gebhart/patrepeval huggingface dataset:
Functional Quantum‐Dot/Dendrimer Nanotubes for Sensitive Detection of DNA Hybridization (2008)

Hybrid nanotubes (NTs) comprising assemblies of quantum dots (QDs) and dendrimer multilayers, with a graded bandgap structure, can be formed using three types of ZnxCd(1−x)Se alloy QDs with luminescence maxima at λ = 561 nm (green), 594 nm (orange), and 614 nm (red). Probe DNA immobilization inside the NTs makes them ideal candidates for biosensor applications, as demonstrated by successful hybridization of labeled target DNA (see figure). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/smll200700453_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Characterization of the murine B7-1 genomic locus reveals an additional exon encoding an alternative cytoplasmic domain and a chromosomal location of chromosome 16, band B5. (1994)

The murine B7-1 (mB7-1) molecule expressed on APCs delivers a costimulatory signal for T cell activation through its T cell counter-receptor CD28, resulting in T cell proliferation and IL-2 production. Signaling through the TCR in the absence of CD28 signaling results in T cell anergy. We have analyzed the genomic structure of mB7-1 and here describe the identification of a previously unrecognized sixth exon at the far 3' end of the locus, which encodes an alternative cytoplasmic domain. Reverse transcriptase-PCR amplification of mB7-1 transcripts demonstrates that exon 6 is functionally spliced to the transmembrane-encoding exon 4. Furthermore, using 5' rapid amplification of cDNA ends, we determined that the 5'-untranslated region extends over 1505 bp beyond the previously reported transcriptional start site. In addition, we report the chromosomal location of mB7-1 to chromosome 16, band B5.
Sympathetic-Nerve Activity during Sleep in Normal Subjects (1993)

REM sleep is associated with profound sympathetic activation in normal subjects, possibly linked to changes in muscle tone. The hemodynamic and sympathetic changes during REM sleep could play a part in triggering ischemic events in patients with vascular disease.
Complement-independent activation of the fifth component (C5) of human complement: limited trypsin digestion resulting in the expression of biological activity. (1982)

Abstract Highly purified human C5 was subjected to limited trypsin digestion (0.42 mol affinity-purified trypsin/mol C5) at pH 7.4 and 37°C. Samples were removed after various time intervals, treated with phenylmethylsulfonyl fluoride to inhibit trypsin activity, and were analyzed by SDS-polyacrylamide slab gel electrophoresis (SDS-PAGE) in the presence or absence of β-mercaptoethanol (βME). The first trypsin-mediated cleavage event was located in the C5α chain and resulted in the production of a 25,000 ± 3000 m.w. (α5) polypeptide and a 90,000 ± 3000 m.w. (α1) fragment. The larger C5α chain fragment, C5α1, produced by trypsin clearly expressed a smaller m.w. than the C5bα chain (102,000 ± 3000 m.w.) produced by the C5 convertase enzymes of either complement activation pathway. The second site of trypsin action resulted in the hydrolysis of the C5α1 chain into C5α2 (58,000 ± 3000 m.w.) and C5α4 (32,000 ± 3000 m.w.) fragments. The C5α2 polypeptide chain was subsequently degraded to a C5α3 fragment (44,000 ± 3000 m.w.). Under the conditions employed in these experiments, only the C5α chain subunit was susceptible to trypsin digestion; the β-subunit was completely resistant. Two-dimensional SDS-PAGE analysis of trypsin-digested C5 (the first dimension was conducted under nonreducing conditions and the second dimension was performed in the presence of βME) demonstrated that all of the C5 fragments produced by the first three trypsin cleavage events (α1 through α5) were disulfide-bonded together, thereby generating a series of trypsin-modified C5 molecules (C5’, C5”, C5’“) possessing the same apparent m.w. as native C5 (210,000 ± 5000). Collectively, these results indicate that limited trypsin digestion of human C5 did not result in the production of C5a and C5b fragments. Nevertheless, limited trypsin digestion did result in the activation of human C5 to induce human neutrophil chemotactic and lysosomal enzyme-releasing activities. Detailed correlation experiments demonstrated that the first trypsin-mediated C5α chain cleavage event, i.e., conversion of C5α to C5α1 and C5α5 polypeptide fragments, resulted in the expression of C5a-like biologic activities by trypsin-modified C5.
Photocleavable peptide-DNA conjugates: synthesis and applications to DNA analysis using MALDI-MS (1999)

The synthesis and characterization of photocleavable peptide-DNA conjugates is described along with their use as photocleavable mass marker (PCMM) hybridization probes for the detection of target DNA sequences by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Three photocleavable peptide-DNA conjugates were synthesized, purified, and characterized using HPLC and denaturing gel electrophoresis, as well as IR-MALDI and UV-MALDI. The hybridization properties of the conjugates were also studied by monitoring their thermal denaturation with absorption spectroscopy. No significant difference in the melting temperature ( T (m)) of the duplexes was observed between the unmodified duplex and the duplex in which one strand was modified with the photocleavable peptide moiety. These conjugates were evaluated as hybridization probes for the detection of immobilized synthetic target DNAs using MALDI-MS. In these experiments, the DNA portion of the conjugate acts as a hybridization probe, whereas the peptide is photoreleased during the ionization/desorption step of UV-MALDI and can serve as a marker (mass tag) to identify a unique target DNA sequence. The method should be applicable to a wide variety of assays requiring highly multiplexed DNA/RNA analysis, including gene expression monitoring, genetic profiling and the detection of pathogens.
SINGLE MODE OSCILLATION OF A PULSED SINGLY RESONANT OPTICAL PARAMETRIC OSCILLATOR (1969)

Single mode oscillation of a pulsed singly resonant optical parametric oscillator was achieved by placing a tilted mode selecting Fabry-Perot etalon inside the oscillator cavity. The output power was 25% of that obtained in multimode oscillation without the etalon. Good agreement was obtained between observed and expected spectral width both with and without the etalon inside the optical cavity.
Neuromodulation of ion transport in porcine distal colon: NPY reduces secretory actions of leukotrienes (1995)

Electrical transmural stimulation (ETS) was used to examine the neuroregulation of electrolyte transport in the porcine distal colon. ETS of the colonic mucosa-submucosa mounted in Ussing chambers produced rapid and transient increases in short-circuit current (Isc) that were inhibited 36% by serosal bumetanide, suggesting that a portion of the response may be attributed to Cl secretion. ETS actions were dependent upon stimulus intensity and frequency and were inhibited by tetrodotoxin and omega-conotoxin. Prazosin and pyrilamine had no effect on the mucosal responses to ETS, whereas atropine reduced the responses by 32%. Neuropeptide Y (NPY) also reduced the mucosal responses to ETS up to 60% (half-maximal effective concentration = 17 nM). In addition, the effects of leukotriene C4, previously shown to stimulate Cl secretion via a neuronal pathway, were also inhibited by NPY. These results indicate that cholinergic submucosal neurons play a role in the regulation of epithelial ion transport and that NPY acts as an inhibitory neuromodulator, particularly on leukotriene-sensitive neurons in the porcine distal colon.
Retiming and resynthesis: optimizing sequential networks with combinational techniques (2002)

A technique is proposed for optimizing a sequential network by moving the registers to the boundary of the network using an extension of retiming, resynthesizing the combinational logic between the registers using existing logic minimization techniques, and replacing the registers throughout the network using retiming algorithms. A sliding-window optimization technique that considers a large number of different combinational blocks is proposed and demonstrated. The theoretical formulation and results on which the approach is based are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
[A new concept for substitutes in vascular surgery]. (1998)

In a tissue engineering approach to develop vascular grafts without disadvantages such as early thrombosis, neointimal hyperplasia, the inability to grow, aneurysm formation, as well as life-long anticoagulation, decellularized matrix tubes which were obtained by enzymatic cell extraction from a porcine aorta were seeded with human endothelial cells in vitro. This procedure led to completely biological vascular grafts with good handling qualities and sufficient burst strength, presumably suitable for implantation in the arterial circuit.
Antigenicity and Immunogenicity of Novel Chimeric Hepatitis B Surface Antigen Particles with Exposed Hepatitis C Virus Epitopes (2001)

The small envelope protein of hepatitis B virus (HBsAg-S) can self-assemble into highly organized virus like particles (VLPs) and induce an effective immune response. In this study, a restriction enzyme site was engineered into the cDNA of HBsAg-S at a position corresponding to the exposed site within the hydrophilic a determinant region (amino acid [aa] 127-128) to create a novel HBsAg vaccine vector allowing surface orientation of the inserted sequence. We inserted sequences of various lengths from hypervariable region 1 (HVR1) of the hepatitis C virus (HCV) E2 protein containing immunodominant epitopes and demonstrated secretion of the recombinant HBsAg VLPs from transfected mammalian cells. A number of different recombinant proteins were synthesized, and HBsAg VLPs containing inserts up to 36 aa were secreted with an efficiency similar to that of wild-type HBsAg. The HVR1 region exposed on the particles retained an antigenic structure similar to that recognized immunologically during natural infection. VLPs containing epitopes from either HCV-1a or -1b strains were produced that induced strain-specific antibody responses in immunized mice. Injection of a combination of these VLPs induced antibodies against both HVR1 epitopes that resulted in higher titers than were achieved by vaccination with the individual VLPs, suggesting a synergistic effect. This may lead to the development of recombinant particles which are able to induce a broad anti-HCV immune response against the HCV quasispecies or other quasispecies-like infectious agents.
A decrease in the wet-dog shakes response to the second administration of kainic acid in juvenile rats. (1991)

The effect of an intermittent administration of kainic acid on the KA-induced behavior, scratching, wet-dog shakes and limbic seizures was studied in the rat. Nine mg/kg kainic acid was injected i.p. at 3, 7, 14 or 21 days after the priming with the same dose of kainic acid at 25 days of age. There was no significant effect of KA-priming on the onset time of scratching. The frequency of wet-dog shakes decreased significantly in all the KA-primed rats. Fourteen day-priming of kainic acid was most effective for reducing the wet-dog shakes response. The onset time of limbic seizures tended to be shorter in all the KA-primed groups; seven day-priming resulted in a significant decrease. Histological findings showed a delay in the formation of dendritic processes of pyramidal cells in the CA3 area of the hippocampus. The results indicated that an intermittent administration of kainic acid with an interval of 3 to 21 days induces a marked tolerance in the wet-dog shakes response to kainic acid in juvenile rats, while no change in the scratching and an acceleration of the onset of limbic seizures were shown, implying that different neuronal systems are involved in these three behaviors induced by kainic acid.
Humoral immunity to human breast cancer: antigen definition and quantitative analysis of mRNA expression. (2001)

The ability of the immune system to recognize structurally altered, amplified or aberrantly expressed proteins can be used to identify molecules of etiologic relevance to cancer and to define targets for cancer immunotherapy. In the current study, ninety-four distinct antigens reactive with serum IgG from breast cancer patients were identified by immunoscreening breast cancer-derived cDNA expression libraries (SEREX). A serological profile was generated for each antigen on the basis of reactivity with allogeneic sera from normal individuals and cancer patients, and mRNA expression profiles for coding sequences were assembled based upon the tissue distribution of expressed sequence tags, Northern blots and real-time RT-PCR. Forty antigens reacted exclusively with sera from cancer patients. These included well-characterized tumor antigens, e.g. MAGE-3, MAGE-6, NY-ESO-1, Her2neu and p53, as well as newly-defined breast cancer antigens, e.g. kinesin 2, TATA element modulatory factor 1, tumor protein D52 and MAGE D, and novel gene products, e.g. NY-BR-62, NY-BR-75, NY-BR-85, and NY-BR-96. With regard to expression profiles, two of the novel gene products, NY-BR-62 and NY-BR-85, were characterized by a high level of testicular mRNA expression, and were overexpressed in 60% and 90% of breast cancers, respectively. In addition, mRNA encoding tumor protein D52 was overexpressed in 60% of breast cancer specimens, while transcripts encoding SNT-1 signal adaptor protein were downregulated in 70% of these cases. This study adds to the growing list of breast cancer antigens defined by SEREX and to the ultimate objective of identifying the complete repertoire of immunogenic gene products in human cancer (the cancer immunome).
A chiral synthesis of D-(+)-2,6-dideoxystreptamine and its microbial incorporation into novel antibiotics (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA chiral synthesis of D-(+)-2,6-dideoxystreptamine and its microbial incorporation into novel antibioticsJeanine Cleophax, Stephan D. Gero, Jean Leboul, Muhammad Akhtar, John E. G. Barnett, and Cedric J. PearceCite this: J. Am. Chem. Soc. 1976, 98, 22, 7110–7112Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/ja00438a079https://doi.org/10.1021/ja00438a079research-articleACS PublicationsRequest reuse permissionsArticle Views125Altmetric-Citations18LEARN 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
Four subtypes of protease‐activated receptors, co‐expressed in rat astrocytes, evoke different physiological signaling (2001)

Protease-activated receptors (PARs) are newly identified members of the superfamily of G-protein-coupled receptors that initiate cell signaling by the proteolytic activity of extracellular serine proteases. Certain proteases are believed to be involved in development and repair processes and most likely regulate multiple functions of the CNS by activating PARs. Three members of this family (PAR-1, PAR-3, and PAR-4) are considered thrombin receptors, whereas PAR-2 is activated by trypsin. In the present study, using reverse transcription-polymerase chain reaction (RT-PCR), immunocytochemistry, and Ca(2+) mobilization studies, we demonstrate that PAR-1, PAR-2, PAR-3, and PAR-4 are functionally co-expressed in cultured rat astrocytes. Short-term stimulation of astrocytes with thrombin, trypsin, and peptides corresponding to the tethered ligand domains of PAR-1, PAR-2, PAR-3, and PAR-4 induced a transient rise of [Ca(2+)](i) in cultured astrocytes. In studying calcium signaling, based on receptor desensitization, and using an antagonist of thrombin receptor PAR-1, we provide evidence that the thrombin-induced [Ca(2+)](i) response in astrocytes in addition to PAR-1 stimulation, involves also stimulation of PAR-3 and PAR-4. Trypsin, in addition to PAR-2, can also activate PAR-1 and PAR-4. Furthermore we find that activation of PAR-1, and PAR-2 induces proliferation of astrocytes while PAR-4 activation exerts toxic effects. This study is the first to show that (1) cultured astrocytes functionally express PAR-3 and PAR-4 together with PAR-1 and PAR-2; (2) PAR-3-activating peptide (TFRGAP) is effective in eliciting Ca(2+) signaling; and (3) activation of different PARs leads to distinct downstream effects.
The use of relative operating characteristic (ROC) curves in test performance evaluation. (1986)

Relative (or receiver) operating characteristic (ROC) curves are a graphical representation of the relationship between sensitivity and specificity of a laboratory test over all possible diagnostic cutoff values. Laboratory medicine has been slow to adopt the use of ROC curves for the analysis of diagnostic test performance. In this tutorial, we discuss the advantages and limitations of the ROC curve for clinical decision making in laboratory medicine. We demonstrate the construction and statistical uses of ROC analysis, review its published applications in clinical pathology, and comment on its role in the decision analytic framework in laboratory medicine.
A study of the self-trapped exciton and F centre in (1997)

The self-trapped excitons (STEs) and F centres in are studied within the extended-ion approximation. It is found that the STE is in fact a nearest-neighbour F - H pair with symmetry. The theoretical results for the spectra of the STEs and F centres are in good agreement with experiments. The stable F - H pairs converted from STEs are generated only at the hole excited state of the STEs according to the calculations of the adiabatical potential energy curve of the STE/FH pair. A model of the excited-hole hopping diffusion is proposed to explain the reorientation of the H centre and the formation of the F - H pair under cascade excitation.
Monitoring and prediction of network performance (2003)

Analysis of network and application performance is traditionally based on mathematical models derived from first principles. Such models are usually complex, difficult to use, and do not exhibit satisfactory accuracy. This paper describes a new way of achieving high accuracy in predicting network performance. The new solution is built on a unique combination of network-component models and probabilistic analysis. The resulting model-based approach provides high fidelity for decision making in both monitoring and prediction modes. This paper discusses key features of the technique and illustrative results. Resulting capabilities are implemented in a system called NetPredictor/sup TM/, which can monitor and predict quality of service (QoS) and compliance with service-level agreements (SLAs). It also empowers users to perform service-level management (SLM) and to make informed decisions about effects of contemplated changes in a network. Networks can be combinations of LANs, WANs, intranets, and the Internet.
Immunogenicity and Epitope Mapping of a Recombinant Soluble gp160 of the Human Immunodeficiency Virus Type 1 Envelope Glycoprotein (1990)

The human immunodeficiency virus 1 envelope glycoprotein is synthesized as a precursor, gp160, which is subsequently cleaved to generate the external gp120 and the transmembrane gp41. Both of these cleavage products are known to mediate critical functions of the virus. In order to define the best strategy for the development of a vaccine against human immunodeficiency virus 1, it could be important to map the crucial epitopes on gp160. This entire gp160 is uneasy to purify because it is readily subjected to proteolytic cleavage. Furthermore, it is anchored on the cell membrane and needs detergent treatment for purification. We thus used a recombinant gp160 which was engineered to remove the cleavage sites between gp120 and gp41 and the hydrophobic transmembrane in order to investigate the murine immune response. We selected a panel of 8 monoclonal antibodies which recognize different epitopes on the immunizing recombinant soluble gp160. The reactivity of the monoclonal antibodies was checked on virus-derived gp160, gp120, and gp41. Three antibodies reacted only with gp120 but the others were shown to react with gp41 epitopes or with discontinuous epitopes bridging gp120 and gp41. One subregion of these epitopes was located using a synthetic peptide corresponding to the sequence of gp41. This epitope is apparently part of an immunodominant site since it is recognized by three different monoclonal antibodies. We used competitive inhibition experiments to map the epitopes on recombinant gp160; therefore, the results are probably indicative of the folding of the recombinant soluble gp160 used for immunization.
Amino acids stimulate phosphorylation of p70 S6k and organization of rat adipocytes into multicellular clusters (1998)

In previous studies we have shown that rat adipocytes suspended in Matrigel and placed in primary culture migrate through the gel to form multicellular clusters over a 5- to 6-day period. In the present study, phosphorylation of the insulin-regulated 70-kDa ribosomal protein S6 kinase (p70S6k) was observed within 30 min of establishment of adipocytes in primary culture. Two inhibitors of the p70S6k signaling pathway, rapamycin and LY-294002, greatly reduced phosphorylation of p70S6k and organization of adipocytes into multicellular clusters. Of all the components of the cell culture medium, amino acids, and in particular a subset of neutral amino acids, were found to promote both phosphorylation of p70S6k and cluster formation. Lowering the concentrations of amino acids in the medium to levels approximating those in plasma of fasted rats decreased both phosphorylation of p70S6k and cluster formation. Furthermore, stimulation of p70S6k phosphorylation by amino acids was prevented by either rapamycin or LY-294002. These findings demonstrate that amino acids stimulate the p70S6k signaling pathway in adipocytes and imply a role for this pathway in multicellular clustering.