gebhart/patrepeval huggingface dataset:
Antibody-inducing properties of a prototype bivalent herpes simplex virus/enterotoxigenic Escherichia coli DNA vaccine (2003)

The antibody-inducing properties of a bacterial/viral bivalent DNA vaccine (pRECFA), expressing a peptide composed of N- and C-terminal amino acid sequences of the herpes simplex virus type 1 (HSV-1) glycoprotein D (gD) fused with an inner segment encoding the major structural subunit of enterotoxigenic Escherichia coli (ETEC) CFA/I fimbriae (CFA/I), was evaluated in BALB/c mice following intramuscular immunization. The bivalent pRECFA vaccine elicited serum antibody responses, belonging mainly to the IgG2a subclass, against both CFA/I and HSV gD proteins. pRECFA-elicited antibody responses cross-reacted with homologous and heterologous ETEC fimbrial antigens as well as with type 1 and type 2 HSV gD proteins, which could bind and inactivate intact HSV-2 particles. On the other hand, CFA/I-specific antibodies could bind but did not neutralize the adhesive functions of the bacterial CFA/I fimbriae. In spite of the functional restriction of the antibodies targeting the bacterial antigen, the present evidence suggests that fusion of heterologous peptides to the HSV gD protein represents an alternative for the design of bivalent DNA vaccines able to elicit serum antibody responses.
Recombinant TCR Ligand Induces Tolerance to Myelin Oligodendrocyte Glycoprotein 35-55 Peptide and Reverses Clinical and Histological Signs of Chronic Experimental Autoimmune Encephalomyelitis in HLA-DR2 Transgenic Mice (2003)

In a previous study, we demonstrated that myelin oligodendrocyte glycoprotein (MOG)-35-55 peptide could induce severe chronic experimental autoimmune encephalomyelitis (EAE) in HLA-DR2(+) transgenic mice lacking all mouse MHC class II genes. We used this model to evaluate clinical efficacy and mechanism of action of a novel recombinant TCR ligand (RTL) comprised of the alpha(1) and beta(1) domains of DR2 (DRB1*1501) covalently linked to the encephalitogenic MOG-35-55 peptide (VG312). We found that the MOG/DR2 VG312 RTL could induce long-term tolerance to MOG-35-55 peptide and reverse clinical and histological signs of EAE in a dose- and peptide-dependent manner. Some mice treated with lower doses of VG312 relapsed after cessation of daily treatment, but the mice could be successfully re-treated with a higher dose of VG312. Treatment with VG312 strongly reduced secretion of Th1 cytokines (TNF-alpha and IFN-gamma) produced in response to MOG-35-55 peptide, and to a lesser degree purified protein derivative and Con A, but had no inhibitory effect on serum Ab levels to MOG-35-55 peptide. Abs specific for both the peptide and MHC moieties of the RTLs were also present after treatment with EAE, but these Abs had only a minor enhancing effect on T cell activation in vitro. These data demonstrate the powerful tolerance-inducing therapeutic effects of VG312 on MOG peptide-induced EAE in transgenic DR2 mice and support the potential of this approach to inhibit myelin Ag-specific responses in multiple sclerosis patients.
Estimation of $K$-Distribution Shape Parameter From Sonar Data: Sample Size Limitations (2009)

The <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distribution has been found to provide a good description of the probability density function (pdf) of the matched filter envelope of sonar signals backscattered from the seafloor. Furthermore, the scale and shape parameters that specify the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distribution, under certain assumptions, have been related to physical descriptors of the seafloor. Specifically, the shape parameter has been related to the number of contributing scatterers and the scale parameter has been related to the average scatterer size. There exists, therefore, the possibility of estimating seafloor scattering properties by determining the shape and scale parameters of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distribution that best fits the signal returned from the seafloor. This paper investigates the relationship between data sample size and the accuracy to which <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distribution shape parameter can be determined. Computer-generated random data are considered and two types of test are used to study the ease with which the data distribution can be described. The Kolmogorov-Smirnov (KS) test and a parameter estimation technique based on the method of moments are used and it is shown that, for these tests, the sample size necessary to distinguish reliably between Rayleigh- and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distributed data is proportional to the square of the shape parameter of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -distribution. It is also shown that the sample size necessary to determine the shape parameter to the nearest integer value is proportional to the shape parameter raised to the fourth power. This proportionality is shown to be consistent with consideration of Cramer-Rao lower bound (CRLB). The implications for practical sonar scenarios are discussed.
Microcomputer Buses and Links (1986)

Keywords: Ordinateurs ; Informatique Reference Record created on 2004-09-07, modified on 2016-08-08
B cell growth-promoting activity of recombinant human interleukin 4. (1987)

Human interleukin 4 (IL-4), also known as B cell stimulatory factor 1, is a T cell-derived glycoprotein consisting of 129 amino acids for which a cDNA has been recently isolated. IL-4 displays little or no B cell growth factor (BCGF) activity in the standard anti-IgM costimulatory assay using suboptimal concentrations of soluble anti-IgM antibody whereas the low m.w. BCGF is very active. When insolubilized anti-IgM was used as the costimulating agent, both IL-4 and the low m.w. BCGF were found to promote B cell proliferation. Human IL-4 is able to induce the proliferation of B lymphocytes preactivated for either 1 day with insolubilized anti-IgM antibody or for 3 days with Staphylococcus aureus strain Cowan I. However, IL-4 is poorly mitogenic for B cells preactivated for 1 day with the Staphylococcus strain whereas the low m.w. BCGF strongly enhances the proliferation of these B cells. These two findings demonstrate that the preactivation signal necessary to induce human B cells to proliferate in response to IL-4 is critical. The increased tritiated thymidine ([3H]dThd) uptake in preactivated B cell cultures with IL-4 reflects cel proliferation because cell cycle analysis demonstrates that IL-4 induces activated B cells to enter the S and G2/M phases of the cell cycle and the addition of IL-4 to preactivated B cell cultures permits the recovery of three- to fourfold more B cells after 4 days of culture. IL-4 and the low m.w. BCGF act in concert to induce the proliferation of anti-IgM-preactivated B cells as demonstrated by [3H]dThd uptake and cell cycle analysis. In striking contrast to the demonstrated antagonistic effect of interferon-gamma on the IL-4-induced expression of the low affinity receptor for IgE (Fc epsilon RL/CD23), on B cells, it was found that interferon-gamma enhanced the IL-4-induced proliferation of anti-IgM-preactivated B cells. Finally, it was found that IL-4 had to be present continuously during the culture period to exert an optimal growth-promoting effect on B cell blasts. As a conclusion, IL-4 is able to induce the proliferation of an appropriately activated subpopulation of human B cells.
Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid (1997)

The genetic basis of heterosis was investigated in an elite rice hybrid by using a molecular linkage map with 150 segregating loci covering the entire rice genome. Data for yield and three traits that were components of yield were collected over 2 years from replicated field trials of 250 F(2:3) families. Genotypic variations explained from about 50% to more than 80% of the total variation. Interactions between genotypes and years were small compared with the main effects. A total of 32 quantitative trait loci (QTLs) were detected for the four traits; 12 were observed in both years and the remaining 20 were detected in only one year. Overdominance was observed for most of the QTLs for yield and also for a few QTLs for the component traits. Correlations between marker heterozygosity and trait expression were low, indicating that the overall heterozygosity made little contribution to heterosis. Digenic interactions, including additive by additive, additive by dominance, and dominance by dominance, were frequent and widespread in this population. The interactions involved large numbers of marker loci, most of which individually were not detectable on single-locus basis; many interactions among loci were detected in both years. The results provide strong evidence that epistasis plays a major role as the genetic basis of heterosis.
Chemical modification and photograft polymerization upon expanded poly(tetrafluoroethylene) (1998)

Poly(tetrafluoroethylene) (PTFE) films were surface-modified by employing a reaction solution of benzophenone and sodium hydride in anhydrous dimethylformamide at a temperature of 150 degrees C for 12 h. Electron spectroscopy for chemical analysis (ESCA) showed defluorination, oxygen incorporation, and extensive unsaturation within the treated PTFE surfaces. The suitably of these reduced PTFE films as substrates for graft polymerization was initially assessed via photograft polymerization of the sodium salt of styrenesulfonic acid (SS-Na), which permitted unequivocal surface analysis by the introduction of a new atom, as well as poly(ethylene glycol) monoacrylate (PEG-Ac). All photograpt polymerization was performed employing ultraviolet irradiation with 2,2-dimethoxy-2-phenylacetophenone as an initiator. Photograft polymerization of SS-Na was verified by further reduction of fluorine atomic content and the appearance of new sulfur and sodium atomic peaks on ESCA survey spectra, and that of PEG-Ac was verified by further reduction of fluorine atomic content and increase of atomic percent ratio of O/C from ESCA survey spectra as well as appearance of a new ester peak on high resolution ESCA C 1s spectra. Dynamic water contact angles on reduced and PEG-Ac photograft polymerized films were measured and showed that the PTFE film surface became more hydrophilic after reduction (from 120 to 89 deg) and the reduced film became more hydrophilic after photograft polymerization with PEG-Ac (from 89 to 36 deg). Modification of the complete surface of expanded PTFE (ePTFE), i.e. of the lumenal, outside and pore surfaces, was performed by employing the reaction described above, except at 105 degrees C for 1 day, followed by photograft polymerization of PEG-Ac. ESCA was performed on the superficial surfaces (i.e. the lumen and exterior) as well as on cross-sections of the ePTFE to permit analysis of the pore surfaces. This analysis showed that both the initial surface reduction and subsequent photograft polymerization were successful as indicated from F/C and O/C atomic percent ratios from ESCA survey spectra, from overall peaks shapes of high resolution ESCA C 1s spectra and from generation of new ester peaks on high resolution ESCA C 1s spectra of ePTFE graft polymerized with PEG-Ac, which demonstrated an O/C atomic percent ratio close to that of PEG-Ac homopolymer. Low voltage scanning electron microscopy confirmed minimal morphological damage to the ePTFE microstructure after reduction and graft polymerization. The approach explored thus provides a means for modulation of biological interactions at ePTFE surfaces with only minimal modification of material morphology, with some surface texture appearing on a length scale of 50-100 nm.
Dynamics of cell wall structure inSaccharomyces cerevisiae (2002)

The cell wall of Saccharomyces cerevisiae is an elastic structure that provides osmotic and physical protection and determines the shape of the cell. The inner layer of the wall is largely responsible for the mechanical strength of the wall and also provides the attachment sites for the proteins that form the outer layer of the wall. Here we find among others the sexual agglutinins and the flocculins. The outer protein layer also limits the permeability of the cell wall, thus shielding the plasma membrane from attack by foreign enzymes and membrane-perturbing compounds. The main features of the molecular organization of the yeast cell wall are now known. Importantly, the molecular composition and organization of the cell wall may vary considerably. For example, the incorporation of many cell wall proteins is temporally and spatially controlled and depends strongly on environmental conditions. Similarly, the formation of specific cell wall protein-polysaccharide complexes is strongly affected by external conditions. This points to a tight regulation of cell wall construction. Indeed, all five mitogen-activated protein kinase pathways in bakers' yeast affect the cell wall, and additional cell wall-related signaling routes have been identified. Finally, some potential targets for new antifungal compounds related to cell wall construction are discussed.
Prognostic Factors for Survival in Previously Treated Patients With Metastatic Renal Cell Carcinoma (2004)

Treatment with novel agents during a clinical trial is indicated for patients with metastatic RCC after progression to cytokine treatment. Three prognostic factors for predicting survival were used to categorize patients into risk groups. These risk categories can be used in clinical trial design and interpretation.
Plasma functionalized PDMS microfluidic chips: towards point-of-care capture of circulating tumor cells (2011)

The main challenge in the isolation of circulating tumor cells (CTCs) resides in their extreme rarity in blood. Here we report on the design of efficient and disposable microfluidic CTC capture devices based on the plasma functionalization of PDMS and its subsequent conjugation with the anti-epithelial-cell adhesion-molecule (EpCAM) mAb. Model studies on planar surfaces demonstrated excellent immuno-specificity of cancer-cell capture using NCI H69 small-cell lung cancer cells and SK-Br-3 breast cancer cells. Taking advantage of the transparency of the PDMS device, direct observation of the capture events on the internal 3D microstructure of the device could be achieved. At a flow rate of 16 μL min−1, an overall capture efficiency of 80 to 90% is determined in cell-spiking experiments in PBS. In accordance with direct microscopic observations, an increased flow rate (48 μL min−1) only has a minor effect (30% reduction) on cell-capture efficiency. Capture efficiency of the device using cancer cells spiked in whole blood is above 70%. The combination of soft lithography and plasma-based functionalization described in this work enables the facile fabrication of efficient and disposable CTC capture devices based on PDMS, which could facilitate the transition of this new technology into the clinical environment.
Receptor Binding, Endocytosis, and Mitogenesis of Insulin‐Like Growth Factors I and II in Fetal Rat Brain Neurons (1991)

Cell surface binding, internalization, and biological effects of insulin-like growth factors (IGFs) I and II have been studied in primary neuronal cultures from developing rat brain (embryonic day 15). Two types of IGF binding sites are present on the cell surface. The IGF-I receptor alpha-subunit (Mr 125,000) binds IGF-I with a KD of 1 nM and IGF-II with 10 times lower affinity. The mannose-6-phosphate (Man-6-P)/IGF-II receptor (Mr 250,000) binds IGF-II with a KD of 0.5 nM and IGF-I with 100 times lower affinity. Surface-bound IGF-I and IGF-II are internalized by their respective receptors binding and internalization of IGF-II but not those of IGF-I. Neuronal synthesis of RNA and DNA is increased twofold by IGF-I with 10 times higher potency than IGF-II. Antibody 3637, which blocks receptor binding of IGF-II, has no effect on the DNA response to IGF-I or IGF-II. Double immunocytochemical staining with antibodies to bromodeoxyuridine and neurofilament shows that greater than 80% of the bromodeoxyuridine-positive cells become neurofilament positive. It is concluded that IGF-I and IGF-II bind to two receptors on the surface of neuronal precursor cells that mediate endocytosis and degradation of IGF-I and IGF-II. Proliferation of neuronal precursor cells is stimulated by IGF-I and IGF-II via activation of the IGF-I receptor.
Protein engineering of Bacillus megaterium CYP102 (2001)

Cytochrome P450 (CYP) enzymes are involved in activating the carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) in mammals, but they are also utilized by microorganisms for the degradation of these hazardous environmental contaminants. Wild-type CYP102 (P450(BM-3)) from Bacillus megaterium has low activity for the oxidation of the PAHs phenanthrene, fluoranthene and pyrene. The double hydrophobic substitution R47L/Y51F at the entrance of the substrate access channel increased the PAH oxidation activity by up to 40-fold. Combining these mutations with the active site mutations F87A and A264G lead to order of magnitude increases in activity. Both these mutations increased the NADPH turnover rate, but the A264G mutation increased the coupling efficiency while the F87A mutation had dominant effects in product selectivity. Fast NADPH oxidation rates were observed (2250 min-1 for the R47L/Y51F/F87A mutant with phenanthrene) but the coupling efficiencies were relatively low (< 13%), resulting in a highest substrate oxidation rate of 110 min-1 for fluoranthene oxidation by the R47L/Y51F/A264G mutant. Mutation of M354 and L437 inside the substrate access channel reduced PAH oxidation activity. The PAHs were oxidized to a mixture of phenols and quinones. Notably mutants containing the A264G mutation showed some similarity to mammalian CYP enzymes in that some 9,10-phenanthrenequinone, the K-region oxidation product from phenanthrene, was formed. The results suggest that CYP102 mutants could be useful models for PAH oxidation by mammalian CYP enzymes, and also potentially for the preparation of novel PAH bioremediation systems.
The Association of Occult Amniotic Fluid Infection With Gestational Age and Neonatal Outcome Among Women in Preterm Labor (1992)

To evaluate the relationships between gestational age, neonatal outcome, and amniotic fluid (AF) bacteria, we obtained AF from women with intact membranes in idiopathic preterm labor. Positive cultures were obtained from 20 (19%) of 105 women. The frequency of positive cultures was inversely related to gestational age: 23-26 weeks, nine of 20; 27-30 weeks, four of 24; and 31-34 weeks, seven of 61 (Χ2 for trend, P < .001).Fusobacterium nucleatum, Bacteroides ureolyticus,andUreaplasma urealyticumwere the most common isolates. Facultative and anaerobic bacteria were more commonly isolated from women at less than 30 weeks' gestation, andUreaplasma urealyticumwas commonly isolated at greater than 30 weeks' gestation. Forty percent of the patients identified as having positive AF facultative and anaerobic cultures by the research laboratory had negative cultures in the clinical laboratory. Clinical characteristics and maternal white blood cell count and differential did not differ between women with and without positive cultures. Elevated C-reactive protein levels and a positive AF Gram stain were the two most sensitive and specific methods to predict positive AF cultures. Women with positive cultures delivered a median of 1.0 day after enrollment, compared with 28.5 days for women with negative cultures. The median gestational age at delivery for women with positive cultures was 27.5 weeks, and the median birth weight was 866 g. Positive AF cultures were associated with respiratory distress syndrome, bronchopulmonary dysplasia, and neonatal death. If occult AF infection among women in preterm labor is a treatable cause of preterm birth, then treatment could markedly reduce both perinatal morbidity and mortality.(Obstet Gynecol 1992;79:351-7)
Methods in Bioengineering: Biomicrofabrication and Biomicrofluidics (2009)

Microfabrication Techniques for Microfluidic Devices. Micropumping and Microvalving. Micromixing and Microfluidic Devices. On-Chip Electrophoresis and Isoelectric Focusing Methods for Quantitative Biology. Electrowetting. Dieletrophoresis for Particle and Cell Manipulations. Optical Microfluidics for Molecular Diagnostics. Neutrophil Chemotaxis Assay from Whole Blood Samples. Microfluidics Immunoassays. Droplet-Based Microfluidics by Shear-Driven Microemulsions. MicroFACS Systems. Optical Flow Characterization - Micro Particle Image Velocimetry (uPIV). Microtubule Motors in Microfluidics.
Enhanced Oil Recovery with Downhole Vibration Stimulation (2001)

Abstract The use of vibration to improve oil recovery has long been investigated. The background for this novel technology is reviewed along with the project rationalizations, designs considerations, and measurements performed in advance of a downhole vibration stimulation field test. This field demonstration will pilot test the potential of downhole vibration to enhance oil recovery from a shallow oilfield in Osage County, Oklahoma. The project is supported by the Department of Energy (DOE), Seismic Recovery LLC, Phillips Petroleum Co., and Grand Resources, Inc. Recent literature has reported successful vibration stimulation in shallow reservoirs with high water oil ratios (WOR). Osage County has, like many areas of the United States, numerous old fields under waterflood, with many wells producing marginal oil with substantial water production.
Platinum Monolayer Electrocatalysts for O2Reduction:  Pt Monolayer on Pd(111) and on Carbon-Supported Pd Nanoparticles (2004)

The kinetics of oxygen reduction was studied in acid solutions on Pt monolayers deposited on a Pd(111) surface and on carbon-supported Pd nanoparticles using the rotating disk-ring electrode technique. These electrocatalysts were prepared by a new method for depositing Pt monolayers involving the galvanic displacement by Pt of an underpotentially deposited Cu monolayer on a Pd substrate and characterized by scanning tunneling and transmission electron microscopies. The kinetics of O2 reduction shows a significant enhancement at Pt monolayers on Pd(111) and Pd nanoparticle surfaces in comparison with the reaction on Pt(111) and Pt nanoparticles. The four-electron reduction, with a first-charge transfer-rate determining step, is operative on both surfaces. The observed increase in the catalytic activity of Pt monolayer surfaces compared with Pt bulk and nanoparticle electrodes may reflect decreased formation of PtOH. An enhanced atomic scale surface roughness and low coordination of some atoms may contribute to the observed activity. The results illustrate that placing a Pt monolayer on a suitable metal nanoparticle substrate is an attractive way of designing better O2 reduction electrocatalysts. Also, by using this method the Pt content is reduced to very low levels. The Pt mass-specific activity of the Pt/Pd/C electrode is 5−8 times higher than that of the Pt/C electrocatalyst. The noble metal (Pt + Pd) mass-specific activity is two times higher than that of Pt/C.