gebhart/patrepeval huggingface dataset:
Cancer Cell Metabolism: There Is No ROS for the Weary (2012)

Using a high-throughput short-hairpin RNA library screen targeting 222 metabolic nodes, Ros and colleagues identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4), a glycolytic enzyme that shunts glucose into the pentose phosphate pathway for NADPH production, as a critical node for the survival of prostate cancer cells. Blocking PFKFB4 induces reactive oxygen species and cancer cell death, suggesting that PFKFB4 could be therapeutically targeted.
Differential effects of oncogenic transformation on N-linked oligosaccharide processing at individual glycosylation sites of viral glycoproteins. (1987)

Hamster sarcoma virus (HSV) transformation of Nil-8 fibroblasts is associated with an increase in the average size of N-acetyllactosamine (complex) type N-linked glycans due to an increase in both the average number of branches/chain and in the fraction of N-linked glycans containing poly(GlcNAc(beta 1,3) Gal-(beta 1,4)) (polylactosaminylglycan) chains. Analysis of glycopeptides from the envelope glycoproteins of Sindbis virus and vesicular stomatitis virus (VSV) grown in Nil-8 and Nil/HSV cells indicated that the transformation-associated shift to larger N-linked oligosaccharides selectively affects some glycosylation sites far more than others. Glycosylation of the Sindbis virus glycoproteins and of Asn-179 of VSV G was similar in Nil-8 and Nil/HSV cells; oligosaccharide processing generally did not proceed beyond the biantennary complex stage. In contrast, Asn-336 of VSV G carried primarily biantennary complex glycans in Nil-8-grown virus (ratio, triantennary, and larger to biantennary complex glycans (tri+/bi) = 0.5) but more highly branched structures in Nil/HSV-grown virus (tri+/bi = 8.1). All of the triantennary or larger oligosaccharides from Asn-336 of Nil/HSV-grown VSV G bound to leukoagglutinating phytohemagglutinin-agarose, indicating the presence of a branch attached to the Man3GlcNAc2 core via a beta 1,6-linked GlcNAc residue and suggesting that increased UDP-GlcNAc:alpha-D-mannoside beta 1,6-N-acetylglucosaminyl transferase V (GlcNAc transferase V) activity accompanied transformation. At least 20% of these leukoagglutinating phytohemagglutinin-binding oligosaccharides were sensitive to an enzyme specific for polylactosaminylglycan chains, Escherichia freundii endo-beta-galactosidase.
Differential antimicrobial activity of human mononuclear phagocytes against the human biovars of Chlamydia trachomatis. (1987)

The antimicrobial activities of human mononuclear phagocytes against Chlamydia trachomatis were investigated. Phagocytes cultured for 7 days or less were efficiently microbicidal. Almost complete inactivation of organisms from both human biovars was observed after 48 hr of incubation. However, organisms from the lymphogranuloma venereum (LGV) biovar survived in mononuclear phagocytes infected after 8 days or more in culture, whereas those from the trachoma biovar continued to be killed by such cells. Phagocytes cultured as long as 21 days killed the trachoma organisms with the same effectiveness as those cultured for 7 days or less. An ultrastructural study of inoculated phagocytes illustrated phagolysosomal fusion with degradation of organisms from either biovar in phagocytes which had been cultured for 24 hr before infection. Phagolysosomal fusion was not observed in cells which had been cultured for 8 days or more and then infected with LGV. The addition of interferon-gamma to these macrophages partially restored the phagocytes' microbicidal activity for LGV. Furthermore, a synergistic effect was observed when eosinophil peroxidase was added with interferon. Specific antibody failed to neutralize the infectivity of LGV organisms in 8-day or older mononuclear phagocytes. The findings may reflect the differences in disease syndromes between the two biovars, with the trachoma biovar causing more peripheral diseases and the LGV biovar causing a more systemic disease, with lymph node involvement as its main syndrome.
Association Between a Functional Catechol O-Methyltransferase Gene Polymorphism and Schizophrenia: Meta-Analysis of Case-Control and Family-Based Studies (2003)

The results of the two types of association studies diverged somewhat, but the evidence from the family-based studies, although based on fewer reports, may be more accurate. The Val allele may be a small but reliable risk factor for schizophrenia for people of European ancestry, but the influence of this polymorphism on risk in Asian populations remains unclear. These results call for more family-based studies to confirm the association between COMT and schizophrenia in European samples and to clarify its contribution to risk in Asian samples. They also suggest that case-control studies should use methods of genomic control to avoid being confounded by population stratification.
Gene Expression, Secretion, and Autocrine Action of C-Type Natriuretic Peptide in Cultured Adult Rat Cardiac Fibroblasts (2003)

C-type natriuretic peptide (CNP), the third member of the natriuretic peptide family, is known to be synthesized in the central nervous system and vascular endothelial cells, in contrast to atrial natriuretic peptide and brain natriuretic peptide. However, there have been no studies concerning CNP production in cultured cardiac cells. Here, we examined the production and the local effect of CNP in cultured ventricular cells. Under serum-free conditions, adult rat cardiac fibroblasts secreted immunoreactive CNP time dependently. TGF-beta1, basic fibroblast growth factor, and endothelin-1 significantly stimulated CNP secretion. Northern blot analysis detected significant expressions of CNP and its specific receptor (guanylyl cyclase-B) mRNA in cardiac fibroblasts. CNP stimulated intracellular cGMP production in fibroblasts more intensely than atrial and brain natriuretic peptides. CNP inhibited both DNA and collagen syntheses of cardiac fibroblasts, and these inhibitory effects by CNP were stronger than by atrial and brain natriuretic peptides. The inhibition by CNP of DNA and collagen syntheses was reproduced by a cGMP analog, 8-bromo cGMP. The present findings demonstrate that CNP is synthesized in and secreted from cardiac fibroblasts and suggest that CNP has a suppressive effect on fibroblast proliferation and extracellular matrix production, probably via the guanylyl cyclase-B-mediated cGMP-dependent process. CNP produced by cardiac fibroblasts may play a role as an autocrine regulator against excessive cardiac fibrosis.
Modeling laser beam-rock interaction. (2003)

The optimal use of lasers requires the understanding of the primary parameters pertinent to laser beam-material interactions. Basically, the laser beam is a heat source that can be controlled to deliver a wide range in intensities and power. When interacting with a material, reflection at the surface, and transmission and absorption through the material occur. The material interaction process is governed by the irradiance (power/unit area) of the incident beam and the interaction time resulting in an amount of heat/energy applied to the material per unit area. The laser beam is a flexible heat source where its intensity and interaction with materials can be controlled by varying the power and size of the beam or the interaction time. For any material, a minimum amount of energy has to be absorbed for the material to be ablated by the laser beam, i.e., a solid has to be heated to liquefy and then vaporize. Under certain conditions, the photon energy may be able to break the molecular bonds of the material directly. In general, the energy absorbed is needed to vaporize the material and account for any heat that may be conducted away. Consequently, the interaction is a heat transfer problem. The relevant parameters are the heat flux and total heat input to the material. The corresponding parameters for the laser beam- material interaction are the irradiance of the beam and the interaction time. The product of these two parameters is the energy applied per unit area. A high irradiance beam may be able to ablate a material rapidly without significant heat transfer to surrounding areas. For drilling or cutting materials, a high intensity beam is required for laser ablation with minimal heat lost to the surrounding areas. However, at high beam irradiance (>1 GW cm{sup -2} for Nd:YAG beams), plasma formed from ionization of gases and vapor will partially absorb or diffract the beam. Reduced penetration of the material results. Similarly, in welding using CO2 lasers where the beam irradiance is {approx}1 MW cm{sup -2}, the plasma plume formed decreases penetration. A high velocity jet of inert gas is usually used to blow away the plasma.
Modulation of Immune Complex–induced Inflammation In Vivo by the Coordinate Expression of Activation and Inhibitory Fc Receptors (1999)

Autoantibodies and immune complexes are major pathogenic factors in autoimmune injury, responsible for initiation of the inflammatory cascade and its resulting tissue damage. This activation results from the interaction of immunoglobulin (Ig)G Fc receptors containing an activation motif (ITAM) with immune complexes (ICs) and cytotoxic autoantibodies which initiates and propagates an inflammatory response. In vitro, this pathway can be interrupted by coligation to FcgammaRIIB, an IgG Fc receptor containing an inhibitory motif (ITIM). In this report, we describe the in vivo consequences of FcgammaRII deficiency in the inflammatory response using a mouse model of IC alveolitis. At subthreshold concentrations of ICs that fail to elicit inflammatory responses in wild-type mice, FcgammaRII-deficient mice developed robust inflammatory responses characterized by increased hemorrhage, edema, and neutrophil infiltration. Bronchoalveolar fluids from FcgammaRII-/- stimulated mice contain higher levels of tumor necrosis factor and chemotactic activity, suggesting that FcgammaRII deficiency lowers the threshold of IC stimulation of resident cells such as the alveolar macrophage. In contrast, complement- and complement receptor-deficient mice develop normal inflammatory responses to suprathreshold levels of ICs, while FcRgamma-/- mice are completely protected from inflammatory injury. An inhibitory role for FcgammaRII on macrophages is demonstrated by analysis of FcgammaRII-/- macrophages which show greater phagocytic and calcium flux responses upon FcgammaRIII engagement. These data reveal contrasting roles for the cellular receptors for IgG on inflammatory cells, providing a regulatory mechanism for setting thresholds for IC sensitivity based on the ratio of ITIM to ITAM FcgammaR expression. Exploiting the FcgammaRII inhibitory pathway could thus provide a new therapeutic approach for modulating antibody-triggered inflammation.
Modification of rabbit corneal curvature with use of carbon dioxide laser burns. (1980)

Carbon dioxide laser burns of varied intensity, location, and pattern were produced on rabbit corneas. Evaluation of the parameters required to produce an optimal corneal lesion showed that lesions made with 8 W caused perforation of rabbit corneas. Various laser burn patterns were studied for their effect on the rabbit corneal curvature. This was followed by comparison of effect of laser burns on corneal curvature with that of untreated contralateral eyes. The effects of the burns on the corneal curvative were measured for 12 weeks with use of a standard keratometer in the 90 degree and 180 degrees axes. No significant changes in the corneal curvature were noted in the experimental versus the control eyes. Carbon dioxide laser burns were not effective in modifying corneal curvature in this study.
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network (2007)

We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.
Dysregulation of JAK-STAT pathway in hematological malignancies and JAK inhibitors for clinical application (2013)

JAK-STAT (Janus associated kinase-signal transducer and activator of transcription) pathway plays a critical role in transduction of extracellular signals from cytokines and growth factors involved in hematopoiesis, immune regulation, fertility, lactation, growth and embryogenesis. JAK family contains four cytoplasmic tyrosine kinases, JAK1-3 and Tyk2. Seven STAT proteins have been identified in human cells, STAT1-6, including STAT5a and STAT5b. Negative regulators of JAK-STAT pathways include tyrosine phosphatases (SHP1 and 2, CD45), protein inhibitors of activated STATs (PIAS), suppressors of cytokine signaling (SOCS) proteins, and cytokine-inducible SH2-containing protein (CIS). Dysregulation of JAK-STAT pathway have been found to be key events in a variety of hematological malignancies. JAK inhibitors are among the first successful agents reaching clinical application. Ruxolitinib (Jakafi), a non-selective inhibitor of JAK1 & 2, has been approved by FDA for patients with intermediate to high risk primary or secondary myelofibrosis. This review will also summarize early data on selective JAK inhibitors, including SAR302503 (TG101348), lestaurtinib (CEP701), CYT387, SB1518 (pacritinib), LY2784544, XL019, BMS-911543, NS-018, and AZD1480.
Estimation of the DNA sequence discriminatory ability of hairpin-linked lexitropsins (1997)

Three- and four-ring polyamides containing N-methylimidazole and N-methylpyrrole, and their hairpin-linked derivatives, bind side-by-side in the minor groove of DNA in a sequence-specific manner. The sequences recognized by side-by-side molecules are dependent on the pairings of the polyamide rings to the bases. In this study we report a mathematical model for estimating the free energies of binding for gamma-aminobutyric acid-linked polyamides to 5- and 6-bp DNA sequences. The model parameters are calibrated by a least-squares fit to 35 experimental binding constants. The model performs well in cross-validation experiments and the parameters are consistent with previously proposed empirical rules of polyamide-DNA binding. We apply the model to the design of targeted polyamides, evaluating the ability of the proposed polyamides to bind to a DNA sequence of interest while minimizing binding to the remaining DNA sequences.
Stabilization of Influenza Vaccine Enhances Protection by Microneedle Delivery in the Mouse Skin (2009)

The functional integrity of hemagglutinin is associated with inducing improved protective immunity against influenza. Simple microneedle influenza vaccination in the skin produced superior protection compared to conventional intramuscular immunization. This approach is likely to be applicable to other vaccines too.
Reduced malignancy of ras-transformed NIH 3T3 cells expressing antisense osteopontin RNA. (1994)

Osteopontin (OPN) is a secreted, calcium-binding phosphoprotein that frequently has been associated with the transformed phenotype. To clarify the function of OPN in tumor cells, we designed experiments to: (a) express antisense OPN RNA in murine PAP2 cells (metastatic, ras-transformed NIH 3T3 cells) and (b) examine the effects of antisense OPN expression on the tumorigenic and metastatic properties of the cells. PAP2 cells were transfected with pNMH-asOPN, an inducible, mammalian expression vector that can generate antisense OPN RNA complementary to the OPN mRNA. Two clones have been identified that expressed antisense OPN RNA in vitro. While reduced OPN protein secretion was not detected when the cells were grown in vitro, the in vivo expression of antisense OPN RNA was associated with reduced tumorigenicity. Tumors that did arise, with greatly extended lag time, had lost expression of antisense OPN RNA in vivo, suggesting that antisense OPN RNA expression was associated with reduced tumorigenicity of these cells.
Pharmacological characterization of a nonpeptide bradykinin B2 receptor antagonist, FR165649, and agonist, FR190997 (1998)

1. The nonpeptide bradykinin (BK) B2 receptor antagonist, FR165649 (8-[2,6-dichloro-3-[N-[(E)-4-(N-methylcarbamoyl)cinnamidoacetyl ]-N-methylamino]benzyloxy]-2-methylquinoline), and agonist, FR190997 (8-[2,6-dichloro-3-[N-[(E)-4-(N-methylcarbamoyl) cinnamidoacetyl]-N-methylamino]benzyloxy]-2-methyl-4-(2-pyridyl methoxy)quinoline) have been identified. These compounds have a common chemical structure, and the 2-pyridylmethoxy group is the only structural difference between them. 2. Both FR165649 and FR190997 displaced [3H]-BK binding to B2 receptors in guinea-pig ileum membranes, with an IC50 of 4.7 x 10(-10) M and 1.5 x 10(-9) M, respectively. They also displaced [3H]-BK binding to B2 receptors in human lung fibroblast IMR-90 cells, with an IC50 of 1.6 x 10(-9) M and 9.8 x 10(-10) M, respectively. 3. In guinea-pig isolated ileum-preparations, FR165649 had no agonistic effect on contraction and caused parallel rightward shifts of the concentration-response curves to BK on contraction. Analysis of the data produced a nominal pA2 value of 9.2+/-0.1 (n=5) and a slope of 1.4+/-0.1 (n=5). On the other hand, FR190997 induced concentration-dependent contraction of guinea-pig ilea with a pD2 of 7.9+/-0.2 and the contraction was inhibited by a specific peptide bradykinin B2 receptor antagonist, Hoe 140 (D-Arg-[Hyp3, Thi5, D-Tic7, Oic8]BK) in a non-competitive manner. 4. In IMR-90 cells, FR165649 had no agonistic effect on phosphatidyl inositol (PI) hydrolysis and caused parallel rightward shifts (approximately 200 fold shift at 10(-7) M) of the concentration-response curves to BK on PI hydrolysis. FR190997 induced concentration-dependent PI hydrolysis in IMR-90 cells with a pD2 of 8.4+/-0.1, and this effect was inhibited by Hoe 140. 5. These results indicate that FR165649 and FR190997 are, respectively, a potent bradykinin B2 receptor antagonist and agonist, and that the agonistic activity depends on the small part of the nonpeptide ligand. FR165649 and FR190997 may be useful tools for studying the relationship between ligands and receptors.
Scheduling and buffering mechanisms for remote rendering streaming in virtual walkthrough class of applications (2006)

With the recent advances of wireless networking and mobile devices technologies, exploration of remote 3D virtual environments has received a great deal of attention nowadays where many applications can be envisioned, such as virtual guides malls, online gaming, just to name a few. The primary objective of this paper is to present the specification of a buffering mechanism and a scheduling solution for on-time image delivery for a class of applications that is based upon a remote virtual environment exploration. Similar to a video buffering, our approach involves buffering the images closest to the user's position within the virtual environment, thereby, providing the client device with the necessary imagery data for rendering future user's viewpoints, removing network jitter, and providing smooth virtual interactionIn this paper, in order to overcome the limitations of current mobile device graphics performance, we propose to use a remote rendering approach that streams the necessary images to a client device as the user explores the virtual environment, leaving only the display and a number of minor image-based rendering tasks to the local, less powerful mobile hardware. Using ns-2, we present and extensive set of simulation experiments to evaluate the performance of our scheme. Our results indicate clearly that our solution is able to guarantee on-time delivery for approximately 40 sessions with a 10 Mbps link
Memory Properties of Nickel Silicide Nanocrystal Layer for Possible Application to Nonvolatile Memory Devices (2009)

The memory properties of nickel silicide (NiSi) nanocrystal (NC) layers, which were directly grown in silicon dioxide by thermal annealing of a simple sandwich structure composed of an ultrathin Ni film sandwiched between two silicon-rich oxide (SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> ) layers, have been investigated for possible nonvolatile memory (NVM) applications. Capacitance-voltage (C-V) measurements on MOS capacitors with a floating gate based on a NiSi NC layer of average diameter of 2.9 nm and areal density of 1.3 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> are shown to have a memory window of ~10 V, a retention time > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> s, and an endurance > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> program/erase cycles. These C-V characteristics demonstrate that the NiSi NC layer has high potential for NVM applications.
Brain-specific expression of an exogenous gene after i.v. administration (2001)

The treatment of brain diseases with gene therapy requires the gene to be expressed throughout the central nervous system, and this is possible by using gene targeting technology that delivers the gene across the blood-brain barrier after i.v. administration of a nonviral formulation of the gene. The plasmid DNA is targeted to brain with pegylated immunoliposomes (PILs) using a targeting ligand such as a peptidomimetic mAb, which binds to a transporting receptor on the blood-brain barrier. The present studies adapt the PIL gene targeting technology to the mouse by using the rat 8D3 mAb to the mouse transferrin receptor. Tissue-specific expression in brain and peripheral organs of different exogenous genes (beta-galactosidase, luciferase) is examined at 1-3 days after i.v. injection in adult mice of the exogenous gene packaged in the interior of 8D3-PIL. The expression plasmid is driven either by a broadly expressed promoter, simian virus 40, or by a brain-specific promoter taken from the 5' flanking sequence of the human glial fibrillary acidic protein (GFAP) gene. The transgene is expressed in both brain and peripheral tissues when the simian virus 40 promoter is used, but the expression of the exogenous gene is confined to the brain when the transgene is under the influence of the brain-specific GFAP promoter. Confocal microscopy colocalizes immunoreactive bacterial beta-galactosidase with immunoreactive GFAP in brain astrocytes. These studies indicate that tissue-specific gene expression in brain is possible after the i.v. administration of a nonviral vector with the combined use of gene targeting technology and tissue-specific gene promoters.