gebhart/patrepeval huggingface dataset:
Regulation of the Macrophage Vacuolar ATPase and Phagosome-Lysosome Fusion by <i>Histoplasma capsulatum</i> (1999)

Histoplasma capsulatum (Hc) maintains a phagosomal pH of about 6.5. This strategy allows Hc to obtain iron from transferrin, and minimize the activity of macrophage (Mo) lysosomal hydrolases. To determine the mechanism of pH regulation, we evaluated the function of the vacuolar ATPase (V-ATPase) in RAW264.7 Mo infected with Hc yeast or the nonpathogenic yeast Saccharomyces cerevisae (Sc). Incubation of Hc-infected Mo with bafilomycin, an inhibitor of the V-ATPase, did not affect the intracellular growth of Hc, nor did it affect the intraphagosomal pH. In contrast, upon addition of bafilomycin, phagosomes containing Sc rapidly changed their pH from 5 to 7. Hc-containing phagosomes had 5-fold less V-ATPase than Sc-containing phagosomes as quantified by immunoelectron microscopy. Furthermore, Hc-containing phagosomes inhibited phagolysosomal fusion as quantified by the presence of acid phosphatase, accumulation of LAMP2, and fusion with rhodamine B-isothiocyanate-labeled dextran-loaded lysosomes. Finally, in Hc-containing phagosomes, uptake of ferritin was equivalent to phagosomes containing Sc, indicating that Hc-containing phagosomes have full access to the early "bulk flow" endocytic pathway. Thus, Hc yeasts inhibit phagolysosomal fusion, inhibit accumulation of the V-ATPase in the phagosome, and actively acidify the phagosomal pH to 6.5 as part of their strategy to survive in Mo phagosomes.
Phagocytes Produce 5-Chlorouracil and 5-Bromouracil, Two Mutagenic Products of Myeloperoxidase, in Human Inflammatory Tissue (2003)

Oxidative damage to DNA has been implicated in carcinogenesis during chronic inflammation. Epidemiological and biochemical studies suggest that one potential mechanism involves myeloperoxidase, a hemeprotein secreted by human phagocytes. In this study, we demonstrate that human neutrophils use myeloperoxidase to oxidize uracil to 5-chlorouracil in vitro. Uracil chlorination by myeloperoxidase or reagent HOCl exhibited an unusual pH dependence, being minimal at pH approximately 5, but increasing markedly under either acidic or mildly basic conditions. This bimodal curve suggests that myeloperoxidase initially produces HOCl, which subsequently chlorinates uracil by acid- or base-catalyzed reactions. Human neutrophils use myeloperoxidase and H2O2 to chlorinate uracil, suggesting that nucleobase halogenation reactions may be physiologically relevant. Using a sensitive and specific mass spectrometric method, we detected two products of myeloperoxidase, 5-chlorouracil and 5-bromouracil, in neutrophil-rich human inflammatory tissue. Myeloperoxidase is the most likely source of 5-chlorouracil in vivo because halogenated uracil is a specific product of the myeloperoxidase system in vitro. In contrast, previous studies have demonstrated that 5-bromouracil could be generated by either eosinophil peroxidase or myeloperoxidase, which preferentially brominates uracil at plasma concentrations of halide and under moderately acidic conditions. These observations indicate that the myeloperoxidase system promotes nucleobase halogenation in vivo. Because 5-chlorouracil and 5-bromouracil can be incorporated into nuclear DNA, and these thymine analogs are well known mutagens, our observations raise the possibility that halogenation reactions initiated by phagocytes provide one pathway for mutagenesis and cytotoxicity at sites of inflammation.
Metabolism of diadenosine tetraphosphate (Ap4A) and related nucleotides in plants; review with historical and general perspective (2004)

This review presents our knowledge of potential biochemical conversions of minor mononucleotides, such as adenosine-5'-tetraphosphate (p4A) and adenosine-5'-pentaphosphate (p5A), and dinucleotides, such as diadenosine-5',5"'-P1,P3-triphosphate (Ap3A) and diadenosine-5',5"'-P1,P4-tetraphosphate (Ap4A), in plants. Although the occurrence of p4A, Ap3A and/or Ap4A has been demonstrated in various bacteria, fungi and animals, identification of these compounds in plants has not been reported as yet. However, the ubiquity of both the compounds and enzymes that can synthesize them (certain ligases and transferases), the demonstration that certain plant ligases can synthesize pnAs and ApnNs in vitro, and the existence in plants of specific and nonspecific degradative enzymes strongly suggest that these various pnNs and NpnN's do indeed occur and play a biological role in plant cells. In fact, some of the plant enzymes involved in the synthesis and degradation of these minor mono- and dinucleotides have been studied even more thoroughly than their counterparts from other organisms.
Dependence of indium–tin–oxide work function on surface cleaning method as studied by ultraviolet and x-ray photoemission spectroscopies (2000)

The effect of the method used to clean indium–tin–oxide (ITO) on its work function was investigated by ultraviolet photoemission spectroscopy (UPS) and x-ray photoemission spectroscopy. With only ultrasonic cleaning in the organic solvent, considerable carbon contamination remained on the ITO surface and the work function was low (4.5 eV). In contrast, ultraviolet (UV)–ozone treatment removed significant carbon contamination, with an increase in the work function to 4.75 eV, which improves the hole-injection efficiency into the organic hole-transport layer in organic electroluminescent devices. Although carbon contamination on the ITO surface was also removed by Ar+ sputtering, it was accompanied by the removal of oxygen from ITO, and the work function was reduced (4.3 eV). Three factors, i.e.,: (i) C-containing contaminants, (ii) the O/In ratio, and (iii) the In/Sn ratio on the ITO surface affect the work function. The present results and those of other workers suggest that these three factors affect the work function in the order: (ii)&gt;(i)&gt;(iii), and (i) is the main cause of the increase in the work function in the UV–ozone or O2 plasma treatments.
An I<sup>2</sup>L watch chip with direct LED drive (1976)

This paper will describe a 86 × 96 mil-chip, using MTL/ I <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> L technology, which divides 32 kHz to 1 Hz, with 7μA drawin in the run mode (without display). With the display on, the average current drain is 50 mA; 10 mA peak current/segment.
Proteolysis Involving Matrix Metalloproteinase 13 (Collagenase-3) Is Required for Chondrocyte Differentiation That Is Associated with Matrix Mineralization (2002)

Collagenases are involved in cartilage matrix resorption. Using bovine fetal chondrocytes isolated from physeal cartilages and separated into a distinct prehypertrophic subpopulation, we show that in serum-free culture they elaborate an extracellular matrix and differentiate into hypertrophic chondrocytes. This is characterized by expression of type X collagen and the transcription factor Cbfal and increased incorporation of 45Ca2+ in the extracellular matrix, which is associated with matrix calcification. Collagenase activity, attributable only to matrix metalloproteinase (MMP) 13 (collagenase-3), is up-regulated on differentiation. A nontoxic carboxylate inhibitor of MMP-13 prevents this differentiation; it suppresses expression of type X collagen, Cbfal, and MMP-13 and inhibits increased calcium incorporation in addition to inhibiting degradation of type II collagen in the extracellular matrix. General synthesis of matrix proteins is unaffected. These results suggest that proteolysis involving MMP-13 is required for chondrocyte differentiation that occurs as part of growth plate development and which is associated with matrix mineralization.
Efficient selection of 3′-terminal exons from vertebrate DNA (1993)

Identification of expressed sequences within genomic DNA is a hurdle in the characterization of complex genomes. We developed an exon trapping scheme that provides a positive selection for vertebrate 3'-terminal exons. A copy of the trapped exon sequence is obtained by RT/PCR amplification. The technique detects valid terminal exons without interference from partial exons or non-specific sequences, including simple human repeated sequences. Application to random human cosmids yielded one unique trapped terminal exon per cosmid on average. Because vertebrate terminal exons average 600-700 nucleotides in length, the technique provides transcribed sequences of sufficient length to assist further mapping efforts.
The Estimation of Biological Populations (1954)

A number of statistical models, underlying the methods used in the estimation of the sizes and other parameters of animal populations, are set up. The relevant estimation equations are given, with their variances and covariances. For the most part the theory is designed for large populations. In setting up the models, consideration has been given to the desideratum of having them conform as closely as possible to the actual practices of animal sampling. To what extent the models do agree with reality is one of the many open questions which are noted in this paper.
Characterization of the thermolysis products of Fe(TPTZ)2Cl2.cntdot.nH2O and the related 2,4,6-tris(2-pyridyl)-1,3,5-triazine complexes Zn(TPTZ)Cl2 and Fe(TPTZ)Cl3 (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of the thermolysis products of Fe(TPTZ)2Cl2.cntdot.nH2O and the related 2,4,6-tris(2-pyridyl)-1,3,5-triazine complexes Zn(TPTZ)Cl2 and Fe(TPTZ)Cl3Diana Sedney, Mina Kahjehnassiri, and William Michael ReiffCite this: Inorg. Chem. 1981, 20, 10, 3476–3481Publication Date (Print):October 1, 1981Publication History Published online1 May 2002Published inissue 1 October 1981https://doi.org/10.1021/ic50224a063RIGHTS & PERMISSIONSArticle Views180Altmetric-Citations21LEARN 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 (610 KB) Get e-Alerts Get e-Alerts
Integrated design of Human-Machine Interfaces for production plants (2015)

During the development of production plants, powerful tools (e.g. for CAD, CAE, or simulation) are used. The resulting engineering data represent the basis for the development of the corresponding HMI. However, this development is usually still performed manually to a great extent. Therefore, this paper describes a model-based approach for the integrated design of HMIs for production plants. Beginning with the aggregation of available engineering data in a plant model, a multi-step transformation workflow is presented. The user is enabled to edit the intermediary results and thus influence the generated HMI. A concrete implementation of the workflow is presented by means of a case study for a sample production plant.
Complete Alanine Scanning of Intersubunit Interfaces in a Foot-and-Mouth Disease Virus Capsid Reveals Critical Contributions of Many Side Chains to Particle Stability and Viral Function (2003)

Spherical virus capsids are large, multimeric protein shells whose assembly and stability depend on the establishment of multiple non-covalent interactions between many polypeptide subunits. In a foot-and-mouth disease virus capsid, 42 amino acid side chains per protomer are involved in noncovalent interactions between pentameric subunits that function as assembly/disassembly intermediates. We have individually truncated to alanine these 42 side chains and assessed their relevance for completion of the virus life cycle and capsid stability. Most mutations provoked a drastic reduction in virus yields. Nearly all of these critical mutations led to virions whose thermal inactivation rates differed from that of the parent virus, and many affected also early steps in the viral cycle. Rapid selection of genotypic revertants or variants with forward or compensatory mutations that restored viability was occasionally detected. The results with this model virus indicate the following. (i). Most of the residues at the interfaces between capsid subunits are critically important for viral function, in part but not exclusively because of their involvement in intersubunit recognition. Each hydrogen bond and salt bridge buried at the subunit interfaces may be important for capsid stability. (ii). New mutations able to restore viability may arise frequently at the subunit interfaces during virus evolution. (iii). A few interfacial side chains are functionally tolerant to truncation and may provide adequate mutation sites for the engineering of a thermostable capsid, potentially useful as an improved vaccine.
Dissecting the molecular mechanisms of olfaction in a malaria-vector mosquito (2002)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Disposable reference electrode (1998)

A disposable reference electrode was developed which can be used for environmental and medical analysis. It is an Ag/AgCl electrode with an integrated junction, prepared using inexpensive materials such as glass-fibre filter medium and heat-sealing film with screen printing and encapsulating by lamination. The potential difference between this electrode and a commercial electrode is hardly influenced by concentration changes and pH (3–11) of the analyte solution. The shelf-life and the operational lifetime of the reference electrode were investigated. Applications with disposable ion selective sensors are demonstrated.
Single-Stage Single-Switch PFC Flyback Converter Using a Synchronous Rectifier (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A single-stage single-switch power factor correction (PFC) flyback converter with a synchronous rectifier (SR) is proposed for improving power factor and efficiency. Using a variable switching-frequency controller, this converter is continuously operated with a reduced turn-on switching loss at the boundary of the continuous conduction mode and discontinuous conduction mode (DCM). The proposed PFC circuit provides relatively low dc-link voltage in the universal line voltage, and also complies with Standard IEC 61000-3-2 Class D limits. In addition, a new driving circuit as the voltage driven-synchronous rectifier is proposed to achieve high efficiency. In particular, since a driving signal is generated according to the voltage polarity, the SR driving circuit can easily be used in DCM applications. The proposed PFC circuit and SR driving circuit in the flyback converter with the reduced switching loss are analyzed in detail and optimized for high performance. Experimental results for a 19 V/90 W adapter at the variable switching-frequency of 30<formula formulatype="inline"><tex>$\sim$</tex></formula>70 kHz were obtained to show the performance of the proposed converter. </para>
Prototype 2-stage magnetic pulse compression modulator for pulse power applications (2002)

A magnetic pulse compression (MPC) scheme using a saturable reactor together with pulse capacitor is a useful technology for shaping input pulses into narrow output pulses of a much higher power level. Modulators with MPC circuits can meet the long life and high reliability requirements which are very important in industrial applications. A prototype modulator with a two-stage MPC switch (assembled with amorphous cores) is constructed to generate repetitive pulses of maximum 500 MW peak power with a pulse width (FWHM) of 500 nsec at a maximum pulse repetition rate of 300 Hz into a 24 /spl Omega/ dummy load. In this paper, the detailed system design and operational characteristics of the prototype MPC modulator are presented.
THE STRUCTURE AND SYNTHESIS OF FIREFLY LUCIFERIN (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE STRUCTURE AND SYNTHESIS OF FIREFLY LUCIFERINEmil H. White, Frank McCapra, George F. Field, and William D. McElroyCite this: J. Am. Chem. Soc. 1961, 83, 10, 2402–2403Publication Date (Print):May 1, 1961Publication History Published online1 May 2002Published inissue 1 May 1961https://pubs.acs.org/doi/10.1021/ja01471a051https://doi.org/10.1021/ja01471a051research-articleACS PublicationsRequest reuse permissionsArticle Views1836Altmetric-Citations168LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A DNA Fragment of Herpes Simplex 2 and Its Transcription in Human Cervical Cancer Tissue (1972)

A human cervical tumor, free of detectable infectious herpes simplex 2 virus, contained a fragment comprising 39% of herpes viral DNA. Renaturation kinetics indicate that an average of 1 to 3.5 DNA fragments of herpes simplex virus are present per cell, depending on the ploidy of the cells in this particular tumor. Virus-specific sequences were found linked to highly repetitive sequences of host DNA, which reassociated under conditions designed to preclude reassociation of viral sequences. The tumor also contained RNA transcripts complementary to 5% of the viral DNA. The fraction of viral DNA template transcribed in the cervical tumor is considerably less than that transcribed in productively infected cells (50%).
Development and Inter-Laboratory Validation of Unlabeled Probe Melting Curve Analysis for Detection of JAK2 V617F Mutation in Polycythemia Vera (2011)

With a high detecting sensitivity, unlabeled probe melting curve analysis is more applicable to disclose JAK2 V617F mutation than conventional methodologies. Verified with the favorable inter- and intra-assay reproducibility, unlabeled probe melting analysis provided a generic mutation detecting alternative for real-time instruments.
Increased cyclic nucleotide phosphodiesterase activity associated with proliferation and cancer in human and murine lymphoid cells. (1977)

Guanosine cyclic 3′:5′-monophosphate phosphodiesterase activity of murine leukemic cells (L1210) was 400 times that of human peripheral blood lymphocytes and 15 times that of murine splenic lymphocytes. Adenosine cyclic 3′:5′-monophosphate (cyclic AMP) phosphodiesterase activity of L1210 cells was 320 times that of human peripheral blood lymphocytes and 24 times that of normal murine lymphocytes. The total cyclic AMP and guanosine cyclic 3′:5′-monophosphate phosphodiesterase activities of rapidly growing cultured human lymphoid cells (normal and leukemic lymphoblastoid cell lines) were also markedly elevated when compared to quiescent peripheral blood lymphocytes. Human peripheral blood lymphocytes stimulated by phytohemagglutinin showed a 10-fold increase in total enzyme activity.

Leukemic and normal murine cells contain a low-affinity cyclic AMP phosphodiesterase as normally observed in most mammalian tissues. In contrast, kinetic analyses of cyclic AMP phosphodiesterase activities of human B and T lymphoblastoid cells were similar to those of peripheral blood lymphocytes in that no evidence of a low-affinity enzyme was found. All the lymphoid cells tested showed a 3 to 4 S enzyme form by linear sucrose gradient fractionation. Proliferating and quiescent human cells also contain a higher-molecular-weight cyclic AMP-specific form (5.9 S), while the murine cells contain a 7.0 S higher-molecular-weight form. Both the 5.9 and 7.0 S forms show anomalous kinetic behavior. These results are discussed with respect to the biochemical nature of cyclic nucleotide phosphodiesterases and the role of this enzyme system in the proliferation of lymphoid cells.
Skill acquisition: Compilation of weak-method problem situations. (1987)

Abstract : Cognitive skills are encoded by a set of productions, which are organized according to a hierarchical goal structure. People solve problems in new domains by applying weak problem-solving procedures to declarative knowledge they have about this domain. From these initial problem solutions, production rules are compiled which are specific to that domain and that use of the knowledge. Numerous experimental results follow from this conception of skill organization and skill acquisition. These experiments include predictions about transfer among skills, differential improvement on problem types, effects of working memory limitations, and applications to instruction. The theory implies that all variety of skill acquisition, including that typically regarded as inductive, conforms to this characterization. Keywords: Artificial intelligence; Cognitive science; Skill acquisition; Production system; LISP.
OMMA: open architecture for Operator-guided Monitoring of Multi-step Attacks (2018)

Current attacks are complex and stealthy. The recent WannaCry malware campaign demonstrates that this is true not only for targeted operations, but also for massive attacks. Complex attacks can only be described as a set of individual actions composing a global strategy. Most of the time, different devices are involved in the same attack scenario. Information about the events recorded in these devices can be collected in the shape of logs in a central system, where an automatic search of threat traces can be implemented. Much has been written about automatic event correlation to detect multi-step attacks but the proposed methods are rarely brought together in the same platform. In this paper, we propose OMMA (Operator-guided Monitoring of Multi-step Attacks), an open and collaborative engineering system which offers a platform to integrate the methods developed by the multi-step attack detection research community. Inspired by a HuMa access (Navarro et al., HuMa: A multi-layer framework for threat analysis in a heterogeneous log environment, 2017) and Knowledge and Information Logs-based System (Legrand et al., Vers une architecture «big-data» bio-inspirée pour la détection d’anomalie des SIEM, 2014) systems, OMMA incorporates real-time feedback from human experts, so the integrated methods can improve their performance through a learning process. This feedback loop is used by Morwilog, an Ant Colony Optimization-based analysis engine that we show as one of the first methods to be integrated in OMMA.