gebhart/patrepeval huggingface dataset:
Purification and characterization of catalase HPII from <i>Escherichia coli</i> K12 (1986)

Catalase (hydroperoxidase II or HPII) of Escherichia coli K12 has been purified using a protocol that also allows the purification of the second catalase HPI in large amounts. The purified HPII was found to have equal amounts of two subunits with molecular weights of 90,000 and 92,000. Only a single 92,000 subunit was present in the immunoprecipitate created when HPII antiserum was added directly to a crude extract, suggesting that proteolysis was responsible for the smaller subunit. The apparent native molecular weight was determined to be 532,000, suggesting a hexamer structure for the enzyme, an unusual structure for a catalase. HPII was very stable, remaining maximally active over the pH range 4-11 and retaining activity even in a solution of 0.1% sodium dodecyl sulfate and 7 M urea. The heme cofactor associated with HPII was also unusual for a catalase, in resembling heme d (a2) both spectrally and in terms of solubility. On the basis of heme-associated iron, six heme groups were associated with each molecule of enzyme or one per subunit.
Deregulation and Mislocalization of the Cytokinesis Regulator ECT2 Activate the Rho Signaling Pathways Leading to Malignant Transformation (2004)

The human ECT2 protooncogene encodes a guanine nucleotide exchange factor for the Rho GTPases and regulates cytokinesis. Although the oncogenic form of ECT2 contains an N-terminal truncation, it is not clear how the structural abnormality of ECT2 causes malignant transformation. Here we show that both the removal of the negative regulatory domain and alteration of subcellular localization are required to induce the oncogenic activity of ECT2. The transforming activity of oncogenic ECT2 was strongly inhibited by dominant negative Rho GTPases, suggesting the involvement of Rho GTPases in ECT2 transformation. Although deletion of the N-terminal cell cycle regulator-related domain (N) of ECT2 did not activate its transforming activity, removal of the small central domain (S), which contains two nuclear localization signals (NLSs), significantly induced the activity. The ECT2 N domain interacted with the catalytic domain and significantly inhibited the focus formation by oncogenic ECT2. Interestingly, the introduction of the NLS mutations in the S domain of N-terminally truncated ECT2 dramatically induced the transforming activity of this otherwise non-oncogenic derivative. Among the known Rho GTPases expressed in NIH 3T3 cells, RhoA was predominantly activated by oncogenic ECT2 in vivo. Therefore, the mislocalization of structurally altered ECT2 might cause the untimely activation of cytoplasmic Rho GTPases leading to the malignant transformation.
Bayesian Nonparametric Regression Modeling of Panel Data for Sequential Classification (2017)

This paper proposes a Bayesian nonparametric regression model of panel data for sequential pattern classification. The proposed method provides a flexible and parsimonious model that allows both time-independent spatial variables and time-dependent exogenous variables to be predictors. Not only this method improves the accuracy of parameter estimation for limited data, but also it facilitates model interpretation by identifying statistically significant predictors with hypothesis testing. Moreover, as the data length approaches infinity, posterior consistency of the model is guaranteed for general data-generating processes under regular conditions. The resulting model of panel data can also be used for sequential classification. The proposed method has been tested by numerical simulation, then validated on an econometric public data set, and subsequently validated for detection of combustion instabilities with experimental data that have been generated in a laboratory environment.
PYK2 in osteoclasts is an adhesion kinase, localized in the sealing zone, activated by ligation of alpha(v)beta3 integrin, and phosphorylated by src kinase. (1998)

Osteoclast activation is initiated by adhesion to the bone surface, followed by cytoskeletal rearrangement, the formation of the sealing zone, and a polarized ruffled membrane. This study shows that PYK2/CAK /RAFTK, a cytoplasmic kinase related to the focal adhesion kinase, is highly expressed in rat osteoclasts in vivo. Using murine osteoclastlike cells (OCLs) or their mononuclear precursors (pOCs), generated in a coculture of bone marrow and osteoblastic MB1.8 cells, we show: ( a ) tyrosine phosphorylation of PYK2 upon ligation of 3 integrins or adhesion of pOCs to serum, vitronectin, osteopontin, or fibronectin but not to laminin or collagen; ( b ) coimmunoprecipitation of PYK2 and c-Src from OCLs; ( c ) PYK2 binding to the SH2 domains of Src; ( d ) marked reduction in tyrosine phosphorylation and kinase activity of PYK2 in OCLs derived from Src ( / ) mice, which do not form actin rings and do not resorb bone; ( e ) PYK2 phosphorylation by exogeneous c-Src; ( f ) translocation of PYK2 to the Triton X-100 insoluble cytoskeletal fraction upon adhesion; ( g ) localization of PYK2 in podosomes and the ring-like structures in OCLs plated on glass and in the sealing zone in OCLs plated on bone; and ( h ) activation of PYK2, in the presence of MB1.8 cells, parallels the formation of sealing zones and pit resorption in vitro and is reduced by echistatin or calcitonin and cytochalasin D. Taken together, these findings suggest that Src-dependent tyrosine phosphorylation of PYK2 is involved in the adhesion-induced formation of the sealing zone, required for osteoclastic bone resorption. ( J. Clin. Invest. 1998. 102: 881-892.) Key words: tyrosine kinase podosome clear zone bone resorption vitronectin receptor
Dichotomal role of inhibition of p38 MAPK with SB 203580 in experimental colitis (2002)

Our results reveal a dichotomy in p38 MAPK action during experimental colitis.
Mapping of receptor binding domains in the envelope protein of spleen necrosis virus (1995)

Spleen necrosis virus (SNV) is an amphotropic retrovirus originally isolated from a duck. Although of avian origin, it also replicates on some mammalian cells. SNV-derived retroviral vectors work with high efficiency and have a high potential for various gene transfer applications. However, little is known about the envelope-receptor interactions of this virus. We constructed a series of recombinant envelope proteins to characterize the SU peptide of SNV. We found that, in contrast to the envelope proteins of other retroviruses, truncated envelope proteins of SNV are transported to the cell surface. Surprisingly, particles displaying truncated envelope proteins can still infect cells, although at reduced efficiencies. Furthermore, these proteins can confer partial superinfection interference. Our data suggest that peptides throughout SU are involved in envelope-receptor interactions. To more precisely determine the localization of the main receptor binding domain, point mutations were introduced at certain regions of the SNV SU which are highly conserved among retroviruses belonging to the same receptor interference group. We identified one point mutation in the middle of SU (position 192) which drastically reduced infectivity and strongly reduced the ability to confer superinfection interference. The level of expression was not abolished, and translocation to the cell membrane of the mutant envelope occurred efficiently. This indicates that amino acid 192 may be directly involved in receptor binding.
Multipoint connection management in high speed networks (1991)

A connection management access protocol (CMAP) for managing multipoint connections in high-speed packet switched networks is described. The protocol is targeted to broadband integrated services digital networks (BISDN) using the asynchronous transfer mode (ATM) communication standard. To establish a multipoint connection, a client first creates a call between itself and the network. The client creating a call is designated the owner of the call. Immediately after creation, the owner is the only endpoint participating in the call. Additional endpoints are added either by invitation from the owner, invitation from another client of the network, or by explicitly requesting to be added. These three modes are sufficient for supporting point-to-point communication (for example, a telephone call), many-to-many communication (for example, a conference call), one-to-many communication (for example, broadcast video), and many-to-one communication (for example, error logging).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Magnetic characterization of a single superparamagnetic bead by phase-sensitive micro-Hall magnetometry (2007)

Employing phase sensitive micro-Hall magnetometry at room temperature, we map the susceptibility of a single superparamagnetic bead, 1.2μm in diameter, as a function of magnetic field. We find that the dependence can be explained by modeling the bead as an ensemble of noninteracting superparamagnetic nanoparticles with log-normal distribution of magnetic moments. We also discuss the effect of possible dipolar interactions between the nanoparticles on the obtained results.
Proton pump inhibitors and risk of gastric cancer: a population-based cohort study (2009)

Proton pump inhibitor (PPI) use leads to hypergastrinaemia, which has been associated with gastrointestinal neoplasia. We evaluated the association between PPI use and risk of gastric cancer using population-based health-care registers in North Jutland, Denmark, during 1990-2003. We compared incidence rates among new users of PPI (n=18,790) or histamine-2-antagonists (H2RAs) (n=17,478) and non-users of either drug. Poisson regression analysis was used to estimate incidence rate ratios (IRRs) adjusted for multiple confounders. We incorporated a 1-year lag time to address potential reverse causation. We identified 109 gastric cancer cases among PPI users and 52 cases among H2RA users. After incorporating the 1-year lag time, we observed IRRs for gastric cancer of 1.2 (95% CI: 0.8-2.0) among PPI users and 1.2 (95% CI: 0.8-1.8) among H2RA users compared with non-users. These estimates are in contrast to significant overall IRRs of 9.0 and 2.8, respectively, without the lag time. In lag time analyses, increased IRRs were observed among PPI users with the largest number of prescriptions or the longest follow-up compared with H2RA users or non-users. Although our results point to a major influence of reverse causation and confounding by indication on the association between PPI use and gastric cancer incidence, the finding of increased incidence among PPI users with most prescriptions and longest follow-up warrants further investigation.
Penetration Testing Tool for Web Services Security (2012)

XML-based SOAP Web Services are a widely used technology, which allows the users to execute remote operations and transport arbitrary data. It is currently adapted in Service Oriented Architectures, cloud interfaces, management of federated identities, eGovernment, or millitary services. The wide adoption of this technology has resulted in an emergence of numerous - mostly complex - extension specifications. Naturally, this has been followed by a rise in large number of Web Services attacks. They range from specific Denial of Service attacks to attacks breaking interfaces of cloud providers [1], [2] or confidentiality of encrypted messages [3]. By implementing common web applications, the developers evaluate the security of their systems by applying different penetration testing tools. However, in comparison to the wellknown attacks as SQL injection or Cross Site Scripting, there exist no penetration testing tools for Web Services specific attacks. This was the motivation for developing the first automated penetration testing tool for Web Services called WS-Attacker. In this paper we give an overview of our design decisions and provide evaluation of four Web Services frameworks and their resistance against WS-Addressing spoofing and SOAPAction spoofing attacks.
VAS2870 and VAS3947 attenuate platelet activation and thrombus formation via a NOX-independent pathway downstream of PKC (2019)

NADPH oxidase (NOX) enzymes are involved in a various physiological and pathological processes such as platelet activation and inflammation. Interestingly, we found that the pan-NOX inhibitors VAS compounds (VAS2870 and its analog VAS3947) exerted a highly potent antiplatelet effect. Unlike VAS compounds, concurrent inhibition of NOX1, 2, and 4 by treatment with ML171, GSK2795039, and GKT136901/GKT137831 did not affect thrombin and U46619-induced platelet aggregation. These findings suggest that VAS compounds may inhibit platelet aggregation via a NOX-independent manner. Thus, we aimed to investigate the detailed antiplatelet mechanisms of VAS compounds. The data revealed that VAS compounds blocked various agonist-induced platelet aggregation, possibly via blocking PKC downstream signaling, including IKKβ and p38 MAPK, eventually reducing platelet granule release, calcium mobilization, and GPIIbIIIa activation. In addition, VAS compounds inhibited mouse platelet aggregation-induced by collagen and thrombin. The in vivo study also showed that VAS compounds delayed thrombus formation without affecting normal hemostasis. This study is the first to demonstrate that, in addition to inhibiting NOX activity, VAS compounds reduced platelet activation and thrombus formation through a NOX-independent pathway downstream of PKC. These findings also indicate that VAS compounds may be safe and potentially therapeutic agents for treating patients with cardiovascular diseases.
Use of ferric ammonium sulfate in serum cholesterol determination. (1973)

Ferric ammonium sulfate, which has advantages over ferric chloride in that it is not deliquescent and does not evolve hydrogen chloride upon addition of sulfuric acid, was used in the ferric chloride—sulfuric acid method for serum cholesterol determination. Comparable results are obtained with these iron salts
Measurement of energy and timing resolution of very highly pixellated LYSO crystal blocks with multiplexed SiPM readout for use in a small animal PET/MR insert (2013)

Arrays of silicon photo-multipliers (SiPMs) are good candidates for the readout of detectors in PET MR inserts due to their high packing density, efficiency, low bias voltage and insensitivity to magnetic fields. In this study we report the readout performance of SensL SiPM arrays in terms of their ability to resolve all elements of pixellated lutetium oxy-orthosilicate (LYSO) crystals, and their energy and timing resolution. A SensL SB4-300-35-CER SiPM array consisting of sixteen 3 × 3 mm elements were used as light sensor. An LYSO crystal block consisting of 10×10 1.2 mm × 1.2 mm × 6.0 mm crystals on the bottom layer and 9×9 1.2 mm × 1.2 mm × 4.0 mm crystals on the top layer (which is offset by ½ the crystal width) was mounted on the SensL array, and covers over 95% of its area. A DPC encoding multiplexor with HDMI cable readout made by the Triumf Instrumentation group with a footprint suitable for allowing 16 modules to form a ring inside a Brooker 7T MR rodent imager was used as a readout. The HDMI cable supplies power, and provides readout of four channels and the device temperature. The average energy resolution for all 100 crystals in the lower layer was 11.3±1.8% and 10.8±1.2% for the 81 crystals in the upper layer. The average timing resolution for all 100 crystals in the lower layer was 2.52±0.23 nsec. and 2.55±0.23 nsec. for the 81 crystals in the upper layer.
An electrostatically actuated gas valve with an S-shaped film element (1994)

A new microvalve actuator driven by electrostatic force is described and shown to be suitable for controlling the flow of a rarefied gas. The actuator consists of a pair of planar electrodes sandwiching a conductive film that has an S-shaped bend in the middle. The S-bend moves back and forth as voltage is alternately applied between each of the electrodes and the film. A manually assembled macromodel actuator having a film 5 mu m thick and 12 mm wide is operated between electrodes separated by 2.5 mm. The propagation speed is 4.0 m s-1 at an applied voltage of 150 V. The large vertical displacement of the film enables the large valve seat lift necessary to allow a certain amount of gas flow. An experimental model of the valve allowed at airflow rate of 10 sccm at a pressure of 60 Pa.
Introduction to IND and recursive partitioning, version 1.0 (1991)

This manual describes the IND package for learning tree classifiers from data. The package is an integrated C and C shell re-implementation of tree learning routines such as CART, C4, and various MDL and Bayesian variations. The package includes routines for experiment control, interactive operation, and analysis of tree building. The manual introduces the system and its many options, gives a basic review of tree learning, contains a guide to the literature and a glossary, lists the manual pages for the routines, and instructions on installation.
What are Web services? (2003)

A Web service, as defined by the W3C Web Services Architecture Working Group, is "a software application identified by a URI, whose interfaces and bindings are capable of being defined, described, and discovered as XML artifacts. A Web service supports direct interactions with other software agents using XML-based messages exchanged via Internet-based protocols." 1 Others refine this definition further by requiring the description be a Web Services Description Language (WSDL) document and the protocol be SOAP.
Characterization of proline endopeptidase from rat brain (1980)

A homogeneous proline endopeptidase from rat brain is characterized with respect to its substrate specificity and the residues essential for catalysis. The two fluorogenic substrate analogues tested, pyroglutamylhistidylprolyl-beta-naphthylamide and pyroglutamy(N-benzylimidazolyl)-histidylprolyl-beta-naphthylamide, have higher Vmax values (19.5 and 26.9 mumol . min-1 . mg-1, respectively) and considerably lower Km values (0.034 and 0.020 mM, respectively) than pyroglutamylhistidylprolylamide (Vmax = 2.9 mumol . min-1 . mg-1 and Km = 4.1 mM). Both fluorogenic substrates give rise to pH optima and pH-rate profiles similar to those of the amide. Values of Km and kcat are determined as a function of pH. Km is pH independent, with the titration curve for kcatKm-1 implicating an active-site residue(s) with a pKa of 6.2. Proline endopeptidase can be completely inactivated by low concentrations of diisopropyl fluorophosphate with an observed second-order rate constant of 2.5 x 10(4) min-1 . M-1. The stoichiometry of the alkylphosphorylation is 0.83 mol/mol of enzyme. The pH dependence of the inactivation by diisopropylfluorophosphate implicates a residue(s) involved in covalent bond formation having a pKa of 6.0. These data suggest that proline endopeptidase is a serine proteinase.
CARBOXYMETHYLCELLULOSE (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCARBOXYMETHYLCELLULOSERodney N. Hader, W. F. Waldeck, and F. W. SmithCite this: Ind. Eng. Chem. 1952, 44, 12, 2803–2812Publication Date (Print):December 1, 1952Publication History Published online1 May 2002Published inissue 1 December 1952https://doi.org/10.1021/ie50516a016RIGHTS & PERMISSIONSArticle Views360Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (5 MB) Get e-Alerts
Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization (2005)

We have detected two paralogs of the tRNA endonuclease gene of Methanocaldococcus jannaschii in the genome of the crenarchaeote Sulfolobus solfataricus. This finding has led to the discovery of a previously unrecognized oligomeric form of the enzyme. The two genes code for two different subunits, both of which are required for cleavage of the pre-tRNA substrate. Thus, there are now three forms of tRNA endonuclease in the Archaea: a homotetramer in some Euryarchaea, a homodimer in other Euryarchaea, and a heterotetramer in the Crenarchaea and the Nanoarchaea. The last-named enzyme, arising most likely by gene duplication and subsequent "subfunctionalization," requires the products of both genes to be active.
The nuclear growth hormone receptor binding protein. Antigenic and physicochemical characterization. (1991)

The mechanisms involved in transcriptional regulation by growth hormone (GH) remain unknown. We report here that GH receptor immunoreactivity can be demonstrated in the nuclei of GH-responsive rat and rabbit tissues at both the light and electron micrograph level using monoclonal antibodies to the receptor extracellular domain. Nuclear staining is heterogeneous and associated with both chromatin and the nuclear membrane. To confirm these observations, nuclei were isolated from rabbit liver by two methods, one involving extensive nonionic detergent washes. Scatchard analysis of nuclear fractions revealed high affinity somatogenic receptor in nuclear membranes, nucleoplasm, and chromatin fractions. A panel of GH receptor monoclonal antibodies was used to further define these nuclear binding sites as being antigenically identical to microsomal receptor in all but one case. In addition, affinity cross-linking experiments showed the somatogenic binding subunit to have a reduced Mr of 67,000, similar to the Mr of the GH binding protein. We propose that the association of a GH binding protein with the nucleus may provide a means whereby GH can regulate the transcription of specific genes either directly or indirectly through nuclear kinase C activation. This speculation is congruent with the recent demonstration of a GH response element by Yoon et al. (Yoon, J. B., Berry, S. A., Seelig, S., and Towle, H. C. (1990) J. Biol. Chem. 265, 19947-19954).
Genetic organization and regulation of the xylose degradation genes in Streptomyces rubiginosus (1991)

The xylose isomerase (xylA) and the xylulose kinase (xylB) genes from Streptomyces rubiginosus were isolated, and their nucleotide sequences were determined. The xylA and xylB genes encode proteins of 388 and 481 amino acids, respectively. These two genes are transcribed divergently from within a 114-nucleotide sequence separating the coding regions. Regulation of the xyl genes in S. rubiginosus was examined by fusing their promoters to the Pseudomonas putida catechol dioxygenase gene and integrating the fusions into the minicircle integration site on the S. rubiginosus chromosome. The expression of catechol dioxygenase was then measured under a variety of conditions. The results indicated that transcription of the xyl genes was induced by D-xylose and repressed by glucose. Data from quantitative S1 mapping were consistent with this conclusion and suggested that xylA had one and xylB had two transcription initiation sites. The transcription initiation site of xylA was 40 bp upstream of the coding region. The two transcription initiation sites of xylB were 20 and 41 bp 5' of its translation initiation codon. Under control of appropriate regulatory elements, the cloned xyl genes are capable of complementing either Escherichia coli xylose isomerase- or xylulose kinase-deficient strains. The deduced amino acid sequence of the S. rubiginosus xylA protein is highly homologous to sequences of other microbial xylose isomerases.