gebhart/patrepeval huggingface dataset:
Accumulation of hyaluronan and tissue edema in experimental myocardial infarction. (1991)

Experimental myocardial infarction was induced in rats. The myocardial accumulation of hyaluronan (HA) and water during the development of infarction was measured. The extractable HA content of the infarcted area increased progressively from day 1 and on day 3 reached a threefold increase compared with the HA amounts in myocardium of sham operated controls. The relative water content of infarcted areas also increased progressively reaching a maximum value by day 3 and was strongly correlated with the HA accumulation. Affinity histochemistry visualized a thin rim of HA in the endoperimysium in healthy myocardium. By day 2 an interstitial edema with inflammatory cells was apparent. The widened endoperimysium stained extensively for HA. By its water-binding ability, interstitial accumulation of HA will contribute to the interstitial edema in infarcted myocardial tissue. An interstitial edema is likely to influence the electromechanical characteristics of the myocardium and facilitate reentry phenomena due to a loss of contact between muscle cells. The edema also induces an increased extracellular pressure and an altered myocardial wall compliance that might impair myocardial microcirculation. The findings are relevant to an understanding of the beneficial effect of hyaluronidase treatment in limiting cellular damage during myocardial ischemia.
Tin‐Free Radical Cyclizations for the Synthesis of 7‐Azaoxindoles, 7‐Azaindolines, Tetrahydro[1,8]naphthyridines, and Tetrahydro‐5H‐pyrido[2,3‐b]azepin‐8‐ones. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Morphoproteomic confirmation of constitutively activated mTOR, ERK, and NF-kappaB pathways in Ewing family of tumors. (2009)

In 3 patients with the Ewing family of tumors (EFT), morphoproteomic analyses of the tumors revealed constitutive activation of the mTOR, ERK, and NF-kappaB pathways, as evidenced by: (a) expression of phosphorylated (p)-mTOR, p-p70S6K, p-ERK 1/2, and p-NF-kappaB proteins using phosphospecific immunohistochemical probes directed against the activation sites; (b) nuclear translocation of p-p70S6K, p-ERK 1/2, and p-NF-kappaB p65; and (c) correlative expression of Ki-67 and Skp2 proteins consistent with cell cycling consequent to signal transduction by these pathways of convergence. This study examines the cytogenetic and molecular correlates and provides insight into therapeutic strategies relevant to this morphoproteomic profile. Based on a literature review, these observations appear to be the first morphoproteomic study of such pathways of convergence in tumors from EFT patients.
Point of care testing for C-reactive protein - a new path for Australian GPs? (2006)

A promising ability of the test in ruling in or out severe infection has been demonstrated in clinical studies. There are still controversies about the use of the CRP test in respiratory tract infections, however clinical research supports its use for some conditions, and therefore introduction into Australian general practice should be considered. Further evaluation of its utility is needed.
Critical assessment of influenza VLP production in Sf9 and HEK293 expression systems (2015)

This study highlights key production hurdles that must be overcome in both expression platforms, namely the presence of contaminants and the ensuing quantification challenges, and brings up the question of what truly constitutes an influenza VLP candidate vaccine.
Host Response to the Attenuated Poxvirus Vector NYVAC: Upregulation of Apoptotic Genes and NF-κB-Responsive Genes in Infected HeLa Cells (2005)

NYVAC has been engineered as a safe, attenuated vaccinia virus (VV) vector for use in vaccination against a broad spectrum of pathogens and tumors. Due to the interest in NYVAC-based vectors as vaccines and current phase I/II clinical trials with this vector, there is a need to analyze the human host response to NYVAC infection. Using high-density cDNA microarrays, we found 368 differentially regulated genes after NYVAC infection of HeLa cells. Clustering of the regulated genes identified six discrete gene clusters with altered expression patterns. Clusters 1 to 3 represented 47.5% of the regulated genes, with three patterns of gene activation kinetics, whereas clusters 4 to 6 showed distinct repression kinetics. Quantitative real-time reverse transcription-PCR analysis of selected genes validated the array data. Upregulated transcripts correlated with genes implicated in immune responses, including those encoding interleukin-1 receptor 2 (IL-1R2), IL-6, ISG-15, CD-80, and TNFSF7. NYVAC upregulated several intermediates of apoptotic cascades, including caspase-9, correlating with its ability to induce apoptosis. NYVAC infection also stimulated the expression of NF-kappaB1 and NF-kappaB2 as well as that of NF-kappaB target genes. Expression of the VV host range K1L gene during NYVAC infection prevented NF-kappaB activation, but not the induction of apoptosis. This study is the first overall analysis of the transcriptional response of human cells to NYVAC infection and provides a framework for future functional studies to evaluate this vector and its derivatives as human vaccines.
<title>Contamination control during shipping, handling, and storage of reticles</title> (2000)

This paper discusses state-of-the-art technology for controlling contamination and defects during shipping, handling, or storage of reticles. Reticles are used for printing IC patterns onto semiconductor wafers. In lithography process, defects in images are converted to wafers after each exposure, leading to classic failures such as short circuits or opens. Since a large batch of wafers might be processed before the defects are detected, high quality pattern images are very important for yield enhancement. Pattern defects can be created through particle deposition or damage of chrome lines due to Electrostatic Discharge (ESD) events. Airborne Molecular Contamination (AMC) may cause problems such as T- topping of photoresists or optics hazing which reduces image homogeneity and energy transmission. As the critical dimensions shrink to deep submicron regime, the susceptibility of reticle patterns to contaminant continuously increases. To meet increasingly stringent requirements of patterning technology, Reticle SMIF Pods (RSP) are developed. Reticles are encapsulated in the sealed pod to avoid particulate contamination in storage, as well as in manual or automatic transport. Constructed exclusively with static dissipative materials, the RSP provides effective protection for reticles from ESD-induced damage. Molecular contamination is minimized by carefully selecting construction materials. Equipped with an electronic data tracking/controlling device, the RSP can be integrated into OEM tools for automatic reticle management. With optional purge capability, the reticle environment is protected by chemically clean inert gas, which offers additional contamination control. These technologies are extensively discussed in this paper. Design principles and experimental data that support performance evaluations of RSP are presented.
Identification and Characterization of a Novel Fibronectin-Binding Protein on the Surface of Group A Streptococci (1999)

Understanding the role surface proteins play in the interaction of group A streptococci with epithelial cells is an important step toward the development of new strategies to fight infections. Fibronectin-binding proteins in streptococci and staphylococci have been described as important mediators for adherence to eukaryotic cells. In the present study we describe a new Streptococcus pyogenes fibronectin-binding protein (PFBP). The gene encoding the PFBP protein (pfbp) was identified from an M12 strain genomic library. It encodes a protein of 127.4 kDa which contains the LPXTGX motif characteristic of cell wall-associated proteins in gram-positive organisms and is among the largest surface molecules described for group A streptococci. The pfbp gene is transcribed during cell growth and was present in several class I and II streptococcal strains tested. The deduced amino acid sequence of PFBP exhibits a variable N-terminal region and a conserved C-terminal region when compared to most fibronectin-binding proteins identified from other gram-positive bacteria. The N-terminal region presents a stretch of 105 amino acids with no homology with N-terminal regions of previously described fibronectin-binding molecules, while the C-terminal region contains three repeat domains that share significant similarity with the repeat regions of fibronectin-binding proteins from S. pyogenes, S. dysgalactiae, and S. equisimilis. The PFBP repeated region, when expressed on the surface of S. gordonii, a commensal organism, binds to soluble and immobilized fibronectin. This study also shows that, in addition to pfbp, a second gene homologous with that of protein F1 (which also codes for a fibronectin-binding protein) is transcribed during cell growth in the same S. pyogenes strain.
Action of Designer Cellulosomes on Homogeneous Versus Complex Substrates (2005)

In recent work, we reported the self-assembly of a comprehensive set of defined "bifunctional" chimeric cellulosomes. Each complex contained the following: (i) a chimeric scaffoldin possessing a cellulose-binding module and two cohesins of divergent specificity and (ii) two cellulases, each bearing a dockerin complementary to one of the divergent cohesins. This approach allowed the controlled integration of desired enzymes into a multiprotein complex of predetermined stoichiometry and topology. The observed enhanced synergy on recalcitrant substrates by the bifunctional designer cellulosomes was ascribed to two major factors: substrate targeting and proximity of the two catalytic components. In the present work, the capacity of the previously described chimeric cellulosomes was amplified by developing a third divergent cohesin-dockerin device. The resultant trifunctional designer cellulosomes were assayed on homogeneous and complex substrates (microcrystalline cellulose and straw, respectively) and found to be considerably more active than the corresponding free enzyme or bifunctional systems. The results indicate that the synergy between two prominent cellulosomal enzymes (from the family-48 and -9 glycoside hydrolases) plays a crucial role during the degradation of cellulose by cellulosomes and that one dominant family-48 processive endoglucanase per complex is sufficient to achieve optimal levels of synergistic activity. Furthermore cooperation within a cellulosome chimera between cellulases and a hemicellulase from different microorganisms was achieved, leading to a trifunctional complex with enhanced activity on a complex substrate.
Runway incursion reduction program (RIRP) surveillance system, NASA/FAA Atlanta demonstration (2002)

Discusses a prototype Airport Movement Area Safety System (AMASS) originally designed to receive ASDE-3 and ARTS-IIIA data. These two data sources were applied to safety logic to provide air traffic controllers with conflict alert advisories on arrival and surface targets. The prototype AMASS was enhanced by software and hardware changes to perform multiple sensor data fusion, which provided a complete track and identification picture of the airport movement area. This surface surveillance system, combined with enhanced data links and displays, demonstrated the capability to maintain situational awareness in the tower and cockpit. This paper describes the performance of this surveillance system, as well as the impact of the system to current FAA airport services.
Foxp3+natural regulatory T cells preferentially form aggregates on dendritic cellsin vitroand actively inhibit their maturation (2008)

Naturally occurring CD4(+)CD25(+) regulatory T cells (Treg) suppress in vitro the proliferation of other T cells in a cell-contact-dependent manner. Dendritic cells (DCs) appear to be a target of Treg-mediated immune suppression. We show here that, in coculture of dye-labeled Treg cells and CD4(+)CD25(-) naïve T cells in the presence of T cell receptor stimulation, Treg cells, which are more mobile than naïve T cells in vitro, out-compete the latter in aggregating around DCs. Deficiency or blockade of leukocyte function-associated antigen-1 (LFA-1) (CD11a/CD18) abrogates Treg aggregation, whereas that of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) (CD152) does not. After forming aggregates, Treg cells specifically down-regulate the expression of CD80/86, but not CD40 or class II MHC, on DCs in both a CTLA-4- and LFA-1-dependent manner. Notably, Treg exerts this CD80/86-down-modulating effect even in the presence of strong DC-maturating stimuli, such as GM-CSF, TNF-alpha, IFN-gamma, type I IFN, and lipopolysaccharide. Taken together, as a possible mechanism of in vitro Treg-mediated cell contact-dependent suppression, we propose that antigen-activated Treg cells exert suppression by two distinct steps: initial LFA-1-dependent formation of Treg aggregates on immature DCs and subsequent LFA-1- and CTLA-4-dependent active down-modulation of CD80/86 expression on DCs. Both steps prevent antigen-reactive naïve T cells from being activated by antigen-presenting DCs, resulting in specific immune suppression and tolerance.
Structural characterization of the lipid A component of pathogenic Neisseria meningitidis (1992)

The lipid A component of meningococcal lipopolysaccharide was structurally characterized by using chemical modification methods, methylation analysis, 31P nuclear magnetic resonance, and laser desorption mass spectroscopy. It was shown that Neisseria meningitidis lipid A consists of a 1,4'-bisphosphorylated beta(1'----6)-linked D-glucosamine disaccharide (lipid A backbone), both phosphate groups being largely replaced by O-phosphorylethanolamine. This disaccharide harbors two nonsubstituted hydroxyl groups at positions 4 and 6', the latter representing the attachment site of the oligosaccharide portion in lipopolysaccharide. In addition, it is substituted by up to six fatty acid residues. In the major lipid A component, representing a hexaacyl species, the hydroxyl groups at positions 3 and 3' carry (R)-3-hydroxydodecanoic acid [12:0(3-OH)], whereas the amino groups at positions 2 and 2' are substituted by (R)-3-(dodecanoyloxy)tetradecanoic acid [3-O(12:0)-14:0]. A minor portion was present as a tetraacyl lipid A component lacking either dodecanoic acid (12:0) or 12:0 and 12:0(3-OH). N. meningitidis lipid A, therefore, significantly differs from Escherichia coli lipid A by the nature and locations of fatty acids and the substitution of O-phosphorylethanolamine for the nonglycosyl (4'-P) and glycosyl phosphate.
Accommodation with higher-order monochromatic aberrations corrected with adaptive optics (2006)

Higher-order monochromatic aberrations in the human eye cause a difference in the appearance of stimuli at distances nearer and farther from best focus that could serve as a signed error signal for accommodation. We explored whether higher-order monochromatic aberrations affect the accommodative response to 0.5 D step changes in vergence in experiments in which these aberrations were either present as they normally are or removed with adaptive optics. Of six subjects, one could not accommodate at all for steps in either condition. One subject clearly required higher-order aberrations to accommodate at all. The remaining four subjects could accommodate in the correct direction even when higher-order aberrations were removed. No subjects improved their accommodation when higher-order aberrations were corrected, indicating that the corresponding decrease in the depth of field of the eye did not improve the accommodative response. These results are consistent with previous findings of large individual differences in the ability to accommodate in impoverished conditions. These results suggest that at least some subjects can use monochromatic higher-order aberrations to guide accommodation. They also show that some subjects can accommodate correctly when higher-order monochromatic aberrations as well as established cues to accommodation are greatly reduced.
Oral bioavailability and brain penetration of (−)‐stepholidine, a tetrahydroprotoberberine agonist at dopamine D1 and antagonist at D2 receptors, in rats (2009)

Although (-)-stepholidine exhibits good brain penetration, future development efforts should aim at improving its oral bioavailability by protecting against pre-systemic glucuronidation or sulphation. In this regard, prodrug approaches may be useful.
Effect of TEI-6720, a Xanthine Oxidase Inhibitor, on the Nucleoside Transport in the Lung Cancer Cell Line A549 (2000)

To examine the effect of 2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazolecarboxylic acid (TEI-6720), an inhibitor of xanthine oxidase, on purine metabolism in the lung cancer cell line A549, the activities of adenosine deaminase, purine nucleoside phosphorylase, adenine phosphoribosyltransferase, hypoxanthine guanine phosphoribosyltransferase, xanthine oxidase, and guanase together with pyrimidine nucleoside phosphorylase were measured with or without the addition of TEI-6720, and the extracellular concentrations of hypoxanthine, xanthine, inosine, uracil, and uridine were measured after the addition of inosine or uridine to the incubation medium with or without TEI-6720. Moreover, the Na-independent nucleoside transport was determined in A549 cells with or without TEI-6720. TEI-6720 inhibited the activity of xanthine oxidase in A549 cells, but did not affect other enzymes. During incubation, TEI-6720 not only prevented a decrease in the inosine concentration in inosine-containing medium, but also a decrease in the uridine concentration in uridine-containing medium. Furthermore, the Na-independent transport of uridine was inhibited by TEI-6720 with a K(i) value of 4.1 micromol/l. These results indicate that TEI-6720 is an inhibitor of the Na-independent nucleoside transport of uridine and inosine, as well as xanthine oxidase.
The Need for Verifiable Visualization (2008)

Visualization is often employed as part of the simulation science pipeline-it's the window through which scientists examine their data for deriving new science, and the lens used to view modeling and discretization interactions within their simulations. We advocate that as a component of the simulation science pipeline, visualization must be explicitly considered as part of the validation and verification (V&V) process. In this article, the authors define V&V in the context of computational science, discuss the role of V&V in the scientific process, and present arguments for the need for verifiable visualization.
Acidity and Lactonization of Xylonic Acid: A Nuclear Magnetic Resonance Study (2010)

In acidic aqueous solutions the xylonic acid/xylonate equilibrium is coupled with the formation of the γ- and δ-lactones. The γ-lactone is formed more readily, whereas the δ-lactone can only be observed in traces at very low pH values (<2.5). By means of 13C NMR, both the lactone hydrolization constant and the acid dissociation constant could be determined (KL = 4.08, = 3.65 ± 0.34). Further, a second deprotonation of one of the hydroxyl groups could be observed at very high pH ( = 13.3 ± 0.76).
Transforming Growth Factor-1 Potentiates Renal Tubular Epithelial Cell Death by a Mechanism Independent of Smad Signaling (2003)

Tubular atrophy resulting from epithelial cell loss is one of the characteristic features in the development of chronic renal interstitial fibrosis. Although the trigger(s) and mechanism for tubular cell loss remain undefined, the hyperactive transforming growth factor (TGF)-beta1 signaling has long been suspected to play an active role. Here we demonstrate that although TGF-beta1 did not induce cell death per se, it dramatically potentiated renal tubular cell apoptosis initiated by other death cues in vitro. Pre-incubation of human kidney epithelial cells (HKC) with TGF-beta1 markedly promoted staurosporine-induced cell death in a time- and dose-dependent manner. TGF-beta1 dramatically accelerated the cleavage and activation of pro-caspase-9, but not pro-caspase-8, in HKC cells. This event was followed by an accelerated activation of pro-caspase-3. To elucidate the mechanism underlying TGF-beta1 promotion of tubular cell death, we investigated the signaling pathways activated by TGF-beta1. Both Smad-2 and p38 mitogen-activated protein (MAP) kinase were rapidly activated by TGF-beta1, as demonstrated by the early induction of phosphorylated Smad-2 and p38 MAP kinase, respectively. We found that overexpression of inhibitory Smad-7 completely abolished Smad-2 phosphorylation and activation induced by TGF-beta1 but did not inhibit TGF-beta1-induced apoptosis. However, suppression of p38 MAP kinase with chemical inhibitor SC68376 not only abolished p38 MAP kinase phosphorylation but also obliterated apoptosis induced by TGF-beta1. These results suggest that hyperactive TGF-beta1 signaling potentiates renal tubular epithelial cell apoptosis by a Smad-independent, p38 MAP kinase-dependent mechanism.
Identification of Genetic Variants in Endothelial Lipase in Persons With Elevated High-Density Lipoprotein Cholesterol (2002)

Six new potentially functional variants in EL were discovered through sequencing of the EL gene in subjects with high HDL-C levels. Differences in allele frequencies exist between blacks and whites and between control subjects and those with high HDL-C levels.
Molecular theory of field‐dependent proton spin‐lattice relaxation in tissue (2006)

A molecular theory is presented for the field-dependent spin-lattice relaxation time of water in tissue. The theory attributes the large relaxation enhancement observed at low frequencies to intermediary protons in labile groups or internal water molecules that act as relaxation sinks for the bulk water protons. Exchange of intermediary protons not only transfers magnetization to bulk water protons, it also drives relaxation by a mechanism of exchange-mediated orientational randomization (EMOR). An analytical expression for T1 is derived that remains valid outside the motional-narrowing regime. Cross-relaxation between intermediary protons and polymer protons plays an important role, whereas spin diffusion among polymer protons can be neglected. For sufficiently slow exchange, the dispersion midpoint is determined by the local dipolar field rather than by molecular motions, which makes the dispersion frequency insensitive to temperature and system composition. The EMOR model differs fundamentally from previous models that identify collective polymer vibrations or hydration water dynamics as the molecular motion responsible for spin relaxation. Unlike previous models, the EMOR model accounts quantitatively for 1H magnetic relaxation dispersion (MRD) profiles from tissue model systems without invoking unrealistic parameter values.
Expression of CD28 on CD8+ and CD4+ Lymphocytes During HIV Infection (1994)

CD28 interaction with B7 molecules, expressed on the membranes of antigen-presenting cells, co-stimulates cytokine production, T-cell proliferation and generation of cytotoxic lymphocytes. The expression of CD28 markers on CD4+ and CD8+ lymphocytes was studied in a group of subjects at various stages of HIV infection. A reduction in the percentage of CD28-bearing CD4+ and CD8+ cell subsets was observed during the asymptomatic stage of the disease. This reduction was more pronounced in AIDS than in non-AIDS patients. At the same time, an increase in the absolute CD8+CD28- cell number (greater in stage A than in stage B and C subjects) was observed in HIV-infected patients. The finding of an altered pattern of CD28 expression on T cells might per se explain certain early defects in the cytokine pattern and in the immune response peculiar to HIV-infected patients.