gebhart/patrepeval huggingface dataset:
The intracellular tyrosine kinase domain of the epidermal growth factor receptor undergoes a conformational change upon autophosphorylation. (1994)

The intracellular portion of the epidermal growth factor receptor consists of a tyrosine kinase domain of approximately 290 amino acids and a COOH-terminal regulatory domain of approximately 230 amino acids that contains five sites of autophosphorylation. The effect of autophosphorylation on the conformation of the intracellular domain has been analyzed using gel filtration. Both phosphorylated and dephosphorylated forms of the intracellular domain exist as monomers and as dimers and appear to have an extended conformation. The Stokes' radii of phosphorylated monomers and dimers were larger than those of the dephosphorylated forms, indicating that the dephosphorylated form is more compact. These results indicate that a significant conformational change occurs in the intracellular portion of the epidermal growth factor receptor upon tyrosine autophosphorylation.
Ferry: An Architecture for Content-Based Publish/Subscribe Services on P2P Networks (2005)

Leveraging DHTs (distributed hash table), we propose Ferry, an architecture for content-based publish/subscribe services. With its novel design in subscription installation, subscription management and event delivery algorithm, Ferry can serve as a scalable platform to host any and many content-based publish/subscribe services: any publish/subscribe service with a unique scheme can run on top of Ferry, and many publish/subscribe services can run together on top of Ferry. For each of the publish/subscribe services running on top of Ferry, Ferry does not need to maintain or dynamically generate any dissemination tree. Instead, it exploits the embedded trees in DHTs such as Chord to deliver events, thereby imposing little overhead. By delivering events along DHT links, Ferry has two main advantages: (1) it eliminates the cost in construction and maintenance of the dissemination trees; (2) it allows further optimization, i.e., the DHT link maintenance messages could be piggybacked onto the event delivery messages to reduce the maintenance cost which is inherent and nontrivial in DHTs. Moreover, Ferry can support a publish/subscribe scheme with a very large number of event attributes.
Properties of single crystalline semiconducting CoSb3 (1996)

A study of the thermoelectric properties of the skutterudite compound CoSb3 was carried out on single crystals grown by the Bridgman gradient freeze technique. p- and n-type samples were obtained over a wide range of carrier concentration. Undoped As-grown crystals show p-type conductivity while n-type samples were obtained by addition of Te or Pd. Samples were characterized by x-ray diffractometry, electron microprobe analysis, and density measurements. The physical properties of CoSb3 such as linear thermal expansion coefficient, sound velocity, and Debye temperature were also determined and are presented. Seebeck coefficient, electrical resistivity, thermal conductivity, and Hall effect measurements were performed between room temperature and about 900 K. Exceptionally high Hall mobilities were obtained on p-type samples with a maximum room-temperature Hall mobility of 3300 cm2 V−1 s−1 at a carrier concentration of 1×1017 cm−3. The results of the transport property measurements are discussed and are in agreement with some recent predictions based on band structure calculations. The potential of CoSb3 for thermoelectric applications is evaluated.
Structure sensitivity and nanoscale effects in electrocatalysis (2011)

This review discusses the role of the detailed nanoscale structure of catalytic surfaces on the activity of various electrocatalytic reactions of importance for fuel cells, hydrogen production, and other environmentally important catalytic reactions, such as carbon monoxide oxidation, methanol and ethanol oxidation, ammonia oxidation, nitric oxide reduction, hydrogen evolution, and oxygen reduction. Specifically, results and insights obtained from surface-science single-crystal-based model experiments are linked to experiments on well-defined shape-controlled nanoparticles. A classification of structure sensitive effects in electrocatalysis is suggested, based both on empirical grounds and on quantum-chemical viz. thermochemical considerations. The mutual relation between the two classification schemes is also discussed. The review underscores the relevance of single-crystal modeling of nanoscale effects in catalysis, and points to the special role of two kinds of active sites for electrocatalysis on nanoparticulate surfaces: (i) steps and defects in (111) terraces or facets, and (ii) long-range (100) terraces or facets.
Antigenically distinct subpopulations of myeloid progenitor cells (CFU-GM) in human peripheral blood and marrow. (1983)

Two types of progenitor cells of the human granulocytic and monocytic lineages (CFU-GM) can be distinguished by using mouse monoclonal antibodies against human hemopoietic cells. Type 1 CFU-GM contribute all of the peripheral blood CFU-GM as well as a small fraction of bone marrow CFU-GM and express surface antigens recognized by "anti-lymphomonocytic" monoclonal antibodies S3-13 and S17-25 but not the antigens recognized by R1B19 and WGHS-29-1 (two monoclonal antibodies that react with all the cells of the granulocytic lineage). Type 2 CFU-GM are present only in the marrow and react with S3-13, R1B19, and WGHS-29-1. Partial reactivity with S17-25 was observed only in the complement-dependent cytotoxicity test. In vitro culture of type 1 CFU-GM in liquid medium in the presence of granulocyte-macrophage colony-stimulatory factor (GM-CSF) generates colony-forming cells that have the surface phenotype of type 2 CFU-GM. This finding supports the idea of two different stages of maturation of myelomonocytic progenitor cells represented by type 1 and type 2 CFU-GM.
Capnocytophaga canimorsus sp. nov. (formerly CDC group DF-2), a cause of septicemia following dog bite, and C. cynodegmi sp. nov., a cause of localized wound infection following dog bite (1989)

CDC group DF-2 is the vernacular name given to a slow-growing gram-negative bacterium that causes septicemia and meningitis in humans. Infections frequently (one-third of cases) occur following dog bites or close contact with dogs or occasionally with cats. Splenectomy and alcoholism appear to be strong predisposing factors for DF-2 infection. In addition to 150 DF-2 strains received for identification, we received 9 DF-2-like strains; 6 were isolated from wound or eye infections, 3 of which were associated with dog bites and 1 of which was associated with a cat scratch, and 3 were isolated from dog mouths. The major characteristics of DF-2 include production of acid but no gas from lactose and maltose and usually D-glucose; positive reactions for oxidase, catalase, arginine dihydrolase, gliding motility, and o-nitrophenyl-beta-D-galactopyranoside; growth enhanced by serum and by incubation in a candle jar atmosphere; and negative reactions for sucrose, raffinose, inulin, melibiose, nitrate reduction, indole, and growth on MacConkey agar. DF-2-like strains had the same characteristics, except that acid was formed from sucrose, raffinose, inulin, and melibiose. By the hydroxyapatite method, DNAs from 12 DF-2 strains were 88% related in 60 degrees C reactions and 84% related in 75 degrees C reactions. Related sequences contained 0.5 to 1.5% unpaired bases (divergence). Three DF-2-like strains were 73 to 80% related at 60 degrees C (with 2.0 to 2.5% divergence) and 68 to 75% related at 75 degrees C. The relatedness of DF-2 and DF-2-like strains was 19 to 31% at 60 degrees Celsius and 13 to 19% at 75 degrees Celsius. The relatedness of DF-2 and DF-2-like strains to Capnocytophaga species was 4 to 7%. The DNA relatedness date indicate that eh DF-2 and the DF-2-like strains are separate, previously undescribed species. Both groups are phenotypically and genetically distinct from Capnocytophaga species, although they do share several characteristics with Capnocytophaga species, including cellular morphology, gliding motility, cellular fatty acid composition, enhancement of growth in a candle jar atmosphere, and G+C content. The new species differ from Capnocytophaga species by their positive oxidase and catalase reactions. We chose to avoid creating a new genus and proposed the names Capnocytophaga canimorsus sp. nov. for group DF-2 and C. cynodegmi sp. nov. for the DF-2-like strains.
Lipoteichoic acid preparations of gram-positive bacteria induce interleukin-12 through a CD14-dependent pathway (1996)

Interleukin 12 (IL-12) strongly augments gamma interferon production by natural killer (NK) and T cells. IL-12 also promotes effective cell-mediated immune responses, which are particularly important against intracellular bacteria such as Listeria monocytogenes. While the lipopolysaccharide (LPS) of gram-negative bacteria induces monocyte production of IL-12, the relevant gram-positive components which induce IL-12 production are uncharacterized. We used the human monocytic cell line THP-1 to study IL-12 induction by gram-positive bacteria. Muramyl dipeptides as well as the major muramyl tetrapeptide component of Streptococcus pneumoniae were inactive for inducing IL-12. In contrast, lipoteichoic acid (LTA), a predominant surface glycolipid of gram-positive bacteria, potently induced IL-12 p40 gene expression. A competitive LPS antagonist, Rhodobacter sphaeroides LPS, inhibited LTA-induced IL-12 production, suggesting a common pathway for LPS and LTA in IL-12 activation. Pretreatment of cells with anti-CD14 monoclonal antibody blocked both LPS and LTA induction of IL-12 p40 expression. LTA also induced Thl development in naive CD4 T cells by an IL-12-dependent mechanism, indicating direct induction of physiologic levels of IL-12. Together, these results show that LTA is a potent surface structure of gram-positive bacteria which induces IL-12 in monocytes through a CD14-mediated pathway.
Pancreatic Adenocarcinoma, Version 2.2012 (2012)

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Pancreatic Adenocarcinoma discuss the workup and management of tumors of the exocrine pancreas. These NCCN Guidelines Insights provide a summary and explanation of major changes to the 2012 NCCN Guidelines for Pancreatic Adenocarcinoma. The panel made 3 significant updates to the guidelines: 1) more detail was added regarding multiphase CT techniques for diagnosis and staging of pancreatic cancer, and pancreas protocol MRI was added as an emerging alternative to CT; 2) the use of a fluoropyrimidine plus oxaliplatin (e.g., 5-FU/leucovorin/oxaliplatin or capecitabine/oxaliplatin) was added as an acceptable chemotherapy combination for patients with advanced or metastatic disease and good performance status as a category 2B recommendation; and 3) the panel developed new recommendations concerning surgical technique and pathologic analysis and reporting.
Toluidine Blue-Mediated Photodynamic Effects on Staphylococcal Biofilms (2007)

Staphylococci are important causes of nosocomial and medical-device-related infections. Their virulence is attributed to the elaboration of biofilms that protect the organisms from immune system clearance and to increased resistance to phagocytosis and antibiotics. Photodynamic treatment (PDT) has been proposed as an alternative approach for the inactivation of bacteria in biofilms. In this study, we have investigated the effect of the photodynamic action of toluidine blue O (TBO) on the viability and structure of biofilms of Staphylococcus epidermidis and of a methicillin-resistant Staphylococcus aureus strain. Significant inactivation of cells was observed when staphylococcal biofilms were exposed to TBO and laser simultaneously. The effect was found to be light dose dependent. Confocal laser scanning microscopic study suggested damage to bacterial cell membranes in photodynamically treated biofilms. In addition, scanning electron microscopy provided direct evidence for the disruption of biofilm structure and a decrease in cell numbers in photodynamically treated biofilms. Furthermore, the treatment of biofilms with tetrasodium EDTA followed by PDT enhanced the photodynamic efficacy of TBO in S. epidermidis, but not in S. aureus, biofilms. The results suggest that photodynamic treatment may be a useful approach for the inactivation of staphylococcal biofilms adhering to solid surfaces of medical implants.
Building Footprint Generation Using Improved Generative Adversarial Networks (2018)

Building footprint information is an essential ingredient for 3-D reconstruction of urban models. The automatic generation of building footprints from satellite images presents a considerable challenge due to the complexity of building shapes. In this letter, we have proposed improved generative adversarial networks (GANs) for the automatic generation of building footprints from satellite images. We used a conditional GAN (CGAN) with a cost function derived from the Wasserstein distance and added a gradient penalty term. The achieved results indicated that the proposed method can significantly improve the quality of building footprint generation compared to CGANs, the U-Net, and other networks. In addition, our method nearly removes all hyperparameters tuning.
Human Cdc34 and Rad6B Ubiquitin-Conjugating Enzymes Target Repressors of Cyclic AMP-Induced Transcription for Proteolysis (1999)

Ubiquitin-mediated proteolysis controls diverse physiological processes in eukaryotes. However, few in vivo targets of the mammalian Cdc34 and Rad6 ubiquitin-conjugating enzymes are known. A yeast-based genetic assay to identify proteins that interact with human Cdc34 resulted in three cDNAs encoding bZIP DNA binding motifs. Two of these interactants are repressors of cyclic AMP (cAMP)-induced transcription: hICERIIgamma, a product of the CREM gene, and hATF5, a novel ATF homolog. Transfection assays with mammalian cells demonstrate both hCdc34- and hRad6B-dependent ubiquitin-mediated proteolysis of hICERIIgamma and hATF5. This degradation requires an active ubiquitin-conjugating enzyme and results in abrogation of ICERIIgamma- and ATF5-mediated repression of cAMP-induced transcription. Consistent with these results, the endogenous ICER protein is elevated in cells which are null for murine Rad6B (mHR6B-/-) or transfected with dominant negative and antisense constructs of human CDC34. Based on the requirement for CREM/ICER and Rad6B proteins in spermatogenesis, we determined expression of Cdc34, Rad6B, CREM/ICER isoforms, and the Skp1-Cullin-F-box ubiquitin protein ligase subunits Cul-1 and Cul-2, which are associated with Cdc34 activity during murine testicular development. Cdc34, Rad6B, and the Cullin proteins are expressed in a developmentally regulated manner, with distinctly different patterns for Cdc34 and the Cullin proteins in germ cells. The Cdc34 and Rad6B proteins are significantly elevated in meiotic and postmeiotic haploid germ cells when chromatin modifications occur. Thus, the stability of specific mammalian transcription factors is the result of complex targeting by multiple ubiquitin-conjugating enzymes and may have an impact on cAMP-inducible gene regulation during both meiotic and mitotic cell cycles.
Exploiting Geometric Restrictions in a PTZ Camera for Finding Point-orrespondences Between Configurations (2010)

A pan-tilt-zoom (PTZ) camera, fixed in location, may perform only rotational movements. There is a class of feature-based self-calibration approaches that exploit the restrictions on the camera motion in order to obtain accurate point-correspondences between two configurations of a PTZ camera. Most of these approaches require extensive computation and yet do not guarantee a satisfactory result. In this paper, we approach this problem from a different perspective. We exploit the geometric restrictions on the image planes, which are imposed by the motion restrictions on the camera. We present a simple method for estimating the camera focal length and finding the point-correspondences between two camera configurations. We compute pan-only, tilt-only and zoom-only correspondences and then combine the three to derive the geometrical relationship between any two camera configurations. We perform radial lens distortion estimation in order to calibrate distorted image coordinates. Our purely geometric approach does not require any intensive computations, feature tracking or training. However, our point-correspondence experiments show that, it still performs well-enough for most computer vision applications of PTZ cameras.
Dual excitation reactive ion etcher for low energy plasma processing (1992)

The influence of the excitation frequency in the parallel plate cathode-coupling equipment has been investigated and it was found that the self-bias voltage of the cathode becomes a logarithmic function of the excitation frequency in two distinct regions. By selecting appropriate excitation frequencies in a dual excitation system, the study found that the plasma density can be controlled by varying the plasma generating rf power without affecting the dc potential of the electrodes. The effect of the plasma generating rf power on plasma density was determined by monitoring the optical emission spectrum, ion current collected at dc biased electrode, and the SiO2 etching rate when the substrate was rf biased to −50 V. Also, the low ion energy etching of Si and SiO2 was demonstrated in CF4 and SiF4 plasmas utilizing the dual excitation system. Then, applied to the plasma cleaning of the fluorocarbon layer subsequent to CF4/H2 plasma etching, i.e., a typical gas combination used for SiO2 etching. SiF4 plasma cleaning as well as H2 plasma were effective in removal of organic contamination of the silicon.
Evidence That the Angiotensin IV (AT4) Receptor Is the Enzyme Insulin-regulated Aminopeptidase (2001)

Central infusion of angiotensin IV or its more stable analogues facilitates memory retention and retrieval in normal animals and reverses amnesia induced by scopolamine or by bilateral perforant pathway lesions. These peptides bind with high affinity and specificity to a novel binding site designated the angiotensin AT(4) receptor. Until now, the AT(4) receptor has eluded molecular characterization. Here we identify the AT(4) receptor, by protein purification and peptide sequencing, to be insulin-regulated aminopeptidase (IRAP). HEK 293T cells transfected with IRAP exhibit typical AT(4) receptor binding characteristics; the AT(4) receptor ligands, angiotensin IV and LVV-hemorphin 7, compete for the binding of [(125)I]Nle(1)-angiotensin IV with IC(50) values of 32 and 140 nm, respectively. The distribution of IRAP and its mRNA in the brain, determined by immunohistochemistry and hybridization histochemistry, parallels that of the AT(4) receptor determined by radioligand binding. We also show that AT(4) receptor ligands dose-dependently inhibit the catalytic activity of IRAP. We have therefore demonstrated that the AT(4) receptor is IRAP and propose that AT(4) receptor ligands may exert their effects by inhibiting the catalytic activity of IRAP thereby extending the half-life of its neuropeptide substrates.
SR 33589, a New Amiodarone-Like Agent (1995)

We have assessed the ability of the new amiodarone-like antiarrhythmic agent, SR 33589, to reduce the incidence of ischemia- and reperfusion-induced arrhythmias, in comparison to amiodarone, D-sotalol, and lignocaine. Rats were anesthetized, artificially ventilated, and the thorax opened by a left thoracotomy. Ischemia was induced by left coronary artery ligation, and reperfusion was achieved (after a 5-min period of ischemia) in a separate group of rats by removing the ligature. Agents were given intravenously 5 min before occlusion or orally 4 h before study. During a 20-min period of ischemia, SR 33589 reduced significantly the incidence of ventricular fibrillation (VF) from 80 to 30% (p < 0.05) at 3 mg/kg i.v. and eliminated VF and mortality at 10 mg/kg i.v. In contrast, amiodarone at 10 mg/kg i.v. reduced significantly only the incidence of mortality during ischemia (from 60 to 0%, p < 0.01), while having no significant effect on 3 mg/kg i.v. On reperfusion (after a 5-min period of ischemia), SR 33589 reduced significantly the incidence of mortality (from 90 to 20%, p < 0.01) at 1 mg/kg and eliminated VF and mortality when administered at 3 and 10 mg/kg. Against both ischemia- and reperfusion-induced arrhythmias, approximately 20% of animals showed AV block at the highest dose of SR 33589 tested. This was not observed with lower doses. Amiodarone (10 mg/kg i.v.) eliminated completely reperfusion-induced VF and mortality while having no significant effect at 1 and 3 mg/kg.(ABSTRACT TRUNCATED AT 250 WORDS)
Formation of Glasses from Liquids and Biopolymers (1995)

Glasses can be formed by many routes. In some cases, distinct polyamorphic forms are found. The normal mode of glass formation is cooling of a viscous liquid. Liquid behavior during cooling is classified between "strong" and "fragile," and the three canonical characteristics of relaxing liquids are correlated through the fragility. Strong liquids become fragile liquids on compression. In some cases, such conversions occur during cooling by a weak first-order transition. This behavior can be related to the polymorphism in a glass state through a recent simple modification of the van der Waals model for tetrahedrally bonded liquids. The sudden loss of some liquid degrees of freedom through such first-order transitions is suggestive of the polyamorphic transition between native and denatured hydrated proteins, which can be interpreted as single-chain glass-forming polymers plasticized by water and cross-linked by hydrogen bonds. The onset of a sharp change in d<r(2)>dT(<r(2)> is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature. The latter may originate in strong anharmonicity in modes ("bosons"), which permits the system to access multiple minima of its configuration space. These modes, the Kauzmann temperature T(K), and the fragility of the liquid, may thus be connected.