gebhart/patrepeval huggingface dataset:
RASSF1A Interacts with Microtubule-Associated Proteins and Modulates Microtubule Dynamics (2004)

The candidate tumor suppressor gene RASSF1A is inactivated in many types of adult and childhood cancers. However, the mechanisms by which RASSF1A exerts its tumor suppressive functions have yet to be elucidated. To this end, we performed a yeast two-hybrid screen to identify novel RASSF1A-interacting proteins in a human brain cDNA library. Seventy percent of interacting clones had homology to microtubule-associated proteins, including MAP1B and VCY2IP1/C19ORF5. RASSF1A association with MAP1B and VCY2IP1/C19ORF5 was subsequently confirmed in mammalian cell lines. This suggested that RASSF1A may exert its tumor-suppressive functions through interaction with the microtubules. We demonstrate that RASSF1A associates with the microtubules, causing them to exist as hyperstabilized circular bundles. We found that two naturally occurring tumor-associated missense substitutions in the RASSF1A coding region, C65R and R257Q, perturb the association of RASSF1A with the microtubules. The C65R and R257Q in addition to VCY2IP1/C19ORF5 showed reduced ability to induce microtubule acetylation and were unable to protect the microtubules against the depolymerizing action of nocodazole. In addition, wild-type RASSF1A but not the C65R or the R257Q is able to block DNA synthesis. Our data identify a role for RASSF1A in the regulation of microtubules and cell cycle dynamics that could be part of the mechanism(s) by which RASSF1A exerts its growth inhibition on cancer cells.
Molecular evolution of herbicide resistance to phytoene desaturase inhibitors in Hydrilla verticillata and its potential use to generate herbicide‐resistant crops (2005)

Hydrilla [Hydrilla verticillata (Lf) Royle] is one of the most serious invasive aquatic weed problems in the USA. This plant possesses numerous mechanisms of vegetative reproduction that enable it to spread very rapidly. Management of this weed has been achieved by the systemic treatment of water bodies with the herbicide fluridone. At least three dioecious fluridone-resistant biotypes of hydrilla with two- to fivefold higher resistance to the herbicide than the wild-type have been identified. Resistance is the result of one of three independent somatic mutations at the arginine 304 codon of the gene encoding phytoene desaturase, the molecular target site of fluridone. The specific activities of the three purified phytoene desaturase variants are similar to the wild-type enzyme. The appearance of these herbicide-resistant biotypes may jeopardize the ability to control the spread of this non-indigenous species to other water bodies in the southern USA. The objective of this paper is to provide general information about the biology and physiology of this aquatic weed in relation to its recent development of resistance to the herbicide fluridone, and to discuss how this discovery might lead to a new generation of herbicide-resistant crops.
Inhibition of Paclitaxel-induced Decreases in Calcium Signaling (2012)

Peripheral neuropathy is one of the most severe and irreversible side effects caused by treatment from several chemotherapeutic drugs, including paclitaxel (Taxol®) and vincristine. Strategies are needed that inhibit this unwanted side effect without altering the chemotherapeutic action of these drugs. We previously identified two proteins in the cellular pathway that lead to Taxol-induced peripheral neuropathy, neuronal calcium sensor-1 (NCS-1) and calpain. Prolonged treatment with Taxol induces activation of calpain, degradation of NCS-1, and loss of intracellular calcium signaling. This paper has focused on understanding the molecular basis for prevention of peripheral neuropathy by testing the effects of addition of two candidate compounds to the existing chemotherapeutic drug regime: lithium and ibudilast. We found that the co-administration of either lithium or ibudilast to neuroblastoma cells that were treated with Taxol or vincristine inhibited activation of calpain and the reductions in NCS-1 levels and calcium signaling associated with these chemotherapeutic drugs. The ability of Taxol to alter microtubule formation was unchanged by the addition of either candidate compound. These results allow us to suggest that it is possible to prevent the unnecessary and irreversible damage caused by chemotherapeutic drugs while still maintaining therapeutic efficacy. Specifically, the addition of either lithium or ibudilast to existing chemotherapy treatment protocols has the potential to prevent chemotherapy-induced peripheral neuropathy.
Recent developments in superhydrophobic surfaces and their relevance to marine fouling: a review (2006)

In this review, a brief synopsis of superhydrophobicity (i.e. extreme non-wettability) and its implications on marine fouling are presented. A short overview of wettability and recent experimental developments aimed at fabricating superhydrophobic surfaces by tailoring their chemical nature and physical appearance (i.e. substratum texture) are reviewed. The formation of responsive/"smart" surfaces, which adjust their physico-chemical properties to variations in some outside physical stimulus, including light, temperature, electric field, or solvent, is also described. Finally, implications of tailoring the surface chemistry, texture, and responsiveness of surfaces on the design of effective marine fouling coatings are considered and discussed.
Comparative myocardial extraction of two technetium-labeled BATO derivatives (SQ30217, SQ32014) and thallium. (1990)

The transcapillary exchange of a new class of 99mTc-labeled compounds (BATO) were compared to 201Tl in isolated, blood perfused rabbit hearts. During variable blood flow (0.15-2.44 ml/min/g), peak and net extraction (Emax and Enet, respectively), and capillary permeability-surface area product (PScap) were determined with paired indicator-dilution techniques. Serial bolus injections of 201Tl, [111In]albumin, and [99mTc]BATO; chloro[tris(cyclohexanedionedioxime)methyl boronic acid]Tc (SQ30217, n = 8) and a hydroxy-substituted derivative (SQ32014, n = 5) were given to a total of 13 hearts. Mean (+/- s.d.) SQ30217 Emax and Enet were 0.72 +/- 0.09 and 0.55 +/- 0.18, respectively, which were higher than thallium values of 0.57 +/- 0.10 and 0.46 +/- 0.17 (p less than 0.03). Mean SQ30217 PScap was 1.1 +/- 0.4 ml/min/g and was also higher than corresponding thallium determinations (0.7 +/- 0.3; p less than 0.001). SQ32014 Emax, Enet, and PScap were all significantly less than thallium values (p less than 0.001). Thallium and SQ30217 values for Emax and PScap were closely correlated with blood flow (r greater than or equal to 0.73), whereas those for SQ32014 were weakly correlated (r = 0.09). A small clinical pilot study (n = 3) was performed, which showed that SQ32014 was a poor myocardial perfusion agent in man. In summary, transcapillary exchange of SQ30217 is greater than thallium, which in turn, is greater than SQ32014. Therefore, SQ30217 appears to have good clinical potential, but SQ32014 does not.
Neutralizing Antibodies Elicited by Immunization of Monkeys with DNA Plasmids and Recombinant Adenoviral Vectors Expressing Human Immunodeficiency Virus Type 1 Proteins (2004)

Immunization with recombinant serotype 5 adenoviral (rAd5) vectors or a combination of DNA plasmid priming and rAd5 boosting is known to elicit potent immune responses. However, little data exist regarding these immunization strategies and the development of anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies. We used DNA plasmids and rAd5 vectors encoding the HIV-1 89.6P or chimeric HxB2/BaL envelope glycoprotein to immunize macaque monkeys. A single rAd5 immunization elicited anti-Env antibody responses, but there was little boosting with subsequent rAd5 immunizations. In contrast, rAd5 boosting of DNA-primed monkeys resulted in a rapid rise in antibody titers, including the development of anti-HIV-1 neutralizing antibodies. The potency and breadth of neutralization were evaluated by testing plasma against a panel of 14 clade B primary isolates. Moderate levels of plasma neutralizing activity were detected against about one-third of the viruses tested, and immunoglobulin G fractionation demonstrated that virus neutralization was antibody mediated. After a challenge with a chimeric simian-human immunodeficiency virus (SHIV89.6P), an anamnestic neutralizing antibody response was observed, although the breadth of the response was limited to the subset of viruses that were neutralized after the primary immunization. These data are the first detailed description of the anti-HIV-1 neutralizing antibody response in nonhuman primates elicited by DNA and rAd5 immunization. In addition to the well-established ability of DNA priming and rAd5 boosting to elicit potent anti-HIV-1 cellular immune responses, this immunization strategy elicits anti-HIV-1 neutralizing antibodies and therefore can be used to study novel Env immunogens designed to elicit more potent neutralizing antibodies.
Ribozyme-Mediated Cleavage of an HIV-1 gag RNA: The Effects of Nontargeted Sequences and Secondary Structure on Ribozyme Cleavage Activity (1991)

Catalytic antisense RNAs, or ribozymes, have great potential as inhibitors of gene expression and as antiviral therapeutic agents. The major advantage of ribozymes versus standard antisense RNAs is their catalytic capability, enabling these RNAs to cleave multiple substrates. We have been investigating the antiviral activity of ribozymes targeted to the HIV-1 genome. The successful use of these antisense agents in an intracellular milieu requires stabilization of the ribozymes by flanking, non-base-pairing sequences, or some modification of the sugar-phosphate backbone. We describe a systematic investigation of the effects of flanking, non-base-pairing sequences on the catalytic activity of an anti-HIV-1 gag ribozyme embedded in radically different transcripts. Amazingly, these complex ribozyme-containing transcripts maintain substantial catalytic activity. Finally, we describe a bacterial gene fusion system that has potential for the large scale production of catalytically active ribozymes.
The use of 7-amino actinomycin D in identifying apoptosis: simplicity of use and broad spectrum of application compared with other techniques (1996)

The detection and quantitation of apoptotic cells is becoming increasingly important in the investigation of the role of apoptosis in cellular proliferation and differentiation. The pathogenesis of hematologic disorders such as aplastic anemia and the development of neoplasia are believed to involve dysregulation of apoptosis. To quantitate accurately the proportion of apoptosis cells within different cell types of a heterogeneous cell population such as blood or bone marrow, a method is required that combines the analysis of large numbers of cells with concurrent immunophenotyping of cell surface antigens. In this study, we have evaluated such a method using the fluorescent DNA binding agent, 7-amino actinomycin D (7AAD), to stain three diverse human cell lines, induced to undergo apoptosis by three different stimuli. Flow cytometric analysis defines three populations on the basis of 7AAD fluorescence and forward light scatter. We have shown by cell sorting and subsequent morphological assessment and terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling that the populations defined by 7AAD represent live, apoptotic, and late-apoptotic/dead cells. This method is quick, simple, reproducible, and cheap and will be a valuable tool in the investigation of the role of apoptosis in normal physiology and in disease states.
In Vitro Activity of Trovafloxacin Compared to Those of Five Antimicrobials against Mycoplasmas Including Mycoplasma hominis and Ureaplasma urealyticum Fluoroquinolone-Resistant Isolates That Have Been Genetically Characterized (2000)

The in vitro activity of trovafloxacin against 125 strains of Mycoplasma species and Ureaplasma urealyticum, including fluoroquinolone-susceptible and fluoroquinolone-resistant species, was compared to those of other fluoroquinolones, doxycycline, and erythromycin. The MIC at which 90% of isolates are inhibited for all fluoroquinolone-susceptible strains was 0.25 microg/ml. Whatever the associated mutations, trovafloxacin exhibited greater activity than the other fluoroquinolones tested against fluoroquinolone-resistant Mycoplasma hominis and U. urealyticum isolates.
Modeling the Dynamics of Cardiac Action Potentials (2000)

The nonlinear dynamics of cardiac action potentials is explained via simple model equations describing the membrane potential and the inward and outward currents through the membrane. The equations approximate ionic models, yet are expressed as polynomial functions, and robustly capture the phase-space dynamics of action potentials.
Synthesis of the Saccharomicin Fucose−Aglycon Conjugate and Determination of Absolute Configuration (2005)

[reaction: see text] Schmidt glycosylation of the appropriately protected 3,4-dihydroxycinnamate methyl ester with 2,3,4-triacetoxyfucopyranosyltrichloroacetimidate gives aryl glycoside in high yield and diastereoselectivity. 2-Sulfation of fucose, installation of taurine, and global deprotection of the remaining protecting groups affords the fucose-aglycon conjugate of saccharomicin. This synthesis which arises from L-fucose also establishes the absolute configuration of the reducing terminus of the saccharomicin oligosaccharide.
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction (2007)

NetCTL-1.2 is demonstrated to have a higher predictive performance than EpiJen, MAPPP, MHC-pathway, and WAPP on all performance measures. The higher performance of NetCTL-1.2 as compared to EpiJen and MHC-pathway is, however, not statistically significant on all measures. In the large-scale benchmark calculation consisting of 216 known HIV epitopes covering all 12 recognized HLA supertypes, the NetCTL-1.2 method was shown to have a sensitivity among the 5% top-scoring peptides above 0.72. On this dataset, the best of the other methods achieved a sensitivity of 0.64. The NetCTL-1.2 method is available at http://www.cbs.dtu.dk/services/NetCTL. All used datasets are available at http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php.
A Multi-Threading Architecture to Support Interactive Visual Exploration (2009)

During continuous user interaction, it is hard to provide rich visual feedback at interactive rates for datasets containing millions of entries. The contribution of this paper is a generic architecture that ensures responsiveness of the application even when dealing with large data and that is applicable to most types of information visualizations. Our architecture builds on the separation of the main application thread and the visualization thread, which can be cancelled early due to user interaction. In combination with a layer mechanism, our architecture facilitates generating previews incrementally to provide rich visual feedback quickly. To help avoiding common pitfalls of multi-threading, we discuss synchronization and communication in detail. We explicitly denote design choices to control trade-offs. A quantitative evaluation based on the system VISPLORE shows fast visual feedback during continuous interaction even for millions of entries. We describe instantiations of our architecture in additional tools.
A scoring system to predict renal outcome in IgA nephropathy: a nationwide 10-year prospective cohort study (2009)

This validated scoring system to quantitatively estimate ESRD risk during the 10-year follow-up of IgAN patients will serve as a useful prognostic tool in clinical practice.
Unaided 2.5 Gb/s silicon bipolar clock and data recovery IC (2002)

We will describe a low cost and low power Si Bipolar IC for clock and data recovery at 2.488 Gb/s that requires no external reference. The design is based on a digital quadri-correlator that has inherent low phase offset and allows the use of passive loop filters. The clock recovery unit (CRU) has broad locking range that makes it robust against power supply and temperature variations.
Electrochemistry of metalloporphyrins and viologens at zeolite Y-modified electrodes: evidence for electron trapping by monomolecular porphyrin layers (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemistry of metalloporphyrins and viologens at zeolite Y-modified electrodes: evidence for electron trapping by monomolecular porphyrin layersZhuyin Li, Chong Mou Wang, Lalchan Persaud, and Thomas E. MalloukCite this: J. Phys. Chem. 1988, 92, 9, 2592–2597Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/j100320a039https://doi.org/10.1021/j100320a039research-articleACS PublicationsRequest reuse permissionsArticle Views361Altmetric-Citations69LEARN 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 options Get e-Alerts
High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2 (2000)

The design of a family shuffling strategy (CLERY: Combinatorial Libraries Enhanced by Recombination in Yeast) associating PCR-based and in vivo recombination and expression in yeast is described. This strategy was tested using human cytochrome P450 CYP1A1 and CYP1A2 as templates, which share 74% nucleotide sequence identity. Construction of highly shuffled libraries of mosaic structures and reduction of parental gene contamination were two major goals. Library characterization involved multiprobe hybridization on DNA macro-arrays. The statistical analysis of randomly selected clones revealed a high proportion of chimeric genes (86%) and a homogeneous representation of the parental contribution among the sequences (55.8 +/- 2.5% for parental sequence 1A2). A microtiter plate screening system was designed to achieve colorimetric detection of polycyclic hydrocarbon hydroxylation by transformed yeast cells. Full sequences of five randomly picked and five functionally selected clones were analyzed. Results confirmed the shuffling efficiency and allowed calculation of the average length of sequence exchange and mutation rates. The efficient and statistically representative generation of mosaic structures by this type of family shuffling in a yeast expression system constitutes a novel and promising tool for structure-function studies and tuning enzymatic activities of multicomponent eucaryote complexes involving non-soluble enzymes.
High quality UV AlGaN/AlGaN distributed Bragg reflectors and microcavities (2007)

We demonstrate high-reflectivity crack-free Al<sub>0.18</sub>Ga<sub>0.82</sub>N/Al<sub>0.8</sub>Ga<sub>0.2</sub>N distributed Bragg reflectors (DBR) and monolithic microcavities grown by molecular beam epitaxy on thick c-axis GaN templates. The elastic strain energy in the epilayer is minimized by compensating the compressive and tensile stress in every period of the DBR structure. A 25 period DBR mirror provides a 26nm-wide stop band centered at 347 nm with the maximum reflectivity higher than 99%. The high-reflectivity DBRs can be used to form high <i>Q</i>-factor monolithic AlGaN/AlGaN microcavities.
The Establishment of Active Chromatin Domains (1998)

It has become obvious during the past several yearsthat the true template for transcription in eukaryotes ischromatin, not bare DNA, and that the processes thatmodify chromatin structure are integral parts of the transcription mechanism. Modification of histones by acetylation, or the ATP-dependent disruption of nucleosomesby a variety of protein complexes, can alter transcriptionrates at specific genes. Enzymes responsible for histoneacetylation or deacetylation can be part of a complexwhich also contains DNA sequence-specific transcriptionfactors, and activation or repression is coupled to bindingof the appropriate acetylase or deacetylase. The involvement of the transcription factor assures that the histonemodification is targeted to the proper gene and may alsomean that the effects of histone modification are confinedto a relatively small region in the neighborhood of thepromoter...
Preparation and characterization of monoclonal antibodies directed to the tumor-associated O-linked sialosyl-2----6 alpha-N-acetylgalactosaminyl (sialosyl-Tn) epitope. (1988)

Two monoclonal antibodies, TKH1 and TKH2, directed toward the sialosyl-Tn structure (NeuAc alpha 2----6GalNAc alpha 1----O-Ser or Thr), which display a remarkable immunohistological tumor specificity, were generated by immunization with ovine submaxillary mucin. The reactivity of these antibodies was monitored by solid phase enzyme-linked immunosorbent assay with different native and glycosidase-treated mucins and glycoproteins. Binding of the antibody to ovine submaxillary mucin glycoprotein was strongly inhibited by the O-linked disaccharide NeuAc alpha 2----6GalNAc alpha 1----O-serine, less strongly by NeuAc alpha 2----6GalNAc beta 1----O-propyl, and weakly by the monosaccharide GalNac. The reactivity was compared with previously established anti-Tn antibodies B72.3, NCC-Lu-35, and NCC-Lu-81. The antibody B72.3 was prepared previously after immunization with metastatic breast adenocarcinoma and its epitope was claimed to be GalNAc alpha 1----O-Ser (or - Thr) by Springer and associates [Springer, G.F., et al. In: T. Dao, et al. (eds.), Tumor Markers and Their Significance in the Management of Breast Cancer, pp. 47-70. New York: A.R. Liss, 1986]. The antibody was found to show very similar reactivity as that of TKH1/TKH2, and its reactivity to ovine submaxillary mucin was inhibited specifically by NeuAc alpha 2----6GalNAc alpha 1----O-serine, indicating that the antibody is clearly directed to sialosyl-Tn antigen. Immunohistological study of the distribution of this antigen in various normal human tissues and carcinomas by TKH1/TKH2 antibodies, as well as B72.3 and monoclonal antibodies NCC-Lu-35/81, which are directed to GalNAc alpha 1----O-Ser or Thr (Tn), was performed. The sialosyl-Tn antigen was not found in normal tissue except for a weak expression in Leydig cells of the testis, goblet cells of the colon, and parietal cells of the stomach. In contrast, the sialosyl-Tn antigen was strongly expressed in a large number of adenocarcinomas. As expected from the specificity studies, B72.3 shows the same reactivity as TKH1 and TKH2. Thus, both sialosyl-Tn (NeuAc alpha 2----6GalNAc alpha 1----O-Ser/Thr) and Tn (GalNAc alpha 1----O-Ser/Thr) are good tumor markers, and combined use of antibodies directed to these structures might be useful in the screening and classification of cancer.