gebhart/patrepeval huggingface dataset:
Expression of De-N-acetyl-gangliosides in Human Melanoma Cells Is Induced by Genistein or Nocodazole (1995)

Neuraminic acid is the core structure of most known sialic acids. In natural systems, the amino group at the 5 position of neuraminic acid residues is usually assumed to be acylated. Previously, synthetic de-N-acetyl-gangliosides (with free amino groups at the 5 position of neuraminic acids) have been shown to modulate cellular proliferation and tyrosine phosphokinase reactions. While indirect evidence has suggested that traces of these molecules exist naturally in certain tumor cells, further exploration has been hampered by the lack of a system showing consistent expression at an easily detectable level. Using synthetic compounds as antigens, we have developed highly specific monoclonal antibodies against de-N-acetyl-GM3 and de-N-acetyl-GD3 that require both the free amino group and the exocyclic side chain of sialic acids for recognition. Cultured human melanoma cells showed low but variably detectable levels of reactivity with these antibodies. The ability of various biologically active molecules to stimulate this reactivity was explored. Of many compounds tested, only the tyrosine kinase inhibitor genistein induced reactivity in a dose-dependent manner. Antibody reactivity with ganglioside extracts from genistein-treated cells was abolished by chemical re-N-acetylation and/or truncation of sialic acid side chains by mild periodate oxidation. High performance thin layer chromatography immuno-overlay analysis confirmed the presence of the novel compound de-N-acetyl-GD3 in these extracts. Several other tyrosine kinase inhibitors tested did not give the same increase in de-N-acetyl-ganglioside expression. However, the microtubule inhibitor nocodazole caused a similar accumulation of these molecules, particularly in non-adherent cells expected to be arrested at metaphase. Thus, genistein may induce de-N-acetyl-ganglioside expression by virtue of its known ability to arrest cells in the G2M phase, rather than as a general consequence of tyrosine kinase inhibition. These studies also provide a system in which to analyze the enzymatic basis of de-N-acetyl-ganglioside expression and their potential roles as growth regulating molecules.
2,3,7,8-Tetrachlorodibenzo-p-dioxin: environmental contaminant and molecular probe. (1976)

The chlorinated dibenzo-p-dioxins and dibenzofurans are formed as trace contaminants during the synthesis of a number of commercially important chemicals. The prototype compound of this group, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), is one of the most potent low molecular weight toxins and teratogens known, and its inadvertent dispersion in the environment has caused concern about the potential hazard to human health. In studying the biochemical effects of TCDD, it was found to be extraordinarily potent as an inducer of two hepatic enzymes: 1) delta-aminolevulinic acid synthetase, the initial and rate-limiting enzyme in heme synthesis, and 2) aryl hydrocarbon hydroxylase, a cytochrome P-450-mediated microsomal monooxygenase. Among a series of halogenated dibenzo-p-dioxins there is an excellent correlation between their toxic potency and their potency as inducers of these two enzymes. The administration of polycyclic aromatic hydrocarbons (e.g., 3-methylcholanthrene (MC)) to certain inbred strains of mice induces aryl hydrocarbon hydroxylase, while other inbred strains fail to respond; and the trait of aryl hydrocarbon responsiveness is inherited as an autosomal dominant. TCDD, about 30,000 times as potent as MC, induces all strains whether responsive or nonresponsive to MC; however, the responsive strains are more sensitive (ED 50 approximately 1 X 10(-9) mole/kg) to TCDD than are the nonresponsive strains (ED50 larger than or equal to 1 X 10(-8) mole/kg). The results suggest that the mutation in the nonresponsive strains results in a ligand binding site (an induction receptor) that has a diminished affinity for MC and TCDD. The correlation among the halogenated dibenzo-p-dioxins, between their potency as toxins and their potency as inducers of aryl hydrocarbon hydroxylase, is discussed in relationship to various proposed mechanisms of toxicity.
Analysis of Double-Stranded Oligonucleotides by Electrospray Mass Spectrometry (1994)

Double-stranded oligonucleotides of different lengths and chemical modification have been analyzed by ion spray mass spectrometry. The non-covalent-bonded duplexes can be detected. Therefore, ion spray mass spectrometry is a useful method for investigation of hybridizations of natural and chemically modified oligonucleotides. Since the exact mass of the double strand can be detected, this method can distinguish between specific and nonspecific interaction.
Cinderella finds her shoe: the first Vps34 inhibitor uncovers a new PI3K–AGC protein kinase connection (2014)

Class II/III PI3Ks (phosphoinositide 3-kinases) produce the PtdIns(3)P lipid that is involved in intracellular vesicular trafficking. In contrast with class I PI3Ks, the potential signalling roles of class II/III PI3Ks are poorly understood. In a recent article in the Biochemical Journal, Bago and co-workers report that Vps34 (vacuolar protein sorting 34), the only class III PI3K, controls the activity of SGK3 (serum- and glucocorticoid-regulated protein kinase 3). Like other AGC kinases, the SGKs (SGK1, SGK2 and SGK3) are activated by dual phosphorylation. Unlike its cousins SGK1 and SGK2, SGK3 contains a PtdIns(3)P-binding domain, providing an additional element of regulation. The study by Bago et al. characterizes and makes extensive use of a Novartis Vps34 inhibitor (VPS34-IN1) that inhibits this PI3K isoform with nanomolar potency, without affecting other lipid kinases or more than 300 protein kinases. The authors show that this compound very rapidly reduced PtdIns(3)P levels at the endosome with concomitant loss of SGK3 phosphorylation. Co-inhibition of class I PI3Ks led to a further reduction in SGK3 activity, indicating that class I PI3Ks may also regulate SGK3 activity through an additional, currently unknown, mechanism. It remains to be assessed whether the novel PI3K-protein kinase connection established by this study is subject to acute cellular stimulation or is part of a constitutive housekeeping function. VPS34-IN1 will provide a useful tool to decipher the kinase-dependent functions of Vps34, with acute changes in SGK3 phosphorylation and subcellular localization being new biomarkers of Vps34 activity.
Immunohistochemical detection of the type I interferon receptor in human fetal, adult, and neoplastic tissues. (1996)

We have used the monoclonal antibody IFNaR3 that recognizes the alpha subunit of the type I interferon (IFN) receptor to study the expression of this receptor in a large series of normal human adult and fetal tissues, as well as in a large number of tumors of diverse origin. Among fetal tissues (8-20 weeks) the type I IFN receptor was expressed in liver, striated muscle, epidermis, renal tubules, choroid plexus of the CNS, and epithelia of different origins (bronchial, gastrointestinal, and pancreatic). Adult tissues showed a similar pattern that includes epithelia from salivary ducts, genital tract, bladder, breast, as well as germinal centers of lymph nodes, tonsils, and spleen. The study of a large series of tumors revealed that the type I IFN receptor is expressed in most, but not all, melanomas, bladder, kidney, small bowel, lung, and breast adenocarcinomas. The majority of lymphomas, sarcomas, and endocrine tumors proved negative. These results support the concept that the type I IFN receptor is rather ubiquitously expressed in normal and malignant epithelial tissues. More interestingly, the expression of the type I IFN receptor was not detected in all tumors, raising the question of whether some cases may fail IFN alpha therapy due to the lack of receptor expression. This report demonstrates that the IFNaR3 monoclonal antibody can be used for receptor detection in paraffin-embedded sections and it could represent a useful tool in the search for correlations between IFN alpha response and receptor expression in different diseases.
Building 3-D city models from multiple unregistered profile maps (2002)

The paper presents an approach for building 3-D city models for virtual environments from multiple 3-D data sets acquired from different viewpoints by light striping. The raw data sets are represented as single valued parametric surfaces called the 3-D profile maps. The profile maps are registered to the same coordinate system by an iterative surface matching algorithm developed previously. The registration proceeds hierarchically from low to high resolution and all the data sets are matched simultaneously but an initial registration is assumed to be known. After having segmented each map by a region growing algorithm, the maps are integrated into a piecewise planar surface model by merging compatible segments in the overlapping areas. The borders of the segments are also traced an the parametric domains of the maps as a step for building a wireframe model. Test results are shown in the case of a scale model of an urban area digitized in laboratory conditions.
A reliable communication switching platform for quick service provisioning (2002)

The paper describes key technologies for establishing a highly reliable communication switching platform, particularly from the viewpoint of service provisioning. For this purpose, a mechanism called the NOSES (nonstop service enhanceable software) plug-in is proposed to ensure partial and dynamic modification of switching system software written in a high-level language without interrupting services. Considering the requirements of reliability, excellent software maintainability and easy operation, a precise mechanism for the modification or addition of software is defined. The relationships between the plug-in mechanisms and the dynamic properties modified software are analyzed and measures to extending applicability of the plug-in to executing switching systems are proposed. The NOSES plug-in is sufficiently applicable for many kinds of software modification and is expected to be used widely for such systems.
The human growth hormone (hGH) antagonist G120RhGH does not antagonize GH in the rat, but has paradoxical agonist activity, probably via the prolactin receptor. (1996)

Human GH (hGH) acts by dimerizing two hGH receptors that bind to different sites in hGH. G120RhGH, an analog mutated in the second binding site to prevent receptor dimerization, acts as an antagonist in vitro. We have now tested the activity of this analog in vivo in rats with low or absent endogenous GH secretion. Surprisingly, treatment with G120RhGH failed to antagonize the effects of infusions or injections of hGH in hypophysectomized (Hx) rats and had little effect on hepatic GH-sensitive CYP2C transcripts in GH-deficient dwarf (dw) rats. Paradoxically, G120RhGH stimulated skeletal growth when infused into Hx rats; a pulsatile iv infusion was more effective than a continuous pattern. Coinfusion of G120RhGH with hGH produced an additive effect on growth. In addition, continuous, but not pulsatile, G120RhGH infusion elevated hepatic 2C12 messenger RNA (mRNA) expression and reduced 2C11 mRNA expression in Hx rats. The direct effects of G120RhGH on hepatic CYP2C transcripts were confirmed in cultured hepatocytes in vitro, which also revealed a significant action of PRL in elevating 2C12 mRNA expression. Binding studies revealed that G120RhGH bound preferentially to hepatic PRL receptors, as [125I]G120hGH was completely displaced by ovine PRL but was unaffected by bGH, a specific GH receptor ligand. The weak growth-promoting effects of G120RhGH were similar to those induced by recombinant hPRL in Hx rats. Our results show that G120RhGH is a poor in vivo GH antagonist in the rat, but shows a paradoxical agonist effect, probably mediated by PRL receptors in this species.
REVIEWS Rimbaud. By PETTTFILSPIERRE. Translated by SHERIDANALAN. Charlottesville, University Press of Virginia, 1987. xxxvi + 388 pp. (1990)

Journal Article REVIEWS Get access Rimbaud. By PIERRE PETTTFILS. Translated by ALAN SHERIDAN. Charlottesville, University Press of Virginia, 1987. xxxvi + 388 pp. MARGARET DAVIES MARGARET DAVIES READING Search for other works by this author on: Oxford Academic Google Scholar French Studies, Volume XLIV, Issue 4, October 1990, Pages 473–474, https://doi.org/10.1093/fs/XLIV.4.473 Published: 01 October 1990
Checkpoint Repair for High-Performance Out-of-Order Execution Machines (1987)

Out-or-order execution and branch prediction are two mechanisms that can be used profitably in the design of supercomputers to increase performance. Proper exception handling and branch prediction miss handling in an out-of-order execution machine do require some kind of repair mechanism which can restore the machine to a known previous state. In this paper we present a class of repair mechanisms using the concept of checkpointing. We derive several properties of checkpoint repair mechanisms. In addition, we provide algorithms for performing checkpoint repair that incur little overhead in time and modest cost in hardware. We also note that our algorithms require no additional complexity or time for use with write-back cache memory systems than they do with write-through cache memory systems, contrary to statements made by previous researchers.
Evolvability (1998)

Evolvability is an organism's capacity to generate heritable phenotypic variation. Metazoan evolution is marked by great morphological and physiological diversification, although the core genetic, cell biological, and developmental processes are largely conserved. Metazoan diversification has entailed the evolution of various regulatory processes controlling the time, place, and conditions of use of the conserved core processes. These regulatory processes, and certain of the core processes, have special properties relevant to evolutionary change. The properties of versatile protein elements, weak linkage, compartmentation, redundancy, and exploratory behavior reduce the interdependence of components and confer robustness and flexibility on processes during embryonic development and in adult physiology. They also confer evolvability on the organism by reducing constraints on change and allowing the accumulation of nonlethal variation. Evolvability may have been generally selected in the course of selection for robust, flexible processes suitable for complex development and physiology and specifically selected in lineages undergoing repeated radiations.
<title>Using the triangle inequality to reduce the number of comparisons required for similarity-based retrieval</title> (1996)

Dissimilarity measures, the basis of similarity-based retrieval, can be viewed as a distance and a similarity-based search as a nearest neighbor search. Though there has been extensive research on data structures and search methods to support nearest-neighbor searching, these indexing and dimension-reduction methods are generally not applicable to non-coordinate data and non-Euclidean distance measures. In this paper we reexamine and extend previous work of other researchers on best match searching based on the triangle inequality. These methods can be used to organize both non-coordinate data and non-Euclidean metric similarity measures. The effectiveness of the indexes depends on the actual dimensionality of the feature set, data, and similarity metric used. We show that these methods provide significant performance improvements and may be of practical value in real-world databases.
Human Parainfluenza Viruses hPIV1 and hPIV3 Bind Oligosaccharides with α2-3-Linked Sialic Acids That Are Distinct from Those Bound by H5 Avian Influenza Virus Hemagglutinin (2007)

We investigated the binding of human parainfluenza virus types 1 and 3 (hPIV1 and hPIV3, respectively) to the glycan array of the Consortium for Functional Glycomics and binding and their release from erythrocytes under conditions where neuraminidase is inactive or active. hPIV1 and hPIV3 bind modifications of Neu5Acalpha2-3Galbeta1-4GlcNAc, including the sialyl-Lewis(x) motif and structures containing 6-sulfogalactose. hPIV1 and hPIV3 thus bind typical N-linked glycans, in contrast to avian influenza virus H5 hemagglutinin (J. Stevens, O. Blixt, T. M. Tumpey, J. K. Taubenberger, J. C. Paulson, and I. A. Wilson, Science 312:404-410, 2006), which binds less-common motifs. While the receptor is not the sole determinant of tropism, hPIV or H5 influenza virus infection of specific cells that express receptors may contribute to their different pathologies.
Identification of a Novel Ligand-Receptor Pair Constitutively Activated by ras Oncogenes (2000)

The Ras signaling pathway is thought to control the expression of a subset of yet to be defined genes that are crucial for cell growth and differentiation. Here we have identified by differential display a novel oncogenic Ras target, mob-5, encoding a 23-kDa cytokine-like secreted protein. Mob-5 expression could be induced by oncogenic Ha-ras and Ki-ras, but not by normal ras activation. Inhibitors of both Ha-Ras and mitogen-activated protein kinase kinase completely abolished the mob-5 expression in ras transformed cells, with concomitant loss of the transformation phenotype. Using an alkaline phosphatase-tagged Mob-5 as ligand, a putative Mob-5 receptor was identified on the cell surface of oncogenic ras transformed cells. Thus, the Mob-5/Mob-5 receptor may represent a novel putative autocrine loop coordinately activated by ras oncogenes.
Evidence of an Association Between the Vasopressin V1b Receptor Gene (AVPR1B) and Childhood-Onset Mood Disorders (2007)

We have found evidence to implicate the AVPR1B gene in the etiology of mood disorders, particularly in females. Antagonists of AVPR1b exhibit antidepressant qualities; hence, genetic variation in AVPR1B may have implications in HPA axis dysregulation in mood disorders.
Two-Stream Convolutional Networks for Action Recognition in Videos (2014)

We investigate architectures of discriminatively trained deep Convolutional Networks (ConvNets) for action recognition in video. The challenge is to capture the complementary information on appearance from still frames and motion between frames. We also aim to generalise the best performing hand-crafted features within a data-driven learning framework. Our contribution is three-fold. First, we propose a two-stream ConvNet architecture which incorporates spatial and temporal networks. Second, we demonstrate that a ConvNet trained on multi-frame dense optical flow is able to achieve very good performance in spite of limited training data. Finally, we show that multi-task learning, applied to two different action classification datasets, can be used to increase the amount of training data and improve the performance on both. Our architecture is trained and evaluated on the standard video actions benchmarks of UCF-101 and HMDB-51, where it is competitive with the state of the art. It also exceeds by a large margin previous attempts to use deep nets for video classification.
Measurement in vivo of proliferation rates of slow turnover cells by 2 H 2 O labeling of the deoxyribose moiety of DNA (2002)

We describe here a method for measuring DNA replication and, thus, cell proliferation in slow turnover cells that is suitable for use in humans. The technique is based on the incorporation of (2)H(2)O into the deoxyribose (dR) moiety of purine deoxyribonucleotides in dividing cells. For initial validation, rodents were administered 4% (2)H(2)O in drinking water. The proliferation rate of mammary epithelial cells in mice was 2.9% per day and increased 5-fold during pregnancy. Administration of estradiol pellets (0-200 microg) to ovariectomized rats increased mammary epithelial cell proliferation, according to a dose-response relationship up to the 100 microg dose. Similarly, proliferation of colon epithelial cells was stimulated in a dose-response manner by dietary cholic acid in rats. Bromodeoxyuridine labeling correlated with the (2)H(2)O results. Proliferation of slow turnover cells was then measured. Vascular smooth muscle cells isolated from mouse aorta divided with a half-life in the range of 270-400 days and die-away values after (2)H(2)O wash-out confirmed these slow turnover rates. The proliferation rate of an adipocyte-enriched fraction from mouse adipose tissue depots was 1-1.5% new cells per day, whereas obese ad libitum-fed obob mice exhibited markedly higher fractional and absolute proliferation rates. In humans, stable long-term (2)H(2)O enrichments in body water were achieved by daily (2)H(2)O intake, without toxicities. Labeled dR from fully turned-over blood cells (monocytes or granulocytes) exhibited a consistent amplification factor relative to body (2)H(2)O enrichment ( approximately 3.5-fold). The fraction of newly divided naive-phenotype T cells after 9 weeks of labeling with (2)H(2)O was 0.056 (CD4(+)) and 0.043 (CD8(+)) (replacement rate <0.1% per day). In summary, (2)H(2)O labeling of dR in DNA allows safe, convenient, reproducible, and inexpensive measurement of cell proliferation in humans and experimental animals and is well suited for slow turnover cells.
The Effects of Heparin and Annexin V on Fibrin Accretion after Injury in the Jugular Veins of Rabbits (1993)

We compared the relative abilities of unfractionated heparin and annexin V to prevent fibrin accretion onto injured jugular veins in vivo. Heparin was used to accelerate the inhibition of thrombin by antithrombin III, and annexin V was used to inhibit the assembly of the prothrombinase complex on phospholipid surfaces, thereby blocking thrombin generation. Rabbit jugular veins were isolated in situ, a 2 cm segment was injured by perfusing it with air, and then blood flow was re-established. Five minutes later, each rabbit was injected with heparin (20 U/kg) or annexin V (0.3 mg/kg) and then with 125I-fibrinogen. The amount of 125I-fibrin accumulation onto each injured vessel wall segment was measured 4 h later. Each injured vessel was completely de-endothelialized as a result of the air perfusion as demonstrated by electron microscopy. 125I-fibrin accretion onto the injured jugular veins was enhanced 2.4-fold as compared to the uninjured veins in sham-operated animals. Heparin treatment did not reduce fibrin accretion, whereas, annexin V treatment decreased fibrin accretion by 60%, p < 0.05. This latter effect was achieved without sustained circulating anticoagulation. Additional experiments confirmed that the inhibitory effect of annexin V on fibrin accretion was associated with a surface specific effect, since more annexin V bound to the injured jugular vein segments as compared to the non-injured jugular veins.(ABSTRACT TRUNCATED AT 250 WORDS)
Adaptive polynomial filters (1991)

Adaptive nonlinear filters equipped with polynomial models of nonlinearity are explained. The polynomial systems considered are those nonlinear systems whose output signals can be related to the input signals through a truncated Volterra series expansion or a recursive nonlinear difference equation. The Volterra series expansion can model a large class of nonlinear systems and is attractive in adaptive filtering applications because the expansion is a linear combination of nonlinear functions of the input signal. The basic ideas behind the development of gradient and recursive least-squares adaptive Volterra filters are first discussed. Adaptive algorithms using system models involving recursive nonlinear difference equations are then treated. Such systems may be able to approximate many nonlinear systems with great parsimony in the use of coefficients. Also discussed are current research trends and new results and problem areas associated with these nonlinear filters. A lattice structure for polynomial models is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>