gebhart/patrepeval huggingface dataset:
Filamentary plasma discharge inside water : initiation and propagation of a plasma in a dense medium (2009)

This thesis presents an experimental study of a filamentary microplasma discharge inside liquid water. Such plasmas are used for liquid electrical insulations tests and for pollution control of water. Plasmas inside dense media are less understood than discharge inside gases. The purpose of the present thesis is to understand the physical mechanisms responsible for initiation and propagation of the discharge. A point to plane electrode configuration submerged in water has been constructed and was submitted to a high voltage pulse. Filaments inception and propagation and several discharges modes have been characterized with electrical measurements and time resolved nanosecond imaging. A Shadow diagnostic using 2 iCCDs was implemented to study the gas content and the shock wave emission from the discharge. The influence of the applied voltage polarity and the water conductivity was investigated. Spectroscopic measurements were performed on the OH emission band and the hydrogen emission lines. At positive high voltage the growth of the discharge begins by the nucleation of a microbubble at the needle electrode within a few microseconds at an applied voltage of 40kV, a hemispheric tree like filamentary structure grows at 3km/s during 100ns and is followed by the propagation of second filamentary structure ten time faster. This continuous propagation on a nanosecond time scale is followed by a stepwise propagation in case of distilled water. When the filaments reach the opposite electrode electrical breakdown occurs. At negative polarity the discharge is much slower 600m/s. The morphology of the gas cavity is driven by interface instability. Curiously, water conductivity has no influence at positive voltage polarity and even inhibits the propagation of the plasma filaments at negative voltage polarity. This thesis made possible to achieve a better understanding of the detailed phenomenology of electrical discharges in water.
Literature as Art, Literature as Text: Exploring the Power and Possibility of a Critical, Literacy‐Based Approach to Citizenship Education (2001)

(2001). Literature as Art, Literature as Text: Exploring the Power and Possibility of a Critical, Literacy‐Based Approach to Citizenship Education. Equity & Excellence in Education: Vol. 34, No. 2, pp. 62-74.
Performance limits of coded diversity methods for transmitter antenna arrays (1999)

Several aspects of the design and optimization of coded multiple-antenna transmission diversity methods for slowly time-varying channels are explored from an information-theoretic perspective. Both optimized vector-coded systems, which can achieve the maximum possible performance, and suboptimal scalar-coded systems, which reduce complexity by exploiting suitably designed linear precoding, are investigated. The achievable rates and associated outage characteristics of these spatial diversity schemes are evaluated and compared, both for the case when temporal diversity is being jointly exploited and for the case when it is not. Complexity and implementation issues more generally are also discussed.
Eosinophils in chronically inflamed human upper airway tissues express transforming growth factor beta 1 gene (TGF beta 1). (1992)

Transforming growth factor beta (TGF beta) is a multifunctional protein which has been suggested to play a central role in the pathogenesis of chronic inflammation and fibrosis. Nasal polyposis is a condition affecting the upper airways characterized by the presence of chronic inflammation and varying degrees of fibrosis. To examine the potential role of TGF beta in the pathogenesis of this condition, we investigated gene expression and cytokine production in nasal polyp tissues as well as in the normal nasal mucosa. By Northern blot analysis using a porcine TGF beta 1 cDNA probe, we detected TGF beta 1-specific mRNA in nasal polyp tissues, as well as in the tissue from a patient with allergic rhinitis, but not in the normal nasal mucosa. By the combination of tissue section staining with chromotrope 2R with in situ hybridization using the same TGF beta 1 probe, we found that approximately 50% of the eosinophils infiltrating the polyp tissue express the TGF beta 1 gene. In addition, immunohistochemical localization of TGF beta 1 was detected associated with extracellular matrix as well as in cells in the stroma. These results suggest that in nasal polyposis where eosinophils are the most prevalent inflammatory cell, TGF beta 1 synthesized by these cells may contribute to the structural abnormalities such as stromal fibrosis and basement membrane thickening which characterize this disease.
Systemic and Central Immunity in Alzheimer's Disease: Therapeutic Implications (2011)

Clinical pharmaceutical trials aimed at modulating the immune system in Alzheimer's Disease have largely focused on either dampening down central proinflammatory innate immunity or have manipulated adaptive immunity to facilitate the removal of centrally deposited beta amyloid. To date, these trials have had mixed clinical therapeutic effects. However, a number of clinical studies have demonstrated disturbances of both systemic and central innate immunity in Alzheimer's Disease and attention has been drawn to the close communication pathways between central and systemic immunity. This paper highlights the need to take into account the potential systemic effects of drugs aimed at modulating central immunity and the possibility of developing novel therapeutic approaches based on the manipulation of systemic immunity and its communication with the central nervous system.
Novel fatty acid beta-oxidation enzymes in rat liver mitochondria. I. Purification and properties of very-long-chain acyl-coenzyme A dehydrogenase. (1992)

Freeze-thawed rat liver mitochondria were extensively washed with potassium phosphate, pH 7.5, and the residue was extracted with 10 mM potassium phosphate, pH 7.5, 1% (w/v) sodium cholate, 0.5 M KCl. The four beta-oxidation enzyme activities of the washes and the last extract were assayed with substrates of various carbon chain lengths. Our data suggest that the last extract contains a novel acyl-CoA dehydrogenase and long-chain 3-hydroxyacyl-CoA dehydrogenase. A novel acyl-CoA dehydrogenase was purified. The molecular masses of the native enzyme and the subunit were estimated to be 150 and 71 kDa, respectively. One mole of enzyme contained 2 mole of FAD. These properties and immunochemical properties of the enzyme differed from those of three other acyl-CoA dehydrogenases: short-, medium-, and long-chain acyl-CoA dehydrogenases. Carbon chain length specificity of the enzyme differed from that of other acyl-CoA dehydrogenases. The enzyme was active toward CoA esters of long- and very-long-chain fatty acids, but not toward those of medium- and short-chain fatty acids. The specific enzyme activity was greater than 10 times that of long-chain acyl-CoA dehydrogenase when palmitoyl-CoA was used as substrate. We propose the name "very-long-chain acyl-CoA dehydrogenase" for this enzyme.
NP and L Proteins of Lymphocytic Choriomeningitis Virus (LCMV) Are Sufficient for Efficient Transcription and Replication of LCMV Genomic RNA Analogs (2000)

ABSTRACT The genome of lymphocytic choriomeningitis virus (LCMV) consists of two negative-sense single-stranded RNA segments, designated L and S. Both segments contain two viral genes in an ambisense coding strategy, with the genes being separated by an intergenic region (IGR). We have developed a reverse genetic system that allows the investigation of cis -acting signals and trans -acting factors involved in transcription and replication of LCMV. To this end, we constructed an LCMV S minigenome consisting of a negative-sense copy of the chloramphenicol acetyltransferase (CAT) reporter gene flanked upstream by the S 5′ untranslated region (UTR) and IGR and downstream by the S 3′ UTR. CAT expression was detected in LCMV-infected cells transfected with the minigenome RNA. Intracellular coexpression of the LCMV minigenome and LCMV L and NP proteins supplied from cotransfected plasmids driven by the T7 RNA polymerase provided by the recombinant vaccinia virus vTF7-3 resulted in high levels of CAT activity and synthesis of subgenomic CAT mRNA and antiminigenome RNA species. Thus, L and NP represent the minimal viral trans -acting factors required for efficient RNA synthesis mediated by LCMV polymerase.
A Control Volume Scheme for Flexible Grids in Reservoir Simulation (1997)

ABSTRACT The commonly used Cartesian and hybrid local grid refinements have the disadvantage that the base grid is always Cartesian, which makes it difficult to align along reservoir heterogeneities. Also, the locally orthogonal Voronoi and A;-orthogonal perpendicular bisector (PEBI) grids are only useful for isotropic or limited anisotropic permeability distributions. The finite-difference approach proposed in this paper overcomes limitations of existing flexible gridding schemes in modeling full, anisotropic and asymmetric permeability tensors and permeability heterogeneity. The new scheme assumes uniform properties inside control-volumes and it can be used for control volumes formed around vertices of triangles in two-dimensions and tetrahedrain three-dimensions. It can thus be used with Voronoi grids in two-dimensions, and median (i.e. CVFE) and boundary adapting grids (BAG) in two- and three-dimensions. Applications of Voronoi grids in three-dimensions are limited due to geometrical considerations. The proposed method can also be used with grids constructed to align along major reservoir heterogeneities, wells and streamlines. Several applications of this method for two- and three-dimensional problems are presented.
Ribozyme-mediated cleavage of the BCRABL oncogene transcript: in vitro cleavage of RNA and in vivo loss of P210 protein-kinase activity. (1993)

The t(9,22) chromosomal translocation generating the Philadelphia chromosome and the BCRABL oncogene has been shown both cytogenetically and molecularly to be the etiologic event in chronic myelogenous leukemia (CML). We have designed a ribozyme to cleave the BCRABL mRNA by targeting a GUU triplet adjacent to the junction of the c-BCR and c-ABL fused genes. This ribozyme efficiently cleaved BCRABL RNA transcripts as demonstrated by in vitro cleavage reactions. To determine the effect of constitutive expression of the ribozyme on the elimination of the BCRABL gene product, the ribozyme cDNA sequence was inserted into different retroviral expression vectors. Introduction of the recombinant retroviruses into the CML blast crisis cell-line K562, resulted in the elimination of the P210 protein-kinase activity in several single cell clones infected with the ribozyme expression cassette. Therefore BCR-ABL specific ribozymes may provide a potential genetic therapy for CML.
NEU1 Sialidase Expressed in Human Airway Epithelia Regulates Epidermal Growth Factor Receptor (EGFR) and MUC1 Protein Signaling (2012)

Epithelial cells (ECs) lining the airways provide a protective barrier between the external environment and the internal host milieu. These same airway epithelia express receptors that respond to danger signals and initiate repair programs. Because the sialylation state of a receptor can influence its function and is dictated in part by sialidase activity, we asked whether airway epithelia express catalytically active sialidase(s). Human primary small airway and A549 ECs expressed NEU1 sialidase at the mRNA and protein levels, and NEU1 accounted for >70% of EC sialidase activity. Blotting with Maackia amurensis and peanut agglutinin lectins established epidermal growth factor receptor (EGFR) and MUC1 as in vivo substrates for NEU1. NEU1 associated with EGFR and MUC1, and NEU1-EGFR association was regulated by EGF stimulation. NEU1 overexpression diminished EGF-stimulated EGFR Tyr-1068 autophosphorylation by up to 44% but enhanced MUC1-dependent Pseudomonas aeruginosa adhesion by 1.6-1.7-fold and flagellin-stimulated ERK1/2 activation by 1.7-1.9-fold. In contrast, NEU1 depletion increased EGFR activation (1.5-fold) and diminished MUC1-mediated bacterial adhesion (38-56%) and signaling (73%). These data indicate for the first time that human airway epithelia express catalytically active NEU1 sialidase that regulates EGFR- and MUC1-dependent signaling and bacterial adhesion. NEU1 catalytic activity may offer an additional level of regulation over the airway epithelial response to ligands, pathogens, and injurious stimuli.
Structure of Recombinant Human Serum Albumin from Pichia pastoris (1997)

The structure of recombinant human serum albumin derived from Pichia pastoris (rHSA) was analyzed in detail. Complete amino acid analysis was performed by the phenyl isothiocyanate precolumn labeling method. The amino terminal sequence was determined by the Edman degradation. The carboxyl terminal amino acid was determined by digestion with carboxypeptidase, and the carboxyl terminal peptide fragment was analyzed by electrospray mass spectrometry. The peptide fragments of rHSA digested with Lysylendopeptidase, Endoproteinase Glu-C, or Endoproteinase Asp-N were analyzed by electrospray mass spectrometry. The complete amino acid composition, the terminal sequences and the complete amino acid sequence of rHSA agreed with the primary structure deduced from its cDNA. The elution pattern of reduced and carboxymethylated rHSA digested with Lysylendopeptidase and the elution pattern of intact rHSA digested with pepsin were respectively similar to those of plasma-derived human serum albumin (pHSA). The pattern of CD spectrum of rHSA was identical in both shape and magnitude to that of pHSA. 1H-NMR spectra of rHSA and pHSA in deuterium oxide showed the same signal patterns in the observed region (delta 10.5-0.5 ppm). Cross peaks assigned to the alpha proton-beta proton of Asp-1 (delta 4.2/2.8 ppm) and the delta proton-epsilon proton of lysine residues (delta 2.8-3.2/1.4-2.0) showed the same cross peak patterns and chemical shifts in two-dimensional phase sensitive double-quantum filtered 1H-1H correlation spectra of rHSA and pHSA.
Ductal Lavage for Breast Cancer Risk Assessment (2002)

Background Effective chemoprevention is available for breast cancer, but it is associated with the potential for life-threatening adverse events. Accurate identification of women facing increased risk of breast cancer is therefore essential. Atypical hyperplasia is a histopathologic pattern that has been consistently associated with an elevated future risk of breast cancer. Methods The literature was reviewed to assess the strength of the association between atypical hyperplasia and breast cancer. The rationale for developing a nonsurgical modality to document the presence of atypia is discussed. Results Ductal lavage identifies atypical hyperplasia by retrieving epithelial cells shed into the ductal system with a specially designed catheter. Women with clinical evidence of increased breast cancer risk may consider ductal lavage as a means of determining whether abnormal proliferative activity is occurring in their breasts at a given point in time from ducts yielding fluid. Conclusions Ductal lavage is a minimally invasive procedure that facilitates the detection of atypia via retrieval of breast ductal fluid that can be evaluated cytologically. It can facilitate the selection of women who may benefit from breast cancer risk reduction intervention.
Properties of MHC Class I Presented Peptides That Enhance Immunogenicity (2013)

T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4-6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses.
Parallel Detection of Autoantibodies with Microarrays in Rheumatoid Diseases (2004)

This microarray system provides results similar to those by conventional methods. Assessment of the diagnostic accuracy of the system remains to be done.
Assessment of Osteoporosis at Autopsy: Mechanical Methods Compared to Radiological and Histological Techniques (1991)

Osteoporosis is a common problem in the elderly female population and pathological fractures are a frequent complication, but how should the pathologist assess the severity of the disease at autopsy? In this study we have compared subjective, semi-quantitative assessments of rib fracturability, vertebral compressibility, Singh index and histomorphometric methods against a 'gold standard' assessment, namely the force required to fracture the femoral neck. We have shown good correlations between rib fracturability. Singh index and the standard chosen. Poor correlation was shown between histomorphometric techniques and the standard. Our findings suggest that gross rib fracturability is a good indicator of osteoporosis in as far as bone fragility is an indicator of the severity of osteoporosis. However, as the population under examination was small, further studies in this area are clearly warranted in order to extend these findings.
Citrobacter freundii produces an 18-amino-acid heat-stable enterotoxin identical to the 18-amino-acid Escherichia coli heat-stable enterotoxin (ST Ia) (1989)

We purified and sequenced the heat-stable enterotoxin produced by Citrobacter freundii. The toxin was detected during purification by reaction with monoclonal antibody to Escherichia coli heat-stable enterotoxin. The C. freundii toxin amino acid sequence was identical to that of the 18-amino-acid heat-stable enterotoxin (STa) produced by toxigenic E. coli.
Crystal structure of inorganic pyrophosphatase from Thermus thermophilus (1994)

The 3-dimensional structure of inorganic pyrophosphatase from Thermus thermophilus (T-PPase) has been determined by X-ray diffraction at 2.0 A resolution and refined to R = 15.3%. The structure consists of an antiparallel closed beta-sheet and 2 alpha-helices and resembles that of the yeast enzyme in spite of the large difference in size (174 and 286 residues, respectively), little sequence similarity beyond the active center (about 20%), and different oligomeric organization (hexameric and dimeric, respectively). The similarity of the polypeptide folding in the 2 PPases provides a very strong argument in favor of an evolutionary relationship between the yeast and bacterial enzymes. The same Greek-key topology of the 5-stranded beta-barrel was found in the OB-fold proteins, the bacteriophage gene-5 DNA-binding protein, toxic-shock syndrome toxin-1, and the major cold-shock protein of Bacillus subtilis. Moreover, all known nucleotide-binding sites in these proteins are located on the same side of the beta-barrel as the active center in T-PPase. Analysis of the active center of T-PPase revealed 17 residues of potential functional importance, 16 of which are strictly conserved in all sequences of soluble PPases. Their possible role in the catalytic mechanism is discussed on the basis of the present crystal structure and with respect to site-directed mutagenesis studies on the Escherichia coli enzyme. The observed oligomeric organization of T-PPase allows us to suggest a possible mechanism for the allosteric regulation of hexameric PPases.
Small-Ring Compounds. XLV. Influence of Vinyl and Phenyl Substituents on the Interconversion of Allylcarbinyl-Type Grignard Reagents1 (1966)

Equilibration of the α and β positions in y,y-diphenylallylcarbinylmagnesium bromide was complete after 5 hr at room temperature. Less than 0.3% of the isomeric cyclopropylcarbinyl derivative, however, is in equilibrium with the ring-opened species. While reactions of the Grignard reagents normally expected to have anionic-type mechanisms were found to lead to allylcarbinyl products only, substantial amounts of cyclic products were formed with molecular oxygen.
p‐Hydroxyphenylacetate decarboxylase from Clostridium difficile (2001)

The human pathogenic bacterium Clostridium difficile is a versatile organism concerning its ability to ferment amino acids. The formation of p-cresol as the main fermentation product of tyrosine by C. difficile is unique among clostridial species. The enzyme responsible for p-cresol formation is p-hydroxyphenylacetate decarboxylase. The enzyme was purified from C. difficile strain DMSZ 1296(T) and initially characterized. The N-terminal amino-acid sequence was 100% identical to an open reading frame in the unfinished genome of C. difficile strain 630. The ORF encoded a protein of the same size as the purified decarboxylase and was very similar to pyruvate formate-lyase-like proteins from Escherichia coli and Archaeoglobus fulgidus. The enzyme decarboxylated p-hydroxyphenylacetate (K(m) = 2.8 mM) and 3,4-dihydroxyphenylacetate (K(m) = 0.5 mM). It was competitively inhibited by the substrate analogues p-hydroxyphenylacetylamide and p-hydroxymandelate with K(i) values of 0.7 mM and 0.48 mM, respectively. The protein was readily and irreversibly inactivated by molecular oxygen. Although the purified enzyme was active in the presence of sodium sulfide, there are some indications for an as yet unidentified low molecular mass cofactor that is required for catalytic activity in vivo. Based on the identification of p-hydroxyphenylacetate decarboxylase as a novel glycyl radical enzyme and the substrate specificity of the enzyme, a catalytic mechanism involving ketyl radicals as intermediates is proposed.
Zinc oxide as an ozone sensor (2004)

This work presents a study of intrinsic zinc oxide thin film as ozone sensor based on the ultraviolet (UV) photoreduction and subsequent ozone re oxidation of zinc oxide as a fully reversible process performed at room temperature. The films analyzed were produced by spray pyrolysis, dc and rf magnetron sputtering. The dc resistivity of the films produced by rf magnetron sputtering and constituted by nanocrystallites changes more than eight orders of magnitude when exposed to an UV dose of 4mW∕cm2. On the other hand, porous and textured zinc oxide films produced by spray pyrolysis at low substrate temperature exhibit an excellent ac impedance response where the reactance changes by more than seven orders of magnitude when exposed to the same UV dose, with a response frequency above 15kHz, thus showing improved ozone ac sensing discrimination.