gebhart/patrepeval huggingface dataset:
Inhibition of Wnt/β‐Catenin Signaling Promotes Engraftment of Mesenchymal Stem Cells to Repair Lung Injury (2013)

We sought to explore the treatment effects and the repair mechanisms of bone marrow derived mesenchymal stem cells (MSCs) during HCl-induced acute lung injury (ALI). MSCs were delivered through the tail veins of rats 24 h after intranasal instillation of HCl. The results showed that MSCs did not ameliorate the histopathologic changes of ALI and pulmonary fibrosis. We found that the activated Wnt/β-catenin signaling may regulate the differentiation of MSCs and is associated with lung fibroblasts activation, pulmonary fibrosis and tissue repair process in ALI rats. Immunofluorescence and histology analysis indicated that activated canonical Wnt/β-catenin signaling induced most MSCs to differentiate into myofibroblasts or fibroblasts in vivo. However, inhibition of Wnt/β-catenin signaling by Dickkopf-1 (DKK1) promotes epithelial differentiation of MSCs induced by native alveolar epithelial cells which are beneficial to repair the injured lung epithelium. Inhibition of Wnt/β-catenin signaling after MSCs transplantation ameliorated pulmonary fibrosis and improved pulmonary function which attenuated the lung injury. In vitro study, activation of the Wnt/β-catenin signaling stimulated MSCs to express myofibroblasts markers, which was attenuated by DKK1. Furthermore, Wnt3α activated Wnt/β-catenin signaling in lung fibroblasts to enhance the expression of collagen I, vimentin and α-smooth muscle actin, but DKK1 attenuated these proteins expression. These findings demonstrated that canonical Wnt/β-catenin signaling plays a key role in regulating differentiation of MSCs in vivo or in vitro and the pathogenesis of fibrotic diseases. Our study suggested that inhibition of abnormal activated Wnt/β-catenin signaling would promote MSCs epithelial differentiation to repair lung injury and reduce pulmonary fibrosis.
Synergistic effects of calcium‐mobilizing agents and adenosine on histamine release from rat peritoneal mast cells (1989)

1. Adenosine and its metabolically stable analogue N-ethyl-carboxamidoadenosine (NECA) enhance histamine release from rat peritoneal mast cells when these are stimulated by calcium-mobilizing agents. NECA and adenosine shift the concentration-response curve of the calcium ionophore A23187 to lower concentrations. 2. The potencies of NECA or adenosine in enhancing A23187-induced histamine release are dependent on the level of stimulated release in the absence of adenosine analogues. At high levels of release their potencies are up to 20 times higher than at low levels. Consequently, averaged concentration-response curves of adenosine and NECA for enhancing histamine release are shallow. 3. The adenosine transport blocker S-(p-nitrobenzyl)-6-thioinosine (NBTI) has no effect by itself at low levels of stimulated histamine release, but abolishes the enhancing effect of adenosine. At high levels of release, however, NBTI alone enhances the release of histamine. 4. It is concluded that adenosine and calcium reciprocally enhance the sensitivity of the secretory processes to the effects of the other agent. The levels of intracellular adenosine obtained by trapping adenosine inside stimulated mast cells are sufficient to enhance histamine release substantially, suggesting that this effect may play a physiological and pathophysiological role.
Mitochondrial β‐oxidation in Aspergillus nidulans (2004)

Beta-oxidation (beta-ox) occurs exclusively in the peroxisomes of Saccharomyces cerevisiae and other yeasts, leading to the supposition that fungi lack mitochondrial beta-ox. Here we present unequivocal evidence that the filamentous fungus Aspergillus nidulans houses both peroxisomal and mitochondrial beta-ox. While growth of a peroxisomal beta-ox disruption mutant (DeltafoxA) was eliminated on a very long-chain fatty acid (C(22:1)), growth was only partially impeded on a long-chain fatty acid (C(18:1)) and was not affected at all on short chain (C4-C6) fatty acids. In contrast, growth of a putative enoyl-CoA hydratase mutant (DeltaechA) was abolished on short-chain and severely restricted on long- and very long-chain fatty acids. Furthermore fatty acids inhibited growth of the DeltaechA mutant but not the DeltafoxA mutant in the presence of an alternate carbon source (lactose). Disruption of echA led to a 28-fold reduction in 2-butenoyl-CoA hydratase activity in a preparation of organelles. EchA was also required for growth on isoleucine and valine. The subcellular localization of the FoxA and EchA proteins was confirmed through the use of red and green fluorescent protein fusions.
Beta tungsten underlayer for low-noise thin-film longitudinal media (1990)

This work investigates the magnetic and media noise properties of Co-15 at. % Cr media having β-W underlayer. These results are correlated with the crystallography and the grain structure of the media. Results show that Hc increases with β-W underlayer thickness up to around 100 nm and becomes constant beyond that. The β-W underlayer seems to influence the epitaxial growth of Co (112̄0) and thus has c axis in the plane. Media noise increases with β-W underlayer film thickness. CoCr/β-W media exhibits almost two times lower media noise than a CoCr/Cr media having identical Hc and Brt. The low noise behavior in CoCr/β-W is due to the unique grain structure which reduces the exchange interaction between the CoCr grains.
BETA3, a Novel Helix-Loop-Helix Protein, Can Act as a Negative Regulator of BETA2 and MyoD-Responsive Genes (1996)

Using degenerate PCR cloning we have identified a novel basic helix-loop-helix (bHLH) transcription factor, BETA3, from a hamster insulin tumor (HIT) cell cDNA library. Sequence analysis revealed that this factor belongs to the class B bHLH family and has the highest degree of homology with another bHLH transcription factor recently isolated in our laboratory, BETA2 (neuroD) (J. E. Lee, S. M. Hollenberg, L. Snider, D. L. Turner, N. Lipnick, and H. Weintraub, Science 268:836-844, 1995; F. J. Naya, C. M. M. Stellrecht, and M.-J. Tsai, Genes Dev. 8:1009-1019, 1995). BETA2 is a brain- and pancreatic-islet-specific bHLH transcription factor and is largely responsible for the tissue-specific expression of the insulin gene. BETA3 was found to be tissue restricted, with the highest levels of expression in HIT, lung, kidney, and brain cells. Surprisingly, despite the homology between BETA2 and BETA3 and its intact basic region, BETA3 is unable to bind the insulin E box in bandshift analysis as a homodimer or as a heterodimer with the class A bHLH factors E12, E47, or BETA1. Instead, BETA3 inhibited both the E47 homodimer and the E47/BETA2 heterodimer binding to the insulin E box. In addition, BETA3 greatly repressed the BETA2/E47 induction of the insulin enhancer in HIT cells as well as the MyoD/E47 induction of a muscle-specific E box in the myoblast cell line C2C12. In contrast, expression of BETA3 had no significant effect on the GAL4-VP16 transcriptional activity. Immunoprecipitation analysis demonstrates that the mechanism of repression is via direct protein-protein interaction, presumably by heterodimerization between BETA3 and class A bHLH factors.
DNA sequences homologous to vertebrate oncogenes are conserved in Drosophila melanogaster. (1981)

Sequences homologous to the oncogene sequences of acute RNA tumor viruses have been shown to be highly conserved within vertebrates. In the present work, eight different oncogene DNA sequences have been used as probes to search for homologous sequences in the DNA of organisms of other phyla. Five of these probes hybridized to the DNA of Drosophila melanogaster. Abelson leukemia virus probe detected a single homologous DNA fragment in Drosophila DNA. In contrast, probes prepared from the genomes of Harvey, avian, and feline sarcoma viruses and avian myelocytomatosis virus hybridized with multiple homologous sequences in Drosophila DNA. The identification of sequences homologous to vertebrate oncogenes in invertebrates demonstrates both a high degree of conservation of these genes and a wide distribution among divergent species. It seems likely that sequences homologous to vertebrate oncogenes play a crucial role in metazoan metabolism.
External beam radiation therapy for prostate cancer (2000)

Men with non-metastatic prostate cancer have many treatment options. For over 35 years, radiation therapy has been a mainstay of treatment for this disease. With improvements in technology and better use of pretreatment prognostic factors, such as prostate specific antigen level and Gleason score, biochemical and clinical results have steadily improved. This article reviews the current status of radiation therapy in the treatment of prostate cancer. Results of treatment utilizing three-dimensional conformal and conventional techniques are compared and contrasted. The appropriate use of adjuvant hormones and particle beam therapy in the management of this disease is also discussed. Finally, the toxicity and future directions of radiation therapy in the treatment of prostate cancer are addressed.
In Vitro Activities of New Quinolones and Oxazolidinones against Actinomadura madurae (2004)

In this work, we studied the in vitro sensitivity of 24 strains of Actinomadura madurae to a new oxazolidinone (DA-7867), gatifloxacin, moxifloxacin, and garenoxacin by using a broth microdilution method. We observed that the A. madurae strains had a high level of sensitivity to all the antimicrobials tested. The most active drug was DA-7867, with a MIC at which 90% of the strains are inhibited (MIC(90)) of 0.125 micro g/ml and a MIC(50) of 0.06 micro g/ml.
Fast and Accurate Ray-Voxel Intersection Techniques for Iso-Surface Ray Tracing (2004)

A new intersection algorithm for iso-surface volume ray tracing increases performance by roughly a factor of three compared to previous accurate intersection algorithms while offering similar performance as previous algorithms that only approximated the solution. The image shows some of the test data sets: Bonsai tree, aneurism, engine, and skull. Visualizing iso-surfaces of volumetric data sets is becoming increasingly important for many practical applications. One crucial task in iso-surface ray tracing is to find the correct intersection of a ray with the trilinear-interpolated implicit surface defined by the data values at the vertices of a given voxel. Currently available solutions are either accurate but slow or they provide fast but only approximate solutions. In this paper, we analyze the available techniques and present a new intersection algorithm. We compare and evaluate the new algorithm against previous approaches using both synthetic test cases and real world data sets. The new algorithm is roughly three times faster but provides the same image quality and better numerical stability as previous accurate solutions. 1
Paternity Exclusion by DNA Markers: Effects of Paternal Mutations (1996)

In parentage testing when one parent is excluded, the distribution of the number of loci showing exclusion due to mutations of the transmitting alleles is derived, and it is contrasted with the expected distribution when the exclusion is caused by nonpaternity. This theory is applied to allele frequency data on short tandem repeat loci scored by PCR analysis, and VNTR data scored by Southern blot RFLP analysis that are commonly used in paternity analysis. For such hypervariable loci, wrongly accused males should generally be excluded based two or more loci, while a true father is unlikely to be excluded based on multiple loci due to mutations of paternal alleles. Thus, when these DNA markers are used for parentage analysis, the decision to infer non-paternity based on exclusions at two or more loci has a statistical support. Our approach places a reduced weight on the combined exclusion probability. Even with this reduced power of exclusion, the probability of exclusion based on combined tests on STR and VNTR loci is sufficiently large to resolve most paternity dispute cases in general populations.
CDK9 inhibition by dinaciclib potently suppresses Mcl-1 to induce durable apoptotic responses in aggressive MYC-driven B-cell lymphoma in vivo (2014)

either as false negatives of the PCR or as false positives of MFC. We can thus conclude that the junction region of the IgH rearrangement in MM is stable and can be used as a target for MRD assessment by ASO RQ-PCR and more, also by deep-sequencing methods, as it constantly identifies the myeloma cells responsible for relapse. n conclusion, our results show that, in the dominant myeloma clone, the CDR3 region of IGH remains constant across all the stages of disease evolution. This major clone signature is not modified by clinical or biological changes in the disease nor under different treatment pressures; accordingly, it would thus be responsible for disease relapses and progression, and could be used as a MRD target. Assuming that the CDR3 region remains stable, the recently raised concept of clonal tiding
Molecular and Conformational Determinants of Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP) for Activation of the PAC1 Receptor (2009)

PAC1 receptor is abundant in the CNS and plays an important role in neuronal survival. To identify the molecular determinants and the conformational components responsible for the activation of the PAC1 receptor, we performed a SAR study focusing on the N-terminal domain of its endogenous ligand, PACAP. This approach revealed that residues Asp(3) and Phe(6) are key elements of the pharmacophore of the PAC1 receptor. This study, supported by NMR structural analyses, suggests that the N-terminal tail of PACAP (residues 1 to 4) adopts a specific conformation similar to a turn when it activates the PAC1 receptor. Moreover, the integrity of the alpha-helix conformation observed at positions 5 to 7 appears crucial to allow the binding of PACAP. Characterization of analogues led to the identification of several superagonists, such as [Bip(6)]PACAP27, and of a new potent PAC1 receptor antagonist, [Sar(4)]PACAP38. The bioactive conformation inferred from this SAR study could constitute an appropriate molecular scaffold supporting the design of nonpeptidic PAC1 receptor agonists.
Effect of Atorvastatin on High-Density Lipoprotein Apolipoprotein A-I Production and Clearance in the New Zealand White Rabbit (2002)

These data suggest that the effect on apoA-I levels observed with atorvastatin at higher drug doses in humans may be caused at least in part by enhanced HDL apoA-I catabolism, which is not entirely offset by a concomitant increase in apoA-I production. Whether this finding results from an effect of atorvastatin on HDL particle composition or on receptors involved in circulating HDL holoparticle clearance will require further study.
Perfume of Texts, Subversive Embraces : A personal retrospect involving "formalist- readings of Ulysses (2005)

The grand and by now legendary James Joyce Symposium celebrating the Bloomsday Centenary in Dublin less than a year ago, in June 2004, for me was a pretext to follow the dusky path of reminiscence and survey at a leasurely and personal pace (even if this happened at the expense of depth and precision), the four decades of my involvement with literary study and contemplate the extent to which it was shaped by the Blooms.In this talk presented at the Bloomsday 100 International Joyce symposium in Dublin in June 2004, Sonja Bai offered a personal retrospect of her involvement in Joyce studies.While fully aware of the need to broaden the field of Joycean theory and criticism, she advocates the use of a formalist approach resting on the pioneering work of the Russian formalists but expanding into kindred fields such as narratology (Genee, Cohn, Barthes), reader-oriented criticism (Iser), etc.She argues that Joyce's greatest innovation was his sudden and frame-breaking juxtaposition of stylistic and narrative registers informed by a supreme awareness of the forms of language.This is why, she concludes,-being the most deliberately formalist of the modernist writers-Joyce will always need the services of formalist critics. I surrender to a sort of retrospective imagination which feeds the analytic faculty with boundless alternatives and which causes each visualized route to fork and re-fork without endNabokov, Lolita (Book One, Ch.
Adaptive Quantization for Transform Domain Wyner-Ziv Residual Coding of Video (2011)

Since prediction processes such as motion estimation motion compensation are not at the WZ video encoder but at its decoder, WZ video compression cannot have better performance than that of conventional video encoder. In order to implement the prediction process with low complexity at the encoder, WZ residual coding was proposed. Instead of original WZ frames, WZ residual coding encodes the residual signal between key frames and WZ frames. Although the proposed WZ residual coding has good performance in pixel domain, it does not have any improvements in transform domain compared to transform domain WZ coding. The WZ residual coding in transform domain is difficult to have better performance, because pre-defined quantization matrices in WZ coding are not compatible with WZ residual coding. In this paper, we propose a new quantization method modifying quantization matrix and quantization step size adaptively for transform domain WZ residual coding. Experimental result shows 22% gain in BDBR and 1.2dB gain in BDPSNR.
Des documents numériques aux « dépôts » numériques (2000)

Au cours des derniers siecles, le reseau des depots d'archives s'est structure sous l'effet des contraintes liees aux caracteres physiques des supports des documents : leur poids, leur nombre, leur encombrement. Les archives devaient quitter tot ou tard le lieu de leur production, mais pour se deposer a proximite, d'ou le maillage territorial des depots. L'avenement du numerique change la donne. Les anciennes contraintes disparaissent. Des tensions nouvelles vont ebranler le systeme d'organisation des archives et modifier profondement son organisation. Notamment les contraintes economiques contradictoires des producteurs et utilisateurs d'archives. L'arbitrage qui sera rendu dessinera le nouveau reseau des « depots numeriques ».
Function of the hypothalamic-pituitary-adrenal axis in patients with fibromyalgia and low back pain. (1998)

The present data validate and substantiate our preliminary evidence for a dysregulation of the HPA axis in patients with FM, marked by mild hypocortisolemia, hyperreactivity of pituitary ACTH release to CRH, and glucocorticoid feedback resistance. Patients with LBP also display hypocortisolemia, but only a tendency toward the disrupted HPA features observed in the patients with FM. We propose that a reduced containment of the stress-response system by corticosteroid hormones is associated with the symptoms of FM.
Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis (2002)

We identified a diverse set of genes that are potentially related to benign prostatic hyperplasia, including genes both previously implicated in BPH pathogenesis as well as others not previously linked to this disease. Further targeted validation and investigations of these genes at the DNA, mRNA, and protein levels are warranted to determine the clinical relevance and possible therapeutic utility of these genes.
Leakage loss and group velocity dispersion in air-core photonic bandgap fibers (2003)

The wavelength dependence and the structural dependence of leakage loss and group velocity dispersion (GVD) in air-core photonic bandgap fibers (PBGFs) are numerically investigated by using a full-vector finite element method. It is shown that at least seventeen rings of arrays of air holes are required in the cladding region to reduce the leakage losses to a level of 0.1 dB/km in 1.55-microm wavelength range even if using large air holes of the diameter to pitch ratio of 0.9 and that the leakage losses in air-core PBGFs decrease drastically with increasing the hole diameter to pitch ratio. Moreover, it is shown that the waveguide GVD and dispersion slope of air-core PBGFs are much larger than those of conventional silica fibers and that the shape of air-core region greatly affects the leakage losses and the dispersion properties.
Proteolytic Cleavage of High Mobility Group Box 1 Protein by Thrombin-Thrombomodulin Complexes (2008)

TM not only binds to HMGB1 but also aids the proteolytic cleavage of HMGB1 by thrombin. These findings highlight the novel antiinflammatory role of TM, in which thrombin-TM complexes degrade HMGB1 to a less proinflammatory form.
Application of Sequence-Specific Labeled 16S rRNA Gene Oligonucleotide Probes for Genetic Profiling of Cyanobacterial Abundance and Diversity by Array Hybridization (2000)

DNA sequence information for the small-subunit rRNA gene (16S rDNA) obtained from cyanobacterial cultures was used to investigate the presence of cyanobacteria and their abundance in natural habitats. Eight planktonic communities developing in lakes characterized by relatively low algal biomass (mesotrophic) and in lakes with correspondingly high biomass (eutrophic) were selected for the study. The organismal compositions of the water samples were analyzed genetically, using multiplex sequence-specific labeling of oligonucleotide probes targeted to 16S rDNA and subsequent hybridization of the labeled probes to their respective complements spotted onto a solid support (DNA array). Ten probes were established to determine the relative abundances of the discernible cyanobacteria encountered in the selected lakes. The probes were generally specific for their targets, as determined through analyses of clone cultures. Reproducible abundance profiles were established for the lakes investigated in the subsequent analyses of natural cyanobacterial communities. The results from the genetic analyses were then compared with information obtained from standard hydrobiological and hydrochemical analyses. Qualitatively, there were relatively good correlations among the groups of organisms (Nostoc, Microcystis, and Planktothrix species) found in the different lakes. The levels of correlation were lower for the quantitative data. This may, however, be due to differences in sample processing technique. The conclusions from these comparisons are that the genetic abundance profiles may provide a foundation for separating and quantifying genetically distinct groups of cyanobacteria in their natural habitats.
Brilliant Sm, Eu, Tb, and Dy Chiral Lanthanide Complexes with Strong Circularly Polarized Luminescence (2006)

The synthesis, characterization, and luminescent behavior of trivalent Sm, Eu, Dy, and Tb complexes of two enantiomeric, octadentate, chiral, 2-hydroxyisophthalamide ligands are reported. These complexes are highly luminescent in solution. Functionalization of the achiral parent ligand with a chiral 1-phenylethylamine substituent on the open face of the complex in close proximity to the metal center yields complexes with strong circularly polarized luminescence (CPL) activity. This appears to be the first example of a system utilizing the same ligand architecture to sensitize four different lanthanide cations and display CPL activity. The luminescence dissymmetry factor, g(lum), recorded for the Eu(III) complex is one of the highest values reported, and this is the first time the CPL effect has been demonstrated for a Sm(III) complex with a chiral ligand. The combination of high luminescence intensity with CPL activity should enable new bioanalytical applications of macromolecules in chiral environments.