gebhart/patrepeval huggingface dataset:
Receptor Protein Tyrosine Kinases and Phosphatases (1992)

It is clear that the number of receptor PTKs and PTPs encoded by a typical vertebrate genome is rather large. Although the signal pathways activated by the receptor PTKs may in many cases be common, specificity is provided by the ligand-binding domain and the availability of ligand. In addition, the precise spectrum of substrates that bind to and are phosphorylated by each receptor PTK can differ based on the number and nature of the autophosphorylation sites and on the repertoire of SH2-containing proteins and other substrates expressed in each cell type. It is also clear that receptor PTKs can activate multiple independent signaling pathways and that the output of these pathways can be integrated to provide a specific cellular response. The role of receptor PTPs in such integrated signaling networks is not yet obvious. In some cases, they may activate nonreceptor PTKs, whereas in other cases, they may counteract the effects of activated receptor and nonreceptor PTKs by dephosphorylating the PTKs themselves or their substrates. We know very little about the substrate specificity of PTPs, but in part this must be dictated by their subcellular location. It is possible that there are specific pairs of receptor PTKs and PTPs, which act in concert at the cell surface to activate and down-regulate specific signal pathways. Progress in understanding the function of receptor PTPs will depend on identifying ligands for receptor PTPs and then determining how ligand binding influences their activity.
Peroxynitrite Inhibits T Lymphocyte Activation and Proliferation by Promoting Impairment of Tyrosine Phosphorylation and Peroxynitrite-Driven Apoptotic Death (1999)

Peroxynitrite (ONOO-) is a potent oxidizing and nitrating agent produced by the reaction of nitric oxide with superoxide. It readily nitrates phenolic compounds such as tyrosine residues in proteins, and it has been demonstrated that nitration of tyrosine residues in proteins inhibits their phosphorylation. During immune responses, tyrosine phosphorylation of key substrates by protein tyrosine kinases is the earliest of the intracellular signaling pathways following activation through the TCR complex. This work was aimed to evaluate the effects of ONOO- on lymphocyte tyrosine phosphorylation, proliferation, and survival. Additionally, we studied the generation of nitrating species in vivo and in vitro during immune activation. Our results demonstrate that ONOO-, through nitration of tyrosine residues, is able to inhibit activation-induced protein tyrosine phosphorylation in purified lymphocytes and prime them to undergo apoptotic cell death after PHA- or CD3-mediated activation but not upon phorbol ester-mediated stimulation. We also provide evidence indicating that peroxynitrite is produced during in vitro immune activation, mainly by cells of the monocyte/macrophage lineage. Furthermore, immunohistochemical studies demonstrate the in vivo generation of nitrating species in human lymph nodes undergoing mild to strong immune activation. Our results point to a physiological role for ONOO- as a down-modulator of immune responses and also as key mediator in cellular and tissue injury associated with chronic activation of the immune system.
Generation of controllable monodispersed sprays using impulse jet and charging techniques (1990)

A technique for producing a tunable monodispersed spray is developed with a combination of impulsed jet and charging techniques. A single orifice impulse-jet droplet generator, of a unique configuration, was used to produce a single stream of uniform droplets over a wide range of diameters. The single stream of droplets is dispersed with an electrostatic charging technique. Control of drop number density was enhanced by a droplet selection technique, in which a number of drops could be removed from the spray.
Evidence that serum NTx (collagen-type I N-telopeptides) can act as an immunochemical marker of bone resorption (1997)

Previous studies have shown that immunoassay of urinary NTx (cross-linked N-telopeptides of type I collagen) provides a responsive index of human bone resorption. Here we report by a sensitive immunoassay that NTx is present in serum and is suppressed appropriately in patients with Paget disease of bone by bisphosphonate antiresorptive therapy. The monoclonal antibody (1H11) developed against urinary NTx was applied in a sensitive chemiluminescence format. Results for human serum and urine showed parallel inhibition curves. The NTx concentrations in paired serum and urine samples from individual patients correlated well when urinary concentrations were normalized to creatinine concentrations (in premenopausal and postmenopausal women and Paget disease patients, r = 0.90, n = 60). The percentage of NTx suppression from baseline values for Paget disease patients on bisphosphonate therapy was similar for serum and urine. Blood samples drawn from bone marrow at the site of Pagetic lesions in three patients with active disease had as much as 10-fold higher concentrations of NTx than did peripheral blood samples drawn at the same time. The latter finding is consistent with other evidence showing that immunoreactive NTx originates directly during the proteolytic cleavage of bone collagen by osteoclasts rather than, e.g., by degradative processes occurring later in the liver and kidney.
Identification of paraxanthine as the most potent caffeine‐derived inhibitor of connective tissue growth factor expression in liver parenchymal cells (2009)

Our data provide an evidence-based suggestion of the caffeine-derived primary metabolite paraxanthine as a potentially powerful antifibrotic drug by its inhibitory effect on (hepatocellular) CTGF synthesis.
Quasimelting and phases of small particles (1988)

Calculations of the Gibbs free energies of single-crystal and multiply twinned small metal particles clearly indicate for the first time both the presence of a quasimolten phase (where the particles are continuously fluctuating between different structures) at temperatures well below the melting point and the existence of distinct phase regions for different particle shapes. These results have important implications for the understanding of epitaxial growth processes; for instance, at temperatures where the quasimolten and single-crystal phases are contiguous one would expect far better epitaxial growth than at temperatures where the multiply twinned phases are stable.
SEQSEE: a comprehensive program suite for protein sequence analysis (1994)

SEQSEE (SEQuence SEEker) is a multi-purpose, menu-driven suite of programs designed to provide a fully integrated, state-of-the-art package for the analysis and display of protein sequences and protein databases. It is currently configured to run on most UNIX-based machines including Sun, SGI and NeXT workstations with conversion to other architectures (e.g. Vax or Cray) being a relatively simple task. SEQSEE is capable of performing nearly all of the analytical and comparative tasks found in most comprehensive commercially available software packages. These include sequence/database searching, sequence retrieval, sequence entry and editing, statistical sequence analysis, multiple sequence alignment, flexible pattern matching, and secondary structure prediction. SEQSEE also integrates a number of unique databases which allow it to perform many additional functions such as structure-based sequence alignments and homology-based secondary structure prediction. Additional enhancements to many previously published algorithms have substantially improved the performance of SEQSEE over that found for most other commercial products. The source code, the documentation and all of the required databases for SEQSEE are freely available and may be obtained by anonymous ftp.
Using the mouse to model human disease: increasing validity and reproducibility (2016)

Experiments that use the mouse as a model for disease have recently come under scrutiny because of the repeated failure of data, particularly derived from preclinical studies, to be replicated or translated to humans. The usefulness of mouse models has been questioned because of irreproducibility and poor recapitulation of human conditions. Newer studies, however, point to bias in reporting results and improper data analysis as key factors that limit reproducibility and validity of preclinical mouse research. Inaccurate and incomplete descriptions of experimental conditions also contribute. Here, we provide guidance on best practice in mouse experimentation, focusing on appropriate selection and validation of the model, sources of variation and their influence on phenotypic outcomes, minimum requirements for control sets, and the importance of rigorous statistics. Our goal is to raise the standards in mouse disease modeling to enhance reproducibility, reliability and clinical translation of findings.
Amplifying four-wavelength combiner, based on erbium/ytterbium-doped waveguide amplifiers and integrated splitters (1997)

We report the successful system demonstration of a four-wavelength integrated-optics amplifying combiner. The arrangement consists of an all-connectorized 4/spl times/1 glass splitter followed by a 4.5-cm-long Er/Yb-doped waveguide amplifier. When injecting 120 mW of 975-nm laser diode pump, we record, in the amplifying section, 11.6 dB of net gain in the single pass configuration and 23 dB in the double pass as well as a noise figure of 4.5 dB. These results show the potentiality of ion-exchange technology for the fabrication of lossless telecommunication devices.
ChemInform Abstract: Reaction of Organic Compounds with SF4‐HF in the Presence of Halogenating Agents. Part 5. Reaction of Unsaturated Acids and Their Esters with SF4‐HF‐Cl2. (1988)

Abstract The reactions between acrylic acid (I), methacrylic acid (IV) or crotonic acid (VIII) and the system SF4/HF/Cl2 afford the polyhalogenated ethers (II), (V) or (IX) and (X) along with polyhalogenoalkanes (III), (VI), (VII) or (XI), which result from addition of one "equivalent" of ClF to the carbon‐carbon double bond with concomitant transformation of the carboxyl group into a trifluoromethyl group.
Extracting relational data from HTML repositories (2004)

There is a vast amount of valuable information in HTML documents, widely distributed across the World Wide Web and across corporate intranets. Unfortunately, HTML is mainly presentation oriented and hard to query. In this paper, we develop a system to extract desired information (records) from thousands of HTML documents, starting from a small set of examples. Duplicates in the result are automatically detected and eliminated. We propose a novel method to estimate the current coverage of results by the system, based on capture-recapture models with unequal capture probabilities. We also propose techniques for estimating the error rate of the extracted information and an interactive the technique for enhancing information quality. To evaluate the method and ideas proposed in this paper, we conducted an extensive set of experiments. Our experimental results validate the effectiveness and utility of our system, and demonstrate interesting tradeoffs between running time of information extraction and coverage of results.
Spatial Organization of Signal Transduction Molecules in the NK Cell Immune Synapses During MHC Class I-Regulated Noncytolytic and Cytolytic Interactions (2001)

The cytolytic activity of NK cells is tightly regulated by inhibitory receptors specific for MHC class I Ags. We have investigated the composition of signal transduction molecules in the supramolecular activation clusters in the MHC class I-regulated cytolytic and noncytolytic NK cell immune synapses. KIR2DL3-positive NK clones that are specifically inhibited in their cytotoxicity by HLA-Cw*0304 and polyclonal human NK cells were used for conjugate formation with target cells that are either protected or are susceptible to NK cell-mediated cytotoxicity. Polarization of talin, microtubule-organizing center, and lysosomes occurred only during cytolytic interactions. The NK immune synapses were analyzed by three-dimensional immunofluorescence microscopy, which showed two distinctly different synaptic organizations in NK cells during cytolytic and noncytolytic interactions. The center of a cytolytic synapse with MHC class I-deficient target is comprised of a complex of signaling molecules including Src homology (SH)2-containing protein tyrosine phosphatase-1 (SHP-1). Closely related molecules with overlapping functions, such as the Syk kinases, SYK, and ZAP-70, and adaptor molecules, SH2 domain-containing leukocyte protein of 76 kDa and B cell linker protein, are expressed in activated NK cells and are all recruited to the center of the cytolytic synapse. In contrast, the noncytolytic synapse contains SHP-1, but is lacking other components of the central supramolecular activation cluster. These findings indicate a functional role for SHP-1 in both the cytolytic and noncytolytic interactions. We also demonstrate, in three-cell conjugates, that a single NK cell forms a cytolytic synapse with a susceptible target cell in the presence of both susceptible and nonsusceptible target cells.
Development and validation of an approach to produce large‐scale quantities of CpG‐methylated plasmid DNA (2007)

The prokaryotic CpG-specific DNA methylase from Spiroplasma, SssI methylase, has been extensively used to methylate plasmid DNA in vitro to investigate the effects of methylation in vertebrate systems. Currently available methods to produce CpG-methylated plasmid DNA have certain limitations and cannot generate large quantities of methylated DNA without cost or problems of purity. Here we describe an approach in which the SssI methylase gene has been introduced into the Escherichia coli bacterial genome under the control of an inducible promoter. Plasmid DNA propagated in this bacterium under conditions which induce the methylase gene result in significant (>90%) CpG methylation. Methylated DNA produced by this approach behaves similarly to methylated DNA produced in vitro using the purified methylase. The approach is scalable allowing for the production of milligram quantities of methylated plasmid DNA.
Coding techniques in Multiview Video Coding and Joint Multiview Video Model (2009)

Since early 2006, Joint Video Team has been devoting on the development of Multiview Video Coding (MVC) standard as an extension of H.264/AVC. This MVC standard has been finalized in 2008. During the standardization of MVC, there was also a project namely Joint Multiview Video Model (JMVM), which focused on the advanced coding tools that are potentially useful. Those coding tools adopted into JMVM, including illumination compensation and motion skip, have not been added into MVC specification. In this paper, coding techniques in MVC as well as the tools in JMVM are described and discussed, focusing on the coding efficiency.
Genetic Programming 1997: Proceedings of the Second Annual Conference (1997)

info:eu-repo/semantics/published
Design and Implementation of an Agent-Based Middleware for Context-Aware Ubiquitous Services (2005)

In ubiquitous computing environment, different kinds of system components including hardware elements, software components and network connections are required to cooperate with each other to provide services that fulfill user requirements. This paper proposes an agent-based middleware for ubiquitous environment that consists of computers and home electric appliances. The middleware, called AMUSE, can take QoS (quality of service) in ubiquitous environment into consideration by coping with not only user context but also resource context, using agent-based computing technology. In this paper we describe concept, design and initial implementation of AMUSE. Simulation results of experimental ubiquitous service using AMUSE has been shown to prove the effectiveness of our proposed scheme. Additionally, we show the initial implementation of multimedia communication application based on AMUSE to confirm the feasibility and effectiveness of our scheme.
Measuring ISP topologies with rocketfuel (2002)

To date, realistic ISP topologies have not been accessible to the research community, leaving work that depends on topology on an uncertain footing. In this paper, we present new Internet mapping techniques that have enabled us to directly measure router-level ISP topologies. Our techniques reduce the number of required traces compared to a brute-force, all-to-all approach by three orders of magnitude without a significant loss in accuracy. They include the use of BGP routing tables to focus the measurements, exploiting properties of IP routing to eliminate redundant measurements, better alias resolution, and the use of DNS to divide each map into POPs and backbone. We collect maps from ten diverse ISPs using our techniques, and find that our maps are substantially more complete than those of earlier Internet mapping efforts. We also report on properties of these maps, including the size of POPs, distribution of router outdegree, and the inter-domain peering structure. As part of this work, we release our maps to the community.
Selective Electrodeposition of Micropatterns on Predefined Surface Defects on p-Si(100) (2001)

NRC publication: Yes
Repressed expression of the HER-2/c-erbB-2 proto-oncogene by the adenovirus E1a gene products. (1991)

The E3 region of adenovirus induces down-regulation of epidermal growth factor receptor (EGFR) through endocytosis. Here we report that an EGFR-related protein, the HER-2/c-erbB-2 gene product, p185, is also down-regulated by adenovirus, but via a different mechanism. We found that the adenovirus E1a gene is responsible for the repression of HER-2/c-erbB-2 at the RNA level.
PI3Kδ Inhibitors in Cancer: Rationale and Serendipity Merge in the Clinic (2011)

A key question is whether compounds targeting a single PI3K catalytic isoform can provide meaningful single agent efficacy in cancer cells that express multiple isoforms. Clinical studies of the drug CAL-101 have provided a significant advance by showing that selective targeting of PI3Kδ achieves efficacy in chronic lymphocytic leukemia, in part through targeting the tumor microenvironment.
Influence of the Structure of the Amino Group and Polarity of the Medium on the Photophysical Behavior of 4-Amino-1,8-naphthalimide Derivatives (2002)

Photophysical behavior of two series of 4-amino-1,8-naphthalimide derivatives differing in the amino functionality has been studied as a function of the polarity of the medium. The location of the lowest singlet state of the systems, intramolecular charge transfer (ICT) in nature, is largely controlled by the conformation of the 4-amino group rather than its electron-donating ability. The fluorescence properties of the systems are strongly dependent on the nature of the amino group as well as on the polarity of the media. An increase in the length of the dialkyl groups connected to the amino nitrogen or an increase in the size of the ring containing the amino nitrogen enhances the nonradiative deactivation of the fluorescent state of the molecule. The nonradiative relaxation process is facilitated by an increase in the polarity of the media. The present results suggest that the radiationless deactivation of the fluorescent state of the systems is dependent on the nitrogen inversion rate at the amino group.
Requirements for IP Version 4 Routers (1995)

This memo defines and discusses requirements for devices that perform
the network layer forwarding function of the Internet protocol suite.
[STANDARDS-TRACK]
Quantum generalisation of feedforward neural networks (2017)

Abstract We propose a quantum generalisation of a classical neural network. The classical neurons are firstly rendered reversible by adding ancillary bits. Then they are generalised to being quantum reversible, i.e., unitary (the classical networks we generalise are called feedforward, and have step-function activation functions). The quantum network can be trained efficiently using gradient descent on a cost function to perform quantum generalisations of classical tasks. We demonstrate numerically that it can: (i) compress quantum states onto a minimal number of qubits, creating a quantum autoencoder, and (ii) discover quantum communication protocols such as teleportation. Our general recipe is theoretical and implementation-independent. The quantum neuron module can naturally be implemented photonically.
Segregation of nucleolar components coincides with caspase-3 activation in cisplatin-treated HeLa cells (2001)

We studied morphological changes of the nucleoli in HeLa cells treated with cisplatin and compared them with induction of markers of programmed cell death and TUNEL staining. We used different light microscopic nucleolar staining methods allowing us to visualize not only nucleolar proteins but also nucleolar RNA. Our results show predominantly compact, centrally localized nucleoli in intact control HeLa cells. In cisplatin-treated HeLa cells, we found an early onset of nucleolar segregation of proteins detected by argyrophilic nucleolar organizer regions and anti-nucleolar monoclonal antibody as well as an increased immunoreactivity for activated caspase-3 after 6 hours. Staining with Toluidine Blue and Methyl-green Pyronine revealed segregated nucleoli 12 hours after the treatment with cisplatin. TUNEL positivity in cisplatin-treated HeLa cells was accompanied by the aggregation of the argyrophilic proteins in the central portion of nucleus, disappearance of nucleolar RNA and shrinkage of the nucleus after 24 hours. Monitoring of the biochemical changes by immunoblotting revealed that activation of distinct caspases and degradation of their downstream protein substrates is executed in two phases. During an early apoptotic stage beginning 4.5 hours post treatment an activation of caspase-9 and caspase-3 was observed. This was accompanied by proteolytic cleavage of poly(ADP-ribose) polymerase-1 (PARP-1). The caspase-9 activation seems to be mediated by recruitment by the activating factor Apaf-1 because the increased accumulation of Apaf-1 and cytochrome C in cytosol preceded the generation of mature caspase-9 form. A second phase of apoptosis occurring between 10 and 15 hours post treatment was characterized by degradation of other nucleolar and nuclear proteins such as nuclear lamins, topoisomerase I and B23. In conclusion, remarkable segregation of nucleolar argyrophilic proteins, nucleolar RNA and a simultaneous activation of the cascade of caspases markedly preceded the TUNEL positivity in cisplatin-treated HeLa cells thereby substantiating the hypothesis that the nucleolus is a preferred target for caspase-3-dependent proteolysis in cisplatin-treated HeLa cells.
In vivo inhibition of estrone sulfatase activity and growth of nitrosomethylurea-induced mammary tumors by 667 COUMATE. (2000)

The development of potent steroid sulfatase inhibitors is an important new therapeutic strategy for the treatment of postmenopausal women with breast cancer. A series of tricyclic coumarin sulfamates were synthesized, and their inhibitory properties were examined in vitro and in vivo. In a placental microsomal assay system, 667 COUMATE emerged as the most potent inhibitor with an IC50 of 8 nM. Administration of a single dose (10 mg/kg, p.o.) of 667 COUMATE inhibited rat liver estrone sulfatase activity by 93%. 667 COUMATE was devoid of estrogenicity, as indicated by its failure to stimulate the growth of uteri in ovariectomized rats. In vivo, estrone sulfate-stimulated growth of uteri in ovariectomized rats was inhibited by 667 COUMATE. Using the nitrosomethylurea-induced mammary tumor model, we found that 667 COUMATE caused regression of estrone sulfate-stimulated tumor growth in a dose-dependent manner. The identification of 667 COUMATE as a potent steroid sulfatase inhibitor will enable the therapeutic potential of this type of therapy to be evaluated.