gebhart/patrepeval huggingface dataset:
Immunogenically Fit Subunit Vaccine Components Via Epitope Discovery from Natural Peptide Libraries (2002)

Antigenic peptides that bind pathogen-specific Abs are a potential source of subunit vaccine components. To be effective the peptides must be immunogenically fit: when used as immunogens they must elicit Abs that cross-react with native intact pathogen. In this study, antigenic peptides obtained from phage display libraries through epitope discovery were systematically examined for immunogenic fitness. Peptides selected from random peptide libraries, in which the phage-displayed peptides are encoded by synthetic degenerate oligonucleotides, had marginal immunogenic fitness. In contrast, 50% of the peptides selected from a natural peptide library, in which phage display segments of actual pathogen polypeptides, proved very successful. Epitope discovery from natural peptide libraries is a promising route to subunit vaccines.
Horizontal Transfer of DNA by the Uptake of Apoptotic Bodies (1999)

In this study we have raised the question of whether DNA can be transferred from one cell to another by phagocytosis of apoptotic bodies. We have used integrated copies of the Epstein-Barr virus (EBV) as a marker to follow the fate and expression pattern of apoptotic DNA in the phagocytotic host. Apoptosis was induced in EBV-carrying cell lines by irradiation before cultivation with either human fibroblasts, macrophages, or bovine aortic endothelial cells. Analysis of the expression pattern of EBV-encoded genes was performed by immunofluorescent staining as well as in situ hybridization. Cocultivation of apoptotic bodies from lymphoid cell lines containing integrated but not episomal copies of EBV resulted in expression of the EBV-encoded genes EBER and EBNA1 in the recipient cells at a high frequency. Fluorescence in situ hybridization analysis showed uptake of human chromatin as well as integrated EBV-DNA into the nuclei of bovine aortic endothelial cells. These data show that DNA may be rescued and reused from apoptotic bodies by somatic cells. In addition, our findings suggest that apoptotic bodies derived from EBV-carrying B lymphocytes may serve as the source of viral transfer to cells that lack receptors for the EBV virus in vivo.
Aliasing Reduction for Modified Discrete Cosine Transform Domain Filtering and its Application to Speech Enhancement (2007)

Efficient combinations of coding and manipulation of audio signals in the spectral domain are often desirable in communication systems. The modified discrete cosine transform (MDCT) represents a popular spectral transform in audio coding as it leads to compact signal representations. However, as the MDCT corresponds to a critically sampled filter bank, it is in general not appropriate to directly apply it to filtering tasks. In this paper we present a method to compensate for aliasing terms that arise from such direct MDCT domain filtering. The discussion is thereby based on a rigorous matrix representation of critically sampled filter banks which also leads to corresponding efficient realizations. As an application showcase, noise reduction for MDCT based speech coding is considered in simulations.
SYNTHESIS OF γ,δ-UNSATURATED KETONES BY THE INTRAMOLECULAR DECARBOXYLATIVE ALLYLATION OF ALLYL β-KETO CARBOXYLATES AND ALKENYL ALLYL CARBONATES CATALYZED BY MOLYBDENUM, NICKEL,AND RHODIUM COMPLEXES (1984)

Abstract Allyl β-keto carboxylates and alkenyl allyl carbonates were converted to γ,δ-unsaturated ketones by the intramolecular decarboxylative allylation catalyzed by molybdenum, nickel, and rhodium complexes.
The Judgment of Paris: Treatment Dilemmas in Advanced Renal Cell Carcinoma (2014)

Article Tools ONCOLOGY GRAND ROUNDS Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2013.53.6029 Journal of Clinical Oncology - published online before print February 10, 2014 PMID: 24516012 The Judgment of Paris: Treatment Dilemmas in Advanced Renal Cell Carcinoma Clara HwangxClara HwangSearch for articles by this author Elisabeth I. HeathxElisabeth I. HeathSearch for articles by this author Show More Henry Ford Health Systems, Detroit, MIWayne State University School of Medicine, Detroit, MI https://doi.org/10.1200/JCO.2013.53.6029 First Page Full Text PDF Figures and Tables © 2014 by American Society of Clinical Oncology
Single-dislocation-based strengthening mechanisms in nanoscale metallic multilayers (2002)

Abstract A breakdown from the dislocation-pile-up-based Hall-Petch model is typically observed in metallic multilayers when the layer thickness (one half of the bilayer period) is of the order of a few tens of nanometres. The multilayer strength, however, continues to increase with decreasing layer thickness to a few nanometres. A model based on the glide of single dislocations is developed to interpret the increasing strength of multilayered metals with decreasing layer thickness when the Hall-Petch model is no longer applicable. The model is built on the hypothesis that plastic flow is initially confined to one layer and occurs by the motion of single ‘hairpin’ dislocation loops that deposit misfit-type dislocations at the interface and transfer load to the other, elastically deforming layer. The composite yield occurs when slip is eventually transmitted across the interface, overcoming an additional resistance from the interface dislocation arrays. In a lower-bound estimate, the stress for the initial glide of ‘hairpin’ dislocation loops, confined to one layer, is similar to the classical Orowan stress. In the upper-bound estimate, the interaction of the glide loop with the existing misfit dislocation arrays at the interface is also considered in deriving the Orowan stress. The effect of in-plane residual stresses in the layers on the Orowan stress calculation is also considered. The model predictions compare favourably with experimentally measured strengths on Cu-based multilayers. When the layer thickness is decreased to a couple of nanometres, the strength reaches a plateau and, in some cases, drops with decreasing layer thickness. The single-dislocation model developed here predicts strengthening with decreasing layer thickness and, therefore, does not explain the deformation behaviour in this regime. In the regime of several nanometres, the deformation behaviour can be explained by dislocation transmission across the interface followed by glide of loops that span several layer thicknesses.
Alport familial nephritis. Absence of 28 kilodalton non-collagenous monomers of type IV collagen in glomerular basement membrane. (1987)

Alport-type familial nephritis (FN), a genetic disorder, results in progressive renal insufficiency and sensorineural hearing loss. Immunochemical and biochemical analyses of the non-collagenous (NC1) domain of type IV collagen isolated from the glomerular basement membranes (GBM) of three males with this disease demonstrate absence of the normally occurring 28-kilodalton (kD) NC1 monomers, but persistence of the 26- and 24-kD monomeric subunits derived from alpha 1 and 2 (both type IV) collagen chains, respectively.
Rapid and sensitive detection of DNA in Southern blots with chemiluminescence. (1990)

A new chemiluminescent Southern blot procedure offers molecular biologists a safe, ultrasensitive and rapid alternative to conventional 32P-based systems. This new DNA detection system, SOUTHERN-LIGHT, has been developed by Tropix, Inc. The luminescent signal is produced from a direct chemiluminescent substrate, disodium 3-(4-methoxyspiro[1,2-dioxetane-3-2'-tricyclo-[3.3.1.1 .3,7]decan]-4-yl) phenyl phosphate (AMPPD), which decomposes upon dephosphorylation with alkaline phosphatase. SOUTHERN-LIGHT is an ultrasensitive, rapid detection kit for use with membrane-bound DNA. It is the first test kit to incorporate AMPPD. It requires no specialized equipment and results can be conveniently imaged on instant film or x-ray film within 5-60 min of exposure.
The sulindac derivatives OSI-461, OSIP486823, and OSIP487703 arrest colon cancer cells in mitosis by causing microtubule depolymerization (2006)

Exisulind (sulindac sulfone) and three highly potent derivatives, OSI-461 (CP461), OSIP486823 (CP248), and OSIP487703, inhibit growth and induce apoptosis in SW480 human colon cancer cells, with IC(50)s of 200, 2, 0.1, and 0.003 micromol/L, respectively. The latter three compounds, but not exisulind, induce marked M-phase cell cycle arrest in these cells. This effect seems to be independent of the known ability of these compounds to cause activation of protein kinase G. When tested at twice their IC(50) concentration for growth inhibition, OSI-461, OSIP486823, and OSIP487703 cause depolymerization of microtubules in interphase cells, inhibit spindle formation in mitotic cells, and induce multinucleated cells. In vitro tubulin polymerization assays indicate that all three compounds interact with tubulin directly to cause microtubule depolymerization and/or inhibit de novo tubulin polymerization. These results suggest that the dual effects of OSI-461, OSIP486823, and OSIP487703 on impairment of microtubule functions and protein kinase G activation may explain the potent antiproliferative and apoptotic effects of these compounds in cancer cells.
The phage T4 nrdB intron: a deletion mutant of a version found in the wild. (1991)

Bacteriophage T4 possesses three self-splicing group I introns. Two of the three introns are mobile elements; the third, in the gene encoding a subunit of the phage nucleotide reductase (nrdB), is not mobile. Because intron mobility offers a reasonable explanation for the paradoxical occurrence of large intervening sequences in a space-efficient eubacterial phage, it is puzzling that the nrdB intron is not mobile like its compatriots. We have discovered a larger nrdB intron in a closely related phage, and we infer from comparative sequence data that the T4 intron is a deletion mutant derived from this larger intron. This larger nrdB intron encodes an open reading frame of 269 codons, which we have cloned and overexpressed. The overexpressed protein shows a dsDNA endonuclease activity specific for the intronless nrdB gene, typical of mobile introns. Thus, we believe that all three introns of T4 are or were mobile "infectious introns" and that they have entered into and been maintained in the phage population by virtue of this efficient mobility.
Combined Tyrosine and Serine/Threonine Kinase Inhibition by Sorafenib Prevents Progression of Experimental Pulmonary Hypertension and Myocardial Remodeling (2008)

The multikinase inhibitor sorafenib prevents pulmonary remodeling and improves cardiac and pulmonary function in experimental pulmonary hypertension. Sorafenib exerts direct myocardial antihypertrophic effects, which appear to be mediated via inhibition of the Raf kinase pathway. The combined inhibition of tyrosine and serine/threonine kinases may provide an option to treat pulmonary arterial hypertension and associated right heart remodeling.
Pyramid Architecture for 3840 X 2160 Quad Full High Definition 30 Frames/s Video Acquisition (2010)

Image pipeline processing is crucial to generating high quality images in applications using complementary metaloxide-semiconductor (CMOS)/charge-coupled device sensors. The on-chip line buffer normally dominates the total area and power dissipation due to the needed filter window buffering. As image resolution and filter support increase, the area and power requirement increase accordingly. This paper presents a novel pyramid architecture to efficiently process a system that the image pipeline is between an image sensor and video coding engine. By utilizing the features of the pyramid structure and block-based video/image encoders, the proposed architecture is scalable from low to high image resolution and filter size. The input image is first partitioned into floors of tiles to reduce the frame line buffer. Two computing schemes, immediate result reuse and vertical snack scan, are utilized to reduce the overlapping redundant computations. A 90 nm CMOS chip design with 7 × 5 filter support for 3840 × 2160 quad full high definition video at 30 frames/s is designed to demonstrate the performance of power and area efficiency. Compared with traditional architectures with frame line buffers, the proposed design has shown that the power consumption is reduced by 25% to 108 mW from 145 mW. The chip area is reduced by 65% to 309 K from 888 K logic gates. The external memory bandwidth increases to 8286 Mbit/s from 5972 Mbit/s for YUV4:2:0, from 7963 Mbit/s for YUV4:2:2, and is reduced by 30% from 11944 Mbit/s for YUV4:4:4.
Immunogenicity evaluation of a lipidic amino acid-based synthetic peptide vaccine for Chlamydia trachomatis . (1993)

Lipidic amino acid-based synthetic peptides derived from the variable domains (VD) of Chlamydia trachomatis outer membrane protein 1 were evaluated as potential candidate sequences in a vaccine. A peptide sequence designated P2 from the VD IV of serovar B contained a B cell epitope capable of eliciting antibodies binding to serovar B elementary bodies (EB) and a T helper site capable of presentation by multiple H-2 alleles. Polymerization of the P2 into polylysine to form lipid core peptides (LCP) significantly enhanced immunogenicity compared with P2 monomer alone. The LCP system incorporates lipidic amino acids into the polylysine system and enhances lipophobicity and membrane binding effects of the peptide. A second peptide sequence derived from the VD I of serovar C was cosynthesized with P2 into lipidic polylysine LCP and was designated LCP-H1. Antibodies to this construct reacted at high titer with EB of the three major trachoma causing C. trachomatis serovars A, B, and C. LCP-H1 was immunogenic among four of five murine H-2 alleles. Pepscan analysis showed that the fine specificity of antibodies generated to LCP-H1 were directed to the predetermined neutralizing epitope sequences. An in vitro HAK cell neutralization assay showed that LCP-H1 elicited neutralizing antibodies to serovars A, B, and C, but these were of low titer. Because LCP-H1 antibodies bound to the peptide sequence with 10-100-fold higher titer than to EB, the low neutralization titers most likely result from conformational differences between the synthetic peptide and antigenic sites on the native organism. Modification of LCP-H1 to incorporate a predefined conformation may result in improved antigenic properties.
Differential Antitumor Activity of Aflibercept and Bevacizumab in Patient-Derived Xenograft Models of Colorectal Cancer (2014)

The recombinant fusion protein aflibercept (ziv-aflibercept in the United States) binds VEGF-A, VEGF-B, and placental growth factor (PlGF). The monoclonal antibody bevacizumab binds VEGF-A. Recent studies hypothesized that dual targeting of VEGF/PlGF is more beneficial than targeting either ligand. We compared activity of aflibercept versus bevacizumab in 48 patient-derived xenograft (PDX) colorectal cancer models. Nude mice engrafted subcutaneously with PDX colorectal cancer tumors received biweekly aflibercept, bevacizumab, or vehicle injections. Differential activity between aflibercept and bevacizumab, determined by mouse (m), human (h), VEGF-A, and PlGF levels in untreated tumors, was measured. Aflibercept induced complete tumor stasis in 31 of 48 models and bevacizumab in 2 of 48. Based on statistical analysis, aflibercept was more active than bevacizumab in 39 of 48 models; in 9 of 39 of these models, bevacizumab was considered inactive. In 9 of 48 remaining models, aflibercept and bevacizumab had similar activity. Tumor levels of hVEGF-A (range 776-56,039 pg/mg total protein) were ∼16- to 1,777-fold greater than mVEGF-A (range 8-159 pg/mg total protein). Tumor levels of mPlGF (range 104-1,837 pg/mg total protein) were higher than hPlGF (range 0-543 pg/mg total protein) in 47 of 48 models. Tumor cells were the major source of VEGF; PlGF was primarily produced by tumor stroma. Because tumor levels of hVEGF-A were far greater than mVEGF-A, bevacizumab's inability to bind mVEGF-A is unlikely to explain higher and more consistent aflibercept activity. Neutralizing PlGF and VEGFR-1 activation may be a factor and should be investigated in future studies. In these colorectal cancer PDX models, aflibercept demonstrated greater antitumor activity than bevacizumab.
The role of intercostal nerve preservation in pain control after thoracotomy† (2012)

ICNP without harvesting an intercostal muscle flap achieves excellent outcomes in controlling acute post-thoracotomy pain and CPTP. ICNP is an effective, simple method to perform, and it should be considered as standard in performing thoracotomy.
Expression and phosphorylation of the Listeria monocytogenes ActA protein in mammalian cells. (1993)

Movement of Listeria monocytogenes within infected eukaryotic cells provides a simple model system to study the mechanism of actin-based motility in nonmuscle cells. The actA gene of L. monocytogenes is required to induce the polymerization of host actin filaments [Kocks, C., Gouin, E., Tabouret, M., Berche, P., Ohayon, H. & Cossart, P. (1990) Cell 68, 521-531; Domann, E., Wehland, J., Rohde, M., Pistor, S., Hartl, M., Goebel, W., Leimeister-Wachter, M., Wuenscher, M. & Chakraborty, T. (1992) EMBO J. 11, 1981-1990]. In this study, an in-frame deletion mutation within the actA gene was constructed and introduced into the L. monocytogenes chromosome by allelic exchange. This mutation resulted in a decrease (3 orders of magnitude) in virulence for mice. In tissue culture cells, the actA mutant was absolutely defective for the nucleation of actin filaments and consequently was impaired in cell-to-cell spread. Antiserum raised to a synthetic peptide encompassing the proline-rich repeat (DFPPPPTDEEL) of ActA was used to characterize the expression of the ActA protein. The ActA protein derived from extracellular bacteria migrated as a 97-kDa polypeptide upon SDS/PAGE, whereas the protein from infected cells migrated as three distinct polypeptides, one that comigrated with the 97-kDa extracellular form and two slightly larger species. Treatment of infected cells with okadaic acid resulted in decreased amounts of all forms of ActA and the appearance of a larger species of ActA. Phosphatase treatment of ActA immunoprecipitated from intracellular bacteria resulted in conversion of the larger two species to the 97-kDa form. Labeling of infected cells with 32Pi followed by immunoprecipitation showed that the largest molecular form of ActA was phosphorylated. Taken together, these data indicate that ActA is phosphorylated during intracellular growth. The significance of the intracellular modification of ActA is not known, but we speculate that it may modulate the intracellular activity of ActA.
Differential control over postganglionic neurons in rat cardiac ganglia by NA and DmnX neurons: anatomical evidence (2004)

In previous single-labeling experiments, we showed that neurons in the nucleus ambiguous (NA) and the dorsal moto nucleus of the vagus (DmnX) project to intrinsic cardiac ganglia. Neurons in these two motor nuclei differ significantly in the size of their projection fields, axon caliber, and endings in cardiac ganglia. These differences in NA and DmnX axon cardiac projections raise the question as to whether they target the same, distinct, or overlapping populations of cardiac principal neurons. To address this issue, we examined vagal terminals in cardiac ganglia and trace injection sites in the brain stem using two different anterograde t ace s 1,1-dioleyl-3,3,3,3-tetramethylindocarbocyanine methanesulfonate and 4-[4-(dihexadecylamino)-styryl]-N-methylpyridinium iodide] and confocal microscopy in male Sprague-Dawley rats. We found that 1) NA and DmnX neurons innervate the same cardiac ganglia, but these axons target separate subpopulations of principal neurons and 2) axons arising from neurons in the NA and DmnX in the contralateral sides of the brain stem enter the cardiac ganglionic plexus through separate bundles and preferentially innervate principal neurons near their entry regions, providing topographic mapping of vagal motor neurons in left and right brain stem vagal nuclei. Because the NA and DmnX project to distinct populations of cardiac principal neurons, we propose that they may play different roles in controlling cardiac function.
Use of a biosensor based on surface plasmon resonance and biotinyl glycans for analysis of sugar binding specificities of lectins. (1995)

We have developed a new method for analysis of the interaction between lectins and biotin-derivatized oligosaccharides involving a biosensor based on surface plasmon resonance. Complex type asialo-bi-, tri-, and tetra-antennary oligosaccharides were quantitatively converted into their biotin derivatives by incubating them with 6-(D-biotinyl)-aminohexanoyl hydrazide. This method was also applicable to sialyl sugar chains without any removal of sialic acid residues. The reaction mixture could be directly injected onto the streptavidin pre-immobilized surface of a sensor chip without any purification because of its fairly low reagent/carbohydrate molar ratio. The amounts of sugar chains required for interaction analysis by this method were as low as 1 pmol. The binding specificities of Sambucus sieboldiana lectin, Maackia amurensis lectin, Ricinus communis agglutinin-120 (RCA120), and concanavalin A could be rapidly determined qualitatively by this method. Furthermore, kinetic analysis of the interaction between RCA120, and complex type asialo-bi-, tri-, and tetra-antennary oligosaccharides revealed that both the association rate constant and the dissociation rate constant (kdiss) decreased with increasing numbers of terminal galactosyl residues. Because the tendency observed for kdiss paralleled the elution order of these oligosaccharides on RCA120 immobilized affinity chromatography, kiss might hold the key to determination of the elution order on affinity chromatography.
Optimal shortest path queries in a simple polygon (1987)

Let P be a simple polygon with n sides. This paper shows how to preprocess the polygon so that, given two query points p and q inside P, the length of the shortest path inside the polygon from p to q can be found in time Ο(log n). The path itself must be polygonal and can be extracted in additional time proportional to the number of turns it makes. The preprocessing consists of triangulation plus a linear amount of additional work.
A Thr359Met mutation in factor VII of a patient with a hereditary deficiency causes defective secretion of the molecule (1996)

We elucidated the genetic basis responsible for factor VII deficiency in an Italian woman with a severe bleeding diathesis. In the allele inherited from the patient's father, we identified a G to A mutation at nucleotide 6070 at the 5' splice site of intron 4 and a G to A substitution at nucleotide 10976 resulting in the Arg353Gln polymorphism. The maternal allele demonstrated a C to T substitution at nucleotide 10994 resulting in Thr359Met. The mutation at nucleotide 6070 alters an invariant GT dinucleotide and disrupts normal mRNA processing. To investigate the mechanism by which Thr359Met reduces factor VIl levels, we expressed wild type factor VII cDNA (FVIIwt) and a mutant factor VII cDNA containing the base substitution resulting in Met359 (FVII359M) in Chinese hamster ovary cells (CHO). In cells transfected with the mutant factor VII cDNA, FVII359M accumulated intracellularly, and no factor VII was detected in the media after 3 hours of chase. The carbohydrate side chains associated with FVII359M were sensitive to Endo H digestion, which indicates that the protein is retained in the endoplasmic reticulum. Analysis of cell lysates also showed that FVII359M was associated with the 78 kD protein corresponding to GRP78/BiP. We conclude that a Thr359Met mutation in factor VII results in a severe secretion defect that probably results from abnormal folding of the molecule.