiPCO and arc-discharge nanotubes. These films have been further exploited as hole-injection electrodes for organic light-emitting diodes (OLEDs) on both rigid glass and flexible substrates. Our experiments reveal that films based on arc-discharge nanotubes are overwhelmingly better than HiPCO-nanotube-based films in all of the critical aspects, including surface roughness, sheet resistance, and transparency. Further improvement in arc-discharge nanotube films has been achieved by using PEDOT passivation for better surface smoothness and using SOCl2 doping for lower sheet resistance. The optimized films show a typical sheet resistance of approximately 160 Omega/ square at 87% transparency and have been used successfully to make OLEDs with high stabilities and long lifetimes.
Cancer Immunotherapy Using Interleukin-2 and Interleukin-2-Activated Lymphocytes (1986)

The development of immunologic approaches to the treatment of cancer has progressed through major changes in the past five years. In the 1970s considerable enthusiasm existed for immunotherapeutic approaches to cancer based on attempts to provide nonspecific stimulation of the host immune system in the hope that this general increase in immune reactiv­ ity would lead to an increased reactivity to putative tumor antigens on growing cancers. This approach was based on minimal experimental data from animal tumor models. A large number of clinical trials in humans utilized attempts to stimulate the immune system nonspecifically. Using substances such as Bacillus Calmette-Guerin (BCG), methenol-extracted residue (MER), Corynebacterium parvum, levamisole, and other immune stimulators, researchers treated patients with extensive tumor, as well as with minimal tumor burdens. This experience was almost universally unsuccessful and, both in animal tumor model systems and in the human, has largely been abandoned (I). An alternate approach to cancer immunotherapy can be categorized as passive or adoptive immunotherapy, in which the tumor-bearing host receives the systemic transfer of immunologic reagents such as antibodies or reactive cells already possessing antitumor reactivity (2-5). Because the
Resveratrol Protects Human Retinal Pigment Epithelial Cells from Acrolein-Induced Damage (2010)

Our results indicated an inhibitory effect of compounds found in cigarette smoke on human RPE phagocytosis, and lutein, zeaxanthin, meclofenamic acid, and resveratrol each offered protection against this inhibition. Therefore, red wine polyphenol, resveratrol, might ameliorate acrolein-induced or age-related RPE degeneration, such as AMD.
Nathalie Heinich, Michael Pollack, « Du conservateur de musée à l'auteur d'expositions : l'invention d'une position singulière », Sociologie du travail, vol. 31, n° 1, 1989, pp. 29-49 (1990)

Lamy Yvon. Nathalie Heinich, Michael Pollack, « Du conservateur de musée à l'auteur d'expositions : l'invention d'une position singulière », Sociologie du travail, vol. 31, n° 1, 1989, pp. 29-49. In: Genèses, 1, 1990. Les voies de l'histoire, sous la direction de Gérard Noiriel. pp. 175-176.