gebhart/patrepeval huggingface dataset:
DNA Interstrand Cross-Link Formation Initiated by Reaction between Singlet Oxygen and a Modified Nucleotide (2005)

DNA is the target of many anti-cancer therapies. These agents damage the biopolymer by oxidation or by alkylation. Interstrand DNA cross-links are believed to be the source of cytotoxicity of anti-tumor agents, such as mitomycin C, which alkylate the biopolymer. In contrast, deoxyguanosine oxidation is the result of reaction between DNA and singlet oxygen, which is the damaging species produced in photodynamic therapy. We have shown that, upon oxidation by singlet oxygen, an analogue of thymidine (2) rearranges to a methide, which forms DNA-DNA interstrand cross-links. This novel process suggests that 2 may be a useful adjuvant in photodynamic therapy.
Myeloperoxidase, a Leukocyte-Derived Vascular NO Oxidase (2002)

Myeloperoxidase (MPO) is an abundant mammalian phagocyte hemoprotein thought to primarily mediate host defense reactions. Although its microbicidal functions are well established in vitro, humans deficient in MPO are not at unusual risk of infection. MPO was observed herein to modulate the vascular signaling and vasodilatory functions of nitric oxide (NO) during acute inflammation. After leukocyte degranulation, MPO localized in and around vascular endothelial cells in a rodent model of acute endotoxemia and impaired endothelium-dependent relaxant responses, to which MPO-deficient mice were resistant. Altered vascular responsiveness was due to catalytic consumption of NO by substrate radicals generated by MPO. Thus MPO can directly modulate vascular inflammatory responses by regulating NO bioavailability.
TRAF Family Proteins Interact with the Common Neurotrophin Receptor and Modulate Apoptosis Induction (1999)

The common neurotrophin receptor, p75(NTR), has been shown to signal in the absence of Trk tyrosine kinase receptors, including induction of neural apoptosis and activation of NF-kappaB. However, the mechanisms by which p75(NTR) initiates these intracellular signal transduction pathways are unknown. Here we report interactions between p75(NTR) and the six members of TRAF (tumor necrosis factor receptor-associated factors) family proteins. The binding of different TRAF proteins to p75(NTR) was mapped to distinct regions in p75(NTR). Furthermore, TRAF4 interacted with dimeric p75(NTR), whereas TRAF2 interacted preferentially with monomeric p75(NTR). TRAF2-p75(NTR), TRAF4-p75(NTR), and TRAF6-p75(NTR) interactions modulated p75(NTR)-induced cell death and NF-kappaB activation with contrasting effects. Coexpression of TRAF2 with p75(NTR) enhanced cell death, whereas coexpression of TRAF6 was cytoprotective. Furthermore, overexpression of TRAF4 abrogated the ability of dimerization to prevent the induction of apoptosis normally mediated by monomeric p75(NTR). TRAF4 also inhibited the NF-kappaB response, whereas TRAF2 and TRAF6 enhanced p75(NTR)-induced NF-kappaB activation. These results demonstrate that TRAF family proteins interact with p75(NTR) and differentially modulate its NF-kappaB activation and cell death induction.
Influence of Tołpa Peat Preparation on gastroprotection and on gastric and duodenal ulcers. (1994)

It was found, that Tołpa Peat Preparation administered prophylactically to rats decreased significantly the size of gastric mucosa damage induced with ethanol. TPP administered to rats with experimental gastric and duodenal ulcers significantly accelerated the healing process.
Isolation and Purification of a Polymeric Form of the Glycoprotein of Rabies Virus (1978)

Of the three major proteins associated with the rabies virus membrane, only the glycoprotein was found to be located on the external surface of the virus membrane. Glycoprotein prepared by treatment of rabies virus with Triton X-100 and purified by isoelectric focusing was found to be homogeneous with respect to size and isoelectric point. This material, which is free of phospholipids, is able to protect in vaccination experiments against a lethal challenge infection with rabies virus. The apparent mol. wt. of this component isolated under non-denaturing conditions is approx. 400000. The same material analysed by SDS polyacrylamide gel electrophoresis (PAGE) was found to consist solely of polypeptide chains of the G protein (mol. wt. 80000). A minor glycoprotein (gp 50), detected by PAGE of the Triton X-100 released material, appeared to be a breakdown product of the G-protein. Therefore the detergent released material represents homopolymers of the G-protein. Whether the antigenic determinants reside on the monomeric subunit or are a property of the polymeric form of the G-protein is discussed.
Isolation and characterization of two hydroxyproline-containing glycoproteins from normal animal lung lavage and lamellar bodies. (1975)

Two glycopeptides, present in particulate material obtained by pulmonary lavage from normal rabbits, were isolated and characterized. The same two glycopeptides were present in preparations of lamellar bodies from rabbit lung. The estimated molecular weights of the two glycopeptides by sodium dodecyl sulfate-acrylamide gel electrophoresis were found to be 62,000 and 36,000 and both were found to contain hydroxyproline and relatively high amount of glycine (11 and 15 per cent, respectively). Carbohydrate analysis of the two glycopeptides demonstrated the presence of glucosamine, sialic acid, mannose, Fucose, and galactose. Similar glycopeptides of the same molecular weights, and amino acid and carbohydrate compositions have been found in layage mateial isolated from lungs of patients with alveolar proteinosis. The data indicate that thses two collagen-like glycopeptides are major intra-alveolar proteins in many mammals, including humans.
Fluorescence Correlation Spectroscopy (2007)

Fluorescence correlation spectroscopy (FCS) is a technique that allows for an extremely sensitive determination of molecular diffusion properties, down to the level of single molecules. It thus provides an attractive alternative to FRAP, requiring much less laser power and lower concentrations of fluorophores. FCS has recently been applied on live cells, and in comparison on domain-forming model membrane systems, to systematically study the influence of cholesterol on local membrane structure by investigating the mobility of selected lipid probes. The findings demonstrate the ability of FCS to sensitively distinguish between different local lipid structures, and emphasize the value of model systems for understanding membrane dynamics in general.
Non-ambipolr electron extraction from a weakly magnetized RF plasma (2006)

Summary form only given. Electron extraction at electron sheaths (i.e. positive going anode sheaths) is studied in weakly magnetized RF inductive plasmas. As with DC plasmas produced with hot filaments, it is shown that all of the electrons created by ionization in the plasma can be extracted from the plasma. The electrons are extracted through a grounded ring and in the presence of a weak axial magnetic field, only a small fraction of the electrons are lost to the ring. All of the ions are lost to a negatively biased conducting cylinder which also serves as a Faraday shield for the RF. Experiments are reported with argon and xenon plasmas having densities of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> to 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">-3</sup> . Magnetic fields were as high as 100 gauss at the extraction ring. Extracted electron currents were as high as 4 A. The necessary condition for all of the electrons to be extracted is that the area ratio between the ion loss area and the electron loss area is at least m <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> m <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> Y, where m <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> is the ion mass and m <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> is the electron mass. The bias on the ion cylinder is chosen so that the biased boundary is much more negative than the floating potential, so that electron losses to the boundary can be neglected
Influence of the mucosal epithelium microenvironment on Langerhans cells: Implications for the development of squamous intraepithelial lesions of the cervix (2001)

We have addressed the notion that the initiation and progression of human papillomavirus associated cancer of the uterine cervix are associated with alterations of Langerhans cells (LC) within the mucosal squamous epithelium. Since the transformation zone (TZ) of the cervix is the site where the majority of squamous intraepithelial lesions (SIL) are initiated, in contrast to the exocervix, we decided to investigate the influence of the local microenvironment within the TZ on the function and density of LC. We show that the TZ is associated with a significant reduction in the density of immature LC (CD1a/LAG) compared to the exocervix. In contrast, the development of SILs is attributed with a relative increased density of immature LC, compared to the TZ. Furthermore, we show that this variability in LC density is correlated with a differential expression of TNFalpha and MIP3alpha within the micro-environment of the TZ and SILs. Both TZ and SIL epithelium-derived LC, in the presence of allogeneic PBMC, induced lower levels of proliferation and IL2 production and higher levels of the immunosuppressive cytokine IL10 in comparison to the exocervix. Nevertheless, the epithelium-derived LC in SILs exhibits a reduction in their functional activity, relative to the TZ. Together our studies suggest that the immunosurveillance within the epithelium of the TZ may be intrinsically perturbed due to the altered expression of chemokines/cytokines and the concomitant diminished density of LC. Furthermore, following HPV infection and the development of SILs, the function of LC may be further incapacitated by viral associated mechanisms.
Surfactant Proteins and Anti-Surfactant Antibodies in Sera from Infants With Respiratory Distress Syndrome With and Without Surfactant Treatment (1991)

The presence of surfactant protein antigenemia and of surfactant protein antibodies was determined in serum from surfactant-treated and control infants with respiratory distress syndrome who were enrolled in a prospective randomized clinical trial. The surfactant used for treatment (surfactant TA) contained surfactant proteins (SPs) B and C and no SP-A. Enzyme-linked immunosorbent assays (ELISAs) that identify surfactant-associated proteins and ELISAs that identify IgG or IgM directed against surfactant proteins were used to investigate sera from these infants obtained prior to treatment, at 1 week of age, and at 2 months of age. There were no significant differences between average values in the surfactant-treated and control groups at each time period. However, in the control group, averaged results from ELISAs that identify SP-A and that identify IgM antibodies to SP-A or to SP-B, C showed significant differences between pretreatment sera and sera obtained at 1 week of age. No significant differences were noted in averaged results for IgG. Positive ELISA values were more frequently found in the control group than in the surfactant-treated group with regard to SP-A, and IgM against SP-A and SP-B, C in sera from neonates at 1 week of age. No positive ELISA values were found in sera from infants at 2 months of age. It is concluded that some patients with severe respiratory distress syndrome presumably leak surfactant proteins into the circulation and that this induces transient low titers of IgM antibody. This occurrence is decreased with surfactant treatment. Surfactant treatment may reduce leak of surfactant proteins into the vascular space by reducing lung damage.
Severity of Optic Nerve Damage in Eyes with POAG Is Correlated with Changes in the Trabecular Meshwork (1997)

Purpose: We wished to determine whether eyes with primary open-angle glaucoma (POAG) and differing severity of optic nerve damage also have differences in severity of trabecular meshwork changes. Methods: The trabecular meshwork and optic nerve from 26 eyes (14 donors) with the clinical diagnosis of POAG were studied. Severity of disease ranged from increased intraocular pressure (IOP) without damage to eyes with severe visual field loss. Optic nerve cross-sections were examined with light microscopy, and axonal counts were determined. We studied the trabecular meshwork around the circumference of each eye, examining sections from each quadrant with light and transmission electron microscopy. Morphometric measurements were made of the components of the cribriform region and statistically correlated with the axonal counts by the Pearson correlation coefficient. Results: In eyes with advanced POAG, as determined by visual field loss, measurements of structures in the cribriform region of the trabecular meshwork and axon counts were in the same range as those reported previously in POAG. Axon counts showed a significant negative correlation with the amount of sheath-derived (SD) plaque material in the cribriform region: eyes with lower axon counts had larger amounts of SD plaques. Six eyes from four donors with increased pressure but no clinical signs of optic nerve damage showed no changes in axon counts and no increase in plaque material. Conclusions: Increasing severity of optic nerve damage in POAG is accompanied by an increase in the amount of SD plaque material in the trabecular meshwork.
Voltage-controlled epitaxial strain in La0.7Sr0.3MnO3∕Pb(Mg1∕3Nb2∕3)O3-PbTiO3(001) films (2005)

Epitaxially grown La0.7Sr0.3MnO3 thin films show resistance modulations induced by the inverse piezoeffect of the employed Pb(Mg1∕3Nb2∕3)O3-PbTiO3(001) (PMN-PT) substrates. The in-plane strain state of the films can continuously be tuned by application of a piezovoltage to PMN-PT. The lattice deformation of a PMN-PT(001) substrate was quantified by x-ray measurements under an electric field. Variation of in-plane lattice parameters by ∼0.06% reversibly changes the resistance of the manganite films by up to 9% at 300 K and shifts the magnetic Curie temperature. Films of different thicknesses from 50 to 290 nm, offering different as-grown strain states, have been studied.
InlA‐ but not InlB‐mediated internalization of Listeria monocytogenes by non‐phagocytic mammalian cells needs the support of other internalins (2002)

To determine the contribution of the previously identified internalins, InlA, InlB, InlC, InlE, InlG, and InlH, to internalization of Listeria monocytogenes by non-professional phagocytic mammalian cells, we constructed mutants with various combinations of deletions in the respective inl genes. Internalization of these mutants into the epithelial-like Caco-2 and the microvascular endothelial HBMEC cell lines were studied. Deletion of the inlGHE gene cluster, or of the single genes, led to a two to fourfold increased internalization by HBMEC and other non-phagocytic mammalian cells. Invasion into HBMEC was totally blocked in the absence of InlB, and InlB-dependent internalization did not require the presence of any of the other internalins. Internalization by Caco-2 cells was reduced to a level of about 1% in the absence of InlA and InlB, and was most efficient in the presence of InlA, InlB and InlC and in the absence of InlG, InlH and InlE. InlB and InlA, in each case in the absence of the other internalins, led (compared with the wild-type strain) to reduced internalization of about 20% and less than 10% respectively. InlA-dependent internalization (in the absence of InlB) required the additional function of InlC and InlGHE. The deletion of inlGHE enhanced the expression of InlA and InlB. The increased amount of InlA led to an increase in early association of L. monocytogenes with Caco-2 cells without enhancing its uptake in the absence of the other internalins, whereas the larger amount of InlB did not enhance early association of L. monocytogenes with HBMEC but led to an increase in internalization of L. monocytogenes. The results suggest that InlB is able to induce phagocytosis in HBMEC and (at a lower efficiency) in Caco-2 cells by itself, but InlA needs the supportive functions of the other internalins to trigger phagocytosis. None of these internalins seems to be required for cell-to-cell spread by L. monocytogenes, as shown by microinjection of Caco-2 cells with appropriate inl mutants.
Avian adenoviruses ‐ a review (1977)

The literature on avian adenoviruses is reviewed with particular reference to the virion, number of serotypes, epidemiology, diagnosis and association with disease. Using the serum neutralisation test there are probably at least 12 serotypes which share a common avian group antigen distinct from the mammalian group antigen. The three disease complexes most often associated with avian adenovirus infections are respiratory disease, falls in egg production and hepatitis.
Anti-inflammatory protein TSG-6 reduces inflammatory damage to the cornea following chemical and mechanical injury (2010)

Previous reports demonstrated that adult stem/progenitor cells from bone marrow (multipotent mesenchymal stem cells; MSCs) can repair injured tissues with little evidence of engraftment or differentiation. In exploring this phenomenon, our group has recently discovered that the therapeutic benefits of MSCs are in part explained by the cells being activated by signals from injured tissues to express an anti-inflammatory protein TNF-α-stimulated gene/protein 6 (TSG-6). Therefore, we elected to test the hypothesis that TSG-6 would have therapeutic effects in inflammatory but noninfectious diseases of the corneal surface. We produced a chemical and mechanical injury of the cornea in rats by brief application of 100% ethanol followed by mechanical debridement of corneal and limbal epithelium. Recombinant human TSG-6 or PBS solution was then injected into the anterior chamber of the eye. TSG-6 markedly decreased corneal opacity, neovascularization, and neutrophil infiltration. The levels of proinflammatory cytokines, chemokines, and matrix metalloproteinases were also decreased. The data indicated that TSG-6, a therapeutic protein produced by MSCs in response to injury signals, can protect the corneal surface from the excessive inflammatory response following injury.
Genotypic and Physiological Characterization of Saccharomyces boulardii , the Probiotic Strain of Saccharomyces cerevisiae (2007)

Saccharomyces boulardii, a yeast that was isolated from fruit in Indochina, has been used as a remedy for diarrhea since 1950 and is now a commercially available treatment throughout Europe, Africa, and South America. Though initially classified as a separate species of Saccharomyces, recent publications have shown that the genome of S. boulardii is so similar to Saccharomyces cerevisiae that the two should be classified as conspecific. This raises the question of the distinguishing molecular and phenotypic characteristics present in S. boulardii that make it perform more effectively as a probiotic organism compared to other strains of S. cerevisiae. This investigation reports some of these distinguishing characteristics including enhanced ability for pseudohyphal switching upon nitrogen limitation and increased resistance to acidic pH. However, these differences did not correlate with increased adherence to epithelial cells or transit through mouse gut. Pertinent characteristics of the S. boulardii genome such as trisomy of chromosome IX, altered copy number of a number of individual genes, and sporulation deficiency have been revealed by comparative genome hybridization using oligonucleotide-based microarrays coupled with a rigorous statistical analysis. The contributions of the different genomic and phenotypic features of S. boulardii to its probiotic nature are discussed.
An Epidermal Growth Factor Receptor Intron 1 Polymorphism Mediates Response to Epidermal Growth Factor Receptor Inhibitors (2004)

This study tested the hypothesis that the number of CA single sequence repeat (CA-SSR) in the intron 1 of the epidermal growth factor receptor (egfr) gene, which affects transcription efficiency of the gene, is associated with the response to EGFR inhibitors. To this end, we determined the number of CA dinucleotides in the intron 1 of the egfr gene in a panel of 12 head and neck cancer cell lines that lack egfr gene amplification and measured the expression of EGFR (mRNA and protein), as well as response to EGFR inhibition. Cells with lower number of CA dinucleotides in the CA-SSR had higher expression of the EGFR gene and protein and were more sensitive to the inhibitory effects of erlotinib, a small molecule inhibitor of the EGFR tyrosine-kinase. Phenotypic modification by silencing EGFR mRNA expression in a susceptible cell line induced resistance to the drug. The number of CA dinucleotide was equivalent in genomic and tumor DNA obtained from 30 patients with head and neck cancer. In a clinical study in colorectal cancer, subjects with lower number of CA dinucleotide frequently developed skin toxicity, a feature that is related to the antitumor activity of this class of drugs. These results suggest that polymorphic variations in the intron 1 of the egfr gene is associated with response to EGFR inhibitors and may provide an explanation as to why the development of skin toxicity is associated with a favorable outcome in patients treated with these agents.
Fecal Lipocalin 2, a Sensitive and Broadly Dynamic Non-Invasive Biomarker for Intestinal Inflammation (2012)

Inflammation has classically been defined histopathologically, especially by the presence of immune cell infiltrates. However, more recent studies suggest a role for "low-grade" inflammation in a variety of disorders ranging from metabolic syndrome to cancer, which is defined by modest elevations in pro-inflammatory gene expression. Consequently, there is a need for cost-effective, non-invasive biomarkers that, ideally, would have the sensitivity to detect low-grade inflammation and have a dynamic range broad enough to reflect classic robust intestinal inflammation. Herein, we report that, for assessment of intestinal inflammation, fecal lipocalin 2 (Lcn-2), measured by ELISA, serves this purpose. Specifically, using a well-characterized mouse model of DSS colitis, we observed that fecal Lcn-2 and intestinal expression of pro-inflammatory cytokines (IL-1β, CXCL1, TNFα) are modestly but significantly induced by very low concentrations of DSS (0.25 and 0.5%), and become markedly elevated at higher concentrations of DSS (1.0 and 4.0%). As expected, careful histopathologic analysis noted only modest immune infiltrates at low DSS concentration and robust colitis at higher DSS concentrations. In accordance, increased levels of the neutrophil product myeloperoxidase (MPO) was only detected in mice given 1.0 and 4.0% DSS. In addition, fecal Lcn-2 marks the severity of spontaneous colitis development in IL-10 deficient mice. Unlike histopathology, MPO, and q-RT-PCR, the assay of fecal Lcn-2 requires only a stool sample, permits measurement over time, and can detect inflammation as early as 1 day following DSS administration. Thus, assay of fecal Lcn-2 by ELISA can function as a non-invasive, sensitive, dynamic, stable and cost-effective means to monitor intestinal inflammation in mice.