gebhart/patrepeval huggingface dataset:
Histamine H4 Receptor Stimulation Suppresses IL-12p70 Production and Mediates Chemotaxis in Human Monocyte-Derived Dendritic Cells (2005)

There is increasing evidence that histamine as an important mediator of immediate type allergic reactions also effects professional APCs. Recent reports showed effects of histamine on human monocyte-derived dendritic cells (MoDC) mediated primarily via histamine H1 receptors (H1R) and H2R. We show here that MoDC also express H3R and H4R at the mRNA and protein level. mRNA of the H3R is down-regulated and mRNA of the H4R is up-regulated during the differentiation from monocytes to MoDC. H4R or H2R stimulation suppressed IL-12p70 production in MoDC. Induction of cAMP was necessary for IL-12p70 inhibition mediated via the H2R. In contrast, H4R stimulation did not affect cAMP production but induced the transcription factor AP-1, and U0126, an inhibitor of AP-1 transactivation and MEK, rescued H4R mediated IL-12p70 suppression. Moreover, MoDC responded to a H4R agonist (and also to a H2R agonist) with increased F-actin polymerization and migration in modified Boyden chamber assays, suggesting a chemotactic effect of histamine via the H2R and the H4R. Thus, H4R stimulation on MoDC results in immunomodulatory and chemotactic effects. Histamine induces chemotaxis and IL-12p70 suppression via different receptors using different signaling pathways, which might be important for the pathogenesis of and therapeutic interventions in allergic diseases.
Effective data mining: a data warehouse-backboned architecture (1998)

An effective Data Mining (DM) system for mining multiple-level knowledge from Data Warehouse (DW), DB and flat files of raw data is proposed. The DW represents the backbone of the proposed architecture. Intermediate, as well as final results of mining are incorporated into the DW for efficient processing of further queries. A Markov Chain mathematical model is developed for managing data dependency and consistency in the DW. An adaptive hybrid view technique is introduced to manage storage space. DM and OLAP technologies are closely integrated. The mining and OLAP kernel includes generic analysis modules for performing a wide spectrum of applications. Active data mining is adopted to support knowledge-driven business processes. Continuously gathered business data is partitioned according to application-dependent time periods. Active mining uses these partitioned data sets to discover rules and key business indicators for each time period.
CD70 Expression in Thymic Carcinoma (2000)

CD70, a type II transmembrane glycoprotein, is a member of the tumor necrosis factor (TNF) family that mediates the interaction between B- and T-lymphocytes. CD70 has been shown to be expressed by malignant lymphoma, especially Hodgkin's disease, and by nasopharyngeal carcinoma, both of which are frequently associated with Epstein-Barr virus (EBV). In this study, we investigated the expression of CD70 in epithelial cells of various types of thymic epithelial tumors and its association with EBV. Immunohistochemical expression of CD70 was studied on frozen tissue. In a series of 27 thymic epithelial tumors, including thymic carcinomas (n = 8), atypical thymomas (n = 5), thymomas (n = 13), and thymic carcinoid (n = 1), 7 (88%) thymic carcinomas and 1 (20%) atypical thymoma showed positive immunoreactivity for CD70, whereas CD70 was not detected in other tumors. Twenty-four intrathoracic malignant epithelial tumors of nonthymic origin, including lung (n = 17), esophagus (n = 5), and mesothelium (n = 2), showed no immunoreactivity for CD70. Northern blot analysis also revealed that CD70 messenger RNA was expressed in 2 of 2 thymic carcinomas, 0 of 2 atypical thymomas. and 0 of 2 thymomas. All of the 27 thymic epithelial tumors were EBV-negative as assessed by EBV-encoded small RNA in situ hybridization. The expression of CD70 is closely related to the pathogenesis of thymic carcinoma but unrelated to EBV infection in the thymus.
Isolated Mitochondria Infusion Mitigates Ischemia-Reperfusion Injury of the Liver in Rats (2013)

A recent study showed that the injection of mitochondria isolated from a nonischemic region mitigated myocardial injury. We tested the protective effects of infusing isolated mitochondria on the reperfusion injury in the liver of rats. A partial liver ischemia-reperfusion (I/R) model in male Wistar rats was used. At the 45th minute of liver ischemia, the recipient's spleen was infused with vehicle (I/R-vehicle group) or vehicle containing isolated mitochondria (7.7 × 10 ± 1.5 × 10/mL, I/R-mito group). After a 240-min reperfusion, the serum and livers were collected to assess tissue injury. Our results show that the elevation of serum alanine aminotransferase (414.3 ± 67.1 vs. 208.8 ± 30.2 U/L), the necrosis of hepatocytes on hematoxylin-eosin staining, increase in positive counts in TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) staining (59.5% ± 4.4% vs. 24.6% ± 9.1%), the expression of cytosolic cytochrome c, cleaved caspase 9, and 4-hydroxynonenal were all reduced in the I/R-mito group, compared with the I/R-vehicle group. The membrane potential of the isolated mitochondria measured by JC-1 fluorescence remained high, and the infused mitochondria were distributed in the liver parenchyma at 240 min after reperfusion. These results demonstrate that an intrasplenic infusion of viable mitochondria isolated from the donor before reperfusion significantly reduced I/R injury in the liver.
Small-sized Mach-Zehnder Interferometer Optical Switch Using Thin Film Ge2Sb2Te5 Phase-change Material (2014)

Small-sized Mach-Zehnder Interferometer optical switch using Ge2Sb2Te5 thin films was fabricated. Two thin films of 1-µm-square were sufficient for switching. The switching operation was successfully demonstrated by pulsed laser irradiation.
Ionic Effects of Sodium Chloride on the Templated Deposition of Polyelectrolytes Using Layer-by-Layer Ionic Assembly (1997)

A new method for the patterning of ionic layer-by-layer assembled films with micron-sized features is presented. Self-assembled monolayers (SAMs) were used as templates to direct the deposition of sulfonated polystyrene (SPS) and poly(diallyldimethylammonium chloride) (PDAC) multilayers onto a surface. Both polyelectrolytes were assembled electrostatically from dilute solutions (10 and 20 mM on a repeat unit basis) with varying amounts of sodium chloride. The ionic content was varied from 0 to 4 M NaCl. The optimal conditions for templating were found at moderate salt contents. At high salt contents (≥1 M NaCl) the templating behavior of the chemically patterned SAM surface completely reversed due to electrostatic screening and dehydration of an oligo(ethylene glycol)surface, indicating that ionic strength can be used to dramatically alter polyion deposition behavior on the functionalized surface.
Mechanisms of induction of cytosolic and microsomal glutathione transferase (GST) genes by xenobiotics and pro-inflammatory agents (2011)

Glutathione transferase (GST) isoezymes are encoded by three separate families of genes (designated cytosolic, microsomal and mitochondrial transferases), with distinct evolutionary origins, that provide mammalian species with protection against electrophiles and oxidative stressors in the environment. Members of the cytosolic class Alpha, Mu, Pi and Theta GST, and also certain microsomal transferases (MGST2 and MGST3), are up-regulated by a diverse spectrum of foreign compounds typified by phenobarbital, 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene, pregnenolone-16α-carbonitrile, 3-methylcholanthrene, 2,3,7,8-tetrachloro-dibenzo-p-dioxin, β-naphthoflavone, butylated hydroxyanisole, ethoxyquin, oltipraz, fumaric acid, sulforaphane, coumarin, 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole, 12-O-tetradecanoylphorbol-13-acetate, dexamethasone and thiazolidinediones. Collectively, these compounds induce gene expression through the constitutive androstane receptor (CAR), the pregnane X receptor (PXR), the aryl hydrocarbon receptor (AhR), NF-E2-related factor 2 (Nrf2), peroxisome proliferator-activated receptor-γ (PPARγ) and CAATT/enhancer binding protein (C/EBP) β. The microsomal T family includes 5-lipoxygenase activating protein (FLAP), leukotriene C(4) synthase (LTC4S) and prostaglandin E(2) synthase (PGES-1), and these are up-regulated by tumour necrosis factor-α, lipopolysaccharide and transforming growth factor-β. Induction of genes encoding FLAP, LTC4S and PGES-1 is mediated by the transcription factors C/EBPα, C/EBPδ, C/EBPϵ, nuclear factor-κB and early growth response-1. In this article we have reviewed the literature describing the mechanisms by which cytosolic and microsomal GST are up-regulated by xenobiotics, drugs, cytokines and endotoxin. We discuss cross-talk between the different induction mechanisms, and have employed bioinformatics to identify cis-elements in the upstream regions of GST genes to which the various transcription factors mentioned above may be recruited.
Solvent-Induced Transition from Micelles in Solution to Cylindrical Microdomains in Diblock Copolymer Thin Films (2007)

It is well-known that block copolymer thin films can be easily prepared on different substrates by spin coating. Here, we show that the cylindrical microdomains of polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) copolymers can be oriented normal to the surface over a large area by spin coating in toluene/THF solvent mixture. The structure and size of the PS-b-P4VP in solution were compared with those in thin films. It was found that the cylindrical microdomains, obtained by spin coating, oriented normal to the film surface depended strongly on the amount of THF in the casting solution. The study was extended to PS-b-P4VP copolymers with different molecular weights and compositions, which allowed the control of the size of the cylindrical domains and the areal density of the arrays.
[ 11 C]PIB in a nondemented population (2006)

Elevated [(11)C]PIB binding in nondemented subjects suggests that [(11)C]PIB amyloid imaging may be sensitive for detection of a preclinical Alzheimer disease state. Longitudinal studies will be required to determine the association of elevated [(11)C]PIB binding and risk of developing dementia of the Alzheimer type.
Bayesian curve fitting using MCMC with applications to signal segmentation (2002)

We propose some Bayesian methods to address the problem of fitting a signal modeled by a sequence of piecewise constant linear (in the parameters) regression models, for example, autoregressive or Volterra models. A joint prior distribution is set up over the number of the changepoints/knots, their positions, and over the orders of the linear regression models within each segment if these are unknown. Hierarchical priors are developed and, as the resulting posterior probability distributions and Bayesian estimators do not admit closed-form analytical expressions, reversible jump Markov chain Monte Carlo (MCMC) methods are derived to estimate these quantities. Results are obtained for standard denoising and segmentation of speech data problems that have already been examined in the literature. These results demonstrate the performance of our methods.
Detection of a Novel Intraneuronal Pool of Insoluble Amyloid β Protein that Accumulates with Time in Culture (1998)

The amyloid-beta peptide (Abeta) is produced at several sites within cultured human NT2N neurons with Abeta1-42 specifically generated in the endoplasmic reticulum/intermediate compartment. Since Abeta is found as insoluble deposits in senile plaques of the AD brain, and the Abeta peptide can polymerize into insoluble fibrils in vitro, we examined the possibility that Abeta1-40, and particularly the more highly amyloidogenic Abeta1-42, accumulate in an insoluble pool within NT2N neurons. Remarkably, we found that formic acid extraction of the NT2N cells solubilized a pool of previously undetectable Abeta that accounted for over half of the total intracellular Abeta. Abeta1-42 was more abundant than Abeta1-40 in this pool, and most of the insoluble Abeta1-42 was generated in the endoplasmic reticulum/intermediate compartment pathway. High levels of insoluble Abeta were also detected in several nonneuronal cell lines engineered to overexpress the amyloid-beta precursor protein. This insoluble intracellular pool of Abeta was exceptionally stable, and accumulated in NT2N neurons in a time-dependent manner, increasing 12-fold over a 7-wk period in culture. These novel findings suggest that Abeta amyloidogenesis may be initiated within living neurons rather than in the extracellular space. Thus, the data presented here require a reexamination of the prevailing view about the pathogenesis of Abeta deposition in the AD brain.
Baculovirus Expression Vectors: the Requirements for High Level Expression of Proteins, Including Glycoproteins (1987)

The requirements for high level expression of three foreign proteins using the polyhedrin gene promoter of Autographa californica nuclear polyhedrosis virus (AcNPV, Baculoviridae) have been investigated. In Spodoptera frugiperda cells infected with the appropriate recombinant baculoviruses, the synthesis of the two S RNA coded genes of lymphocytic choriomeningitis virus (LCMV; i.e. the nucleoprotein, N, and glycoprotein precursor, GPC), or the haemagglutinin gene of influenza A virus, appears to be related to the degree of integrity of the 5' upstream sequence of the polyhedrin gene. No effect on the level of N protein expression was detected when all the polyhedrin gene coding sequences or some of the immediate 3' downstream sequences were deleted. Using the most efficient expression viruses derived from a new transfer vector, pAcYM1, it has been estimated that LCMV N protein represented approximately 50% of the total cellular protein, an observation consistent with the presence of numerous inclusion bodies in the cytoplasm of infected cells. For recombinant viruses derived from the pAcYM1 transfer vector containing the LCMV GPC gene, the level of synthesis of the arenavirus glycoprotein was equivalent to approximately 20% of the cellular protein. Thin sections of cells infected with the GPC recombinant revealed a highly vacuolated cytoplasm.
Adult stem cells in the endometrium (2010)

Rare cells with adult stem cell activity were recently discovered in human endometrium. Endometrial stem/progenitor cell candidates include epithelial, mesenchymal and endothelial cells, and all may contribute to the rapid endometrial regeneration following menstruation, rather than a single candidate. Endometrial mesenchymal stem-like cells (eMSC) are prospectively isolated as CD146(+)PDGF-Rβ(+) cells and are found in both basalis and functionalis as perivascular cells. Epithelial progenitor cells are detected in colony forming unit assays but their identity awaits elucidation. They are postulated to reside in the basalis in gland bases. Endometrial stem/progenitor cells may be derived from endogenous stem cells, but emerging evidence suggests a bone marrow contribution. Endometrial endothelial progenitor cells are detected as side population cells, which express several endothelial cell markers and differentiate into endometrial glandular epithelial, stromal and endothelial cells. Investigating endometrial stem cell biology is crucial to understanding normal endometrial physiology and to determine their roles in endometrial proliferative diseases. The nature of endometriosis suggests that initiation of ectopic endometrial lesions involves endometrial stem/progenitor cells, a notion compatible with Sampson's retrograde menstruation theory and supported by the demonstration of eMSC in menstrual blood. Evidence of cancer stem cells (CSC) in endometrial cancer indicates that new avenues for developing therapeutic options targeting CSC may become available. We provide an overview of the accumulating evidence for endometrial stem/progenitor cells and their possible roles in endometrial proliferative disorders, and discuss the unresolved issues.
Lipotoxicity and Decreased Islet Graft Survival (2009)

OBJECTIVE To evaluate if baseline serum lipids are associated with islet graft survival in type 1 diabetes islet transplant (ITx) recipients. RESEARCH DESIGN AND METHODS Baseline fasting lipid profile was collected from 44 ITx recipients. Comparisons were performed between subjects below and above the median values of each lipid fraction. Differences in outcomes were compared by Kaplan-Meier curves and Cox regression analysis. RESULTS Subjects with baseline fasting plasma triglycerides and VLDL cholesterol above the median had shorter islet graft survival (triglycerides: 39.7 +/- 6.1 vs. 61.3 +/- 6.6 months, P = 0.029, and VLDL: 41.5 +/- 5.7 vs. 62.8 +/- 7.3 months, P = 0.032). Total, LDL, and HDL cholesterol did not influence islet function. Triglycerides (odds ratio 2.97 [95% CI 1.03-8.52], P = 0.044) maintained its association with graft failure after adjustments for confounders. CONCLUSIONS Higher baseline triglycerides are associated with earlier decline in islet graft function. Prospective clinical trials should address whether it is directly caused by lipotoxicity and if strategies focusing on lowering serum lipids may prolong islet graft survival.
Hospital anxiety and depression scale assessment of 100 patients before and after using low vision care: A prospective study in a tertiary eye-care setting (2017)

Low vision correction can significantly improve anxiety and depression indicators in visually impaired patients.
Activated Leukocytes Oxidatively Damage DNA, RNA, and the Nucleotide Pool through Halide-Dependent Formation of Hydroxyl Radical (2000)

A variety of chronic inflammatory conditions are associated with an increased risk for the development of cancer. Because of the numerous links between DNA oxidative damage and carcinogenesis, a potential role for leukocyte-generated oxidants in these processes has been suggested. In the present study, we demonstrate a novel free transition metal ion-independent mechanism for hydroxyl radical ((*)OH)-mediated damage of cellular DNA, RNA, and cytosolic nucleotides by activated neutrophils and eosinophils. The mechanism involves reaction of peroxidase-generated hypohalous acid (HOCl or HOBr) with intracellular superoxide (O(2)(*)(-)) forming (*)OH, a reactive oxidant species implicated in carcinogenesis. Incubation of DNA with either isolated myeloperoxidase (MPO) or eosinophil peroxidase (EPO), plasma levels of halides (Cl(-) and Br(-)), and a cell-free O(2)(*)(-) -generating system resulted in DNA oxidative damage. Formation of 8-hydroxyguanine (8-OHG), a mutagenic base which is a marker for (*)OH-mediated DNA damage, required peroxidase and halides and occurred in the presence of transition metal chelators (DTPA +/- desferrioxamine), and was inhibited by catalase, superoxide dismutase (SOD), and scavengers of hypohalous acids. Similarly, exposure of DNA to either neutrophils or eosinophils activated in media containing metal ion chelators resulted in 8-OHG formation through a pathway that was blocked by peroxidase inhibitors, hypohalous acid scavengers, and catalytically active (but not heat-inactivated) catalase and SOD. Formation of 8-OHG in target cells (HA1 fibroblasts) occurred in all guanyl nucleotide-containing pools examined following exposure to both a low continuous flux of HOCl (at sublethal doses, as assessed by [(14)C]adenine release and clonogenic survival), and hyperoxia (to enhance intracellular O(2)(*)(-) levels). Mitochondrial DNA, poly A RNA, and the cytosolic nucleotide pool were the primary targets for oxidation. Moreover, modest but statistically significant increases in the 8-OHG content of nuclear DNA were also noted. These results suggest that the peroxidase-H(2)O(2)-halide system of leukocytes is a potential mechanism contributing to the well-established link between chronic inflammation, DNA damage, and cancer development.
Infrared luminescence of residual iron deep level acceptors in gallium nitride (GaN) epitaxial layers (1994)

A characteristic infrared luminescence band, dominated by a zero-phonon line at 1.30 eV has been consistently detected in gallium nitride (GaN) epitaxial layers. It is assigned to the intra-3d-shell transitions 4T1(G)→6A1(S) of omnipresent iron trace impurities, Fe3+Ga(3d5). Another infrared emission is often also observed at 1.19 eV. This is tentatively assigned to chromium trace impurities, Cr4+Ga(3d2). The role of iron and chromium as minority-carrier lifetime killers in GaN-based optoelectronic devices is suggested from these data.
A Novel Local Recycling Mechanism That Enhances Enteric Bioavailability of Flavonoids and Prolongs Their Residence Time in the Gut (2012)

Recycling in the gastrointestinal tract is important for endogenous substances such as bile acids and for xenobiotics such as flavonoids. Although both enterohepatic and enteric recycling mechanisms are well recognized, no one has discussed the third recycling mechanism for glucuronides: local recycling. The intestinal absorption and metabolism of wogonin and wogonoside (wogonin-7-glucuronide) was characterized by using a four-site perfused rat intestinal model, and hydrolysis of wogonoside was measured in various enzyme preparations. In the perfusion model, the wogonoside and wogonin were interconverted in all four perfused segments. Absorption of wogonoside and conversion to its aglycon at the upper small intestine was inhibited in the presence of a glucuronidase inhibitor (saccharolactone) but was not inhibited by lactase phlorizin hydrolase (LPH) inhibitor gluconolactone or antibiotics. Further investigation indicated that hydrolysis of wogonoside in the blank intestinal perfusate was not correlated with bacterial counts. Kinetic studies indicated that K(m) values from blank duodenal and jejunal perfusate were essentially identical to the K(m) values from intestinal S9 fraction but were much higher (>2-fold) than those from the microbial enzyme extract. Lastly, jejunal perfusate and S9 fraction share the same optimal pH, which was different from those of fecal extract. In conclusion, local recycling of wogonin and wogonoside is the first demonstrated example that this novel mechanism is functional in the upper small intestine without significant contribution from bacteria β-glucuronidase.
The Effects of Four Different Tyrosine Kinase Inhibitors on Medullary and Papillary Thyroid Cancer Cells (2011)

There is indeed specificity for different RET mutations, with XL184 being the most potent inhibitor in MEN2A and PTC and vandetanib the most effective in MEN2B in vitro. No TK inhibitor was superior for all the cell lines tested, indicating that mutation-specific therapies could be beneficial in treating MTC and PTC.
Characteristics of Nucleic Acids (2000)

This appendix is a compilation of information from Current Protocols in Molecular Biology (John Wiley & Sons, Inc.) and provides information about the major nucleoside/nucleotide constituents and structures for A-, B-, and Z-DNA. Tables and figures provide (1) experimentally useful properties of the nucleoside/nucleotide building blocks; (2) chemical structures of the nucleosides; (3) aspects of nucleotide stereochemistry that are important to an understanding of base pairing and secondary structure; (4) alternative (non-Watson-Crick) base pairings; and (5) the three best characterized helix structures for DNA: A-, B-, and Z-DNA.