gebhart/patrepeval huggingface dataset:
Salicylic Acid-Dependent Expression of Host Genes in Compatible Arabidopsis-Virus Interactions (2005)

Plant viruses elicit the expression of common sets of genes in susceptible hosts. Studies in Arabidopsis (Arabidopsis thaliana) and tomato (Lycopersicon esculentum) indicate that at least one-third of the genes induced in common by viruses have been previously associated with plant defense and stress responses. The genetic and molecular requirements for the induction of these stress and defense-related genes during compatible host-virus interactions were investigated with a panel of Arabidopsis mutant and transgenic plants defective in one or more defense signaling pathways. pad4, eds5, NahG, npr1, jar1, ein2, sid2, eds1, and wild-type Columbia-0 and Wassilewskija-2 plants were infected with two different viruses, cucumber mosaic virus and oilseed rape mosaic virus. Gene expression was assayed by a high-throughput fiber-optic bead array consisting of 388 genes and by RNA gel blots. These analyses demonstrated that, in compatible host-virus interactions, the expression of the majority of defense-related genes is induced by a salicylic acid-dependent, NPR1-independent signaling pathway with a few notable exceptions that did require NPR1. Interestingly, none of the mutant or transgenic plants showed enhanced susceptibility to either cucumber mosaic virus or oilseed rape mosaic virus based on both symptoms and virus accumulation. This observation is in contrast to the enhanced disease susceptibility phenotypes that these mutations or transgenes confer to some bacterial and fungal pathogens. These experimental results suggest that expression of many defense-related genes in compatible host plants might share components of signaling pathways involved in incompatible host-pathogen interactions, but their increased expression has no negative effect on viral infection.
Transfection of interleukin-12 cDNAs into tumor cells induces cytotoxic immune responses against native tumor: implications for tumor vaccination. (1998)

Interleukin-12 (IL-12) is a heterodimeric cytokine that is central to the development of T helper 1-dependent cellular immunity. Although this cytokine has potential therapeutic application as an antineoplastic agent, the systemic infusion of IL-12 has led to toxic fatalities; hence, restriction of expression of IL-12 to the microenvironment of target tumor cells has obvious appeal. In this study, we examined whether tumor cells that were liposome-transfected with IL-12 could enhance the induction of cytolytic lymphocyte immunity to the native tumor. The plasmid expression vector that we used has several useful features including replication to high copy number as an episome and a polycistronic message enabling the production of both the p35 and p40 subunits of IL-12 without alternative splicing; up to 3 ng/mL/10(6)/48 hours of IL-12 was produced following transfection. Tumor cells transfected with IL-12 were superior to untransfected cells in the induction of lymphocyte-mediated cytolysis. IL-12 transfectants induced a heterogeneous population of natural killer, lymphokine activated killer, and cytolytic T lymphocytes, the latter of which exhibited tumor-specific activity. Our studies suggest that liposome-mediated transfection of tumor cells with an episomal, high copy number plasmid vector expressing both IL-12 subunits is a promising approach to cancer vaccination, a strategy that could be implemented ex vivo in treating malignancies such as metastatic ovarian cancer.
Perovskites: The Emergence of a New Era for Low-Cost, High-Efficiency Solar Cells (2013)

Over the last 12 months, we have witnessed an unexpected breakthrough and rapid evolution in the field of emerging photovoltaics, with the realization of highly efficient solid-state hybrid solar cells based on organometal trihalide perovskite absorbers. In this Perspective, the steps that have led to this discovery are discussed, and the future of this rapidly advancing concept have been considered. It is likely that the next few years of solar research will advance this technology to the very highest efficiencies while retaining the very lowest cost and embodied energy. Provided that the stability of the perovskite-based technology can be proven, we will witness the emergence of a contender for ultimately low-cost solar power.
Suppression of Radiation Sensitivity and Capsular Polysaccharide Synthesis in Escherichia coli K-12 by Ochre Suppressors (1967)

A class of suppressors effective on nonsense polarity mutations suppresses several independent mutations in a gene (capR) that controls ultraviolet-radiation sensitivity and capsular polysaccharide synthesis. Since these ochre suppressors function at the level of translation of messenger ribonucleic acid into protein, the results provide evidence that the product of the capR gene is a protein.
In vitro and in vivo growth of clonal sublines of human small cell lung carcinoma is modulated by polysialic acid of the neural cell adhesion molecule. (1994)

Poly Sia does not occur on all N-CAM immunoreactive cells of SCLC. Poly Sia on SCLC cells is a clonable trait and high poly Sia expression correlates with reduced cell-cell adherence, a greater clonogenic ability in semisolid media, and a significantly higher incidence of intracutaneous metastases in nude mice.
Fat Absorption in Commercial French Fries Depending on Oil Type and Coating (2013)

This study examines the effect of edible coatings, type of oil used, and cooking method on the fat content of commercially available French fries. In contrast to earlier studies that examined laboratory prepared French fries, this study assesses commercially available French fries and cooking oils. This study also measured the fat content in oven baked French fries, comparing the two cooking methods in addition to the comparisons of different coatings’ oil uptake. The findings of this study were that the type of oil used did have a significant impact on the final oil content of the uncoated and seasoned fries. The fries coated in modified food starch and fried in peanut and soy oils had what appeared to be significantly higher oil content than those fried in corn oil or baked, but the difference was not statistically significant. Additionally, fat content in French fries with hydrocollidial coatings that were prepared in corn oil were not significantly different than French fries with the same coating that were baked.
Oxidation of Polynuclear Aromatic Hydrocarbons in Water. 4. Ozone Combined with Hydrogen Peroxide (1996)

Three polynuclear aromatic hydrocarbons, fluorene, phenanthrene, and acenaphthene, have been treated in water with ozone combined with hydrogen peroxide. The effect of hydrogen peroxide concentration, pH, and bicarbonate ions has been investigated. The process goes through direct and radical reactions in the case of fluorene and phenanthrene oxidation, while acenapthene is removed exclusively by direct ozonation. At concentrations of hydrogen peroxide higher than 10-5 M, ozone mass transfer controls the process rate, regardless of pH. In any case, however, the presence of hydrogen peroxide does not improve the oxidation rate compared to ozonation alone due to the importance of the direct reactions. Intermediate compounds identified during oxidation with ozone alone and combined with UV radiation or hydrogen peroxide are similar and justify the high consumption of ozone in these processes.
Microtubule-associated protein 1B (2001)

Myelin-associated glycoprotein (MAG) is expressed in periaxonal membranes of myelinating glia where it is believed to function in glia-axon interactions by binding to a component of the axolemma. Experiments involving Western blot overlay and coimmunoprecipitation demonstrated that MAG binds to a phosphorylated neuronal isoform of microtubule-associated protein 1B (MAP1B) expressed in dorsal root ganglion neurons (DRGNs) and axolemma-enriched fractions from myelinated axons of brain, but not to the isoform of MAP1B expressed by glial cells. The expression of some MAP1B as a neuronal plasma membrane glycoprotein (Tanner, S.L., R. Franzen, H. Jaffe, and R.H. Quarles. 2000. J. Neurochem. 75:553-562.), further documented here by its immunostaining without cell permeabilization, is consistent with it being a binding partner for MAG on the axonal surface. Binding sites for a MAG-Fc chimera on DRGNs colocalized with MAP1B on neuronal varicosities, and MAG and MAP1B also colocalized in the periaxonal region of myelinated axons. In addition, expression of the phosphorylated isoform of MAP1B was increased significantly when DRGNs were cocultured with MAG-transfected COS cells. The interaction of MAG with MAP1B is relevant to the known role of MAG in affecting the cytoskeletal structure and stability of myelinated axons.
USP9X deubiquitylating enzyme maintains RAPTOR protein levels, mTORC1 signalling and proliferation in neural progenitors (2017)

USP9X, is highly expressed in neural progenitors and, essential for neural development in mice. In humans, mutations in USP9X are associated with neurodevelopmental disorders. To understand USP9X's role in neural progenitors, we studied the effects of altering its expression in both the human neural progenitor cell line, ReNcell VM, as well as neural stem and progenitor cells derived from Nestin-cre conditionally deleted Usp9x mice. Decreasing USP9X resulted in ReNcell VM cells arresting in G0 cell cycle phase, with a concomitant decrease in mTORC1 signalling, a major regulator of G0/G1 cell cycle progression. Decreased mTORC1 signalling was also observed in Usp9x-null neurospheres and embryonic mouse brains. Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR. EdU incorporation assays confirmed Usp9x maintains the proliferation of neural progenitors similar to Raptor-null and rapamycin-treated neurospheres. Interestingly, loss of Usp9x increased the number of sphere-forming cells consistent with enhanced neural stem cell self-renewal. To our knowledge, USP9X is the first deubiquitylating enzyme shown to stabilize RAPTOR.
Deep Unordered Composition Rivals Syntactic Methods for Text Classification (2015)

Mohit Iyyer, Varun Manjunatha, Jordan Boyd-Graber, Hal Daumé III. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments (1987)

Dissolved DNA and a series of microbial biomass and activity parameters were measured in offshore, coastal, estuanne and coral reef environments of the southeast Gulf of Mexico. Oceanic concentrations of dissolved DNA ranged from 0.2 to 19 vg 1-' and decreased as a function of distance from shore and depth in the water column. Dissolved DNA concentrations were greater than half the particulate DNA content in offshore environments (Z = 63 + 45 O/O), but were a smaller percentage of particulate DNA in nearshore and estuarine environments (Z = 35 f 21 %). Dissolved DNA correlated better with bacterial parameters (i.e. bacterial direct counts, particulate DNA and thymidine incorporation) than with phytoplankton parameters (chlorophyll a, primary productivity). The molecular weight (MW) of dissolved DNA (determined by agarose gel electrophoresis) ranged from 0.12 kilobase pairs (kb; 7.75 X 104 daltons) to 35.2 kb (2.32 X 10' daltons) for estuarine samples, while an oligotrophic environment contained smaller MW DNA (range 0.24 to 14.27 kb). DNA fragments in this size range are sufficient to contain gene sequences. These results are discussed in terms of the potential for transformation by dissolved DNA.
Rivaroxaban (BAY 59‐7939) – an oral, direct Factor Xa inhibitor – has no clinically relevant interaction with naproxen (2006)

There appeared to be no clinically relevant interaction between rivaroxaban and naproxen in healthy subjects, although some individuals may be more sensitive to the combination. Large-scale Phase III clinical studies will be required to confirm whether there is an increased risk of bleeding during treatment with rivaroxaban and concomitant NSAIDs.
Stochastic Similarity Selections from Large Combinatorial Libraries (2000)

A stochastic procedure for similarity searching in large virtual combinatorial libraries is presented. The method avoids explicit enumeration and calculation of descriptors for every virtual compound, yet provides an optimal or nearly optimal similarity selection in a reasonable time frame. It is based on the principle of probability sampling and the recognition that each reagent is represented in a combinatorial library by multiple products. The method proceeds in three stages. First, a small fraction of the products is selected at random and ranked according to their similarity against the query structure. The top-ranking compounds are then identified and deconvoluted into a list of "preferred" reagents. Finally, all the cross-products of these preferred reagents are enumerated in an exhaustive manner, and systematically compared to the target to obtain the final selection. This procedure has been applied to produce similarity selections from several virtual combinatorial libraries, and the dependency of the quality of the selections on several selection parameters has been analyzed.
Proteins of the Troponin Complex (1992)

The troponin complex is a group of three protein subunits located on the thin filament of the contractile apparatus. These three subunits—troponin T, troponin I, and troponin C—different in genetic and protein structure, act together to regulate muscle contraction. The distribution, function, and detection of these subunits in different muscle tissue and blood components, as well as their relation to myocardial damage, will be reviewed in this article.
Valine of the YVDD Motif of Moloney Murine Leukemia Virus Reverse Transcriptase: Role in the Fidelity of DNA Synthesis (2000)

The YXDD motif is highly conserved in the reverse transcriptase family. The variable X residue is occupied by valine and methionine in MuLV RT and HIV-1 RT, respectively. Previous studies have shown that Tyr 222, the Y residue of the YXDD motif in MuLV RT, constitutes a major component of the fidelity center of the enzyme [Kaushik, N., Singh, K., Alluru, I., and Modak, M. J. (1999) Biochemistry 38, 2617-2627]. In this work, we present evidence that reverse transcriptases containing valine in the "X" position of the YXDD motif generally catalyze DNA synthesis with greater fidelity than those containing methionine or alanine. In the MuLV RT system, the two mutants V223M and V223A exhibited an overall reduced fidelity of DNA synthesis, specifically for RNA-templated reactions. Further analysis revealed that these mutants exhibit a higher efficiency of misinsertion on MS2 RNA than the wild-type enzyme for every mispair tested. However, unlike HIV-1 RT, the insensitivity of the wild-type MuLV RT to all four ddNTPs remained unchanged by mutation of V223 to Met or Ala. A 3D molecular model of the ternary complex of MuLV RT, template primer, and dNTP suggests that Val 223 along with its neighboring Tyr 222 stabilizes the substrate binding pocket via hydrophobic interactions with the dNTP substrate and template-primer.
Experience with biliary atresia disease at AIIMS during the past decade. (1999)

ABSTRACT: Extrahepatic biliary atresia remains a challenge to the pediatric surgeons till. The early enthusiasm with the Kasai procedure is now tempered with the realization of significant morbidity and mortality in long term follow up. There is still a controversy regarding the etiology, the ideal investigative modality and also the best possible treatment for this condition. We reviewed our experience with biliary atresia over the last 10 years to assess the clinical presentation and early outcome following Kasai's portoenterostomy.
A Network Map of FGF-1/FGFR Signaling System (2014)

Fibroblast growth factor-1 (FGF-1) is a well characterized growth factor among the 22 members of the FGF superfamily in humans. It binds to all the four known FGF receptors and regulates a plethora of functions including cell growth, proliferation, migration, differentiation, and survival in different cell types. FGF-1 is involved in the regulation of diverse physiological processes such as development, angiogenesis, wound healing, adipogenesis, and neurogenesis. Deregulation of FGF-1 signaling is not only implicated in tumorigenesis but also is associated with tumor invasion and metastasis. Given the biomedical significance of FGFs and the fact that individual FGFs have different roles in diverse physiological processes, the analysis of signaling pathways induced by the binding of specific FGFs to their cognate receptors demands more focused efforts. Currently, there are no resources in the public domain that facilitate the analysis of signaling pathways induced by individual FGFs in the FGF/FGFR signaling system. Towards this, we have developed a resource of signaling reactions triggered by FGF-1/FGFR system in various cell types/tissues. The pathway data and the reaction map are made available for download in different community standard data exchange formats through NetPath and NetSlim signaling pathway resources.
Risk factors of stroke incidence and mortality. A 12-year follow-up of the Oslo Study. (1993)

Reduction of blood pressure, cessation of smoking, lowered cholesterol, and increased physical activity at leisure are individual measures to reduce the risk of stroke.
Complement activation during extracorporeal therapy: biochemistry, cell biology and clinical relevance. (1994)

Complement is a principal mediator of the acute inflammatory response and contributes to the non-specific recognition and elimination of foreign substances from the body. The system evolved to protect the host from invasion by various pathogens. However, due to the non-selective nature of the alternative pathway, biomaterial surfaces in any medical device used in contact with blood will also activate the system. This review summarizes our current understanding of the biochemistry and cell biology of complement. The relationship of this basic information to clinical observations is discussed in order to affirm the relevance of complement as a critical parameter of biocompatibility.
Cost-Effective Remote iPhone-Teathered Telementored Trauma Telesonography (2010)

McBeth, Paul B. MD; Hamilton, Trevor MD; Kirkpatrick, Andrew W. MD, FRCSC, FACS Author Information
Investigation of the ultradrawing properties of gel spun fibers of ultra‐high molecular weight polyethylene/carbon nanotube blends (2008)

Abstract The carbon nanotubes (CNTs) contents, ultrahigh‐molecular‐weight polyethylene (UHMWPE) concentrations and temperatures of UHMWPE, and CNTs added gel solutions exhibited significant influence on their rheological and spinning properties and the drawability of the corresponding UHMWPE/CNTs as‐prepared fibers. Tremendously high shear viscosities (ηs) of UHMWPE gel solutions were found as the temperatures reached 140°C, at which their ηs values approached the maximum. After adding CNTs, the ηs values of UHMWPE/CNTs gel solutions increase significantly and reach a maximum value as the CNTs contents increase up to a specific value. At each spinning temperature, the achievable draw ratios obtained for UHMWPE as‐prepared fibers prepared near the optimum concentration are significantly higher than those of UHMWPE as‐prepared fibers prepared at other concentrations. After addition of CNTs, the achievable draw ratios of UHMWPE/CNTs as‐prepared fibers prepared near the optimum concentration improve consistently and reach a maximum value as their CNTs contents increase up to an optimum value. To understand these interesting drawing properties of the UHMWPE and UHMWPE/CNTs as‐prepared fibers, the birefringence, thermal, morphological, and tensile properties of the as‐prepared and drawn fibers were investigated. Possible mechanisms accounting for these interesting properties are proposed. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Akt and Autophagy Cooperate to Promote Survival of Drug-Resistant Glioma (2010)

Although the phosphatidylinositol 3-kinase to Akt to mammalian target of rapamycin (PI3K-Akt-mTOR) pathway promotes survival signaling, inhibitors of PI3K and mTOR induce minimal cell death in PTEN (phosphatase and tensin homolog deleted from chromosome 10) mutant glioma. Here, we show that the dual PI3K-mTOR inhibitor PI-103 induces autophagy in a form of glioma that is resistant to therapy. Inhibitors of autophagosome maturation cooperated with PI-103 to induce apoptosis through the mitochondrial pathway, indicating that the cellular self-digestion process of autophagy acted as a survival signal in this setting. Not all inhibitors of mTOR synergized with inhibitors of autophagy. Rapamycin delivered alone induced autophagy, yet cells survived inhibition of autophagosome maturation because of rapamycin-mediated activation of Akt. In contrast, adenosine 5'-triphosphate-competitive inhibitors of mTOR stimulated autophagy more potently than did rapamycin, with inhibition of mTOR complexes 1 and 2 contributing independently to induction of autophagy. We show that combined inhibition of PI3K and mTOR, which activates autophagy without activating Akt, cooperated with inhibition of autophagy to cause glioma cells to undergo apoptosis. Moreover, the PI3K-mTOR inhibitor NVP-BEZ235, which is in clinical use, synergized with the lysosomotropic inhibitor of autophagy, chloroquine, another agent in clinical use, to induce apoptosis in glioma xenografts in vivo, providing a therapeutic approach potentially translatable to humans.
A low third order intermodulation amplifier with harmonic feedback circuitry (2002)

This paper describes a novel technique for reducing the third-order intermodulation product levels in a nonlinear amplifier. This technique is based on feeding the second harmonic signal produced at the output of the amplifier back to its input. Mathematical analysis and computer simulation are presented. The results of the related experiment which gave a measurement of 16 dB reduction in the level of the third order intermodulation is reported.
Structural and electrical properties of crystalline (1−x)Ta2O5–xAl2O3 thin films fabricated by metalorganic solution deposition technique (1997)

Polycrystalline (1−x)Ta2O5–xAl2O3 thin films were fabricated by metalorganic solution deposition technique on Pt-coated Si substrate at a temperature of 750 °C. Thin films with 0.9Ta2O5–0.1Al2O3 composition exhibited improved dielectric and insulating properties compared to Ta2O5 thin films. The measured small signal dielectric constant and dissipation factor at 100 kHz were 42.8 and 0.005, respectively. The temperature coefficient of capacitance was 20 ppm/°C in the measured temperature range of 25–125 °C. The leakage current density was lower than 6×10−8 A/cm2 up to an applied electric field of 1 MV/cm. A charge storage density of 18.9 fC/μm2 was obtained at an applied electric field of 0.5 MV/cm. The high dielectric constant, low dielectric loss, low leakage current density, and good temperature and bias stability suggest (1−x)Ta2O5–xAl2O3 thin films to be a suitable dielectric layer in integrated electronic devices in place of conventional dielectrics such as SiO2 or Si3N4.