gebhart/patrepeval huggingface dataset:
Six chains of the human T cell antigen receptor.CD3 complex are necessary and sufficient for processing the receptor heterodimer to the cell surface. (1991)

The T cell antigen receptor (TCR) plays a key role in the process of antigen recognition. It is a complex of at least seven peptide chains (alpha beta gamma delta epsilon zeta-zeta). It is found on the surface of mature T cells and functions in antigen binding in the presence of the major histocompatibility complex. It has been known for some time that physical associations between the CD3 proteins and the TCR chains are essential for efficient transport of either component to the surface of T cells. For example, T cells that lack either the alpha, beta, or delta chains synthesize partial complexes that are eventually degraded. cDNAs encoding the six chains of receptor have become available recently. We have used transfection techniques to generate a panel of Chinese hamster ovary cells that contain partial receptor complexes of known composition and also cells that express all six subunits of the TCR.CD3 complex. Cells in this panel were analyzed for the ability to form alpha-beta heterodimers and also an ability to transport the synthesized chains to the plasma membrane. These studies have allowed us to define the minimum requirements for TCR.CD3 expression on the cell surface.
Gold Nanorods: From Synthesis and Properties to Biological and Biomedical Applications (2009)

Noble metal nanoparticles are capable of confining resonant photons in such a manner as to induce coherent surface plasmon oscillation of their conduction band electrons, a phenomenon leading to two important properties. Firstly, the confinement of the photon to the nanoparticle's dimensions leads to a large increase in its electromagnetic field and consequently great enhancement of all the nanoparticle's radiative properties, such as absorption and scattering. Moreover, by confining the photon's wavelength to the nanoparticle's small dimensions, there exists enhanced imaging resolving powers, which extend well below the diffraction limit, a property of considerable importance in potential device applications. Secondly, the strongly absorbed light by the nanoparticles is followed by a rapid dephasing of the coherent electron motion in tandem with an equally rapid energy transfer to the lattice, a process integral to the technologically relevant photothermal properties of plasmonic nanoparticles. Of all the possible nanoparticle shapes, gold nanorods are especially intriguing as they offer strong plasmonic fields while exhibiting excellent tunability and biocompatibility. We begin this review of gold nanorods by summarizing their radiative and nonradiative properties. Their various synthetic methods are then outlined with an emphasis on the seed-mediated chemical growth. In particular, we describe nanorod spontaneous self-assembly, chemically driven assembly, and polymer-based alignment. The final section details current studies aimed at applications in the biological and biomedical fields.
Screening for mutations in the open reading frame and promoter of the β-amyloid precursor protein gene in familial Alzheimer's disease: identification of a further family with APP717 Val→lle (1992)

Following the identification of mutations in the beta-amyloid precursor protein (APP) gene in familial, early onset Alzheimer's disease (AD), we have developed a screening protocol using single strand conformation analysis (SSCA) to screen exon 17 for the known mutations within APP. In addition, we used this protocol to screen the other seventeen exons of APP and a three hundred and thirty base pair regulatory region of the promoter for new mutations in 9 families with early onset AD. Exons 16 and 17, which encode the deposited beta-amyloid peptide, were screened in a further 10 families. Our screening procedure identifies all the reported mutations within APP. While we have identified a further family with APP717 Val-->Ile, we did not find any previously undescribed mutations. Screening of other exons of APP in 2 families in which we have previously reported mutations at APP717, failed to reveal other sequence abnormalities supporting the hypothesis that the mutations at APP717 cause the disease in these families. These data suggest that mutations in APP are a rare cause of familial early onset AD (3/21 families tested) and that within APP most, possibly all, mutations which cause AD are in exon 17.
MHC class I expression and CD8+ T cell development in TAP1/β2-microglobulin double mutant mice (1995)

We have bred to homozygosity gene disruptions for the transporter associated with antigen processing 1 (TAP1) and beta 2-microglobulin (beta 2m), each of which plays a distinct role in providing class I MHC subunits. Surface expression of H-2Kb or Db on cells derived from TAP1/beta 2m -/- mice was undetectable by immunofluorescence or immunoprecipitation, unlike the situation observed for TAP1 -/- and beta 2m -/- single mutant mice. Yet, TAP1/beta 2m -/- cells were able to elicit a CD8+ cytotoxic T cell (CTL) response in mice of different H-2 haplotypes and could be killed by anti-H-2b specific CTL. Furthermore, TAP1/beta 2m -/- skin grafts were rejected by bm1 mutant mice. This suggests that very low levels of conformed class I heavy chains can reach the cell surface even in the complete absence of TAP1 and beta 2m gene products, and that these molecules may select a functional CD8+ T cell repertoire. Indeed, CD4-CD8+ T cells were detected in TAP1/beta 2m -/- mice, but in numbers lower than in either of the single mutant mice. Nonetheless, it was possible to elicit a CD8+ allospecific and H-2b reactive CTL response in TAP1/beta 2m -/- mice. In line with this, TAP1/beta 2m -/- mice rapidly rejected TAP1/beta 2m +/- skin grafts. Our results suggest that some MHC class I heavy chains in TAP1/beta 2m -/- cells can reach the cell surface in a form that allows recognition by allospecific CTL and positive selection of CD8+ T cells.
Membrane Localization of Phosphatidylinositol 3-Kinase Is Sufficient To Activate Multiple Signal-Transducing Kinase Pathways (1996)

Phosphatidylinositol (PI) 3-kinase is a cytoplasmic signaling molecule recruited to the membrane by activated growth factor receptors. The p85 subunit of PI 3-kinase links the catalytic p110 subunit to activated growth factor receptors and is required for enzymatic activity of p110. In this report, we describe the effects of expressing novel forms of p110 that are targeted to the membrane by either N-terminal myristoylation or C-terminal farnesylation. The expression of membrane-localized p110 is sufficient to trigger downstream responses characteristic of growth factor action, including the stimulation of pp70 S6 kinase, Akt/Rac, and Jun N-terminal kinase (JNK). These responses can also be triggered by expression of a form of p110 (p110*) that is cytosolic but exhibits a high specific activity. Finally, targeting of pl10* to the membrane results in maximal activation of downstream responses. Our data demonstrate that either membrane-targeted forms of p110 or a form of p110 with high specific activity can act as constitutively active PI 3-kinases and induce PI 3-kinase-dependent responses in the absence of growth factor stimulation. The results also show that PI 3-kinase activation is sufficient to stimulate several kinases that appear to function in different signaling pathways.
Purification and characterization of initiation factor IF-E3 from rabbit reticulocytes. (1976)

Initiation factor IF-E3 from rabbit reticulocytes was isolated from a high salf extract of ribosomes prepared according to the procedure of Schreier and Staehelin (J. Mol9 Biol, 73, 329-349, 1973). The factor was highly purified from the crude extract by ammonium sulfate fractionation, sucrose gradient centrifugation, salf gradient elution from DEAE-cellulose and phosphocellulose columns, and glycerol gradient centrifugation. IF-E3 stimulated cell-free protein synthesis dependent on an exogenous globin mRNA fraction 4- to 5-fold. The factor under nondenaturing conditions behaved as a large multipolypeptide complex, but was separated into 11 major protein components by two-dimensional polyacrylamide gel electrophoresis with urea and sodium dodecyl sulfate. The stoichiometry and molecular weights (range: 28,000-140,000) of the IF-E3 proteins were determined. None of the components corresponded to ribosomal proteins found in high salt-washed ribosomes. 14CH3-IF-E3 was prepared by reductive alkylation without detectable loss of its initiation factor activity, and bound stoichiometrically to 40S ribosomal subunits, but not to 60S or 80S ribosomes. 14CH3-IF-E3 isolated from the 40S complex contained only nine of the 11 original protein components.
Massively Parallel Single-Molecule and Single-Cell Emulsion Reverse Transcription Polymerase Chain Reaction Using Agarose Droplet Microfluidics (2012)

A microfluidic device for performing single copy, emulsion Reverse Transcription Polymerase Chain Reaction (RT-PCR) within agarose droplets is presented. A two-aqueous-inlet emulsion droplet generator was designed and fabricated to produce highly uniform monodisperse picoliter agarose emulsion droplets with RT-PCR reagents in carrier oil. Template RNA or cells were delivered from one inlet with RT-PCR reagents/cell lysis buffer delivered separately from the other. Efficient RNA/cell encapsulation and RT-PCR at the single copy level was achieved in agarose-in-oil droplets, which, after amplification, can be solidified into agarose beads for further analysis. A simple and efficient method to graft primer to the polymer matrix using 5'-acrydite primer was developed to ensure highly efficient trapping of RT-PCR products in agarose. High-throughput single RNA molecule/cell RT-PCR was demonstrated in stochastically diluted solutions. Our results indicate that single-molecule RT-PCR can be efficiently carried out in agarose matrix. Single-cell RT-PCR was successfully performed which showed a clear difference in gene expression level of EpCAM, a cancer biomarker gene, at the single-cell level between different types of cancer cells. This work clearly demonstrates for the first time, single-copy RT-PCR in agarose droplets. We believe this will open up new possibilities for viral RNA detection and single-cell transcription analysis.
Effects of the inclusion of yeast culture (Saccharomyces cerevisiae plus growth medium) in the diet of dairy cows on milk yield and forage degradation and fermentation patterns in the rumen of steers (1991)

The effects of including yeast culture (YC; Saccharomyces cerevisae plus growth medium; 5 x 10(9) organisms/g) in diets for ruminants was examined in two experiments. In Exp. 1, 32 multiparous Friesian dairy cows were fed between wk 7 to 12 of lactation one of four completely mixed diets based on either hay or straw plus rolled barley (mixed to give concentrate:forage ratios of either 50:50 or 60:40, respectively) with or without 10 g YC/d in a 2(3) factorial design. Supplementation with YC increased DM intake of the cows by a mean of 1.2 kg/d (P less than or equal to .062) and increased milk yield by 1.4 liters/d (corrected to 4% butterfat; P less than or equal to .05). There was an interaction (P less than .05) between diet composition and YC addition; effects of YC were greatest in diets containing 60:40 (concentrate:forage) ratio. In Exp. 2, three steers were fed a diet of 50% hay and 50% rolled barley (DM basis). Hay was available for the major part of the day but barley was fed in two meals/d. Addition of YC to the diet increased (P less than .05) ruminal pH for 4 h after the barley meal. This elevation in pH probably was due to a reduction (P less than or equal to .01) in the concentration of L-lactate in the ruminal liquor of steers given YC (1.43 vs 3.55 mM; P less than or equal to .01). Peak ruminal L-lactate concentration (7.75 mM) in the controls coincided with time of minimum pH values (2 h after the meal of barley); this peak was absent in steers given YC. YC had no effect on the concentration of VFA in ruminal liquor, but the ratio of acetate to propionate was reduced (P less than or equal to .01) from 3.3:1 to 2.8:1 in steers given YC. The extent of DM degradation of hay incubated in the rumen of steers fed the hay and rolled barley diet was increased (P less than .05) in the presence of YC at 12 h of incubation, but degradation was similar in all treatment groups after 24 h of incubation. Presence of yeast culture in the rumen had effects on ruminal stoichiometry. An increased rate of forage degradation may have increased forage intake and productivity of these dairy cows.
Synthesis of Dinucleotide Thiophosphoramidates as Anti-HIV New Prodrugs (2003)

Sequential transesterification of diphenyl phosphite with 5′-O-(4,4′-dimethoxytrityl)thymidine (1) and hydrogen sulfide gave O-[5′-O-(4,4′-dimethoxytrityl)thymidine-3′-yl] H-thiophosphonate (2), and subsequent condensation of 2 with AZT or d4T in the presence of diphenyl chlorophosphoate provided the dinucleotide H-thiophosphonates 3 or 3′. The Antherton-Todd reaction of 3 or 3′ with l-amino acid methyl ester in a solution of CCl4-Et3N-H2O-MeCN gave the dinuleotide thiophosphoramidates 4 or 4′, and removal of the dimethoxytrityl protecting group in formic acid yielded the target products AZT/d4T thiophosphoramidates 5 and 5′.
Tumor Endothelial Cells Express Epidermal Growth Factor Receptor (EGFR) but not ErbB3 and Are Responsive to EGF and to EGFR Kinase Inhibitors (2006)

Epidermal growth factor (EGF) receptor family members are expressed by tumor cells and contribute to tumor progression. The expression and activity of EGF receptors in endothelial cells are less well characterized. Analysis of tumor-derived endothelial cells showed that they express EGFR, ErbB2, and ErbB4, whereas their normal counterparts express ErbB2, ErbB3, and ErbB4. The gain in expression of EGFR and the loss of ErbB3 expression in tumor vasculature was also observed in vivo. As a consequence of their expressing EGFR, tumor endothelial cells responded to EGF and other EGF family members by activating both EGFR and ErbB2, by activating the downstream mitogen-activated protein kinase pathway, and by enhanced proliferation. On the other hand, normal endothelial cells did not respond to EGF but instead were responsive to neuregulin (NRG), a ligand for ErbB3 and ErbB4. NRG activated ErbB3 in normal endothelial cells and inhibited growth of these cells. In contrast, tumor endothelial cells, which do not express ErbB3, were not growth inhibited by NRG. Furthermore, due to their expression of EGFR, tumor endothelial cells, unlike normal endothelial cells, are direct targets for EGFR kinase inhibitors. These low-molecular-weight compounds block EGF-induced EGFR activation and proliferation of tumor endothelial cells. These results suggest that a gain of EGF-induced endothelial cell proliferation, and loss of NRG-induced growth inhibition in tumor endothelial cells constitutes a switch that promotes tumor angiogenesis. In addition, these results suggest that EGFR kinase inhibitors may be effective for antiangiogenesis therapy by specifically targeting the tumor, but not the normal, vasculature.
Characterization of herpes simplex virus 1 alpha proteins 0, 4, and 27 with monoclonal antibodies (1984)

Analyses of the reactivity and patterns of synthesis of infected cell polypeptides (ICPs) specified by herpes simplex virus (HSV) 1 and 2 and by HSV-1 X HSV-2 recombinants indicated that monoclonal antibody H1183 reacted with HSV-1 alpha ICP0, whereas monoclonal antibody H1113 reacted with both HSV-1 and HSV-2 alpha ICP27. H1083 and H1113 and a monoclonal antibody to ICP4 (H640) similar to one previously described (D. K. Braun et al., J. Virol. 46:103-112.) were then used to study the properties of these alpha proteins. The results were as follows: alpha ICP0, ICP4, and ICP27 accumulated primarily in the nuclei of infected cells. ICP4 and ICP27 were poorly soluble in nondenaturing buffer solutions. ICP0 was considerably more soluble than ICP4 and ICP27. ICP0, ICP4, and ICP27 were readily partially purified by immunoaffinity chromatography from lysates of infected cells solubilized with denaturing agents such as sodium dodecyl sulfate. ICP0 and ICP27 were phosphorylated in cells overlaid with medium containing 32P early (1 to 3 h) or late (18 to 20 h) postinfection. A fraction, but not all, 32P that was incorporated early was chased in the presence of unlabeled phosphate. ICP0, ICP4, and ICP27 labeled with either 32P or [35S]methionine yielded multiple spots upon two-dimensional separations. However, ICP4 quantitatively precipitated at the origin when the migration in the first dimension was from acid to base, and both ICP4 and ICP27 partially precipitated at the origin when the direction of migration was reversed.
Automatic Music Transcription and Audio Source Separation (2002)

Abstract In this article, we give an overview of a range of approaches to the analysis and separation of musical audio. In particular, we consider the problems of automatic music transcription and audio source separation, which are of particular interest to our group. Monophonic music transcription, where a single note is present at one time, can be tackled using an autocorrelation-based method. For polyphonic music transcription, with several notes at any time, other approaches can be used, such as a blackboard model or a multiple-cause/sparse coding method. The latter is based on ideas and methods related to independent component analysis (ICA), a method for sound source separation.
Carbon nanotube‐enhanced thermal destruction of cancer cells in a noninvasive radiofrequency field (2007)

The current results suggested that SWNTs targeted to cancer cells may allow noninvasive RF field treatments to produce lethal thermal injury to the malignant cells. Now, the authors are developing SWNTs coupled with cancer cell-targeting agents to enhance SWNT uptake by cancer cells while limiting uptake by normal cells.
Allosteric Modulation of Protease-Activated Receptor Signaling (2012)

The protease-activated receptors (PARs) are G protein-coupled receptors (GPCRs) that are uniquely activated by proteolysis. PARs mediate hemostasis, thrombosis, inflammation, embryonic development and progression of certain malignant cancers. The family of PARs include four members: PAR1, PAR2, PAR3 and PAR4. PARs harbor a cryptic ligand sequence within their N-terminus that is exposed following proteolytic cleavage. The newly formed PAR Nterminus functions as a tethered ligand that binds intramolecularly to the receptor to trigger transmembrane signaling. This unique mechanism of activation would indicate that regardless of the activating protease, cleavage of PARs would unmask a tethered ligand sequence that would induce a similar active receptor conformation and signaling response. However, this is not the case. Recent studies demonstrate that PARs can be differentially activated by synthetic peptide agonists, proteases or through dimerization, that ultimately result in distinct cellular responses. In some cases, allosteric modulation of PARs involves compartmentalization in caveolae, plasma membrane microdomains enriched in cholesterol. Here, we discuss some mechanisms that lead to allosteric modulation of PAR signaling.
Analysis of full-length cDNA clones carryingGALIofSaccharomyces cerevisiae:a model system for cDNA expression (1984)

A cDNA cloning vector that allows expression in Saccharomyces cerevisiae has been developed using the plasmid primer approach described by Okayama and Berg [Mol. Cell. Biol. 2:161-170(1982)]. The vector contains ARS1 and TRP1 for plasmid maintenance in yeast and the ADC1 or GAL1 promoter and the TRP5 terminator for expression of the cloned cDNA. Using this system, several recombinants with nearly full-length GAL1 cDNA inserts in a cDNA library made with galactose-induced yeast mRNA were identified. By measurement of galactokinase mRNA and its protein, the expression of GAL1 cDNA was shown to be under the control of the promoter placed upstream of the cDNA insert. Nucleotide sequence analysis revealed that the 3'-ends of the GAL1 cDNA inserts were not unique, indicating that polyA tails were added to GAL1 transcripts at multiple sites in the GAL1 gene. Genetic complementation of appropriate yeast mutants permitted the isolation of clones containing the coding sequences for GAL1, HIS3, and LEU2 from the same cDNA library.
Molecular cloning and characterization of DNA sequences encoding rat and human atrial natriuretic factors. (1984)

A cDNA copy of the message encoding rat atrial natriuretic factor (ANF) has been cloned in Escherichia coli, and its nucleotide sequence was determined. ANF appears to be synthesized as a larger precursor, atrial pronatriodilatin. The cDNA has an open reading frame potentially encoding a protein of 152 amino acids, of which the first 24 amino acids strongly resemble a signal sequence. This is followed by a sequence with 80% homology to a second vasoactive protein, porcine cardiodilatin. The ANF peptide is contained in the COOH-terminal portion of the protein. The DNA sequence corresponding to human ANF is also presented and displays a high degree of homology to its rat counterpart. These data provide further evidence for the expression in cardiac atria of a multifactor system that may contribute to the regulation of blood pressure and extracellular fluid volume.
Transient stimulation expands superior antitumor T cells for adoptive therapy (2017)

Adoptive cell therapy is a potentially curative therapeutic approach for patients with cancer. In this treatment modality, antitumor T cells are exponentially expanded in vitro prior to infusion. Importantly, the results of recent clinical trials suggest that the quality of expanded T cells critically affects their therapeutic efficacy. Although anti-CD3 mAb-based stimulation is widely used to expand T cells in vitro, a protocol to generate T cell grafts for optimal adoptive therapy has yet to be established. In this study, we investigated the differences between T cell stimulation mediated by anti-CD3/CD28 mAb-coated beads and cell-based artificial antigen-presenting cells (aAPCs) expressing CD3/CD28 counter-receptors. We found that transient stimulation with cell-based aAPCs, but not prolonged stimulation with beads, resulted in the superior expansion of CD8<sup>+</sup> T cells. Transiently stimulated CD8<sup>+</sup> T cells maintained a stem cell-like memory phenotype and were capable of secreting multiple cytokines significantly more efficiently than chronically stimulated T cells. Importantly, the chimeric antigen receptor-engineered antitumor CD8<sup>+</sup> T cells expanded via transient stimulation demonstrated superior persistence and antitumor responses in adoptive immunotherapy mouse models. These results suggest that restrained stimulation is critical for generating T cell grafts for optimal adoptive immunotherapy for cancer.
Synthesis of biologically active, novel monosaccharide analogs of lipid A. (1984)

(LPS) possess a variety of biological activities, e.g., endotoxicity, adjuvanticity, antitumor activity and so on, and many of these activities have been suggested to be localized in the lipid A component.la) The fundamental structure of
Randomized Multicenter Trial of the Effects of Melanoma-Associated Helper Peptides and Cyclophosphamide on the Immunogenicity of a Multipeptide Melanoma Vaccine (2011)

Melanoma-associated helper peptides paradoxically decreased CD8(+) T-cell responses to a melanoma vaccine (P < .001), and CY pretreatment had no immunologic or clinical effect. Prior work showed immunologic and clinical activity of 6MHP alone. Possible explanations for negative effects on CD8 responses include modulation of homing receptor expression or induction of antigen-specific regulatory T cells.