gebhart/patrepeval huggingface dataset:
HomeRF™ and SWAP (1998)

The Shared Wireless Aaccess Protocol (SWAP) specification for wireless voice and data networking within the home will enable a new class of mobile consumer devices that draw from the power and content of the Internet and the Home PC. If cable modems and xDSL represent the "last mile" access to the home, then HomeRFTM's mission with SWAP could be called the "very last 150 feet" within and around the home. HomeRFTM has the broad backing of the major corporate stakeholders for networking within the home and is optimized specifically for the cost/performance point needed for consumers. The technology leverages the existing PC-industry infrastructure around the Internet, TCP/IP and Ethernet and adds a standard way to connect to the Public Switched Telephone Network (PSTN) for voice telephony. First products should appear in late 1999 and future versions with enhanced features and/or higher data rates should follow by 1--2 years.
Synthesis and antiproliferative activity of 3α-hydroxyl-3β-methoxymethyl-5α-pregnan-20-one with a C-21 hydrophilic substituent (2017)

A series of 3α-hydroxyl-3β-methoxymethyl-5α-pregnan-20-ones 7-15 possessing C-21 hydrophilic substituents were synthesized from the corresponding C21-bromo steroid 6 in 24%-89% yields. The hydrophilic groups include amino group from Delepine reaction, hydroxyl group from the hydrolysis by cesium formate in anhydrous MeOH, and amino acids, hydrazinecarboxamide, piperazine, and imidazolyl from nucleophilic substitution. Acylation and O-glycosylation of the resulting C-21 hydroxylsteroid also afforded the corresponding acylated and glycosylated products in excellent yield (77%-89%). Among the compounds, aminosteroid 7 and piperazinyl steroid 14 were most potent against the proliferation of human prostate cancer PC-3 cells with IC50 values of 42 and 82 μmol L−1, respectively.
Real-Time Microchip PCR for Detecting Single-Base Differences in Viral and Human DNA (1998)

This report describes real-time 5' nuclease PCR assays to rapidly distinguish single-base polymorphism using a battery-powered miniature analytical thermal cycling instrument (MATCI). Orthopoxviruses and the human complement component C6 gene served as targets to demonstrate the feasibility of using the MATCI for diagnosis of infectious diseases and genetic disorders. In the Orthopoxvirus assay, consensus Orthopoxvirus PCR primers were designed to amplify 266-281 base-pair (bp) segments of the hemagglutinin (HA) gene in camelpox, cowpox, monkeypox, and vaccinia viruses. A vaccinia virus-specific fluorogenic (TaqMan) probe was designed to detect a single-base (A/G) substitution within the HA gene. In the C6 gene assay, a 73-bp segment of the C6 gene was PCR-amplified from human genomic DNA, and TaqMan probes were used to detect a single-base (A/C) polymorphism in the second position of codon 98. The MATCI correctly identified the nucleotide differences in both viral DNA and human genomic DNA. In addition, using a rapid DNA preparation method, it was possible to achieve sample, preparation of human genomic DNA, DNA amplification, and real-time detection in less than 1 h.
Cutting Edge: Differential Roles for Phosphoinositide 3-Kinases, p110γ and p110δ, in Lymphocyte Chemotaxis and Homing (2004)

Despite the established role for PI3Ks in cell migration, the PI3Ks involved in lymphocyte chemotaxis are poorly defined. In this study, we report that p110gamma-deficient T cells, but not B cells, show reduced chemotactic responses to the lymphoid chemokines, CCL19, CCL21, and CXCL12. As B cell and T cell chemotactic responses were both sensitive to the general PI3K inhibitors, wortmannin (WMN) and LY294002, we explored whether B cell responses were affected in mice lacking p110delta, a major PI3K isoform in lymphocytes. B cells deficient in p110delta showed diminished chemotactic responses, especially to CXCL13. Adoptive transfer experiments with WMN-treated wild-type B cells and with p110delta-deficient B cells revealed diminished homing to Peyer's patches and splenic white pulp cords. WMN selectively inhibited CXCR5-dependent B cell homing to Peyer's patches. These observations establish that p110gamma and p110delta function in lymphocyte chemotaxis, and show differential roles for PI3K family members in B and T cell migration.
Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain, Ochrobactrum sp. Strain SJY1 (2014)

A newly isolated strain, SJY1, identified as Ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated vppB, vppD, and vppE, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The vppB gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-N-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-l-nicotine oxidase, 24%) from the pyridine pathway. The vppD gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from Pseudomonas putida strain S16, whereas the specific activity of VppD is ∼10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation.
A fine-grained access control system for XML documents (2002)

Web-based applications greatly increase information availability and ease of access, which is optimal for public information. The distribution and sharing of information via the Web that must be accessed in a selective way, such as electronic commerce transactions, require the definition and enforcement of security controls, ensuring that information will be accessible only to authorized entities. Different approaches have been proposed that address the problem of protecting information in a Web system. However, these approaches typically operate at the file-system level, independently of the data that have to be protected from unauthorized accesses. Part of this problem is due to the limitations of HTML, historically used to design Web documents. The extensible markup language (XML), a markup language promoted by the World Wide Web Consortium (W3C), is de facto the standard language for the exchange of information on the Internet and represents an important opportunity to provide fine-grained access control. We present an access control model to protect information distributed on the Web that, by exploiting XML's own capabilities, allows the definition and enforcement of access restrictions directly on the structure and content of the documents. We present a language for the specification of access restrictions, which uses standard notations and concepts, together with a description of a system architecture for access control enforcement based on existing technology. The result is a flexible and powerful security system offering a simple integration with current solutions.
Crystalline and Paracrystalline Order in High Polymers (1963)

The mathematical treatment of light scattering by regular and random arrays of points is outlined. The diffraction patterns of two-dimensional models are compared with patterns from ideal crystals, imperfect crystals, and paracrystalline lattices. The effects of various types of crystalline imperfections and paracrystalline order on the diffraction pattern are analyzed and examples are presented. It is shown that both natural and synthetic polymers can be treated as paracrystalline materials. The diffraction patterns of polyethylene after various thermal and mechanical treatments are discussed. A detailed model of the structure of polyethylene is presented and various features of the structure of other polymers are pointed out.
High‐level expression of full‐length antibodies using trans‐complementing expression vectors (2003)

Recombinant antibodies are increasingly used as therapeutics for a wide variety of diseases. Generation of cell lines expressing high levels of recombinant antibody typically requires labor-intensive cloning and screening steps. We describe a mammalian expression system for the high-level production of full-length antibody molecules. It has been shown that the dihydrofolate reductase (DHFR) selectable marker can be divided into two fragments that, with the aid of a leucine zipper, can re-associate to form an active molecule. Using bicistronic vectors, we linked the expression of each antibody chain to the expression of a DHFR fragment. Survival in selective media requires expression of both DHFR fragments that, by virtue of these vectors, also selects for the expression of both antibody chains. Initial pools produced 5 microg of Ab/10(6) cells/d (qP = microg/10(6) cells/d). Expression of each antibody chain in conjunction with a portion of DHFR also leads to concurrent amplification of both antibody chains in the presence of methotrexate, a DHFR inhibitor, and results in a two- to fivefold increase in antibody production with basal qPs ranging from 10-25 ug/10(6) cells/d. Shake-flask cultures of amplified pools produced up to 600 mg/L of antibody in 7 days. This system allows for rapid generation of antibodies without cloning and greatly simplifies selection of cell lines for the production of potential antibody therapeutics.
Epidemiology and Risk Factors for Clostridium difficile Infection in Children (2011)

Recent antibiotic exposure and certain comorbid conditions (solid organ transplant, presence of a gastrostomy or jejunostomy tube) were associated with CDI. Diagnostic testing has less utility in patients being treated with C. difficile-active antibiotics.
Charged collagen structure mediates the recognition of negatively charged macromolecules by macrophage scavenger receptors. (1993)

Macrophage scavenger receptors mediate the recognition of a wide range of negatively charged macromolecules including modified low density lipoproteins (LDL). Truncated bovine receptors lacking residues 330-342, which include the conserved lysine cluster of a collagen-like domain, were unable to degrade modified LDL in spite of their expression on the cell surface. Substitution of lysine 337 into alanine abolished the acetyl-LDL degradation and binding at 37 degrees C, but did not abolish the 4 degrees C binding. In contrast, substitution of more than 2 lysines in this region are needed to abolish the oxidized LDL degradation and 37 degrees C binding. Based on computational modeling of this domain, we propose that a "charged collagen" structure containing a lysine cluster forms a positively charged groove which specifically interacts with negatively charged ligands.
Formation of a ternary complex between thrombin, fibrin monomer, and heparin influences the action of thrombin on its substrates. (1990)

The consequences of the combined effects of fibrin II monomer (FnIIm) and heparin (H) on the hydrolysis of peptidyl p-nitroanilide substrates by thrombin (IIa), the cleavage of prothrombin by thrombin and the thrombin-catalyzed release of fibrinopeptides from fibrinogen have been studied at pH 7.4 and I 0.15. The effects of fibrin II monomer and heparin on chromogenic substrate hydrolysis can be described by a hyperbolic mixed inhibition model in which substrate can interact with four possible enzyme species (IIa, IIa.H, IIa.FnIIm, and IIa.FnIIm.H) that arise as a result of random formation of a ternary complex among thrombin, fibrin II monomer, and heparin (Hogg, P. J. and Jackson, C. M. (1990) J. Biol. Chem. 265, 241-247). The formation of the ternary IIa.FnIIm.H complex results in an increase in the Km values of 7.03 +/- 1.17-fold (1.37-9.65 microM) and 1.94 +/- 0.60-fold (38.1-73.9 microM) for H-D-Ile-Pro-Arg-pNA and Cbz-Gly-Pro-Arg-pNA hydrolysis, respectively, and a decrease in the kc values of 0.45 +/- 0.08-fold (49.5-22.3 s-1) and 0.52 +/- 0.05-fold (93.1-48.4 s-1). Fibrin II monomer and heparin in combination also decrease the efficiency (kc/Km) with which thrombin cleaves prothrombin to produce Fragment 1 and Prethrombin 1 by 2.3-fold from 607 +/- 30 to 264 +/- 13 M-1 s-1. In contrast to the effects of fibrin II monomer and heparin on thrombin hydrolysis of chromogenic substrates, its proteolysis of prothrombin and its inactivation by antithrombin III (Hogg, P. J., and Jackson, C. M. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 3619-3623), these components have no discernible influence on the ability of thrombin to cleave fibrinogen. These observations indicate that the substrate specificity of thrombin is altered when it is bound in a complex with fibrin II monomer and heparin and suggest that the catalytic efficiency of thrombin for its physiological substrates will be affected differentially by these interactions. Such ternary complex formation involving thrombin, fibrin II monomer, and heparin may provide a mechanism for selectively regulating thrombin action.
In Silico Analysis of the Lateral Organ Junction (LOJ) Gene and Promoter of Arabidopsis Thaliana (2007)

A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of a few genes involved in lateral organ development and meristem related expression reveals a few common relevant regulatory motifs. The coding region of the LOJ gene is intron-less and contains 19 PPR units. Based on in silico analysis, LOJ protein is predicted to be hydrophobic in nature and targeted to mitochondria. A partial 3D model of LOJ protein has been suggested using a homology-based modeling program.
Quantitation of CD38 expression using QuantiBRITE? beads (1998)

The QuantiBRITE bead method was compared with the CD4 biological calibration method for quantitation of CD38 expression on CD8+ T-lymphocytes of Multicenter AIDS Cohort Study participants. Results were expressed as CD38 antibodies bound per cell (ABCs) and were the same with the two methods provided two conditions were met. These were the use of repurified (> 95% of the monoclonal antibodies [mAbs] have 1 phycoerythrin [PE] molecule per mAb) CD38-PE for both methods and use of repurified CD4-PE to calculate the relative fluorescence intensity multiplier for the CD4 biological calibration method. Our results indicate that the prognostic significance of CD38 values obtained using the QuantiBRITE method can be interpreted using previously published reports (Liu et al.: J Acquir Immune Defic Syndr Hum Retrovirol 16:83-92, 1997 and 18:332-340, 1998). Sample preparation using NH4Cl and FACS lysing solution gave similar results for CD38 relative fluorescence intensity. Dilution into either phosphate-buffered saline with 2% fetal calf serum and 0.1% sodium azide or fixation in 1% paraformaldehyde for 1 or 24 h also gave similar results. In experiments using Raji cells, which express high levels of CD38, the valence of binding of the intact Leu 17 antibody was approximately 68% bivalent and approximately 32% monovalent. This emphasizes the complexity of determining antigen density from ABCs. We conclude that repurified PE conjugates of CD38, which can be consistently made, together with QuantiBRITE PE beads, provide a convenient and reliable method for quantitation of CD38 expression as ABCs.
The Apertos reflective operating system (1992)

Article Free Access Share on The Apertos reflective operating system: the concept and its implementation Author: Yasuhiko Yokote View Profile Authors Info & Claims OOPSLA '92: Conference proceedings on Object-oriented programming systems, languages, and applicationsOctober 1992Pages 414–434https://doi.org/10.1145/141936.141970Published:31 October 1992Publication History 177citation925DownloadsMetricsTotal Citations177Total Downloads925Last 12 Months83Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Specific targeting of human peripheral blood T cells by heteroaggregates containing anti-T3 crosslinked to anti-target cell antibodies. (1986)

Antibody heteroaggregates have been used to render human peripheral blood T cells lytic for specified targets. The heteroaggregates contain anti-T3 covalently linked to antibodies against nominal target cell antigens. Such heteroaggregates bind target cells directly to T3 molecules on effector cells and trigger target cell lysis. Freshly prepared human PBL, when coated with anti-T3-containing heteroaggregates, are lytic without further stimulation, although brief exposure to crude lymphokine-containing supernatants or recombinant IL-2, but not recombinant IFN-gamma, enhances the activity. The effector cells are T8+, and when fully stimulated, their lytic activity approaches that of some cloned CTL. When T cells are treated with heteroaggregate, washed, and incubated at 37 degrees C in medium not containing heteroaggregate, they retain activity for at least 24 h. The results of this study suggest a strategy in which heteroaggregate-coated T cells could be used in vivo to mount a lytic response against pathogenic cells such as tumor cells or virus-infected cells.
miR-19 is a key oncogenic component of mir-17-92 (2009)

Recent studies have revealed the importance of multiple microRNAs (miRNAs) in promoting tumorigenesis, among which mir-17-92/Oncomir-1 exhibits potent oncogenic activity. Genomic amplification and elevated expression of mir-17-92 occur in several human B-cell lymphomas, and enforced mir-17-92 expression in mice cooperates with c-myc to promote the formation of B-cell lymphomas. Unlike classic protein-coding oncogenes, mir-17-92 has an unconventional gene structure, where one primary transcript yields six individual miRNAs. Here, we functionally dissected the individual components of mir-17-92 by assaying their tumorigenic potential in vivo. Using the Emu-myc model of mouse B-cell lymphoma, we identified miR-19 as the key oncogenic component of mir-17-92, both necessary and sufficient for promoting c-myc-induced lymphomagenesis by repressing apoptosis. The oncogenic activity of miR-19 is at least in part due to its repression of the tumor suppressor Pten. Consistently, miR-19 activates the Akt-mTOR (mammalian target of rapamycin) pathway, thereby functionally antagonizing Pten to promote cell survival. Our findings reveal the essential role of miR-19 in mediating the oncogenic activity of mir-17-92, and implicate the functional diversity of mir-17-92 components as the molecular basis for its pleiotropic effects during tumorigenesis.
DNA Prime–Canarypox Boost with Polycistronic Hepatitis C Virus (HCV) Genes Generates Potent Immune Responses to HCV Structural and Nonstructural Proteins (2000)

DNA vaccination was employed to study immune responses to hepatitis C virus (HCV) proteins. As an immunizing strategy, we studied immune responses of BALB/c (H-2d) and C57BL/6 mice (H-2b) to HCV genes delivered intramuscularly as a polycistronic construct capsid/E1/E2/NS2/NS3 (pRC/C-NS3) encoding 5 structural and nonstructural proteins. We also evaluated canarypox virus containing the same HCV genes as a means for potentiating immune responses to naked DNA. Our results indicate that mice that received a polycistronic pRC/C-NS3 with canarypox booster had enhanced antibody and cellular responses to HCV proteins. Immunodominant CD8(+) T cell responses to several HCV structural and nonstructural proteins, characterized by cytotoxicity and interferon (IFN)-gamma production or IFN-gamma production without significant cytotoxicity, were observed in both strains of mice. The combination of naked DNA with a nonreplicating canarypox booster encoding HCV polycistronic pRC/C-NS3 genes appears to diversify and enhance T cell responses to HCV proteins.
Addition of Modified Bentonites in Polymer Gel Formulation of 2,4-D for Its Controlled Release in Water and Soil (2009)

Carboxymethylcellulose (CMC) gel was used for encapsulating anionic herbicide 2,4-D for its controlled release. The slower release rate of 2,4-D in water and soil was obtained by adding in the gel formulation some modified bentonites, which were prepared by intercalating inorganic or organic cations in interlayers of Na(+)-saturated bentonite. The higher encapsulation efficiencies of 2,4-D were observed on the bentonite/CMC gel formulations due to the sorption of 2,4-D on modified bentonites. The time taken for 50% of 2,4-D to be released in water, t(50), showed a variation (8.8-19.8 h) for these gel formulations, the largest value corresponding to the formulation incorporated with hydroxy-iron intercalated bentonite that has the highest sorption capacity to 2,4-D. The gel formulations could also control the release of 2,4-D when applied to a thin soil layer and demonstrated potential to reduce leaching of such anionic herbicides in soil.
Finding question-answer pairs from online forums (2008)

Online forums contain a huge amount of valuable user generated content. In this paper we address the problem of extracting question-answer pairs from forums. Question-answer pairs extracted from forums can be used to help Question Answering services (e.g. Yahoo! Answers) among other applications. We propose a sequential patterns based classification method to detect questions in a forum thread, and a graph based propagation method to detect answers for questions in the same thread. Experimental results show that our techniques are very promising.
Possible Mechanisms of Action of Transurethral Needle Ablation of the Prostate on Benign Prostatic Hyperplasia Symptoms: A Neurohistochemical Study (1997)

Our study demonstrated severe thermal damage to intraprostatic nerve fibers caused by transurethral needle ablation. A long-term denervation of alpha-receptors and/or sensory nerves could explain the clinical effects of transurethral needle ablation of the prostate. Theoretically, the best location to produce necrotic lesions should include submucosal and subcapsular nerve endings. Differences in the distribution of the adrenoreceptors and morphometry of the prostate transition zone could partly explain differences in clinical outcome observed after transurethral needle ablation of the prostate.