gebhart/patrepeval huggingface dataset:
Endothelin-1 Impairs Nitric Oxide Signaling in Endothelial Cells Through a Protein Kinase Cδ-Dependent Activation of STAT3 and Decreased Endothelial Nitric Oxide Synthase Expression (2009)

In an ovine model of persistent pulmonary hypertension of the newborn (PPHN), endothelin-1 (ET-1) expression is increased, while endothelial nitric oxide synthase (eNOS) expression is decreased. However, the molecular mechanisms by which ET-1 attenuates eNOS expression in endothelial cells are not completely understood. Thus, the goal of this study was to determine if the overexpression of ET-1 decreases eNOS expression in pulmonary arterial endothelial cells isolated from fetal lambs. To increase the ET-1 expression, cells were transfected with a plasmid coding for Prepro-ET-1, a precursor of ET-1. After overexpression of Prepro-ET-1, ET-1 levels in the culture medium were significantly increased (control = 805.3 +/- 69.8; Prepro-ET-1 overexpression = 1351 +/- 127.9). eNOS promoter activity, protein levels, and NO generation were all significantly decreased by the overexpression of Prepro-ET-1. The decrease in transcription correlated with increased activity of protein kinase Cdelta (PKCdelta) and STAT3. Further, DNA binding activity of STAT3 was also increased by Prepro-ET-1 overexpression. The increase in STAT3 activity and decrease in eNOS promoter activity were inhibited by the overexpression of dominant negative mutants of PKCdelta or STAT3. Further, a 2 bp mutation in the STAT3 binding site in the eNOS promoter inhibited STAT3 binding and led to enhanced promoter activity in the presence of Prepro-ET-1 overexpression. In conclusion, ET-1 secretion is increased by Prepro-ET-1 overexpression. This results in activation of PKCdelta, which phosphorylates STAT3, increasing its binding to the eNOS promoter. This in turn decreases eNOS promoter activity, protein levels, and NO production. Thus, ET-1 can reduce eNOS expression and NO generation in fetal pulmonary artery endothelial cells through PKCdelta-mediated activation of STAT3.
Supervised classification in high-dimensional space: geometrical, statistical, and asymptotical properties of multivariate data (1998)

The recent development of more sophisticated remote-sensing systems enables the measurement of radiation in many more spectral intervals than was previously possible. An example of this technology is the AVIRIS system, which collects image data in 220 bands. The increased dimensionality of such hyperspectral data greatly enhances the data's information content, but provides a challenge to the current techniques for analyzing such data. Human experience in 3D space tends to mislead our intuition of geometrical and statistical properties in high-dimensional space, properties which must guide our choices in the data analysis process. Using Euclidean and Cartesian geometry, high-dimensional space properties are investigated in this paper, and their implication for high-dimensional data and its analysis is studied in order to illuminate the differences between conventional spaces and hyperdimensional space.
SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines (2008)

Translational research hinges on the ability to make observations in model systems and to implement those findings into clinical applications, such as the development of diagnostic tools or targeted therapeutics. Tumor cell lines are commonly used to model carcinogenesis. The same tumor cell line can be simultaneously studied in multiple research laboratories throughout the world, theoretically generating results that are directly comparable. One important assumption in this paradigm is that researchers are working with the same cells. However, recent work using high throughput genomic analyses questions the accuracy of this assumption. Observations by our group and others suggest that experiments reported in the scientific literature may contain pre-analytic errors due to inaccurate identities of the cell lines employed. To address this problem, we developed a simple approach that enables an accurate determination of cell line identity by genotyping 34 single nucleotide polymorphisms (SNPs). Here, we describe the empirical development of a SNP panel identification assay (SPIA) compatible with routine use in the laboratory setting to ensure the identity of tumor cell lines and human tumor samples throughout the course of long term research use.
A natural classification of the basic helix–loop–helix class of transcription factors (1997)

A natural (evolutionary) classification is provided for 242 basic helix-loop-helix (bHLH) motif-containing proteins. Phylogenetic analyses of amino acid sequences describe the patterns of evolutionary change within the motif and delimit evolutionary lineages. These evolutionary lineages represent well known functional groups of proteins and can be further arranged into five groups based on binding to DNA at the hexanucleotide E-box, the amino acid patterns in other components of the motif, and the presence/absence of a leucine zipper. The hypothesized ancestral amino acid sequence for the bHLH transcription factor family is given together with the ancestral sequences of the subgroups. It is suggested that bHLH proteins containing a leucine zipper are not a natural, monophyletic group.
The first valve-less diffuser gas pump (2002)

The first valve-less gas pump based on the fluid directing properties of diffusers has been fabricated and tested. The pump, fabricated in brass, consists of two flat-wall diffusers connected to a pump chamber with two diaphragms excited by piezo discs. The pump dimensions are 20/spl times/16/spl times/2.3 mm. The measured maximum pump pressure and volume flow are 5 kPa (0.5 mH/sub 2/O) and 8 ml/min, respectively. An electrical analogy is used to calculate the pump resonance frequencies and the pump flow.
Phase-aware optimization in approximate computing (2017)

This paper shows that many applications exhibit execution-phase-specific sensitivity towards approximation of the internal subcomputations. Therefore, approximation in certain phases can be more beneficial than others. Further, this paper presents Opprox, a novel system for application's execution-phase-aware approximation. For a user provided error budget and target input parameters, Opprox identifies different program phases and searches for profitable approximation settings for each phase of the application execution. Our evaluation with five benchmarks and four existing transformations show that our phase-aware optimization on average does 14% less work for a 5% error tolerance bound and 42% less work for a 20% tolerance bound.
Derivation of completely cell culture-derived mice from early-passage embryonic stem cells. (1993)

Several newly generated mouse embryonic stem (ES) cell lines were tested for their ability to produce completely ES cell-derived mice at early passage numbers by ES cell <==> tetraploid embryo aggregation. One line, designated R1, produced live offspring which were completely ES cell-derived as judged by isoenzyme analysis and coat color. These cell culture-derived animals were normal, viable, and fertile. However, prolonged in vitro culture negatively affected this initial totipotency of R1, and after passage 14, ES cell-derived newborns died at birth. However, one of the five subclones (R1-S3) derived from single cells at passage 12 retained the original totipotency and gave rise to viable, completely ES cell-derived animals. The total in vitro culture time of the sublines at the time of testing was equivalent to passage 24 of the original line. Fully potent early passage R1 cells and the R1-S3 subclone should be very useful not only for ES cell-based genetic manipulations but also in defining optimal in vitro culture conditions for retaining the initial totipotency of ES cells.
Inhibition of Hepatitis C Virus RNA Replication by 2′-Modified Nucleoside Analogs (2003)

The RNA-dependent RNA polymerase (NS5B) of hepatitis C virus (HCV) is essential for the replication of viral RNA and thus constitutes a valid target for the chemotherapeutic intervention of HCV infection. In this report, we describe the identification of 2'-substituted nucleosides as inhibitors of HCV replication. The 5'-triphosphates of 2'-C-methyladenosine and 2'-O-methylcytidine are found to inhibit NS5B-catalyzed RNA synthesis in vitro, in a manner that is competitive with substrate nucleoside triphosphate. NS5B is able to incorporate either nucleotide analog into RNA as determined with gel-based incorporation assays but is impaired in its ability to extend the incorporated analog by addition of the next nucleotide. In a subgenomic replicon cell line, 2-C-methyladenosine and 2'-O-methylcytidine inhibit HCV RNA replication. The 5'-triphosphates of both nucleosides are detected intracellularly following addition of the nucleosides to the media. However, significantly higher concentrations of 2'-C-methyladenosine triphosphate than 2'-O-methylcytidine triphosphate are detected, consistent with the greater potency of 2'-C-methyladenosine in the replicon assay, despite similar inhibition of NS5B by the triphosphates in the in vitro enzyme assays. Thus, the 2'-modifications of natural substrate nucleosides transform these molecules into potent inhibitors of HCV replication.
Changes in passive mechanical stiffness of myocardial tissue with aneurysm formation. (1994)

The findings indicate that infarcted myocardium becomes more stiff during the first 1 to 2 weeks after anteroapical infarction and then more compliant. The infarct also exhibits directional anisotropy. These observations underscore the importance of ventricular material properties during the remodeling process after acute myocardial infarction and may partially explain the progressive left ventricular dilatation and functional deterioration that occur in some patients after anteroapical infarction.
Bombesin and epidermal growth factor stimulate the mitogen-activated protein kinase through different pathways in Swiss 3T3 cells (1993)

Both bombesin and epidermal growth factor (EGF) are potent mitogens in Swiss 3T3 cells that nonetheless have dissimilar receptor structures. To explore possible common intracellular events involved in the stimulation of cellular growth by these two peptides, we have evaluated the regulation of the mitogen-activated protein (MAP) kinase. Exposure of Swiss 3T3 cells to bombesin, EGF or the protein kinase C activator phorbol 12-myristate 13-acetate (PMA) causes the rapid and transient stimulation of the enzyme activity. Pretreatment of cells with the protein kinase inhibitor H-7, or down-regulation of cellular protein kinase C by prolonged exposure to PMA, causes a decrease of over 90% in the activation of MAP kinase by bombesin. In contrast, these treatments have no effect on the stimulation of MAP kinase by EGF. The stimulation of MAP kinase activity by bombesin is dose-dependent, occurring over a narrow concentration range of the peptide. Both EGF and bombesin stimulate the phosphorylation of an immunoprecipitable MAP kinase protein migrating at 42 kDa on SDS/PAGE. Phosphoamino acid analysis of this phosphorylated protein reveals that EGF and bombesin stimulate phosphorylation on tyrosine, threonine and serine residues. Tyrosine phosphorylation of the enzyme, as evaluated by antiphosphotyrosine blotting of the immunoprecipitated protein, reveals that the time course of phosphorylation by both mitogens correlates with stimulation of enzyme activity. These results provide further evidence for the convergence of discrete pathways emanating from tyrosine kinase and G-protein-linked receptors in the regulation of MAP kinase.
Enhancement of interferon antitumor action by sodium butyrate. (1979)

Sodium butyrate together with interferon enhances the antitumor effect of interferon in vivo. When Sarcoma 180 TG cells are inoculated in mice, the mean survival time and final survival rate are greatly increased compared to those for treatment with interferon alone. Similarly, a significant delay in the mean survival time is observed when mice inoculated with L1210 cells are treated with sodium butyrate and interferon. This effect could be due at least in part to a potentiation of interferon action on the tumor cells.
Electron Mobility Model for Strained-Si Devices (2005)

Strained-Si material has emerged as a strong contender for developing transistors for next-generation electronics, because this material system offers superior transport properties. We suggest a model describing the low-field bulk mobility tensor for electrons in strained-Si layers as a function of strain. Our analytical model includes the effect of strain-induced splitting of the conduction band valleys in Si, intervalley scattering, and doping dependence. Intervalley scattering has been modeled on the equilibrium electron distribution and the valley splitting for a given strain tensor. The effect of different substrate orientations is considered by performing coordinate transformations for the strain tensor and effective masses. Monte Carlo simulations accounting for various scattering mechanisms and the splitting of the anisotropic conduction band valleys due to strain in combination with an accurate ionized impurity scattering model were carried out to verify the results for the complete range of Ge contents and for a general orientation of the SiGe buffer layer. Our mobility model is suitable for implementation into a conventional technology CAD simulation tool.
Primary High-Dose Murine Norovirus 1 Infection Fails To Protect from Secondary Challenge with Homologous Virus (2009)

Human noroviruses in the Caliciviridae family are the major cause of nonbacterial epidemic gastroenteritis worldwide. Primary human norovirus infection does not elicit lasting protective immunity, a fact that could greatly affect the efficacy of vaccination strategies. Little is known regarding the pathogenesis of human noroviruses or the immune responses that control them because there has previously been no small-animal model or cell culture system of infection. Using the only available small-animal model of norovirus infection, we found that primary high-dose murine norovirus 1 (MNV-1) infection fails to afford protection against a rechallenge with a homologous virus. Thus, MNV-1 represents a valuable model with which to dissect the pathophysiological basis for the lack of lasting protection against human norovirus infection. Interestingly, the magnitude of protection afforded by a primary MNV-1 infection inversely correlates with the inoculum dose. Future studies will elucidate the mechanisms by which noroviruses avoid the induction of protective immunity and the role played by the inoculum dose in this process, ultimately translating this knowledge into successful vaccination approaches.
The Tryptophanase Gene Cluster of Haemophilus influenzae Type b: Evidence for Horizontal Gene Transfer (1998)

Among strains of Haemophilus influenzae, the ability to catabolize tryptophan (as detected by indole production) varies and is correlated with pathogenicity. Tryptophan catabolism is widespread (70 to 75%) among harmless respiratory isolates but is nearly universal (94 to 100%) among strains causing serious disease, including meningitis. As a first step in investigating the relationship between tryptophan catabolism and virulence, we have identified genes in pathogenic H. influenzae which are homologous to the tryptophanase (tna) operon of Escherichia coli. The tna genes are located on a 3.1-kb fragment between nlpD and mutS in the H. influenzae type b (Eagan) genome, are flanked by 43-bp direct repeats of an uptake signal sequence downstream from nlpD, and appear to have been inserted as a mobile unit within this sequence. The organization of this insertion is reminiscent of pathogenicity islands. The tna cluster is found at the same map location in all indole-positive strains of H. influenzae surveyed and is absent from reference type d and e genomes. In contrast to H. influenzae, most other Haemophilus species lack tna genes. Phylogenetic comparisons suggest that the tna cluster was acquired by intergeneric lateral transfer, either by H. influenzae or a recent ancestor, and that E. coli may have acquired its tnaA gene from a related source. Genomes of virulent H. influenzae resemble those of pathogenic enterics in having an island of laterally transferred DNA next to mutS.
Immunologic recognition of malignant melanoma by autologous T lymphocytes (1993)

T lymphocytes specifically recognizing autologous tumor cells in vitro can be generated from melanoma patients. Recognition of tumor cells by both CD4 and CD8 lymphocytes is mediated through the T-cell receptor and is restricted by HLA antigens. Although HLA-A2 has been identified as a restricting allele for many melanoma-specific cytotoxic T lymphocytes, T cells directed against antigens unique to each patient's tumor as well as antigens common to melanomas from unrelated individuals can be restricted by several different HLA alleles. A common melanoma antigen recognized in association with HLA-A1 has now been identified. The antigen is a nonapeptide derived from the gene MAGE1, a normal cellular gene preferentially expressed in a variety of solid tumors. Melanoma cells have been found to produce a soluble form of the intracellular adhesion molecule-1. Soluble intercellular adhesion molecule-1 effectively inhibits cell-mediated cytotoxicity in vitro, raising the possibility that its expression in vivo could promote escape of the tumor cells from immune effectors.
The genome of melon ( Cucumis melo L.) (2012)

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.
Aspartyl-tRNA Synthetase Is the Target of Peptide Nucleotide Antibiotic Microcin C (2006)

Microcin C is a ribosome-synthesized heptapeptide that contains a modified adenosine monophosphate covalently attached to the C-terminal aspartate. Microcin C is a potent inhibitor of bacterial cell growth. Based on the in vivo kinetics of inhibition of macromolecular synthesis, Microcin C targets translation, through a mechanism that remained undefined. Here, we show that Microcin C is a subject of specific degradation inside the sensitive cell. The product of degradation, a modified aspartyl-adenylate containing an N-acylphosphoramidate linkage, strongly inhibits translation by blocking the function of aspartyl-tRNA synthetase.
Pulmonary Inflammation and Emphysema (2007)

Our results indicate that IL-18 and IL-13 may have an important role in the pathogenesis of COPD.
Magnetoelectric Properties in Piezoelectric and Magnetostrictive Laminate Composites (2001)

Magnetoelectric laminate composites of piezoelectric-magnetostrictive materials were investigated. The composites were prepared by stacking and bonding Pb(Zr, Ti)O 3 (PZT) and Terfenol-D disks. Experimental results indicated that the magnetoelectric voltage coefficient, dE/dH , increased with decreasing thickness and increasing piezoelectric voltage constant ( g 31 ) of the PZT layer. We obtained the highest magnetoelectric voltage coefficient of 4.68 V/cm·Oe at room temperature for the sample with high g 33 PZT of 0.5 mm in thickness. This value is about 36 times higher than the best reported value.
Nonequilibrium Antifreeze Peptides and the Recrystallization of Ice (1995)

Evidence is presented that the nonequilibrium antifreeze peptide (AFP) from winter flounder has a special ability to inhibit recrystallization in ice only when an appreciable amount of liquid is present, as is the case when the system contains salts and the temperature is not too low. In this circumstance the AFP binds to the ice surface at the ice-solution interfaces in grain boundaries, preventing migration of the solution and effectively immobilizing the boundaries. In the absence of liquid, recrystallization inhibition appears to be a common property of many peptides. This is consistent with the view that the special effects of AFPs require a structural fit onto ice, and therefore require the AFP molecules to have the mobility to achieve that fit. Since the concentration of salt required to induce the special recrystallization inhibition effects of AFPs is lower (< 10 mM) than that found normally in physiological fluids, AFPs could play a role in the survival of organisms by preventing damage due to recrystallization. The proposition that mobility is needed for AFP molecules to produce their special influence upon ice growth argues against any special effects of AFPs in devitrification.
The effect of acid mucopolysaccharides and acid mucopolysaccharide–proteins on fibril formation from collagen solutions (1968)

1. The effects of acid mucopolysaccharides and acid mucopolysaccharide-proteins on the size and rate of formation of fibril aggregates from collagen solutions in pH7.6 buffers were studied by turbidimetric and light-scattering methods. 2. Serum albumin, orosomucoid, methylated cellulose, chondroitin sulphate A and chondroitin sulphate C of molecular weight less than 20000, and hyaluronate of molecular weight less than 40000 did not influence rates of fibril formation. Chondroitin sulphate A, chondroitin sulphate C and hyaluronate of high molecular weight retarded the rate of fibril formation. This effect of high-molecular-weight chondroitin sulphate C decreased with increasing ionic strength. Heparin, though of low molecular weight (13000), was highly effective, as was also heparitin sulphate. The chondroitin sulphate-proteins of very high molecular weight were highly effective, despite the fact that for some preparations the component chondroitin sulphate chains had molecular weights much less than 20000. 3. Agents that had delayed fibril formation were also effective in producing an increase in degree of aggregation of fibrillar collagen, as indicated by dissymmetry changes observed in light-scattering experiments at low collagen concentrations. Methylated cellulose and heparin at 2.5mug./ml. were unusual in decreasing aggregation, but heparin at 0.25mug./ml. increased aggregation. Electron microscopy of gels showed fibrils and fibril aggregates with ;normal' collagen spacing and dimensions consistent with the light-scattering results. 4. The rates of electrical transport of agents and of solvent (electro-osmosis) through collagen gels indicated a contribution of molecular entanglement that increased with increase in molecular size of the agents. Electrostatic binding of heparin to collagen was noted. Binding to collagen during fibril formation was also found for heparitin sulphate and a chondroitin sulphate with extra sulphate groups. 5. Electrostatic binding of acid mucopolysaccharide-proteins to collagen may be an important factor in the organization and functioning of connective tissues at all stages of growth and development. Excluded-volume (molecular-entanglement) effects may also be important. These factors operate simultaneously and interact mutually so that precise assessment of their relative importance is difficult.