gebhart/patrepeval huggingface dataset:
Harpin induces disease resistance in Arabidopsis through the systemic acquired resistance pathway mediated by salicylic acid and the NIM1 gene (1999)

Harpin, the product of the hrpN gene of Erwinia amylovora, elicits the hypersensitive response and disease resistance in many plants. Harpin and known inducers of systemic acquired resistance (SAR) were tested on five genotypes of Arabidopsis thaliana to assess the role of SAR in harpin-induced resistance. In wild-type plants, harpin elicited systemic resistance to Peronospora parasitica and Pseudomonas syringae pv. tomato, accompanied by induction of the SAR genes PR-1 and PR-2. However, in experiments with transgenic Arabidopsis plants containing the nahG gene which prevents accumulation of salicylic acid (SA), harpin neither elicited resistance nor activated SAR gene expression. Harpin also failed to activate SAR when applied to nim1 (non-inducible immunity) mutants, which are defective in responding to SA and regulation of SAR. In contrast, mutants compromised in responsiveness to methyl jasmonate and ethylene developed the same resistance as did wild-type plants. Thus, harpin elicits disease resistance through the NIM1-mediated SAR signal transduction pathway in an SA-dependent fashion. The site of action of harpin in the SAR regulatory pathway is upstream of SA.
Chemical Imaging of Microstructured Self-Assembled Monolayers with Nanometer Resolution (2007)

We report on the infrared spectroscopic characterization of microstructured self-assembled monolayers by scanning near-field infrared microscopy. Using a CO laser as the radiation source in the characteristic amide band (at 1711 cm-1 (λ = 5.85 μm)), we were able to image self-assembled monolayers of thiols. The measurements were carried out on well-defined microcontact printed line patterns of monomolecular films of 1-octadecanethiolate and biotinylated alkylthiolate (BAT). The lateral resolution was ∼90 × 90 nm2, which is well below the Abbe limit. The detection limit was 5 × 10-20 mol corresponding to 27 attogram or 30 000 molecules of BAT. This demonstrates the high sensitivity of our setup, which allows recording IR spectra of a single monolayer.
Structure of the single-strand annealing domain of human RAD52 protein (2002)

In eukaryotic cells, RAD52 protein plays a central role in genetic recombination and DNA repair by (i) promoting the annealing of complementary single-stranded DNA and (ii) stimulation of the RAD51 recombinase. The single-strand annealing domain resides in the N-terminal region of the protein and is highly conserved, whereas the nonconserved RAD51-interaction domain is located in the C-terminal region. An N-terminal fragment of human RAD52 (residues 1-209) has been purified to homogeneity and, similar to the full-size protein (residues 1-418), shown to promote single-strand annealing in vitro. We have determined the crystal structure of this single-strand annealing domain at 2.7 A. The structure reveals an undecameric (11) subunit ring with extensive subunit contacts. A large, positively charged groove runs along the surface of the ring, readily suggesting a mechanism by which RAD52 presents the single strand for reannealing with complementary single-stranded DNA.
Vector unpacking as a potential barrier for receptor-mediated polyplex gene delivery (2000)

Ligand-conjugated polymer (polyplex) gene delivery vectors have strong potential as targeted, in vivo gene transfer vehicles; however, they are currently limited by low delivery efficiency. A number of barriers to polyplex-mediated delivery have been previously identified, including receptor binding, internalization, endosomal escape, and nuclear localization. However, based on understanding of viral gene delivery systems, yet another potential barrier may exist; a limited ability to unpackage the plasmid DNA cargo following localization to the nucleus. We have developed a model system that employs a cationic polymer linked to epidermal growth factor (EGF) as a ligand to target delivery of plasmid DNA encoding the green fluorescent protein to mouse fibroblasts bearing the EGF receptor. Using fluorescence microscopy to simultaneously trace both the plasmid and polymer during gene delivery in combination with an in vitro transcription assay, we provide evidence that plasmid unpackaging can indeed be a limiting step for gene expression for sufficiently large polymer constructs. Short-term expression is significantly enhanced by using short polycations that dissociate from DNA more rapidly both in vitro and in vivo. Finally, we describe a thermodynamic model that supports these data by showing that shorter polycations can have a higher probability of dissociating from DNA. This work demonstrates that vector unpackaging should be added to the list of barriers to receptor-mediated polyplex gene delivery, thus providing an additional design principle for targeted synthetic delivery vehicles.
Bovine papillomavirus type 1 alters the processing of host glucose- and calcium-modulated endoplasmic reticulum proteins (1991)

We have previously characterized five proteins induced by the presence of the E2 open reading frame (ORF) region of bovine papillomavirus type 1 (BPV-1) in C127 mouse fibroblasts (R. M. Levenson, U. G. Brinckmann, M. K. O'Banion, E. J. Androphy, J. T. Schiller, F. Tabatabai, L. P. Turek, K. Neary, M. T. Chin, T. R. Broker, L. T. Chow, and D. A. Young, Virology 172:170-179, 1989). By specific immunoprecipitation, we now find that one of the papillomavirus-associated proteins (pvp1) is a highly glycosylated form of glucose-regulated protein 100 (grp100), a major constituent of the endoplasmic reticulum. A second set of pvps (2, 3, and 4) are shown to be related precursors of another protein already present in C127 cells (protein B). Based on their induction by the calcium ionophore A23187 and their positions on giant two-dimensional gels, we have tentatively identified pvp2, -3, and -4 and B as forms of calcium-regulated protein 55, another constituent of the endoplasmic reticulum (D. R. J. Macer and G. L. E. Koch, J. Cell Sci. 91:61-70, 1988). The mechanism by which BPV-1 brings about these changes is not yet defined; however, it is unlikely to involve calcium level perturbations or transformation per se, since ionophore treatment changes other proteins in C127 cells not seen with BPV and the papillomavirus-associated proteins are found in nontransformed cells harboring the E2 ORF region. Furthermore, the BPV changes are not associated with increased grp mRNA levels, as occurs in ionophore-treated cells. Rather, it appears that BPV-1 somehow retards the normal processing of these resident endoplasmic reticulum proteins that are believed to serve as critical regulators of host protein processing and assembly.
Mutual Solubilities for Water−o-Nitrotoluene System and Distribution Coefficients for Furfural and Acetic Acid in Water−o-Nitrotoluene System (2010)

Ten high boiling solvents were evaluated as the extraction solvent of furfural. o-Nitrotoluene with a high furfural distribution coefficient, high thermal stability, and having no azeotrope with furfural was chosen as a furfural extraction solvent for further study. The mutual solubilities for the water−o-nitrotoluene system were experimentally determined from (383.15 to 483.15) K at 25.0 bar using a static method. According to the results, it can be seen that the solubilities are temperature-dependent and can be correlated with a quadratic equation well. The distribution coefficients for furfural and acetic acid in the water−o-nitrotoluene system were determined from (303.15 to 483.15) K at 25.0 bar using a static method, respectively. The results show that the distribution coefficients are temperature-dependent and can be correlated with van’t Hoff equation well. Considering the high selectivity for furfural, the low selectivity for acetic acid and negligible mutual solubilities with water, o-nitrotoluene was considered as a suitable solvent for furfural production in the solvent extraction process.
3'-Substituted 2',3'-dideoxynucleoside analogs as potential anti-HIV (HTLV-III/LAV) agents (1987)

A series of 2',3'-unsaturated and 3'-substituted 2',3'-dideoxynucleoside analogues of purines and pyrimidines have been synthesized and evaluated for their inhibitory activity against human immunodeficiency virus (HIV). The 2',3'-unsaturated analogues of 2',3'-dideoxycytidine (ddeCyd) and 2',3'-dideoxythymidine (ddeThd), 3'-azido-2',3'-dideoxythymidine (AzddThd), 3'-fluoro-2',3'-dideoxythymidine, 2',3'-dideoxycytidine (ddCyd), and 2',3'-dideoxyadenosine (ddAdo) emerged as the most potent inhibitors of HIV-induced cytopathogenicity in the human T lymphocyte cell lines ATH8 and MT4. In ATH8 cells ddCyd, ddeCyd, and ddAdo had the highest therapeutic index whereas in MT4 cells AzddThd, ddThd, ddCyd, and ddAdo were the most selective. Derivatives from ddThd in which the substituent group was linked to the 3'-carbon atom via a thio, sulfonyl, or oxygen bridge were far less inhibitory to HIV than was AzddThd.
Binding of gastrin(17) to human gastric carcinoma cell lines. (1988)

The hormone gastrin stimulates acid secretion by gastric parietal cells and acts as a growth factor for the gastric mucosa. Gastrin receptors with dissociation constants of approximately 0.5 nM have been detected on isolated gastric parietal cells, and on some cell lines derived from colon carcinomas. We now report that gastrin is also bound by five cell lines derived from human gastric carcinomas, but that the affinities of these lines for gastrin range from 0.2 to 1.3 microM. Cholecystokinin8 binds to the cell line Okajima with an affinity similar to gastrin17, while shorter gastrin analogues bind with reduced affinity. Binding of gastrin is unaffected by acetylcholine, histamine, or a number of other hormones with the exception of insulin which inhibits binding with an IC50 value of 0.5 microM. The ability to bind gastrin with affinities in the microM range appears to be a property widespread among other tumor cell lines.
Rheology of Hyaluronate (1987)

Solutions containing high molecular weight hyaluronate at concentrations around 10 mg/ml exhibit interesting rheological properties due to formation of a highly entangled network of flexible polysaccharide molecules. We have performed an extensive study of the rheological properties of hyaluronate solutions as a function of concentration and molecular weight. In this paper we review some basic rheological concepts, and discuss the rheological properties of hyaluronate solutions at high concentrations and medium to high molecular weights (1-5 million). The bulk viscosity (zero shear viscosity) of hyaluronate solutions is strongly dependent both on concentration and molecular weight. A 2-fold increase in concentration or molecular weight results in a 10-fold increase in bulk viscosity. For application in body compartments, the concentration of hyaluronate cannot be increased much above 10 mg/ml due to the highly non-ideal colloid osmotic behaviour of hyaluronate. High viscosity hyaluronate solutions must therefore be based on high molecular weight material.
Coordinate Regulation of the Production and Signaling of Retinoic Acid by Estrogen in the Human Endometrium (2003)

To determine whether estrogen regulates retinoic acid (RA) production and signaling in the human endometrium as it does in the rodent uterus, we investigated the effects of estrogens on the expression of RA-metabolizing enzymes, retinoid receptors, and biomarker genes in the post- and premenopausal human endometrium. Real-time quantitative PCR revealed that retinaldehyde dehydrogenase (RALDH) 2, a critical enzyme in RA biosynthesis, was induced 4-fold by estrogen replacement therapy with either Premarin or a mixture of estrone and equilin sulfates for 3 months. Estrogen replacement therapy also increased the expression of the RA receptor RAR alpha 1.9-fold. In parallel, there was a marked increase in the expression of two RA-regulated genes, cellular retinoic acid-binding protein II and tissue transglutaminase. In the premenopausal endometrium, the levels of RALDH1, RALDH2, RAR alpha, and cellular retinoic acid-binding protein II were increased in the estrogen-dominated proliferative phase, and the transcripts for the RA catabolic enzyme retinoic acid 4-hydroxylase (CYP26A1) and tissue transglutaminase were significantly increased in the secretory phase. Our results suggest that estrogen coordinately up-regulates RA production and signaling in the human endometrium. This coordinate mechanism may play a role in the antiproliferative effects that counterbalance the estrogen-induced endometrial proliferation.
Generation of hair cells in neonatal mice by β-catenin overexpression in Lgr5-positive cochlear progenitors (2013)

Mammalian hair cells do not regenerate, and their loss is a major cause of deafness. We recently identified leucine-rich repeat containing, G-protein-coupled receptor 5 (Lgr5)-expressing cochlear supporting cells with the capacity for self-renewal and hair cell differentiation in vitro. We found that these cells, a subset of cochlear supporting cells, were responsive to Wnt signaling. Here we asked whether these Lgr5-positive cells, despite their lack of contribution to hair cell replacement after degenerative loss, could be driven by forced expression of β-catenin to act as hair cell progenitors in vivo. We showed that forced stabilization of β-catenin in supporting cells in neonatal animals resulted in proliferation of supporting cells and generation of hair cells. Although β-catenin expression was increased by genetic means in all supporting cells, entry to the cell cycle and differentiation to hair cells of the normally postmitotic cells was restricted to the Lgr5-positive population. Our finding suggests that Wnt/β-catenin can drive Lgr5-positive cells to act as hair cell progenitors, even after their exit from the cell cycle and apparent establishment of cell fate.
Production and Characterization of Monoclonal Antibodies against Human Malignant Melanoma (1983)

The specific immunoreactivities of 31 monoclonal antibodies against human malignant melanoma were analyzed on a variety of malignant and nonmalignant human cells. Seven distinct groups were defined based on reactivity in radioimmunoassay and in mixed hemadsorption assay. The Group A antibody bound to 33% of short- and long-term cultured melanomas; Group B antibodies reacted with the majority of melanomas, astrocytomas, neuroblastomas, and fetal polygonal cells; and Group C antibodies bound to melanomas, teratocarcinomas, and to melanocytes grown in the presence of tumor-promoting phorbol esters. Antibodies of Groups D-G showed a less restricted binding pattern. In all groups, antibodies of IgG2b and IgM isotypes mediated complement-dependent lysis (CDC) and antibodies of IgG1, IgG2a, and IgG2b isotypes mediated antibody-dependent cell-mediated cytotoxicity (ADCC). Biochemical analysis indicated that 16 different proteins with molecular weights ranging between 28,000 and 500,000 were detected by the monoclonal antimelanoma antibodies.
ChemInform Abstract: Lithiation of Methoxypyridines Directed by α‐Amino Alkoxides. (1990)

Abstract Various methoxypyridinecarbaldehydes are consecutively treated with lithium amides and alkyl‐ or aryllithium agents to generate α‐amino alkoxide lithium complexes which are quenched with methyl iodide (II), producing methylated pyridine derivatives.
Cloning and expression of the Vibrio cholerae neuraminidase gene nanH in Escherichia coli (1988)

A cosmid gene bank of Vibrio cholerae 395, classical Ogawa, was screened in Escherichia coli HB101 for expression of the vibrio neuraminidase (NANase) gene nanH (N-acylneuraminate glycohydrolase). Positive clones were identified by their ability to cleave the fluorogenic NANase substrate 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid. Seven NANase-positive clones were detected after screening 683 cosmid isolates with a rapid, qualitative plate assay method. The nanH gene was subcloned from one of the cosmids and was located within a 4.8-kilobase-pair BglII restriction endonuclease fragment. Evidence that nanH was the NANase structural gene was obtained by transposon mutagenesis and by purification and comparison of the cloned gene product with the secreted NANase purified from the parent V. cholerae strain. The sequence of the first 20 amino-terminal amino acids of the secreted NANase purified from V. cholerae was determined by automated Edman degradation and matched perfectly with the amino acid sequence predicted from nucleotide sequencing of nanH. The sequence data also revealed the existence of a potential signal peptide that was apparently processed from NANase in both V. cholerae and E. coli. In contrast to V. cholerae, E. coli nanH+ clones did not secrete NANase into the growth medium, retaining most of the enzyme in the periplasmic compartment. Kinetic studies in V. cholerae showed that nanH expression and NANase secretion were temporally correlated as cells in batch culture entered late-exponential-phase growth. Similar kinetics were observed in at least one of the E. coli nanH+ clones, suggesting that nanH expression in E. coli might be controlled by some of the same signals as in the parent V. cholerae strain.
Production of pharmaceutical‐grade recombinant aprotinin and a monoclonal antibody product using plant‐based transient expression systems (2010)

Plants have been proposed as an attractive alternative for pharmaceutical protein production to current mammalian or microbial cell-based systems. Eukaryotic protein processing coupled with reduced production costs and low risk for mammalian pathogen contamination and other impurities have led many to predict that agricultural systems may offer the next wave for pharmaceutical product production. However, for this to become a reality, the quality of products produced at a relevant scale must equal or exceed the predetermined release criteria of identity, purity, potency and safety as required by pharmaceutical regulatory agencies. In this article, the ability of transient plant virus expression systems to produce a wide range of products at high purity and activity is reviewed. The production of different recombinant proteins is described along with comparisons with established standards, including high purity, specific activity and promising preclinical outcomes. Adaptation of transient plant virus systems to large-scale manufacturing formats required development of virus particle and Agrobacterium inoculation methods. One transient plant system case study illustrates the properties of greenhouse and field-produced recombinant aprotinin compared with an US Food and Drug Administration-approved pharmaceutical product and found them to be highly comparable in all properties evaluated. A second transient plant system case study demonstrates a fully functional monoclonal antibody conforming to release specifications. In conclusion, the production capacity of large quantities of recombinant protein offered by transient plant expression systems, coupled with robust downstream purification approaches, offers a promising solution to recombinant protein production that compares favourably to cell-based systems in scale, cost and quality.
Research advances in intelligent collision avoidance and adaptive cruise control (2003)

This paper looks into recent developments and research trends in collision avoidance/warning systems and automation of vehicle longitudinal/lateral control tasks. It is an attempt to provide a bigger picture of the very diverse, detailed and highly multidisciplinary research in this area. Based on diversely selected research, this paper explains the initiatives for automation in different levels of transportation system with a specific emphasis on the vehicle-level automation. Human factor studies and legal issues are analyzed as well as control algorithms. Drivers' comfort and well being, increased safety, and increased highway capacity are among the most important initiatives counted for automation. However, sometimes these are contradictory requirements. Relying on an analytical survey of the published research, we will try to provide a more clear understanding of the impact of automation/warning systems on each of the above-mentioned factors. The discussion of sensory issues requires a dedicated paper due to its broad range and is not addressed in this paper.
Characterization of a cellobiose dehydrogenase in the cellulolytic fungus Sporotrichum (Chrysosporium) thermophile (1982)

An extracellular enzyme from culture filtrates of Sporotrichum (Chrysosporium) thermophile (A.T.C.C. 42 464) after growth on cellulose or cellobiose was shown to oxidize cellobiose to cellobionic acid in vitro. Lactose and cellodextrins were also efficiently oxidized, but the enzyme was not active against most mono- and di-saccharides. Several redox substances could act as electron acceptors, but molecular oxygen, tetrazolium salts and NAD(P) were not reduced. Activity was stimulated up to 2-fold in the presence of 0.05 M-Mg2+. The pH optimum of the enzymic reaction was acidic when the activity was tested with dichlorophenol-indophenol or Methylene Blue, but was neutral to alkaline for 3,5-di-t-butyl-1,2-benzoquinone or phenazine methosulphate as electron acceptors. As the enzyme was formed inductively in parallel with the endocellulase, its possible function in relation to cellulolysis is discussed.
Hybrid selection for sequencing pathogen genomes from clinical samples (2011)

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.
Basicity of, SN2 reactivity of, and basic catalysis by 1-azabicyclo[2.2.1]heptane (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBasicity of, SN2 reactivity of, and basic catalysis by 1-azabicyclo[2.2.1]heptaneJack Hine and Yao Jung ChenCite this: J. Org. Chem. 1987, 52, 10, 2091–2094Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://doi.org/10.1021/jo00386a036RIGHTS & PERMISSIONSArticle Views328Altmetric-Citations15LEARN 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 (509 KB) Get e-Alertsclose Get e-Alerts
Management Information Base for Version 2 of the Simple Network Management Protocol (SNMPv2) (1996)

It is the purpose of this document to define managed objects which
describe the behavior of a SNMPv2 entity. [STANDARDS-TRACK]