gebhart/patrepeval huggingface dataset:
Retroviral Vector Producer Cell Killing in Human Serum Is Mediated by Natural Antibody and Complement: Strategies for Evading the Humoral Immune Response (1996)

The introduction of retroviral vector producer cells (VPC) into tumors as a means of increasing transduction efficiency has recently been employed in human gene therapy trials. However, the fate of these xenogeneic cells in humans is not well understood. In the present study, we used an in vitro model to examine the survival of commonly used VPC lines in serum from humans and various other species. VPC derived from the murine NIH-3T3 cell line, including PA317, Psi CRIP, and GP + E-86, were effectively killed in sera from Old World primates, including human and baboon. Conversely, the same murine cell lines survived exposure to sera from dog, rabbit, rat, and mouse. This pattern of serum killing parallels the occurrence of the anti-alpha-galactosyl natural antibody (Ab) found exclusively in Old World primates. The anti-alpha-galactosyl Ab targets the terminal glycosidic structure Gal alpha 1-3Gal beta 1-4GlcNAc-R (alpha-galactosyl epitope) found on the surface of mammalian cells, excluding Old World primates. All murine-derived VPC tested expressed high levels of the alpha-galactosyl epitope as determined by FACS analysis. VPC killing was complement-mediated, because preincubation of human serum with a functionally blocking anti-C5 mAb completely abolished cell lysis. Furthermore, addition of soluble galactose(alpha 1-3)galactose (Gal alpha 1-3Gal) to human serum or down-regulation of the alpha-galactosyl epitope on the surface of VPC effectively reduced VPC killing, indicating that complement activation by these cells is primarily initiated by natural antibody recognition of the alpha-galactosyl epitope. Finally, VPC incubated with human serum for 8 hr in the presence of complement inhibition continued to produce viable retroviral particles, thus demonstrating a correlation between VPC and particle survival. Taken together, these data suggest that elimination of the alpha-galactosyl epitope or complement blockade may provide a strategy to prolong the survival of VPC and the particles that they produce in vivo.
Transgenic approaches to crop improvement (2000)

Transgenic crops are now grown commercially on several million hectares, principally in North America. To date, the predominant crops are maize (corn), soybean, cotton, and potatoes. In addition, there have been field trials of transgenics from at least 52 species including all the major field crops, vegetables, and several herbaceous and woody species. This review summarizes recent data relating to such trials, particularly in terms of the trends away from simple, single gene traits such as herbicide and insect resistance towards more complex agronomic traits such as growth rate and increased photosynthetic efficiency. Much of the recent information is derived from inspection of patent databases, a useful source of information on commercial priorities. The review also discusses the time scale for the introduction of these transgenes into breeding populations and their eventual release as new varieties.
VKORC1 Polymorphisms, Haplotypes and Haplotype Groups on Warfarin Dose Among African–Americans and European–Americans (2008)

Our findings support the use of CYP2C9, VKORC1 polymorphisms (rs9934438 or rs9923231) and clinical covariates to predict warfarin dose in both African- and European-Americans. A uniform set of common polymorphisms in CYP2C9 and VKORC1, and limited clinical covariates can be used to improve warfarin dose prediction for a racially diverse population.
Chimeric RNA/Ethylene-Bridged Nucleic Acids Promote Dystrophin Expression in Myocytes of Duchenne Muscular Dystrophy by Inducing Skipping of the Nonsense Mutation-Encoding Exon (2004)

Editing of dystrophin mRNA by induction of exon skipping, using antisense oligonucleotides, has been proposed as one way to generate dystrophin expression in Duchenne muscular dystrophy (DMD) patients. Here, antisense chimeric oligonucleotides consisting of RNA and a new modified nucleic acid are tested for activity to induce skipping of an exon containing a nonsense mutation. In a Japanese DMD case, a nonsense mutation (R1967X) due to a single nucleotide change in exon 41 of the dystrophin gene (C5899T) was identified. Oligonucleotides consisting of 2'-O-methyl RNA and a new 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) were designed to bind the mutation site of exon 41, and their ability to induce exon 41 skipping in dystrophin mRNA was evaluated. Finally, among the specific oligonucleotides tested, an 18-mer RNA/ENA chimera was found to have the strongest activity, inducing exon 41 skipping in nearly 90% of dystrophin mRNA. Accordingly, nearly 90% of cultured myocytes were shown to be dystrophin positive by immunohistochemical analysis. Western blot analysis disclosed the presence of nearly normal-sized dystrophin up to 1 week after the transfection. Our results suggest that an RNA/ENA chimera can be used to express dystrophin in DMD.
Solid-phase synthesis and cyclization of a large branched peptide from IgG Fc with affinity for FcγRI (1999)

A solid phase approach has been used to synthesize a large branched disulphide peptide from IgG Fc, Ac-F-C*-A-K-V-N-N-K-D-L-P-A-P-I-E-K(Ac-E-L-L-G-G-P-S-V-F)-C*-I-NH2. This peptide combines the lower hinge region of IgG and a proximal beta-hairpin loop, both implicated in binding to Fc gammaRI. Solid phase Tl(tfa)3 cyclization of the linear branched peptide resulted in a poor yield of cyclic hinge-loop peptide (11%) most likely due to steric hindrance caused by the branch. However, if addition of the branch was preceded by solid phase Tl(tfa)3 cyclization of the loop, the yield was excellent at 75%. Cyclic hinge-loop peptide was active in displacing IgG2a from Fc gammaRI expressed on monocyte cell lines with an IC50 of 40 microM, whereas the linear form of this peptide was inactive. The Fc hinge-loop peptide demonstrates the potential for a non-mAb high affinity, immunomodulatory ligand for Fc gammaRI.
Single-Trial Analysis of EEG during Rapid Visual Discrimination: Enabling Cortically Coupled Computer Vision (2007)

We describe our work using linear discrimination of multi-channel electroencephalography for single-trial detection of neural signatures of visual recognition events. We demonstrate the approach as a methodology for relating neural variability to response variability, describing studies for response accuracy and response latency during visual target detection. We then show how the approach can be utilized to construct a novel type of brain-computer interface, which we term cortically-coupled computer vision. In this application, a large database of images is triaged using the detected neural signatures. We show how ‘corticaltriaging’ improves image search over a strictly behavioral response.
Specific modelling of regulatory units in DNA sequences. (1997)

Transcriptional control regions are usually composed of a complex arrangement of individual transcriptional elements like protein binding sites. This modular structure allows generation of enormous functional diversity of regulatory regions with a limited set of individual elements. We implemented simple formal representations of these general features of regulatory regions into an algorithm capable of developing complex models reflecting both the element composition and the functional organization of individual elements. Our method (ModelGenerator) requires a training set of at least 10 sequences containing the regulatory regions to be modelled and a very simple initial model which may consist of just two characteristic transcription factor binding sites. We show the capability of our algorithm to expand the initial model solely by comparative sequence analysis leading to complex, biologically meaningful models. A second program (ModelInspector) is capable to scan new sequence data for matches to models defined by ModelGenerator. We show two models for retroviral transcriptional control regions to be highly specific. A search against GenBank using one of the models is shown to be free of false negatives and to produce less than 2 false positives/million nucleotides. Thus, our algorithms appear to be useful tools for the analysis of extremely long genomic sequences which are now becoming available as results of various genome sequencing projects.
Epsilon-near-zero Al-doped ZnO for ultrafast switching at telecom wavelengths (2015)

Transparent conducting oxides have recently gained great attention as CMOS-compatible materials for applications in nanophotonics due to their low optical loss, metal-like behavior, versatile/tailorable optical properties, and established fabrication procedures. In particular, aluminum doped zinc oxide (AZO) is very attractive because its dielectric permittivity can be engineered over a broad range in the near infrared and infrared. However, despite all these beneficial features, the slow (> 100 ps) electron-hole recombination time typical of these compounds still represents a fundamental limitation impeding ultrafast optical modulation. Here we report the first epsilon-near-zero AZO thin films which simultaneously exhibit ultra-fast carrier dynamics (excitation and recombination time below 1 ps) and an outstanding reflectance modulation up to 40% for very low pump fluence levels (< 4 mJ/cm2) at the telecom wavelength of 1.3 {\mu}m. The unique properties of the demonstrated AZO thin films are the result of a low temperature fabrication procedure promoting oxygen vacancies and an ultra-high carrier concentration. As a proof-of-concept, an all-optical AZO-based plasmonic modulator achieving 3 dB modulation in 7.5 {\mu}m and operating at THz frequencies is numerically demonstrated. Our results overcome the traditional "modulation depth vs. speed" trade-off by at least an order of magnitude, placing AZO among the most promising compounds for tunable/switchable nanophotonics.
Phase Variation ofCampylobacter jejuni81-176 Lipooligosaccharide Affects Ganglioside Mimicry and Invasiveness In Vitro (2002)

The outer cores of the lipooligosaccharides (LOS) of many strains of Campylobacter jejuni mimic human gangliosides in structure. A population of cells of C. jejuni strain 81-176 produced a mixture of LOS cores which consisted primarily of structures mimicking GM(2) and GM(3) gangliosides, with minor amounts of structures mimicking GD(1b) and GD(2). Genetic analyses of genes involved in the biosynthesis of the outer core of C. jejuni 81-176 revealed the presence of a homopolymeric tract of G residues within a gene encoding CgtA, an N-acetylgalactosaminyltransferase. Variation in the number of G residues within cgtA affected the length of the open reading frame, and these changes in cgtA corresponded to a change in LOS structure from GM(2) to GM(3) ganglioside mimicry. Site-specific mutation of cgtA in 81-176 resulted in a major LOS core structure that lacked GalNAc and resembled GM(3) ganglioside. Compared to wild-type 81-176, the cgtA mutant showed a significant increase in invasion of INT407 cells. In comparison, a site-specific mutation of the neuC1 gene resulted in the loss of sialic acid in the LOS core and reduced resistance to normal human serum but had no affect on invasion of INT407 cells.
SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex (2014)

SARS coronavirus (SARS-CoV) develops an antagonistic mechanism by which to evade the antiviral activities of interferon (IFN). Previous studies suggested that SARS-CoV papain-like protease (PLpro) inhibits activation of the IRF3 pathway, which would normally elicit a robust IFN response, but the mechanism(s) used by SARS PLpro to inhibit activation of the IRF3 pathway is not fully known. In this study, we uncovered a novel mechanism that may explain how SARS PLpro efficiently inhibits activation of the IRF3 pathway. We found that expression of the membrane-anchored PLpro domain (PLpro-TM) from SARS-CoV inhibits STING/TBK1/IKKε-mediated activation of type I IFNs and disrupts the phosphorylation and dimerization of IRF3, which are activated by STING and TBK1. Meanwhile, we showed that PLpro-TM physically interacts with TRAF3, TBK1, IKKε, STING, and IRF3, the key components that assemble the STING-TRAF3-TBK1 complex for activation of IFN expression. However, the interaction between the components in STING-TRAF3-TBK1 complex is disrupted by PLpro-TM. Furthermore, SARS PLpro-TM reduces the levels of ubiquitinated forms of RIG-I, STING, TRAF3, TBK1, and IRF3 in the STING-TRAF3-TBK1 complex. These results collectively point to a new mechanism used by SARS-CoV through which PLpro negatively regulates IRF3 activation by interaction with STING-TRAF3-TBK1 complex, yielding a SARS-CoV countermeasure against host innate immunity.
Pottery Production and Microcosmic Organization: The Residential Structure of la Quemada, Zacatecas (2000)

Incised-engraved pottery and clays from the Malpaso Valley region of northwest Mexico are chemically characterized to investigate the nature of residential organization of the capital settlement, La Quemada, during the Epiclassic period, ca. A.D. 600-900. Scanning-electron microprobe analysis of 115 pottery and 10 clay samples from settlements in the valley, and from middens associated with the civic-ceremonial core of La Quemada and flanking residential terraces, identifies locations of pottery production and indicates patterns of pottery circulation. The distribution of pottery at La Quemada, manufactured in specific outlying settlements, suggests that the social composition of the polity was reproduced in microcosm at the site, and that activities in civic-ceremonial zones involved a greater degree of separation among social groups than those in flanking residential areas.
Distinct Patterns of Dendritic Cell Cytokine Release Stimulated by Fungal β-Glucans and Toll-Like Receptor Agonists (2009)

beta-Glucans derived from fungal cell walls have potential uses as immunomodulating agents and vaccine adjuvants. Yeast glucan particles (YGPs) are highly purified Saccharomyces cerevisiae cell walls composed of beta1,6-branched beta1,3-d-glucan and free of mannans. YGPs stimulated secretion of the proinflammatory cytokine tumor necrosis factor alpha (TNF-alpha) in wild-type murine bone marrow-derived myeloid dendritic cells (BMDCs) but did not stimulate interleukin-12p70 (IL-12p70) production. A purified soluble beta1,6-branched beta1,3-d-glucan, scleroglucan, also stimulated TNF-alpha in BMDCs. These two beta-glucans failed to stimulate TNF-alpha in Dectin-1 (beta-glucan receptor) knockout BMDCs. Costimulation of wild-type BMDCs with beta-glucans and specific Toll-like receptor (TLR) ligands resulted in greatly enhanced TNF-alpha production but decreased IL-12p70 production compared with TLR agonists alone. The upregulation of TNF-alpha and downregulation of IL-12p70 required Dectin-1, but not IL-10. Gamma interferon (IFN-gamma) priming did not overcome IL-12p70 reduction by beta-glucans. Similar patterns of cytokine regulation were observed in human monocyte-derived dendritic cells (DCs) costimulated with YGPs and the TLR4 ligand lipopolysaccharide. Finally, costimulation of BMDCs with YGPs and either the TLR9 ligand, CpG, or the TLR2/1 ligand, Pam(3)CSK(4), resulted in upregulated secretion of IL-1alpha and IL-10 and downregulated secretion of IL-1beta, IL-6, and IFN-gamma-inducible protein 10 but had no significant effects on IL-12p40, keratinocyte-derived chemokine, monocyte chemotactic protein 1, or macrophage inflammatory protein alpha, compared with the TLR ligand alone. Thus, beta-glucans have distinct effects on cytokine responses following DC stimulation with different TLR agonists. These patterns of response might contribute to the skewing of immune responses during mycotic infections and have implications for the design of immunomodulators and vaccines containing beta-glucans.
The Lyt-2 molecule recognizes residues in the class I alpha 3 domain in allogeneic cytotoxic T cell responses. (1988)

The involvement of the different domains of the MHC class I molecule in CTL recognition was investigated. mAbs specific for the alpha 1/alpha 2 domains of H-2Ld interfered with both the primary and secondary generation and effector function of in vitro Ld-specific CTL. mAbs specific for the alpha 3 domain of H-2Ld interfered with the generation and function of primary in vitro Ld-specific CTL; however, there was no effect on the in vitro generation of secondary CTL and only partial inhibition of their function. In vivo treatment with graft-specific antibodies to both the alpha 3 domain and the alpha 1/alpha 2 domains together resulted in a dramatic enhancement of Ld- or Dd-disparate skin grafts, whereas the individual mAbs showed minimal effects. This suggested that the class I alpha 3 domain is recognized by alloreactive CTL. Several approaches were undertaken to examine whether recognition of the alpha 3 domain determinants is mediated by the Lyt-2 molecule. When mAbs specific for the alpha 3 domain of either H-2Ld or H-2Dd were used in vivo and in vitro, the resulting CTL population was not inhibited by antibody to the alpha 3 domain and was only partially inhibited by antibody to Lyt-2. We therefore observed a correlation between the effects of antibody to the class I alpha 3 domain of the target molecule and antibody to the Lyt-2 molecule on the CTL. To further test the relationship between CTL recognition of the alpha 3 domain and the involvement of Lyt-2, we used a cell expressing a mutation in the alpha 3 domain of the Dd molecule. The mutation resulted in a single amino acid substitution of glu to lys at residue 227 of the alpha 3 domain. Consistent with an earlier report, cells expressing the mutant Dd lys molecule were not lysed by CTL from a primary stimulation against the wild-type Dd glu molecule. However, this same cell line was killed by the Lyt-2-independent secondary Dd-specific CTL generated in the presence of antibody to the alpha 3 domain in vivo and in vitro. Furthermore, cells expressing the mutant Dd lys molecule failed to stimulate a primary response. In conclusion, several independent lines of evidence indicate that residues in the alpha 3 domain of the class I molecule are involved in recognition by the Lyt-2 molecule, and that Lyt-2-mediated recognition can be specifically blocked using mAb to determinants in the alpha 3 domain.
Peroxisome proliferator-activated receptor γ transcriptional regulation is involved in platelet-derived growth factor-induced proliferation of human hepatic stellate cells (2000)

During liver injury, hepatic stellate cells (HSC) acquire a myofibroblast-like phenotype associated with reduction of lipid droplets, increased collagen synthesis, and proliferation. Peroxisome proliferator-activated receptor gamma (PPARgamma) regulates adipocyte differentiation and controls gene transcription in response to various activators including prostanoids and antidiabetic thiazolidinediones. We explored whether the presence of PPARgamma and its transcriptional activity were involved in control of HSC proliferation in vitro. PPARgamma ligands, 15-deoxy-triangle up(1214) prostaglandin J(2) (15d-PGJ(2)) and ciglitizone, significantly decrease platelet-derived growth factor (PDGF)-induced proliferation in activated human HSC and inhibit alpha smooth muscle actin (alpha-SMA) expression during HSC transdifferentiation. Treatment with 9-cis retinoic acid (9-cisRA) and LG268, ligands of the heterodimerization partner retinoic X receptor (RXR), had a negligible effect in PDGF-treated cells but caused a further reduction of proliferation when used in combination with ciglitizone. Transfection experiments with a reporter gene consisting of 3 copies of a PPAR response element (peroxisome proliferator response element [PPRE](3)-tk-luciferase) showed a progressive reduction of PPAR transcriptional activity during plastic-induced HSC transdifferentiation. Cotransfection with human PPARgamma expression vector restored the PPRE(3)-tk-luciferase reporter expression and the increased level of the receptor in activated HSC-inhibited cell proliferation in a dose-dependent manner. Incubation of human PPARgamma-cotransfected HSC with PDGF strongly inhibited luciferase activity and this effect was blocked by the inhibition of the mitogen-activated protein (MAP) kinase signal cascade. Our results indicate that depression of PPARgamma expression and activity is involved in HSC proliferation and that the PPARgamma ligand-mediated activation exerts a previously unrecognized inhibition of PDGF-induced mitogenesis in activated human HSC.
The Role of Oxidative Stress in Alzheimer Disease (1999)

Increasing evidence demonstrates that oxidative stress causes damage to cell function with aging and is involved in a number of age-related disorders including atherosclerosis, arthritis, and neurodegenerative disorders. In the neurodegenerative diseases, oxidative stress has been implicated in amyotrophic lateral sclerosis, Parkinson disease, Huntington disease, and Alzheimer disease (AD). The neurodegenerative disorder receiving the most attention has been AD, in which an increase occurs in oxidation of brain lipids, carbohydrates, proteins, and DNA. Some of the products of oxidation have been found in the major histopathologic alterations in AD: the neurofibrillary tangles (NFTs) and senile plaques (reviewed in Markesbery and Carney 1 and Ceballos-Picot 2 ). These oxidative modifications are closely associated with a subtle inflammatory process in the brain in AD. Oxidative stress refers to a state in which free radicals and their products are in excess of antioxidant defense mechanisms. This imbalance can occur as a result of increased free radical production or a decrease in antioxidant defenses. Free radicals are defined as any atom or molecule that has one or more unpaired electrons in its outer shell. The reduction of molecular oxygen to water is a major source of potent radicals. The initial step in this reaction yields the superoxide radical, which produces hydrogen peroxide by addition of an electron. The reduction of hydrogen peroxide yields the highly reactive hydroxyl radical. These radicals plus singlet oxygen are called reactive oxygen species (ROS). Several reactive nitrogen species, nitric oxide, and peroxynitrite also are important modulators of oxidative stress. These free radicals and others are capable of reacting with lipids, proteins, nucleic acids, and other molecules and altering their structure and function. Oxidative stress can lead to alterations in cells with an accumulation of oxidized products such as aldehydes and isoprostanes from lipid peroxidation, protein carbonyls from protein oxidation, and base ad
Synthesis and biological evaluation of a (99m)Tc-labelled cyclic RGD peptide for imaging the alphavbeta3 expression. (2004)

(99m)Tc-DKCK-RGD allows imaging of alphavbeta3-positive tumours in mice. However, pharmacokinetics as well as metabolic stability of the tracer have to be improved for potential clinical application.
The intron requirement for immunoglobulin gene expression is dependent upon the promoter (1988)

Transfection assays were used to assess the need for an intron in order to obtain expression of cytoplasmic immunoglobulin p mRNA. An intron is required when transcription is driven by an immunoglobulin promoter/enhancer combination, although this requirement is not specific for a particular intron. However, this need for an intron is dependent upon the promoter used. Whilst an intron is required in the case of immunoglobulin or $-globin promoters, it is not in the case of cytomegalovirus or heat-shock promoters. The data point to a connection between the promoter and RNA processing or export.