gebhart/patrepeval huggingface dataset:
Induction of endonucleolytic DNA cleavage in human acute myelogenous leukemia cells by etoposide, camptothecin, and other cytotoxic anticancer drugs: a cautionary note. (1989)

Treatment of human HL-60 or KG1A leukemia cells with the topoisomerase II inhibitor etoposide resulted in extensive DNA degradation. When DNA integrity was analyzed by agarose gel electrophoresis, a nucleosomal ladder became evident 1.5-2 h after addition of etoposide to cells, increased in intensity over 6 h, and persisted at 24 h. Six h after addition of the drug, 94 +/- 4% of the cells excluded trypan blue even though as much as 90% of the DNA had been degraded to oligosomal fragments. Exposure of cells to 10 micrograms/ml (17 microM) etoposide for as little as 45 min was sufficient to induce this DNA damage 4 h later. Preincubation with dinitrophenol abolished the effect of etoposide, suggesting that an energy-requiring step occurred prior to or during the endonucleolytic cleavage. In contrast, the effect of etoposide was not prevented by preincubation of HL-60 cells with the RNA synthesis inhibitor 5,6-dichloro-1-beta-ribofuranosylbenzimidazole or the protein synthesis inhibitors cycloheximide or puromycin. On the contrary, high concentrations of 5,6-dichloro-1-beta-ribofuranosylbenzimidazole, cycloheximide, or puromycin by themselves induced the same endonucleolytic cleavage, as did a variety of diverse cytotoxic agents, including camptothecin (0.1 microM), colcemid (0.1 microgram/ml), cis-platinum (20 microM), methotrexate (1 microM), and 1-beta-D-arabinofuranosylcytosine (3 microM). These results suggest that endonucleolytic DNA damage by a preexisting cellular enzyme occurs soon after treatment of HL-60 cells with any of a variety of cytotoxic agents. The observation that a variety of nuclear proteins [including poly(ADP-ribose) polymerase, lamin B, topoisomerase I, topoisomerase II, and histone H1] are degraded concomitant with the DNA fragmentation calls into question the selectivity of the degradative process for DNA. The implications of these results for (a) current theories which focus upon endonucleolytic damage of DNA as a critical early event during cell death, and (b) use of topoisomerase-directed drugs to map topoisomerase-binding sites in active chromatin are discussed.
ChemInform Abstract: Preparation of 2‐Amino‐1,6‐anhydro‐2,3‐dideoxy‐β‐D‐arabino‐hexopyranose. 1H‐and 13C‐NMR Spectra of Deoxy Derivatives of 2‐Amino‐1,6‐anhydro‐2‐deoxy‐D‐glucose and 2‐Amino‐1,6‐anhydro‐2‐deoxy‐D‐mannose. (1984)

Abstract Die literaturbekannte Anhydromannose (Ia) wird in das Derivat (Ib) übergeführt, das nach Mesylierung zu (Ic) zum Epoxid (II) umgesetzt wird.
Measurement of Surface Tension of Epoxy Resins Used in Dispensing Process for Manufacturing Thin Film Transistor-Liquid Crystal Displays (2008)

This paper presents an inverse method for measuring the surface tension of the epoxy resins used in the dispensing process for manufacturing TFT-LCD based on droplet images. A direct method, which is capable of predicting the profile of an axisymmetric liquid droplet, is developed, and then the direct method is incorporated with a droplet imaging system to build up a measurement system for determination of the surface tension of the epoxy resins. When applying the surface tension measurement method, one only needs to give the density of the liquid and identify the geometric parameters of the liquid droplet, such as the droplet volume and the contact angle, through the imaging system. This approach has been used to determine surface tension of various epoxy resins. Finally, for testing the accuracy of the approach, some commonly used fluids are tested. Results show that the approach leads to satisfactory accuracy.
Premature and accelerated aging: HIV or HAART? (2013)

Highly active antiretroviral therapy (HAART) has significantly increased life expectancy of the human immunodeficiency virus (HIV)-positive population. Nevertheless, the average lifespan of HIV-patients remains shorter compared to uninfected individuals. Immunosenescence, a current explanation for this difference invokes heavily on viral stimulus despite HAART efficiency in viral suppression. We propose here that the premature and accelerated aging of HIV-patients can also be caused by adverse effects of antiretroviral drugs, specifically those that affect the mitochondria. The nucleoside reverse transcriptase inhibitor (NRTI) antiretroviral drug class for instance, is known to cause depletion of mitochondrial DNA via inhibition of the mitochondrial specific DNA polymerase-γ. Besides NRTIs, other antiretroviral drug classes such as protease inhibitors also cause severe mitochondrial damage by increasing oxidative stress and diminishing mitochondrial function. We also discuss important areas for future research and argue in favor of the use of Caenorhabditis elegans as a novel model system for studying these effects.
COOL PLASMA ACTIVATED SURFACE IN SILICON WAFER DIRECT BONDING TECHNOLOGY (1988)

A novel cool plasma surface activation method has been developed for high quality SOI/SDB (Silicon wafer Direct Bonding) preparation. The activation effectiveness of different plasma gases, espetially of O2 plsma gases were investigated. The measurements of H.V-PMOS and L.V.-NMOS devices made on the SOI/SDB and on a bulk Silicon indicate that ratios of electron and hole mobility of SOI to those of bulk Silicon are 0.92 and 0.88, respectively. It was proved that our SOI substrate produced by SDB is of device level quality.
Robustness Analysis of an Aircraft Design for Short Takeoff and Landing (2015)

As part of the Collaborative Research Center 880, preliminary aircraft design activities are carried out for a new class of low-noise cruise-efficient short takeoff and landing (CESTOL) transport aircraft. A corresponding aircraft is quite different from a state-of-the-art commercial aircraft because of the use of a high-lift system with active flow control. The fact that new technologies are not sufficiently understood yet in combination with the assumption of common design data and the use of classical calculation methods expresses itself in uncertainties that are of epistemic character. The robustness of a deterministic CESTOL aircraft design toward parameters such as the necessary engine thrust, direct operating costs, and the maximum takeoff and landing distances is investigated here concerning the mentioned uncertainties. For this purpose, a stochastic description of parameter variations of the design is formulated. Stochastic quantities are computed by Monte Carlo sampling to rate the robustness. A distributed component-based software implementation is used to perform the Monte Carlo sampling. The software system is installed on a Linux cluster with several multi-CPU computers; a deterministic sample is simulated through the design program PrADO.
Development of Selective Inhibitors against Plasma Kallikrein. (1991)

Specific plasma kallikrein inhibitors were designed and synthesized and their structure-activity relationship was studied. trans-4-Aminomethylcyclohexanecarbonyl (Tra)-lysyl-4-ethoxycarbonylanilide inhibited plasma kallikrein and plasmin with IC50 values of 23 and 210 microM, respectively, indicating that this compound is fairly specific to plasma kallikrein. Tra-arginyl-4-ethoxycarbonylanilide inhibited plasma kallikrein and plasmin with IC50 values of 16 and 480 microM, respectively. Tra-homoarginyl-4-carboxyanilide inhibited plasma kallikrein and plasmin with IC50 values of 14 microM and 1 mM, respectively. Finally, Tra-Arg(Mts)-4-acetylanilide (ACA) exhibited potent and selective inhibitory activity against plasma kallikrein (IC50 value for plasma kallikrein: 2 microM and for plasmin: 42 microM).
Synthesis and physical analysis of DNA (1992)

Chemical Synthesis of DNA: M.H. Caruthers, G. Beaton, J.V. Wu, and W. Wiesler, Chemical Synthesis of Deoxyoligonucleotides and Deoxyoligonucleotide Analogs. T. Brown and D.J.S. Brown, Purification of Synthetic DNA. B.A. Connolly, Synthetic Oligodeoxynucleotides Containing Modified Bases. P.S. Miller, Preparation of Psoralen-Derivatized Oligodeoxyribonucleodise Methylphosphonates. Nonstandard DNA Structures and Their Analysis: R.E. Dickerson, DNA Structure from A to Z. V.I. Ivanov and D.Y. Krylov, A-DNA in Solution as Studied by Diverse Approaches. B.H. Johnston, Generation and Detection of Z-DNA. A.H. Murchie and D.M.J. Lilley, Supercoiled DNA and Cruciform Structures. M.D. Frank-Kamenetskii, Protonated DNA Structures. D. Sen and W. Gilbert, Guanine Quartet Structures. K. Rippe and T.M. Jovin, Parallel-Stranded Duplex DNA. W.N. Hunter, Crystallographic Studies of DNA Containing Mismatches, Modified, and Unpaired Bases. Spectroscopic Methods for Analysis of DNA: J. Feigon, V. Sklenar, E. Wang, D.E. Gilbert, R.F. Macaya, and P. Schultze, 1H NMR Spectroscopy of DNA. D.G. Gorenstein, 31P NMR of DNA. J.Van Wijk, B.D. Huckriede, J.H. Ippel, and C. Altona, Furanose Sugar Conformations in DNA from NMR Coupling Constants. E. Taillandier and J. Liquier, Infrared Spectroscopy of DNA. W.L. Peticolas and E. Evertsz, Conformation of DNA in Vitro and in Vivo from Laser Raman Scattering. R.M. Clegg, Fluorescence Resonance Energy Transfer and Nucleic Acids. D.M. Gray, R.L. Ratliff, and M.R. Vaughan, Circular Dichroism Spectroscopy of DNA. Structural Methods of DNA Analysis: Y. Timsit and D. Moras, Crystallization of DNA. J. Langowski, W. Kremer, and U. Kapp, Dynamic Light Scattering for Study of Solution Conformation and Dynamics of Superhelical DNA. E. von Kitzing, Modeling DNA Structures: Molecular Mechanics and Molecular Dynamics. A.V. Vologodskii and M.D. Frank-Kamenetskii, Modeling Supercoiled DNA. R. Thresher and J. Griffith, Electron Microscopic Visualization of DNA and DNA-Protein Complexes as Adjunct to Biochemical Studies. P.G. Arscott and V.A. Bloomfield, Scanning Tunneling Microscopy of Nucleic Acids. J. Dubochet, M. Adrian, I. Dustin, P. Furrer, and A. Stasiak, Cryoelectron Microscopy of DNA Molecules in Solution. J. Torbet, Solution Behavior of DNA Studied with Magnetically Induced Birefringence. K.J. Breslauer, E. Freire, and M. Straume, Calorimetry: A Tool for DNA and Ligand-DNA Studies. Author Index. Subject Index.
Role of the renal nerves in one-kidney, one clip hypertension in rats. (1984)

The effects of renal denervation on the onset and maintenance of one-kidney, one clip Goldblatt (1K1C) hypertension were determined. Renal denervation was performed at the time of 1K1C surgery, and was repeated at 3-week intervals to prevent renal nerve regeneration. Denervation delayed the onset of 1K1C hypertension by about 5 weeks, but the final hypertensive state was unaltered. Mean arterial pressure (MAP) averaged 196 +/- 11.4 mm Hg in six rats at 9 weeks after 1K1C surgery and 194 +/- 11.3 mm Hg in eight renal-denervated rats at this time. The delay in the development of 1K1C hypertension following renal denervation could not be explained by interference with renin release. This delay in the development of hypertension could be prevented, however, in renal-denervated 1K1C rats by substituting saline for the drinking water. Two weeks after 1K1C surgery and a high sodium diet, MAP averaged 164 +/- 6.4 mm Hg in eight rats rats with intact renal nerves and 173 +/- 4.8 mm Hg in nine renal-denervated rats. Intact renal nerves are not necessary for the development or maintenance of 1K1C hypertension. Renal denervation delays development of 1K1C hypertension, possibly by delaying the ability of these rats to retain sodium.
A role for heterodimerization of μ and δ opiate receptors in enhancing morphine analgesia (2004)

Opiates such as morphine are the choice analgesic in the treatment of chronic pain. However their long-term use is limited because of the development of tolerance and dependence. Due to its importance in therapy, different strategies have been considered for making opiates such as morphine more effective, while curbing its liability to be abused. One such strategy has been to use a combination of drugs to improve the effectiveness of morphine. In particular, delta opioid receptor ligands have been useful in enhancing morphine's potency. The underlying molecular basis for these observations is not understood. We propose the modulation of receptor function by physical association between mu and delta opioid receptors as a potential mechanism. In support of this hypothesis, we show that mu-delta interacting complexes exist in live cells and native membranes and that the occupancy of delta receptors (by antagonists) is sufficient to enhance mu opioid receptor binding and signaling activity. Furthermore, delta receptor antagonists enhance morphine-mediated intrathecal analgesia. Thus, heterodimeric associations between mu-delta opioid receptors can be used as a model for the development of novel combination therapies for the treatment of chronic pain and other pathologies.
Commensal Clostridia: leading players in the maintenance of gut homeostasis (2013)

The gastrointestinal tract is a complex and dynamic network where an intricate and mutualistic symbiosis modulates the relationship between the host and the microbiota in order to establish and ensure gut homeostasis. Commensal Clostridia consist of gram-positive, rod-shaped bacteria in the phylum Firmicutes and make up a substantial part of the total bacteria in the gut microbiota. They start to colonize the intestine of breastfed infants during the first month of life and populate a specific region in the intestinal mucosa in close relationship with intestinal cells. This position allows them to participate as crucial factors in modulating physiologic, metabolic and immune processes in the gut during the entire lifespan, by interacting with the other resident microbe populations, but also by providing specific and essential functions. This review focus on what is currently known regarding the role of commensal Clostridia in the maintenance of overall gut function, as well as touch on their potential contribution in the unfavorable alteration of microbiota composition (dysbiosis) that has been implicated in several gastrointestinal disorders. Commensal Clostridia are strongly involved in the maintenance of overall gut function. This leads to important translational implications in regard to the prevention and treatment of dysbiosis, to drug efficacy and toxicity, and to the development of therapies that may modulate the composition of the microflora, capitalizing on the key role of commensal Clostridia, with the end goal of promoting gut health.
Last clock (2005)

The Last clock displays a space's history and rhythm. Trails behind its hands paint the clock face with a video feed, creating a mandala of archived time. The Last clock began as an investigation into representations of time. The goal was to use the mutable properties of digital technology, hoping to create something aesthetically pleasing, interesting, and ever changing without having to succumb to randomness. The clock reveals the rhythm of events and spaces. It provides a record of and a means of reflection for what is happening and what has happened. With the Internet-connected streaming version, the clock can connect two or more remote spaces so that people feel a sense of each other's presence. The clock does not show precisely the activity in the space, just a filtered version of it. Beyond being an aesthetic object, Last serves a real purpose as a display that shows an overview of a given space's dynamics and history. By borrowing the form of a traditional analog clock, Last becomes an easy-to-read visualization of complex information, which includes the type of activity captured, the pace and volume of motion, and the point in time that this activity happened. it shows all this information in a continuously updated, live, single image. This article is available with a short video documentary on CD-ROM.
Focused ion beam/optical-merged lithographic technique using ladder silicone spin-on glass (1995)

Focused ion beam (FIB) optical-merged lithography has been developed to improve the throughput in delineating the gate pattern of the metal–oxide–semiconductor field-effect transistor. In this process, only the critical part of the pattern is delineated with FIB and merged with optically printed noncritical parts. Ladder silicone spin-on glass (LS-SOG) has been used as the negative resist for the 200 keV Si2+-focused ion beam. The 100 nm polysilicon gate was successfully fabricated using the single-level resist process. The film characteristics of the LS-SOG were also investigated.
Gamma delta T lymphocytes regulate the induction and maintenance of oral tolerance (1997)

Oral administration of Ag, over a period of several days, induces a state of tolerance that is associated with activation of CD8+ T cells that can transfer unresponsiveness to naive syngeneic hosts. We previously demonstrated that these T cells are not CTL precursors and that they inhibit responses by CD8+ CTL, as well as Ab and CD4+ T cell responses. Activation of noncytolytic, CD8+ suppressor T cells by oral Ag is a process that is not understood. In these studies, we asked whether depletion of the gamma delta T cells altered induction of oral tolerance. Injection of the anti-delta-chain Ab (GL3) down-modulated the expression of gamma delta TCR and inhibited the induction of oral tolerance to OVA, as measured by Ab, CD4+, and CD8+ T cell responses. GL3 did not activate IL-2 secretion that could be detected in the serum, nor did it induce IL-2R expression by intraepithelial lymphocytes, suggesting that GL3 inhibited the function of gamma delta T cells rather than activating them. This interpretation is supported by our observation that oral administration of Ag did not induce tolerance in TCR-delta knockout mice. These data suggest that gamma delta T cells play a critical, active role in tolerance induced by orally administered Ag.
Sulfur-Oxidizing Bacteria in Soap Lake (Washington State), a Meromictic, Haloalkaline Lake with an Unprecedented High Sulfide Content (2006)

Culture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genus Thioalkalimicrobium, which are common inhabitants of soda lakes. A dense population of Thioalkalimicrobium (up to 10(7) cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. Twelve Thioalkalimicrobium strains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups according to 16S rRNA gene sequence analysis. One of the groups was closely related to T. cyclicum, which was isolated from Mono Lake (California), a transiently meromictic, haloalkaline lake. The second group, consisting of four isolates, was phylogenetically and phenotypically distinct from known Thioalkalimicrobium species and unique to Soap Lake. It represented a new species, for which we suggest the name Thioalkalimicrobium microaerophilum sp. nov.
Role of Monocytes in Atherogenesis (2003)

This review focuses on the role of monocytes in the early phase of atherogenesis, before foam cell formation. An emerging consensus underscores the importance of the cellular inflammatory system in atherogenesis. Initiation of the process apparently hinges on accumulating low-density lipoproteins (LDL) undergoing oxidation and glycation, providing stimuli for the release of monocyte attracting chemokines and for the upregulation of endothelial adhesive molecules. These conditions favor monocyte transmigration to the intima, where chemically modified, aggregated, or proteoglycan- or antibody-complexed LDL may be endocytotically internalized via scavenger receptors present on the emergent macrophage surface. The differentiating monocytes in concert with T lymphocytes exert a modulating effect on lipoproteins. These events propagate a series of reactions entailing generation of lipid peroxides and expression of chemokines, adhesion molecules, cytokines, and growth factors, thereby sustaining an ongoing inflammatory process leading ultimately to lesion formation. New data emerging from studies using transgenic animals, notably mice, have provided novel insights into many of the cellular interactions and signaling mechanisms involving monocytes/macrophages in the atherogenic processes. A number of these studies, focusing on mechanisms for monocyte activation and the roles of adhesive molecules, chemokines, cytokines and growth factors, are addressed in this review.
Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae. (1990)

We have purified to near homogeneity a site-specific, double-stranded DNA endonuclease (I-Sce II) encoded by intron 4 alpha (aI4 alpha) of the yeast mitochondrial coxI gene. Our purification starts with a high salt extract of mitochondria isolated from a yeast strain that overproduces the enzyme because of a block in splicing of aI4 alpha. The final step of purification is an affinity column consisting of covalently bound double-stranded DNA multimers of a synthetic sequence, 5'-TTGGTCATCCAGAAGTAT-3', which contains the I-Sce II cleavage/recognition site. Typical yields of enzyme are 3-5% with a specific activity of approximately 500,000 units/mg, where 1 unit of activity cleaves 50 ng of DNA substrate/h at 30 degrees C. I-Sce II has a monomer molecular mass of 31 kDa as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Active enzyme purifies as a 55-kDa species, which we presume to be a homodimer. I-Sce II monomer comigrates with an in vivo synthesized mitochondrial translation product made in the strain that overproduces the enzyme. We conclude that I-Sce II is derived by proteolytic processing of a precursor polypeptide, p62, encoded by an in-frame fusion of coxI exons 1-4 with the downstream aI4 alpha reading frame. I-Sce II is most active at pH 7.5 and at 20-30 degrees C. Endonuclease activity is sensitive to salt and is dependent upon Mg2+ or Mn2+, but is unaffected by inclusion of ATP or GTP. I-Sce II is the first intron-encoded protein to be purified and characterized from yeast mitochondria.
Complementary Adhesion Molecules Promote Neutrophil- Kupffer Cell Interaction and the Elimination of Bacteria Taken Up by the Liver (2002)

Most bacteria that enter the bloodstream are taken up by the liver. Previously, we reported that such organisms are initially bound extracellularly and subsequently killed by immigrating neutrophils, not Kupffer cells as widely presumed in the literature. Rather, the principal functions of Kupffer cells demonstrated herein are to clear bacteria from the peripheral blood and to promote accumulation of bactericidal neutrophils at the principal site of microbial deposition in the liver, i.e., the Kupffer cell surface. In a mouse model of listeriosis, uptake of bacteria by the liver at 10 min postinfection i.v. was reduced from approximately 60% of the inoculum in normal mice to approximately 15% in mice rendered Kupffer cell deficient. Immunocytochemical analysis of liver sections derived from normal animals at 2 h postinfection revealed the massive immigration of neutrophils and their colocalization with Kupffer cells. Photomicrographs of the purified nonparenchymal liver cell population derived from these infected mice demonstrated listeriae inside neutrophils and neutrophils within Kupffer cells. Complementary adhesion molecules promoted the interaction between these two cell populations. Pretreatment of mice with mAbs specific for CD11b/CD18 (type 3 complement receptor) or its counter-receptor, CD54, inhibited the accumulation of neutrophils in the liver and the elimination of listeriae. Complement was not a factor; complement depletion affected neither the clearance of listeriae by Kupffer cells nor the antimicrobial activity expressed by infiltrating neutrophils.