gebhart/patrepeval huggingface dataset:
Instability of expression of lipooligosaccharides and their epitopes in Neisseria gonorrhoeae (1988)

We assessed variation in the expression of lipooligosaccharide (LOS) components and their epitopes within populations of a strain of Neisseria gonorrhoeae by using the monoclonal antibodies (MAbs) O6B4 and 3F11 and immunoenzymatic, immuno-colloidal gold electron microscopic, and sodium dodecyl sulfate-polyacrylamide gel electrophoretic procedures. Wild-type organisms varied in binding of both MAbs. We used the intensity of immunoenzymatic colony blot color to distinguish four binding variants for each MAb: red (R), pink (P), and colorless (nonreactive [N]) and an N back to R (N-R) revertant. R to P to R and R to N to R variation occurred at frequencies of 0.2% and 0.02%, respectively. The electrophoretic LOS profiles and MAb immunoblot patterns of the R, P, and N-R variants were the same as those of the wild type. LOSs of the N variants, in contrast, were of lower Mr, bound neither 3F11 nor O6B4 MAb, and contained as their major component the 3.6-kilodalton LOS that bears the L8LOS epitope of N. meningitidis. Results of immunoelectron microscopic studies were consistent with LOS binding patterns. Large number of colloidal gold particles were deposited about both R and P variants, distally from R organisms, but proximally from P organisms. N variant organisms, like their LOS, bound neither of the MAbs. N-R variant organisms were like the wild type in that they showed much variation in the amounts of MAb they bound.
Comparison of Two Recombinant Major Outer Membrane Proteins of the Human Granulocytic Ehrlichiosis Agent for Use in an Enzyme-Linked Immunosorbent Assay (2000)

Enzyme-linked immunosorbent assay (ELISA) for human granulocytic ehrlichiosis (HGE) using two different recombinant P44 proteins (rP44 and rP44-2hv) of the HGE agent as antigens was evaluated. Sera from a total of 72 healthy humans both from regions where HGE is nonendemic and regions where HGE is endemic were used as negative controls to determine the cutoff value for ELISA. Sera from a total of 14 patients (nine from whom the HGE agent was isolated and five who were HGE-PCR positive) were used as positive controls. One hundred nine sera from 72 patients in an area where HGE is endemic who were suspected of having HGE were examined by ELISA and indirect immunofluorescence assay (IFA). All IFA-negative sera were negative by both ELISAs. Of 39 sera that were IFA positive, 35 and 27 were positive by ELISA using rP44 and rP44-2hv, respectively, indicating that the use of rP44 is more sensitive. Western blot analysis of the four rP44-ELISA-negative IFA-positive sera using whole HGE agent as antigen suggests that these four sera were false IFA positive. There was no difference in results with or without the preabsorption of sera with Escherichia coli or with or without the cleavage of the fused protein derived from the vector. There was a significant positive correlation between IFA titers and optical densities of ELISAs. Four Ehrlichia chaffeensis-positive and 10 Borrelia burgdorferi-positive sera were negative by ELISA. However, two Babesia microti-positive sera showed strong cross-reactivity to the fused vector protein, which was eliminated after cleavage of the protein. Thus, ELISA using rP44 nonfusion protein would provide a simple, specific, and objective HGE serologic test which can be easily automated.
Hypoxia Regulates Vascular Endothelial Growth Factor Gene Expression in Endothelial Cells (1995)

Vascular endothelial growth factor (VEGF) is a potent mitogen specific for endothelial cells. Its expression is dramatically induced by low oxygen tension in a variety of cell types, and it has been suggested to be a key mediator of hypoxia-induced angiogenesis. Although VEGF action is targeted to endothelial cells, it is generally believed that these cells do not express VEGF. In addition, the mechanisms by which hypoxia regulates VEGF production remain unclear. We report in the present study that pulmonary artery endothelial cells do not express VEGF under basal conditions; however, significant VEGF mRNA levels accumulate when these cells are exposed to hypoxia. Using a DNA fragment containing human VEGF promoter sequence, we identified a 28-bp element that is necessary and sufficient to upregulate transcription in response to hypoxia. This element can act as a hypoxia-specific enhancer when placed upstream or downstream from a heterologous promoter. The enhancer includes, in addition to an octamer homologous to the hypoxia-inducible factor-1 (HIF-1) consensus, a sequence that resides 3' to the consensus. Although this sequence may not be involved in the binding of HIF-1, it is absolutely required for the enhancer activity and may be the binding site for certain constitutive binding proteins. The expression of VEGF by endothelial cells in response to hypoxia may provide an important mechanism by which endothelial cell permeability and proliferation is regulated in an autocrine manner.
Nano- and micro-fiber combined scaffolds: A new architecture for bone tissue engineering (2005)

One possible interesting way of designing a scaffold for bone tissue engineering is to base it on trying to mimic the biophysical structure of natural extracellular matrix (ECM). This work was developed in order to produce scaffolds for supporting bone cells. Nano and micro fiber combined scaffolds were originally produced from starch based biomaterials by means of a fiber bonding and a electrospinning, two step methodology. The cell culture studies with SaOs-2 human osteoblast-like cell line and rat bone marrow stromal cells demonstrated that presence of nanofibers influenced cell shape and cytoskeletal organization of the cells on the nano/micro combined scaffolds. Moreover, cell viability and Alkaline Phosphatase (ALP) activity for both cell types was found to be higher in nano/micro combined scaffolds than in control scaffolds based on fiber meshes without nanofibers. Consequently, the developed structures are believed have a great potential on the 3D organization and guidance of cells that is provided for engineering of 3-dimensional bone tissues.
Protection from Fluorescein Isothiocyanate-Induced Fibrosis in IL-13-Deficient, but Not IL-4-Deficient, Mice Results from Impaired Collagen Synthesis by Fibroblasts (2004)

Intratracheal injection of FITC results in acute lung injury and progresses to fibrosis by day 21 postchallenge. In response to FITC, BALB/c mice produce IL-4 and IL-13 in the lung. To investigate whether IL-4 and/or IL-13 were important profibrotic mediators in this model, we examined the fibrotic response to FITC in mice that were genetically deficient in IL-4 (IL-4(-/-)), IL-13 (IL-13(-/-)), or IL-4 and IL-13 combined (IL-4/13(-/-)). Baseline levels of collagen were similar in all mice. In response to FITC, both BALB/c and IL-4(-/-) mice developed fibrosis, whereas the IL-13(-/-) and IL-4/13(-/-) mice were significantly protected, as measured by total lung collagen levels and histology. Total leukocyte recruitment to the lung was similar in all four strains of mice when measured on days 7, 14, and 21 post-FITC. BALB/c mice showed prominent eosinophilia on day 7 that was absent in IL-4(-/-), IL-13(-/-), and IL-4/13(-/-) mice, suggesting that eosinophilia is not necessary for development of a fibrotic response. There were no significant differences in the percentages of any other leukocytes analyzed between the genotypes. Similarly, protection in IL-13(-/-) mice was not associated with alterations in cytokine or eicosanoid profiles. Interestingly, TGF-beta1 production was not reduced in IL-13(-/-) mice. Analyses of fibroblasts isolated from the four genotypes demonstrated that although there were similar numbers of fibroblasts present in cultures of lung minces, fibroblasts from IL-13-deficient strains have reduced basal and stimulated levels of collagen production. IL-13Ralpha1 expression increases on fibroblasts during fibrotic responses in vivo, and IL-13 increases collagen synthesis in fibroblasts. Thus, IL-13 mediates its profibrotic actions through direct effects on fibroblast production of extracellular matrix.
Ribonuclease mimics (1991)

The cleavage of the ribonucleotide UpU by imidazole buffers shows kinetic behavior that indicates a sequential bifunctional mechanism, in which the imidazolium ion acts first. Similar results are obtained for the cleavage of ApA. This mechanism is related to the simultaneous bifunctional cleavage of RNA by the enzyme ribonuclease, and has guided us to the synthesis of an improved cyclodextrin-bis-imidazole enzyme mimic that also uses a simultaneous bifunctional mechanism.
MCPIC: a video coding algorithm for transmission and storage applications (1990)

The Moving Picture Experts Group (MPEG) of ISO is considering a standard for storage applications below 1.5 Mb/s. A video coding algorithm developed at Bellcore that has been proposed as a contribution to the standardization activity of ISO/MPEG is described. The following characteristics of the algorithm are described. The following characteristics of the algorithm are described in detail: frequent periodic reset of the temporal predictor (to provide random access), interpolative coding of every second frame, flexibility of providing adaptive Huffman code tables for digital-storage-media (DSM)-based applications (not feasible for real-time transmissions), 1/2-pel accuracy in motion estimation, and optional quantization matrix. Additional features of reverse playback, fast searches, and random access are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biochemical Methods: A Concise Guide for Students and Researchers (2002)

Preface. BIOCHEMICAL LITERATURE. Accessing the biochemical literature. Access to the methodologically based biochemical literature. Reference works and handbooks. Literature searches. Documentation of practical work. Literature. GENERAL LABORATORY PROCEDURES. The biochemistry laboratory. Routine biochemical procedures. Working with radioactivity. Literature. SAMPLE PREPARATION. Cell and tissue disruption. Solubilisation. Precipitation procedures for proteins and nucleic acids. Dialysis, ultrafiltration and lyophilisation. Literature. SEPARATION METHODS. Chromatography. Electrophoresis. Centrifugation. Literature. ANALYTICAL METHODS. Protein analysis. Nucleic acid analysis. Enzymatic analysis. Literature. IMMUNOLOGICAL METHODS. Antibodies. Antibody antigen interactions. Literature. BIOPHYSICAL METHODS. Spectroscopy. Scattering techniques. Interactions. Determination of structure. Literature. MATHEMATICAL METHODS. Statistics. Quantitative evaluation of experimental results. Sequence analysis. Literature. QUANTITATIVE ANALYSIS OF BIOCHEMICAL DATA. Introduction. Applications. Guide to the compact disc. Appendix I: SI Units. Appendix II: Conversions into SI Units. Index.
Metabolism of the calcium antagonist, mibefradil (POSICOR™, Ro 40-5967). Part II. Metabolism in hepatic microsomes from rat, marmoset, cynomolgus monkey, rabbit and man (1997)

1. The calcium antagonist, mibefradil, is converted to some 30 metabolites after incubation with hepatic microsomes from the rat, marmoset, cynomolgus monkey, rabbit and man. 2. The wide inter-species differences in metabolic profile stem mainly from variations in the activity of the microsomal esterase, which hydrolyses the ester side-chain of mibefradil to give the alcohol metabolite, Ro 40-5966. Hydrolysis is especially marked in the cynomolgus monkey and rabbit, less in man and least in the rat and marmoset. 3. The biotransformation of this alcohol metabolite by cytochromes P450 is more facile than that of the parent compound, leads to fewer metabolites and the metabolic profiles in all species are similar. 4. The most important cytochrome P450-mediated metabolic process in microsomes in all species is hydroxylation at the benzylic carbon atom of the tetrahydronaphthyl group; further oxidation of the resultant secondary alcohol to a ketone also occurs. These reactions indicate the route of the biosynthetic pathway which leads to the major, naphthyl-glucuronide metabolites previously isolated from rat bile. 5. Dealkylation of the tertiary amino group is also important and leads to compounds lacking either the N-methyl group or the propylbenzimidazole moiety. 6. Hydroxylation of the benzimidazole ring at both the 4- and 5-positions is largely restricted to mibefradil and does not occur to a significant extent with Ro 40-5966.
The Premium Economizer: An Idea Whose Time Has Come (2006)

Several field studies have found that more than half of outside air economizers on packaged rooftop cooling units are not providing optimal savings, either because dampers or controls have failed, changeover is set incorrectly, or the improper type of controls for the local climate have been installed. Analysis of economizer operation indicates that, at best, only onethird of potential savings is being achieved. Eugene Water & Electric Board (EWEB) has developed “premium” economizer requirements that result in increased economizer savings in the field. Meeting the stricter requirements is rewarded by larger utility rebates. A brief literature review of packaged rooftop cooling unit studies is followed by results from a full cooling season field test of ten packaged units equipped with either standard or premium outside air economizers. Extended field monitoring shows that properly operating premium economizers provide more savings than standard economizers. Results also show that better commissioning is required to improve economizer reliability. Three years of utility program experience in providing rebates for a “premium” economizer are also discussed.
Mammalian SWI-SNF Complexes Contribute to Activation of the hsp70 Gene (2000)

ATP-dependent chromatin-remodeling complexes are conserved among all eukaryotes and function by altering nucleosome structure to allow cellular regulatory factors access to the DNA. Mammalian SWI-SNF complexes contain either of two highly conserved ATPase subunits: BRG1 or BRM. To identify cellular genes that require mammalian SWI-SNF complexes for the activation of gene expression, we have generated cell lines that inducibly express mutant forms of the BRG1 or BRM ATPases that are unable to bind and hydrolyze ATP. The mutant subunits physically associate with at least two endogenous members of mammalian SWI-SNF complexes, suggesting that nonfunctional, dominant negative complexes may be formed. We determined that expression of the mutant BRG1 or BRM proteins impaired the ability of cells to activate the endogenous stress response gene hsp70 in response to arsenite, a metabolic inhibitor, or cadmium, a heavy metal. Activation of hsp70 by heat stress, however, was unaffected. Activation of the heme oxygenase 1 promoter by arsenite or cadmium and activation of the cadmium-inducible metallothionein promoter also were unaffected by the expression of mutant SWI-SNF components. Analysis of a subset of constitutively expressed genes revealed no or minimal effects on transcript levels. We propose that the requirement for mammalian SWI-SNF complexes in gene activation events will be specific to individual genes and signaling pathways.
The role of tea and tea flavonoids in cardiovascular health (2006)

Consumption of green or black tea has been inversely associated with the development and progression of cardiovascular diseases. In this review, the current knowledge about protective effects of tea and tea constituents, particularly flavonoids, on the cardiovascular system is summarized. Underlying mechanisms for the beneficial effects of tea include vasculoprotective, antioxidative, antithrombogenic, anti-inflammatory, and lipid-lowering properties of tea flavonoids. Although promising experimental data on beneficial effects of tea in various cardiovascular diseases are available, results of clinical studies in humans are not uniform. A number of factors are discussed which may contribute to inconsistent data in humans. Overall, tea represents a promising tool for the prevention and treatment of cardiovascular disorders.
Apolipoprotein genetic variation and human disease (1988)

Atherosclerosis is the major public health problem in much of the world today. The information summarized in this review, based on the recognized apolipoprotein structural variants appreciated at both the protein and gene levels, indicates that apolipoprotein genetic variation plays a major role in determining human genetic susceptibility to this disease. With the use of cloned apolipoprotein genes, it should, in the near future, be possible to determine how their expression is regulated; this should provide insight into other classes of mutations of a regulatory nature that might have clinical significance. In addition, the many association and linkage studies currently being undertaken will provide the rationale for cloning defective alleles and determining specific causative mutations. Both structural and regulatory mutations can then be described either with restriction enzymes and Southern blotting or by direct oligonucleotide hybridization techniques in the general population. This will allow the identification of presymptomatic atherosclerosis-susceptible individuals who would be targets for primary preventative therapy.
Tamoxifen-associated eye disease. A review. (1996)

Ocular toxicity is uncommon in the current clinical setting of long-term, low-dose tamoxifen use. Physicians should be aware of the potential for ocular toxicity among patients receiving the drug and should assure appropriate surveillance and prompt evaluation of visual complaints.
Mapping the mouse ZP3 combining site for sperm by exon swapping and site-directed mutagenesis. (1995)

During fertilization in mice, sperm bind to mouse ZP3 (mZP3), a M(r) approximately 83,000 glycoprotein present in the ovulated egg extracellular coat, or zona pellucida. Sperm recognize and bind to specific serine/threonine-linked (O-linked) oligosaccharides present at the mZP3 combining site for sperm. Binding to mZP3 induces sperm to undergo a form of exocytosis, the acrosome reaction. To map the mZP3 combining site for sperm, we examined the effect of exon swapping and site-directed mutagenesis on the glycoprotein's two activities, sperm binding and induction of the acrosome reaction. Stably transfected embryonal carcinoma cell lines were established that synthesized recombinant glycoproteins and secreted them into the culture medium. The glycoproteins were partially purified from culture medium and assayed for sperm-binding and acrosome reaction-inducing activities. Results of these assays suggest that glycosylation of one or more of five serine residues, clustered together in a polypeptide region encoded by mZP3 gene exon 7, is required for activity. Interestingly, this polypeptide region exhibits considerable sequence divergence during evolution and may be related to the proposed role for oligosaccharides in species-specific gamete adhesion during mammalian fertilization.
Overexpression of Plasma Membrane-associated Sialidase Attenuates Insulin Signaling in Transgenic Mice (2003)

Plasma membrane-associated sialidase is a key enzyme for ganglioside hydrolysis, thereby playing crucial roles in regulation of cell surface functions. Here we demonstrate that mice overexpressing the human ortholog (NEU3) develop diabetic phenotype by 18-22 weeks associated with hyperinsulinemia, islet hyperplasia, and increased beta-cell mass. As compared with the wild type, insulin-stimulated phosphorylation of the insulin receptor (IR) and insulin receptor substrate I was significantly reduced, and activities of phosphatidylinositol 3-kinase and glycogen synthase were low in transgenic muscle. IR phosphorylation was already attenuated in the younger mice before manifestation of hyperglycemia. Transient transfection of NEU3 into 3T3-L1 adipocytes and L6 myocytes caused a significant decrease in IR signaling. In response to insulin, NEU3 was found to undergo tyrosine phosphorylation and subsequent association with the Grb2 protein, thus being activated and causing negative regulation of insulin signaling. In fact, accumulation of GM1 and GM2, the possible sialidase products in transgenic tissues, caused inhibition of IR phosphorylation in vitro, and blocking of association with Grb2 resulted in reversion of impaired insulin signaling in L6 cells. The data indicate that NEU3 indeed participates in the control of insulin signaling, probably via modulation of gangliosides and interaction with Grb2, and that the mice can serve as a valuable model for human insulin-resistant diabetes.
WHT/OFDM - an improved OFDM transmission method for selective fading channels (2002)

The application of the Walsh-Hadamard transformation is proposed as the means to combat the influence of selective fading on the OFDM system performance. Substantial improvement as compared with the OFDM system applying the adaptive equalizer at the receiver is shown by simulation.
The relationship between the cone photoreceptor mosaic and visual acuity in normal observers and blue cone monochromat carriers (2010)

Purpose: Determine the relationship between the photoreceptor mosaic and visual acuity (VA) in normal observers and blue cone monochromat (BCM) carriers. Methods: The adaptive optics scanning laser ophthalmoscope (AOSLO) was used to project an AO-corrected stimulus onto the retina of 9 observers (6 normal; 3 BCM carriers). High contrast photopic letter acuity was measured using a 4AFC tumbling E test at the preferred retinal locus (PRL) and temporal parafovea. Stimuli were presented at 840 or 658 nm with simultaneous photoreceptor imaging at 840 nm. Results: Cones were well resolved at the PRL for all BCM carriers and two normal observers. BCM carriers had lower cone density and greater cone spacing than normal observers. Voronoi analysis revealed irregular cone packing and cone loss in BCM carriers. Power spectra of mosaic images confirmed irregular packing, with no Yellot's ring at test locations of BCM carriers. BCM carriers performed worse in the VA task than normal observers. VA was better than or matched the Nyquist limit for all normal observers and one BCM carrier at the PRL, but worse than the Nyquist limit beyond the PRL. Conclusions: VA is not sampling limited (ie. limited by the spacing of rows of photoreceptors) beyond the PRL. Cone spacing closely matches VA outside the PRL, but there is a trend toward underperformance (VA drops faster than spacing). Although these BCM carriers had normal VA tested conventionally, their performance with AO-correction shows that AO-corrected tests may reveal cone loss before such loss is detectable with conventional methods. A large discrepancy between cone spacing and VA in two BCM carriers may indicate a post-receptoral deficit.
Development of Fiber Optic and Electrochemical pH Sensors to Monitor Brain Tissue (2000)

This article describes fiber optic and electrochemical pH sensors that could become part of a therapeutic arsenal to quickly and aggressively treat stroke victims as well as people who have suffered brain trauma. The fiber optic sensor design was based on the immobilization of a pH-sensitive dye, seminaphthorhodamine-1 carboxylate (SNARF-1C), onto the end of a 125-microm-diameter silica optical fiber using the sol-gel method. A miniature bench-top fluorimeter system was developed for use with the optical fiber to obtain pH measurements. The electrochemical sensor was based on sputter-coated iridium oxide thin films. Linear and reproducible responses for both sensors were obtained in human blood with pH varying between 6.8 ato 8.0, which encompasses the clinically relevant range. In vivo studies were also performed and results indicated that both types of sensors tracked pH with very little drift.
Comparison of Roche Cell-Free DNA collection Tubes to Streck Cell-Free DNA BCT s for sample stability using healthy volunteers (2019)

The findings of this study indicate that the Roche Cell-Free DNA Collection Tubes<sup>®</sup> are a suitable alternative for sample collection and storage at room temperature, albeit for a duration of less than 7 days.