gebhart/patrepeval huggingface dataset:
Immunoproteasomes Shape Immunodominance Hierarchies of Antiviral Cd8+ T Cells at the Levels of T Cell Repertoire and Presentation of Viral Antigens (2001)

Vertebrates express three cytokine-inducible proteasome subunits that are incorporated in the place of their constitutively synthesized counterparts. There is increasing evidence that the set of peptides generated by proteasomes containing these subunits (immunoproteasomes) differs from that produced by standard proteasomes. In this study, we use mice lacking one of the immunoproteasome subunits (LMP2) to show that immunoproteasomes play an important role in establishing the immunodominance hierarchy of CD8(+) T cells (T(CD8+)) responding to seven defined determinants in influenza virus. In LMP2(-/)- mice, responses to the two most dominant determinants drop precipitously, whereas responses to two subdominant determinants are greatly enhanced. Adoptive transfer experiments with naive normal and transgenic T(CD8+) reveal that the reduced immunogenicity of one determinant (PA(224-233)) can be attributed to decreased generation by antigen presenting cells (APCs), whereas the other determinant (NP(366-374)) is less immunogenic due to alterations in the T(CD8+) repertoire, and not, as reported previously, to the decreased capacity of LMP2(-/)- APCs to generate the determinant. The enhanced response to one of the subdominant determinants (PB1F2(62-70)) correlates with increased generation by LMP2(-)(/)- virus-infected cells. These findings indicate that in addition to their effects on the presentation of foreign antigens, immunoproteasomes influence T(CD8+) responses by modifying the repertoire of responding T(CD8+).
Developing GIS-supported location-based services (2002)

Mobile networking is developing and proliferating at a high speed. Many estimates say that the number of mobile telecom subscribers will exceed 1 billion in the year 2003. Among the terminals deployed, there will be hundreds of millions of Internet-enabled ones making Mobile Internet a reality for the big masses. The terminals and/or the mobile networks are now able to determine the position of the terminal on the earth with more and more precision. This is the basis for the new class of services called Location-Based Services (LBS). The paper discusses this new emerging application area that some people consider the central novel application class of Mobile Internet. The main topic of the paper is the question, how Geographic Information Systems (GIS) and the data hosted currently by them could be used in the context of LBS. We analyze their properties and relate them with the needs of LBS. We also present our LBS pilot system that is using XML-based vector formal for city maps and runs on Java-enabled mobile terminals, PDAs and smartphones.
Differentiation of Strains of Xylella fastidiosa Infecting Grape, Almonds, and Oleander Using a Multiprimer PCR Assay (2006)

Xylella fastidiosa is a xylem-limited, nutritionally fastidious bacterium that causes several plant diseases including Pierce's disease (PD) in grape and leaf scorch in almond (ALS) and oleander (OLS). OLS strains belong to X. fastidiosa subsp. sandyi, PD strains belong to X. fastidiosa subsp. fastidiosa, and strains from almond designated as ALS strains are of two general types belonging either to X. fastidiosa subsp. multiplex or X. fastidiosa subsp. fastidiosa. The ALS strains assigned to X. fastidiosa subsp. multiplex belong to two different genotypes (ALSI and ALSII) below the subspecies level. The OLS strains do not infect grape or almond. PD strains produce diseases in grape, alfalfa, almond, and some weeds, but they do not infect oleander, oak, peach, or citrus. ALS strains that belong to X. fastidiosa subsp. multiplex do not produce disease on grape. In this study, a relatively simple polymerase chain reaction (PCR) based method was developed to distinguish among PD, OLS, and ALS strains. PCR performed with primers XF1968-L and XF1968-R amplified a 638-bp fragment from OLS strains but not from PD strains or ALS strains that belong to X. fastidiosa subsp. fastidiosa. PCR with primers XF2542-L and XF2542-R amplified a 412-bp fragment from PD strains, but not from OLS strains. PCR with primers ALM1 and ALM2 produced a fragment of 521 bp from strains isolated from almond that belong to X. fastidiosa subsp. multiplex. The combination of the three primer sets allowed the distinction of the two ALS genotypes of X. fastidiosa subsp. multiplex. These results are in agreement with those obtained from analysis of sequences of 16S-23S rDNA intergenic spacer regions sequence analysis and with previous results based on randomly amplified polymorphic DNA analysis.
The genetic design of signaling cascades to record receptor activation (2007)

We have developed an experimental strategy to monitor protein interactions in a cell with a high degree of selectivity and sensitivity. A transcription factor is tethered to a membrane-bound receptor with a linker that contains a cleavage site for a specific protease. Activation of the receptor recruits a signaling protein fused to the protease that then cleaves and releases the transcription factor to activate reporter genes in the nucleus. This strategy converts a transient interaction into a stable and amplifiable reporter gene signal to record the activation of a receptor without interference from endogenous signaling pathways. We have developed this assay for three classes of receptors: G protein-coupled receptors, receptor tyrosine kinases, and steroid hormone receptors. Finally, we use the assay to identify a ligand for the orphan receptor GPR1, suggesting a role for this receptor in the regulation of inflammation.
Method of Injection of OnabotulinumtoxinA for Chronic Migraine: A Safe, Well‐Tolerated, and Effective Treatment Paradigm Based on the PREEMPT Clinical Program (2010)

Chronic migraine (CM) is a prevalent and disabling neurological disorder. Few prophylactic treatments for CM have been investigated. OnabotulinumtoxinA, which inhibits the release of nociceptive mediators, such as glutamate, substance P, and calcitonin gene-related peptide, has been evaluated in randomized, placebo-controlled studies for the preventive treatment of a variety of headache disorders, including CM. These studies have yielded insight into appropriate patient selection, injection sites, dosages, and technique. Initial approaches used a set of fixed sites for the pericranial injections. However, the treatment approach evolved to include other sites that corresponded to the location of pain and tenderness in the individual patient in addition to the fixed sites. The Phase III REsearch Evaluating Migraine Prophylaxis Therapy (PREEMPT) injection paradigm uses both fixed and follow-the-pain sites, with additional specific follow-the-pain sites considered depending on individual symptoms. The PREEMPT paradigm for injecting onabotulinumtoxinA has been shown to be safe, well-tolerated, and effective in well-designed, controlled clinical trials and is the evidence-based approach recommended to optimize clinical outcomes for patients with CM.
Automated screening using microfluidic chip‐based PCR and product detection to assess risk of BK virus‐associated nephropathy in renal transplant recipients (2006)

The cost-effective detection of viral particles in bodily fluids could enable more effective responses to viral outbreaks, whether isolated clinical cases, or influenza epidemics. In renal transplant recipients, complications arising from high levels of BK virus can lead to graft dysfunction, graft loss, and/or reduced patient survival. We describe a microfluidic system for the sensitive analysis of BK virus (viral load) in unprocessed urine samples that are applied directly onto the chip, thus avoiding labor-intensive processing and sources of inter-assay variability. Integration of small volume genetic amplification (PCR) and electrophoretic analysis detects as few as 1-2 viral copies, distinguishes between high, medium and low levels of virus and reliably identifies viral loads requiring clinical intervention. As a first step to wider application in the clinic and in the field, the present work presents an entirely microchip-based system, validated against conventional clinical methods using clinical samples.
Development of Zeptomole and Attomolar Detection Sensitivity of Biotin−Peptide Using a Dot−Blot GoldNanoparticle Immunoassay (2006)

An ultrasensitive, simple, and fast immunoassay for biotin-peptide detection using gold nanoparticles conjugated with antibodies has been developed. Biotin was covalently attached to a peptide and the biotin-peptide bound on a nitrocellulose membrane. Antibody-coated gold nanoparticles bound to the biotin-peptide formed red dots. With this method, 100 amol of the biotin-peptide was detected and no immunogold was bound to the membrane in the absence of biotin. The relative intensity of each dot was scored using Quantity One, a quantitative analysis software program. The linear working range of this assay was between 1 pmol and 1 micromol. The assay sensitivity was increased by silver enhancement to 100 zmol, and the linear working range was between 100 zmol and 100 fmol. This assay can be extended to detect target molecules, such as dioxin, digoxin, mercury, and so on, with matched antibodies and has potential broad applications in immunoassay.
Human interleukin-5 (IL-5) regulates the production of eosinophils in human bone marrow cultures: comparison and interaction with IL-1, IL-3, IL-6, and GMCSF (1989)

Recombinant human interleukin-5 (rhIL-5), in either liquid or semi-solid cultures, selectively induced eosinophil production from normal human bone marrow, with no activity on other cell lineages. The time course of eosinophil production induced by murine IL-5, rhIL-3, and rh granulocyte-macrophage colony stimulating factor (GMCSF) was similar to rhIL-5. The rate of eosinophil maturation in vitro was independent of the stimulating cytokine, mature eosinophils being produced after 4 to 5 weeks in liquid culture with each of these cytokines. The eosinophils produced in response to each cytokine were morphologically indistinguishable, and had the ultrastructural features of maturity except that the electron-dense material in the granules had not formed into crystalline cores. Neither rhIL-1 nor rhIL-6 alone, or in combination with rhIL-5 or rhIL-3, induced eosinophil differentiation or proliferation under the conditions used. rhIL-3 and rhGMCSF induced more eosinophil colonies than rhIL-5, rhIL-5 had an additive, not synergistic, effect on eosinophil colony production when combined with either rhIL-3 or rhGMCSF, suggesting that rhIL-5 stimulates a smaller and possibly different population of eosinophil progenitors. However, rhIL-5 induced the greatest eosinophil production in liquid cultures, suggesting that although it may act on a smaller population of precursors, it is able to stimulate more proliferative steps than either rhIL-3 or rhGMCSF.
The primary structure of thermostable D-amino acid aminotransferase from a thermophilic Bacillus species and its correlation with L-amino acid aminotransferases (1989)

The gene for thermostable D-amino acid aminotransferase from a thermophile, Bacillus species YM-1 was cloned and expressed efficiently in Escherichia coli. The entire covalent structure of the enzyme was determined from the nucleotide sequence of the cloned gene and mostly confirmed by amino acid sequences of tryptic peptides from the gene product. The polypeptide is composed of 282 amino acid residues with a calculated molecular weight of 32,226. Comparison of the primary structure with those of various proteins registered in a protein data bank revealed a significant sequence homology between D-amino acid aminotransferase and the L-branched chain amino acid aminotransferase of E. coli (Kuramitsu, S., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) J. Biochem. (Tokyo) 97, 993-999); the active site lysyl residue is located in an equivalent position in both enzyme sequences of similar size. Despite the difference in subunit composition and no immunochemical cross-reactivity, the sequences of the two enzymes show similar hydropathy profiles, and spectrophotometric properties of the enzyme-bound cofactor are also similar. The sequence homology suggests that the structural genes for D-amino acid and L-branched chain amino acid aminotransferases evolved from a common ancestral gene.
Boron-containing nucleic acids. Synthesis of cyanoborane adducts of 2'-deoxynucleosides (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBoron-containing nucleic acids. Synthesis of cyanoborane adducts of 2'-deoxynucleosidesAnup Sood, Barbara Ramsay Shaw, and Bernard F. SpielvogelCite this: J. Am. Chem. Soc. 1989, 111, 26, 9234–9235Publication Date (Print):December 1, 1989Publication History Published online1 May 2002Published inissue 1 December 1989https://pubs.acs.org/doi/10.1021/ja00208a019https://doi.org/10.1021/ja00208a019research-articleACS PublicationsRequest reuse permissionsArticle Views276Altmetric-Citations49LEARN 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
Grandifolione: a novel tetranortriterpenoid (1966)

J. D. Connolly, K. L. Handa, R. McCrindle and K. H. Overton, Chem. Commun. (London), 1966, 867 DOI: 10.1039/C19660000867
Prophylactic Oophorectomy in Carriers ofBRCA1orBRCA2Mutations (2002)

Bilateral prophylactic oophorectomy reduces the risk of coelomic epithelial cancer and breast cancer in women with BRCA1 or BRCA2 mutations.
Hybridoma cells containing intracellular anti-ricin antibodies show ricin meets secretory antibody before entering the cytosol. (1987)

Hybridoma cells which synthesize monoclonal antibodies (mAb) that block ricin toxicity were 50-300-fold resistant to ricin compared with other hybridomas. Two of the mAb blocked two isozymes of ricin, D and E, to different and opposite extents, and the hybridoma cell resistance to the two forms of ricin closely corresponded with the mAb reactivity. The hybridoma cell resistance to ricin was therefore due to the binding activity of the mAb produced by the cells. Neither rabbit polyclonal antibodies, which neutralized extracellular anti-ricin mAb, nor quantitative removal of hybridoma cell surface IgG with papain affected the cellular resistance to ricin. Therefore, neither extracellular or cell surface antibodies contributed to the resistance of the hybridoma cells. In contrast, inhibition of protein synthesis by cycloheximide or puromycin, which selectively decreased levels of intracellular secretory IgG, decreased the hybridoma cell resistance to ricin. We conclude that intracellular mAb, synthesized de novo for subsequent secretion, block ricin toxicity. Ricin therefore must meet intracellular secretory antibodies before reaching the cytosol. The monoclonal antibodies can also be used to study toxin function within intracellular compartments. An antibody specific for the galactose-binding site of ricin blocks ricin intracellularly, showing that the ricin galactose-binding activity is required in an intracellular compartment for transport of ricin A chain to the cytosol.
Modeling of Threading Dislocation Reduction in Growing GaN Layers (2000)

In this work, a model is developed to treat threading dislocation (TD) reduction in (0001) wurtzite epitaxial GaN thin films. The model is based on an approach originally proposed for (001) f.c.c. thin film growth and uses the concepts of mutual TD motion and reactions. We show that the experimentally observed slow TD reduction in GaN can be explained by low TD reaction probabilities due to TD line directions practically normal to the film surface. The behavior of screw dislocations in III-nitride films is considered and is found to strongly impact TD reduction. Dislocation reduction data in hydride vapor phase epitaxy (HVPE) grown GaN is well-described by this model. The model provides an explanation for the non-saturating TD density in thick GaN films.
Melting of Isolated Tin Nanoparticles (2000)

The melting of isolated neutral tin cluster distributions with mean sizes of about 500 atoms has been investigated in a molecular beam experiment by calorimetrically measuring the clusters' formation energies as a function of their internal temperature. For this purpose the possibility to adjust the temperature of the clusters' internal degrees of freedom by means of the temperature of the cluster source's nozzle was exploited. The melting point of the investigated tin clusters was found to be lowered by 125 K and the latent heat of fusion per atom is reduced by 35% compared to bulk tin. The melting behavior of the isolated tin clusters is discussed with respect to the occurrence of surface premelting.
Direct Gene Transfer into Nonhuman Primate Myofibers In Vivo (1992)

Previously, we showed that rodent muscle has the ability to take up and express plasmid genes injected intramuscularly. This study now demonstrates that nonhuman primate muscle also has this ability to express injected plasmids. A scaled-up version of the standard large preparation of plasmid DNA allowed several tens of milligrams of CCC plasmid DNA to be relatively easily produced and administered to monkeys. After the injection of the E. coli beta-galactosidase reporter gene in pRSVLac-Z, foreign gene expression was localized to both type I and type II myofibers. The luciferase reporter gene in pRSVL was used to quantify the amount of expression. The multiple implantation of plasmid DNA pellets was more efficient in expressing luciferase than the injection of DNA in normal saline. Luciferase activity persisted for at least 4 months after injection. However, the luciferase expression was considerably less than that in rodents. Preliminary studies explored why expression was less in monkeys. Of particular interest was the increased thickness of the perimysium of monkeys as compared to that in rodents. This increased connective tissue may decrease delivery of the plasmid DNA to the myofibers. Anti-nuclear or anti-DNA antibodies were not observed, even after repetitive DNA administrations, and no adverse effects were observed in any of the monkeys.
Phosphorylation of deoxyribonucleic acid dependent RNA polymerase II by nuclear protein kinase N II: mechanism of enhanced ribonucleic acid synthesis (1982)

RNA polymerase II was purified from Morris hepatoma 3924A by a series of ion-exchange and affinity column chromatographic fractionations, followed by sucrose gradient centrifugation in the presence of 0.3 M KC1. Purified RNA polymerase II had a specific activity of greater than 400 nmol of UMP incorporated (30 min)-1 (mg of protein)-1 by using double-stranded DNA as template. The purified enzyme contained five polypeptides (Mr 214 000, 140 000, 33 000, 25 000, and 21 000) that were present in molar quantities and two additional polypeptides (Mr 19 000 and 18 000) that had a combined molar ratio of 1.0. The cyclic AMP independent nuclear protein kinase NII, also purified from hepatoma 3924A, was able to phosphorylate RNA polymerase II polypeptides of Mr 214 000, 140 000, and 21 000. Phosphorylation of the polymerase was accompanied by enhanced transcription of double-stranded DNA, heat-denatured DNA, and poly[d-(A-T)]. The elevation in RNA polymerase activity was dependent upon the presence of hydrolyzable ATP and resulted from an increased number of RNA molecules synthesized in vitro. The average length of RNA chains was not affected by the kinase. Under similar conditions, protein kinase NII also stimulated homologous RNA polymerase I. In contrast to the phosphorylation of polymerase II, modification of polymerase I resulted in an increase in the average size, but not number, of RNA chains synthesized. The specificity of the NII kinase-catalyzed reaction was demonstrated by the inability of another homologous protein kinase, NI, to phosphorylate or activate RNA polymerase II.
Observation of polarization-gate based reconstruction quality improvement during the process of turbidity suppression by optical phase conjugation (2009)

We present experiments that study the impact of polarization selection on the phenomenon of turbidity suppression by optical phase conjugation. Counter to intuition, we discovered that the preferential utilization of multiply scattered light field components over their sparsely scattered counterparts via appropriate polarization selection can lead to better image reconstruction quality. This effect was observed with tissue phantoms and biological tissue sections. The physical origin of this effect and its dependence on scatterer properties are discussed.
Role of Fe-hydrogenase in biological hydrogen production (2006)

Fe-hydrogenase is a distinct class of hydrogen-producing metalloenzyme, present in a wide variety of prokaryotes and eukaryotes. It functions either in the utilization of hydrogen as a growth substrate (H 2 uptake) or in the disposing of excess electrons by combining them with protons to form hydrogen (H 2 evolution). The reversible conversion of molecular hydrogen (H 2 ) to protons (H + ) and electrons is a central reaction in the biological energy cycle of all hydrogenproducing organisms. The active centre of the Fe-hydrogenases contains a unique bimetallic (Fe-Fe) centre with non-protein ligands (CO, CN). X-ray crystallography and spectroscopic studies reveal that Fe-hydrogenase is a simpler system than the Ni-Fe counterpart. The present work summarizes the role of Fe-hydrogenase in the microbial production of hydrogen. Classification, distribution and localization of Fe-hydrogenase enzymes and their structural diversity have also been highlighted.
Superconductivity at 90 K in the Tl-Ba-Cu-O system (1988)

Stable and reproducible superconductivity has been unambiguously observed in a new Tl-Ba-Cu-O system containing no group-IIIB elements. Resistance in these rare-earth--free oxides starts to drop sharply above 90 K and reaches zero at 81 K. Meissner flux expulsion and diamagnetic shielding show bulk superconductivity. Further substitutions of elements for this system may lead to even higher-temperature superconductors.