gebhart/patrepeval huggingface dataset:
In situ detection of DNA damage : methods and protocols (2002)

Detection and analysis of DNA damage is critically important in the study of the widest variety of biological phenomena, ranging from apoptosis and aging to heart diseases and anticancer drug development. In In Situ Detection of DNA Damage: Methods and Protocols, Vladimir Didenko and a panel of experts describe all the major in situ techniques for studying DNA damage and apoptosis, and show how approaches originally designed to label apoptotic cells can be used for DNA damage analysis (and vice versa). The readily reproducible techniques presented here include all those designed to detect specific single- and double-stranded DNA breaks in tissue sections while using polymerases, ligases, nucleases, and kinases. In-depth protocols for single-cell electrophoresis (comet assay) are presented, as well as those for the detection of indirect markers of DNA damage and modified bases. Technical reviews discuss specificity, sensitivity, advantages, and limitations of the techniques described, and compare them with alternative approaches. State-of-the-art and highly practical, In Situ Detection of DNA Damage: Methods and Protocols presents for the first time a complete set of enzymatic methods for determining DNA breaks, and will greatly facilitate the work of all those studying not only the in situ detection of DNA damage but also the labeling of apoptotic cells
Principles and Application of High Pressure–Based Technologies in the Food Industry (2015)

High pressure processing (HPP) has emerged as a commercially viable food manufacturing tool that satisfies consumers' demand for mildly processed, convenient, fresh-tasting foods with minimal to no preservatives. Pressure treatment, with or without heat, inactivates pathogenic and spoilage bacteria, yeast, mold, viruses, and also spores and extends shelf life. Pressure treatment at ambient or chilled temperatures has minimal impact on product chemistry. The product quality and shelf life are often influenced more by storage conditions and packaging material barrier properties than the treatment itself. Application of pressure reduces the thermal exposure of the food during processing, thereby protecting a variety of bioactive compounds. This review discusses recent scientific advances of high pressure technology for food processing and preservation applications such as pasteurization, sterilization, blanching, freezing, and thawing. We highlight the importance of in situ engineering and thermodynamic properties of food and packaging materials in process design. Current and potential future promising applications of pressure technology are summarized.
Sphingosine 1‐phosphate induces Chemotaxis of immature dendritic cells and modulates cytokine‐release in mature human dendritic cells for emergence of Th2 immune responses (2002)

Sphingosine 1-phosphate (S1P) is a potent extracellular lysolipid phosphoric acid mediator that is released after IgE-stimulation of mast cells. Here we investigated the biological activity and intracellular signaling of S1P on human dendritic cells (DC), which are specialized antigen presenting cells with the ability to migrate into peripheral tissues and lymph nodes, as well as control the activation of naive T cells. We show that immature and mature DC express the mRNA for different S1P receptors, such as endothelial differentiation gene (EDG)-1, EDG-3, EDG-5, and EDG-6. In immature DC, S1P stimulated pertussis toxin-sensitive Ca2+ increase actin-polymerization and chemotaxis. These responses were lost by DC matured with lipopolysaccharide. In maturing DC, however, S1P inhibited the secretion of tumor necrosis factor alpha and interleukin (IL)-12, whereas it enhanced secretion of IL-10. As a consequence, mature DC exposed to S1P showed a reduced and increased capacity to generate allogeneic Th1 and Th2 responses, respectively. In summary, our study implicates that S1P might regulate the trafficking of DC and ultimately favor Th2 lymphocyte-dominated immunity.
Anti-cholinergic effects of quinidine, disopyramide, and procainamide in isolated atrial myocytes: mediation by different molecular mechanisms. (1989)

Effects of quinidine, disopyramide, and procainamide on the acetylcholine (ACh)-induced K+ channel current were examined in single atrial cells, using the tight-seal, whole-cell clamp technique. The pipette solution contained guanosine-5'-triphosphate (GTP) or guanosine-5'-O-(3-thiotriphosphate) (GTP-gamma S, a nonhydrolysable GTP analogue). In GTP-loaded cells, not only ACh but also adenosine induced a specific K+ channel current via GTP-binding proteins (G) by activating muscarinic ACh or adenosine receptors. Quinidine and disopyramide depressed the ACh-induced K+ current quite effectively. Procainamide had a weak inhibitory effect. Quinidine also depressed adenosine-induced K+ current, while the effect of disopyramide on adenosine-induced current was much smaller than that on ACh-induced current. In GTP-gamma S-loaded cells, the K+ channel was uncoupled from the receptors and was activated irreversibly, probably due to direct activation of G proteins by GTP-gamma S. Quinidine depressed the GTP-gamma S-induced K+ current just as in the cases of ACh- and adenosine-induced currents of GTP-loaded cells. Disopyramide had only a weak inhibitory effect and procainamide showed no effect. From these results, it is strongly suggested that the major mechanisms underlying the anti-cholinergic effects of quinidine, disopyramide, and procainamide are different; quinidine may inhibit the muscarinic K+ channel itself and/or G proteins, while disopyramide and high doses of procainamide may mainly block functions of muscarinic ACh receptors in atrial myocytes.
A Molecularly Imprinted Fluoral-P/Polyaniline Double Layer Sensor System for Selective Sensing of Formaldehyde (2014)

We demonstrate the capacity of a double layer thin-film system, composed of polyaniline and fluoral-p, to sensitively detect and selectively bind formaldehyde vapor using an interdigitated electrode assembly. The sensor response scales with the concentration of formaldehyde vapor and does not respond significantly to other potentially interfering molecules. This heightened response and selectivity result from imprinting the polyaniline layer with a molecular memory for ammonia. The chemistry of the double layer detection is discussed in terms of the Hantzsch reaction and the p-type semiconducting activity of polyaniline.
Models of autoimmune demyelination in the central nervous system: on the way to translational medicine (2009)

Multiple sclerosis (MS) is the most common neurologic disease of young adults. In the recent years, our understanding on disease pathomechanisms has considerably improved and new therapies have emerged. Yet a cure for this devastating disorder is still a far cry away and human resources on ex vivo specimens are limited. More than 70 years after its first description, experimental autoimmune encephalomyelitis (EAE) remains an important tool to understand concepts of T cell mediated autoimmunity as well as the roles of the innate and the humoral immune systems. Some EAE models also well reflect mechanisms of tissue damage including demyelination, axonal injury and also cortical changes. A limitation of the classical EAE model is a neglect of CD8 T cell mediated immune mechanisms. Moreover, well characterized models for primary progressive MS or demyelination patterns involving primary oligodendrocyte dystrophy are still not available. Yet many current therapeutic concepts including glatiramer acetate or natalizumab stem from their successful first application in EAE models. New strategies include the widespread use of conditional knockout mice to understand the cell-type specific function of single genes, innovative approaches to establish models on the roles of B cells and CD8 T cells as well as on the relation of inflammation to primary degeneration. In summary, EAE models continue to play an important role in neuroimmunology thereby also stimulating research in other fields of the neurosciences and immunobiology.
Interleukin-2-transduced lymphocytes grow in an autocrine fashion and remain responsive to antigen (1995)

The maintenance of T lymphocytes in vivo after adoptive transfer for immunotherapy requires the systemic administration of interleukin-2 (IL-2), but prolonged administration of IL-2 is associated with substantial toxicity. The constitutive production of IL-2 by T cells may be an alternative method to prolong T-cell survival and potentially augment antitumor responses. To study the effects of constitutive production of IL-2 on the growth and antigen reactivity of a murine T cell, the sperm-whale myoglobin (SWM) specific T-cell line 14.1 was retrovirally transduced with the cDNA for IL-2. Cells that were transduced with vectors without an internal promoter were able to proliferate in the absence of exogenously added IL-2, and to grow in an autocrine fashion. These vectors used an internal ribosomal entry site (IRES) to allow translation of the neomycin phosphotransferase (neor) gene. In contrast, the cells transduced with an IL-2 vector in which the neor gene was under the transcriptional control of an internal SV-40 promoter failed to proliferate or grow in the absence of exogenously added IL-2. The proliferation of the cells growing without IL-2 could be inhibited with antibodies to the IL-2 receptor or to human IL-2, indicating that they were still IL-2 dependent. Despite their autocrine growth, no tumor formation was observed in syngeneic mice injected subcutaneously with the transduced cells, and the cells retained their antigen reactivity and specificity. These results suggest that autocrine growth of T cells for therapy will not interfere with effector function.
Generating Suspended Single-Walled Carbon Nanotubes Across a Large Surface Area via Patterning Self-Assembled Catalyst-Containing Block Copolymer Thin Films (2006)

Using self-assembled block copolymers as templates, catalytically active nanostructures with controlled size and space have been produced. A self-assembled polystyrene-b-polyferrocenylsilane thin film and monolayer of surface micelles of cobalt-complexed polystyrene-b-poly(2-vinylpyridine) are fully compatible with novolac-based conventional photoresists. Combining bottom-up self-assembly of catalyst-containing block copolymers with top-down microfabrication processing, plateaus covered with arrays of catalytically active nanostructures have been generated. Spatially selective growth of suspended single-walled carbon nanotubes over a large surface area has been achieved. Greatly enhanced Raman signals have been detected from the suspended tubes. This facile method of creating highly ordered catalyst nanostructures on top of posts enables the rational synthesis of suspended carbon nanotubes, thus facilitating the study of CNT properties by optical methods and enabling the fabrication of devices based on suspended CNTs.
Genetically encoded sensors for ions and metabolites (2004)

Abstract Many of the genes encoding important trans porters and metabolic enzymes have been identified over the last ten years. Moreover it has been possible to study the biochemical properties of the corresponding proteins in great detail. It is expected that by 2,010 biochemical functions will have been assigned to many of the products of the approximately 30,000 Arabidopsis genes. We will get closer to understanding the biological function of the gene products by systematic analysis of mutants using knock-out and TILLING approaches. Metabolomics initiatives complement these approaches by providing insight into the changes in cellular ion and metabolite profiles in the mutants, thus giving information essential for the construction of cellular and whole plant models. However, one important dataset especially relevant to multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of ions and metabolite levels at cellular and subcell ular levels. To address this issue, we have developed protein-based nanosensors for several metabolites, providing a set of tools for the determination of cytosolic and subcellular ion (e.g. iron and zinc) and metabolite levels in real time using fluorescence-based microscopy. The prototypes of these sensors were shown to function in vitro and also in vivo, i.e. in yeast and in mammalian cell cultures. One future goal is to expand the set of sensors to a wider spectrum of targets by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets. Application of nanosensor technology to plant cells and tissues will help to elucidate the special and temporal distribution of ions and metabolites.
Posttranslational Processing of Endogenous and of Baculovirus-Expressed Human Gastrin-Releasing Peptide Precursor (1988)

The 27-amino-acid gastrin-releasing peptide (GRP1-27) is a neuropeptide and growth factor that is synthesized by various neural and neuroendocrine cells. The major pro-GRP hormone (isoform I) contains both GRP1-27 and a novel C-terminal extension peptide termed pro-GRP31-125. In order to define potentially active neuropeptides that could be generated from this novel protein domain, we analyzed the posttranslational processing of endogenous human pro-GRP1-125 in a small-cell lung cancer cell line. Because such studies are much easier in an overexpression system, we investigated at the same time the posttranslational processing of baculovirus-expressed human pro-GRP1-125 in an insect ovary cell line. In the small-cell lung cancer cell line, GRP1-27 was cleaved as expected from the endogenous prohormone at a pair of basic amino acids (29 and 30) and alpha-amidated at its C-terminal methionine; however, a number of novel peptides were generated by additional cleavages in the pro-GRP31-125 domain. In the insect ovary cell line, GRP1-27 was cleaved from the expressed prohormone by a different mechanism, as were a number of other peptides that appeared to be similar in size to those produced by the human neuroendocrine tumor cell line. These data show for the first time that an insect ovary cell line that is widely used to overexpress proteins can process a human neuropeptide precursor. They also reveal the existence of novel pro-GRP-derived peptides that are candidates for biologically active ligands.
Photocrosslinking of polyethylene. I. Photoinitiators, crosslinking agent, and reaction kinetics (1989)

Abstract High density polyethylene has been photocrosslinked in the melt by using 4‐chlorobenzophenone (4‐CBP) as photoinitiator and triallylcyanurate (TAC) as crosslinking agent. Various factors affecting the crosslinking process (photoinitiator used and its concentration, irradiation temperature and time, atmosphere, UV light source, light intensity) were examined. By optimizing the irradiation conditions, it was found that samples up to 2 mm thick could readily be crosslinked to high gel content (≈ 90%) with satisfactory homogeneity within very short irradiation times (≈ 15 s). The kinetic analysis of the crosslinking process showed a linear relation between log S and log t ( S is the sol fraction t is the irradiation time). An induction period was observed, the length of which decreased with increasing concentration of 4‐CBP and increasing light intensity. An upper limit of gel content was also found for long irradiation times at a level depending on the concentration of 4‐CBP. The crosslinking rate was proportional to the second order of light intensity at lower intensity and changed to first order at higher light intensity. A mechanism based on the recombination of chain radicals through both allyl and alkyl type radicals of TAC was proposed.
Differences in tumor microvessel density between squamous cell carcinomas and basal cell carcinomas may relate to their different biologic behavior (1997)

Tumor microvessel density (TMVD) has been recognized as an important indicator for the metastatic risk in certain tumors. The purpose of this study was to analyse whether there is an association of TMVD in epithelial neoplasms of the skin with their clinical behavior. Paraffin sections of keratoacanthomas (KA, n = 10), squamous cell carcinomas (SCC, n = 9), nodular (nod-BCC, n = 13), and sclerosing (scl-BCC, n = 12) basal cell carcinomas were immunohistochemically stained for factor-VIII-related antigen and TMVD was determined. In all SCC, KA and nod-BCC, TMVD significantly exceeded perilesional skin microvessel density (PSMVD) (SCC:TMVD/PSMVD = 20.54:11.25, p < 0.0001; KA:TMVD/PSMVD = 20.90:12.17, p < 0.0001; nod-BCC:TMVD/PSMVD = 16.77:13.34, p = 0.03). In contrast, no significant difference between TMVD and PSMVD was found in scl-BCC (15.44:12.86, p = 0.22). TMVD was significantly higher in SCC and KA compared to nod-BCC (p = 0.036 and 0.006, respectively). Our data demonstrate that SCC and KA are highly vascularized tumors. The fact that TMVD does not differ significantly between SCC and KA (p = 0.80) suggests that MVD is not an indicator for the metastatic risk or aggressive growth behavior of epithelial skin tumors. The finding that MVD in both nod- and scl-BCC is significantly lower than in SCC and KA, might at least in part explain the slow growth of BCC.
Review: LAN Technologies Explained (2001)

LAN Technologies Explained Philip Miller and Michael Cummins Digital Press ISBN 1-55558 234 6 £27.50
Adaptive intra block update for robust transmission of H.263 (2000)

An adaptive block based intra refresh algorithm for increasing error robustness in an interframe coding system is described. The goal of this algorithm is to allow the intra update rates for different image regions to vary according to various channel conditions and image characteristics. The update scheme is based on an "error-sensitivity metric," accumulated at the encoder, representing the vulnerability of each coded block to channel errors. As each new frame is encoded, the accumulated metric for each block is examined, and those blocks deemed to have an unacceptably high metric are sent using intra coding as opposed to inter coding. This approach requires no feedback channel and is fully compatible with H.263. It involves a negligible increase in encoder complexity and no change in the decoder complexity. Simulations performed using an H.263 bitstream corrupted by channel errors demonstrate a significant improvement in terms of error recovery time over nonadaptive intra update strategies.
The Staphostatin-Staphopain Complex (2003)

Staphostatins are the endogenous inhibitors of the major secreted cysteine proteases of Staphylococcus aureus, the staphopains. Our recent crystal structure of staphostatin B has shown that this inhibitor forms a mixed, eight-stranded beta-barrel with statistically significant similarity to lipocalins, but not to cystatins. We now present the 1.8-A crystal structure of staphostatin B in complex with an inactive mutant of its target protease. The complex is held together through extensive interactions and buries a total surface area of 2300 A2. Unexpectedly for a cysteine protease inhibitor, staphostatin B binds to staphopain B in an almost substrate-like manner. The inhibitor polypeptide chain runs through the protease active site cleft in the forward direction, with residues IG-TS in P2 to P2' positions. Both in the free and complexed forms, the P1 glycine residue of the inhibitor is in a main chain conformation only accessible to glycines. Mutations in this residue lead to a loss of affinity of the inhibitor for protease and convert the inhibitor into a substrate.
Highly Efficient Phosphate Diester Transesterification by a Calix[4]arene-Based Dinuclear Zinc(II) Catalyst (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTHighly Efficient Phosphate Diester Transesterification by a Calix[4]arene-Based Dinuclear Zinc(II) CatalystPeter Molenveld, Susan Kapsabelis, Johan F. J. Engbersen, and David N. ReinhoudtView Author Information Laboratory of Supramolecular Chemistry and Technology University of Twente, P.O. Box 217 7500 AE Enschede, The Netherlands Cite this: J. Am. Chem. Soc. 1997, 119, 12, 2948–2949Publication Date (Web):March 26, 1997Publication History Received8 November 1996Published online26 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ja9638770https://doi.org/10.1021/ja9638770rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1165Altmetric-Citations151LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Catalysts,Ligands,Peptides and proteins,Phosphates,Surface interactions Get e-Alerts
Molecular cloning, sequence, and specificity of expression of the gene encoding the low molecular weight human salivary mucin (MUC7). (1993)

Previous biochemical studies have determined that human saliva contains high and low molecular weight mucin glycoproteins (MG1 and MG2, respectively) that are structurally distinct. In this study, we describe the isolation and characterization of overlapping cDNA clones which code for the MG2 protein core. DNA sequencing revealed a translated region of 1131 nucleotides encoding a protein of 377 amino acid residues with a molecular mass of 39 kDa. The first 20 N-terminal residues were very hydrophobic and probably comprise the MG2 leader peptide. The region encoding the secreted protein can be divided into three distinct domains; unique 5'- and 3'-translated regions containing 4 and 1 potential N-glycosylation sites, respectively, and a central region of six almost perfect tandem repeats of 23 amino acid residues with a high number of Thr and Ser. No sequence homology with any other human or animal mucins, and no significant homology to any other proteins was found. MG2 mRNA is about 2.5 kilobases long, and its expression appears to be species-, tissue-, and cell-specific. We propose to name this gene MUC7 in accordance with the mucin genes cloned to date named MUC1-MUC6.
On secret sharing systems (1983)

A "secret sharing system" permits a secret to be shared among <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> trustees in such a way that any <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> of them can recover the secret, but any <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k-1</tex> have complete uncertainty about it. A linear coding scheme for secret sharing is exhibited which subsumes the polynomial interpolation method proposed by Shamir and can also be viewed as a deterministic version of Blakley's probabilistic method. Bounds on the maximum value of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> for a given <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> and secret size are derived for any system, linear or nonlinear. The proposed scheme achieves the lower bound which, for practical purposes, differs insignificantly from the upper bound. The scheme may be extended to protect several secrets. Methods to protect against deliberate tampering by any of the trustees are also presented.