gebhart/patrepeval huggingface dataset:
Coagulation Abnormalities in Acute Lung Injury and Sepsis (2000)

Intraalveolar and intravascular fibrin deposition is frequently found in the setting of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) (1, 2). Fibrin deposits enhance inflammatory response by increasing vascular permeability, activating endothelial cells to produce proinflammatory cytokines and other mediators, inducing the accumulation of activated neutrophils, and modulating immunoregulatory responses in the lung. Infusions of endotoxin produce fibrin deposits in the lung and other organs, and these widespread intravascular alterations are postulated to contribute to multiple organ dysfunction in sepsis (3, 4, 5). Fan and colleagues now show that hemorrhagic shock can potentiate the effects of small doses of endotoxin, creating a procoagulant milieu in the lungs, in which reactive oxygen intermediates (ROI) and tumor necrosis factora (TNFa ) produced by alveolar macrophages have important roles (6). Procoagulant activity is enhanced in the lungs of patients with ARDS (7, 8). Levels of tissue factor, a pivotal mediator in the extrinsic coagulation pathway, are increased in ARDS bronchoalveolar lavage (BAL) specimens, and tissue factor appears to occupy an important role in the ARDS-associated procoagulant state (9, 10). In addition, fibrinolytic processes are inhibited in ALI, as shown by increased BAL concentrations of plasminogen activator inhibitor 1 (PAI-1), and may also contribute to fibrin generation in ALI (11). In experimental models of endotoxemia, early increases in the anticoagulant tissue plasminogen activator are rapidly followed by sustained elevations in PAI-1, leading to a prolonged antifibrinolytic state (12).
Asparaginase Entrapped in Red Blood Cells: Action and Survival (1976)

As a strategy to avoid serious allergic reactions to the antitumor agent asparaginase, this enzyme was entrapped in autologous red blood cells before intravenous injection into monkeys. Additional advantages of this approach are prolonged enzyme half-life and targeting of this agent into the reticuloendothelial system.
Ceramide-Induced Apoptosis in Renal Tubular Cells: A Role of Mitochondria and Sphingosine-1-Phoshate (2015)

Ceramide is synthesized upon stimuli, and induces apoptosis in renal tubular cells (RTCs). Sphingosine-1 phosphate (S1P) functions as a survival factor. Thus, the balance of ceramide/S1P determines ceramide-induced apoptosis. Mitochondria play a key role for ceramide-induced apoptosis by altered mitochondrial outer membrane permeability (MOMP). Ceramide enhances oligomerization of pro-apoptotic Bcl-2 family proteins, ceramide channel, and reduces anti-apoptotic Bcl-2 proteins in the MOM. This process alters MOMP, resulting in generation of reactive oxygen species (ROS), cytochrome C release into the cytosol, caspase activation, and apoptosis. Ceramide regulates apoptosis through mitogen-activated protein kinases (MAPKs)-dependent and -independent pathways. Conversely, MAPKs alter ceramide generation by regulating the enzymes involving ceramide metabolism, affecting ceramide-induced apoptosis. Crosstalk between Bcl-2 family proteins, ROS, and many signaling pathways regulates ceramide-induced apoptosis. Growth factors rescue ceramide-induced apoptosis by regulating the enzymes involving ceramide metabolism, S1P, and signaling pathways including MAPKs. This article reviews evidence supporting a role of ceramide for apoptosis and discusses a role of mitochondria, including MOMP, Bcl-2 family proteins, ROS, and signaling pathways, and crosstalk between these factors in the regulation of ceramide-induced apoptosis of RTCs. A balancing role between ceramide and S1P and the strategy for preventing ceramide-induced apoptosis by growth factors are also discussed.
CGA-7 and HHF, two monoclonal antibodies that recognize muscle actin and react with adherent cells in human long-term bone marrow cultures (1985)

The CGA-7, a monoclonal antibody that reacts with smooth muscle cell actin but not with endothelial cell or fibroblast actin, and HHF, a monoclonal antibody that reacts with smooth muscle, skeletal muscle, and cardiac muscle actin, both recognize microfilaments present within adherent cells from actively hematopoietic human long-term marrow cultures. Macrophages, monocytes, and cultured marrow fibroblasts do not react with either antibody. These data suggest that the anti-actin antibodies may serve as useful markers for in vitro microenvironmental cells and lend support to the hypothesis that stromal cells from long- term marrow cultures are different from marrow fibroblasts and may constitute a unique cell lineage.
Pathogenic Natural Antibodies Propagate Cerebral Injury Following Ischemic Stroke in Mice (2011)

Self-reactive natural Abs initiate injury following ischemia and reperfusion of certain tissues, but their role in ischemic stroke is unknown. We investigated neoepitope expression in the postischemic brain and the role of natural Abs in recognizing these epitopes and mediating complement-dependent injury. A novel IgM mAb recognizing a subset of phospholipids (C2) and a previously characterized anti-annexin IV mAb (B4) were used to reconstitute and characterize injury in Ab-deficient Rag1(-/-) mice after 60 min of middle cerebral artery occlusion and reperfusion. Reconstitution with C2 or B4 mAb in otherwise protected Rag1(-/-) mice restored injury to that seen in wild-type (wt) mice, as demonstrated by infarct volume, demyelination, and neurologic scoring. IgM deposition was demonstrated in both wt mice and reconstituted Rag1(-/-) mice, and IgM colocalized with the complement activation fragment C3d following B4 mAb reconstitution. Further, recombinant annexin IV significantly reduced infarct volumes in wt mice and in Rag1(-/-) mice administered normal mouse serum, demonstrating that a single Ab reactivity is sufficient to develop cerebral ischemia reperfusion injury in the context of an entire natural Ab repertoire. Finally, C2 and B4 mAbs bound to hypoxic, but not normoxic, human endothelial cells in vitro. Thus, the binding of pathogenic natural IgM to postischemic neoepitopes initiates complement-dependent injury following murine cerebral ischemia and reperfusion, and, based also on previous data investigating IgM reactivity in human serum, there appears to be a similar recognition system in both mouse and man.
Subcellular localization of acyl carrier protein in leaf protoplasts of Spinacia oleracea. (1979)

This communication demonstrates that all de novo fatty acid biosynthesis in spinach leaf cells requires acyl carrier protein (ACP) and occurs specifically in the chloroplasts. Antibodies raised to purified spinach ACP inhibited at least 98% of malonyl CoA-dependent fatty acid synthesis by spinach leaf homogenates. Therefore, the presence of ACP in a compartment of the spinach leaf cell would serve as a marker for de novo fatty acid biosynthesis. A radioimmunoassay capable of detecting 10(15) mol (10(-11) g) of spinach ACP was developed to measure the levels of ACP in leaf cell components isolated by sucrose gradient centrifugation of a gentle lysate of spinach leaf protoplasts. All of the ACP of the leaf cell could be attributed to the chloroplast. Less than 1% of the ACP associated with chloroplasts resulted from binding of free ACP to chloroplasts. Of interest, ACP from Escherichia coli, soybean, and sunflower showed only partial crossreactivity with spinach ACP by the radioimmunoassay. These results strongly suggest that, in the leaf cell, chloroplasts are the sole site for the de novo synthesis of C16 and C18 fatty acids. These fatty acids are then transported into the cytoplasm for further modification and are either inserted into extrachloroplastic membrane lipids or returned to the chloroplast for insertion into lamellar membrane lipids.
Analysis of lymphocyte-target conjugates by flow cytometry. I. Discrimination between killer and non-killer lymphocytes bound to targets and sorting of conjugates containing one or multiple lymphocytes. (1986)

The use of flow cytometric analysis and sorting techniques for the enumeration and purification of lymphocyte-target conjugates was investigated. Murine cytotoxic T-lymphocytes (CTL) with killer effector function were identified and quantitated during a 3-hour cell-mediated cytotoxicity reaction using multiparameter analysis. Resolution of conjugates containing single and multiple lymphocytes was achieved by two-color fluorescence, and individual conjugate subpopulations were subsequently sorted for further analysis. To measure total and cytotoxic conjugate frequencies, CTL were labelled with FITC-conjugated Thy 1.2 antibody and dead target cells were stained with propidium iodide (PI). Size difference between the CTL and P815 tumor target cells, as measured by Coulter volume and axial light loss, facilitated detection of conjugates which were identified as both large and Thy 1.2-positive. Conjugates containing dead target cells possessed red fluorescence due to PI uptake. The frequency of conjugates containing cytotoxic activity increased with time during the cytotoxicity period and correlated with frequencies obtained in single-cell assays. Analysis of the distribution of single and multiple lymphocyte-bound conjugates was done by co-centrifugation of Hoechst-stained CTL and FITC-labeled P815 target cells. Analysis by two-color fluorescence effectively resolved conjugate populations containing different numbers of CTL and allowed their purification by cell sorting. The purity of the separate populations was confirmed by fluorescence microscopic inspection. The results of these studies demonstrate that flow cytometry can resolve target-bound and free CTL, measure cytolytic efficiency and specifically sort out cytometrically defined subgroups within the effector cell population.
Chemistry of Polyvalent Iodine (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTChemistry of Polyvalent IodineViktor V. Zhdankin*† and Peter J. Stang‡View Author Information Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota 55812, and Department of Chemistry, 315 S 1400 E, Rm 2020, University of Utah, Salt Lake City, Utah 84112*Corresponding author (e-mail, [email protected]).†University of Minnesota Duluth.‡University of Utah.Cite this: Chem. Rev. 2008, 108, 12, 5299–5358Publication Date (Web):November 6, 2008Publication History Received5 May 2008Published online6 November 2008Published inissue 10 December 2008https://pubs.acs.org/doi/10.1021/cr800332chttps://doi.org/10.1021/cr800332creview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views29668Altmetric-Citations1638LEARN 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:Alcohols,Iodine,Oxidation,Reagents,Salts Get e-Alerts
The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella (2011)

The multitude of physical barriers that likely must be overcome for diatoms to successfully colonize freshwaters suggests that the physiological traits of T. pseudonana, and the genes underlying those traits, might differ from those of strictly marine diatoms. The freshwater ancestry of T. pseudonana might therefore confound generalizations about the physiological and metabolic properties of marine diatoms. The freshwater component of T. pseudonana's history merits careful consideration in the interpretation of experimental data collected for this important model species.
Protein Targeting to the Bacterial Cytoplasmic Membrane (1999)

Proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. In bacteria, several targeting routes are known; the SecB- and the signal recognition particle-dependent pathways are the best characterized. Recently, evidence for the existence of a third major route, the twin-Arg pathway, was gathered. Proteins that use either one of these three different pathways possess special features that enable their specific interaction with the components of the targeting routes. Such targeting information is often contained in an N-terminal extension, the signal sequence, but can also be found within the mature domain of the targeted protein. Once the nascent chain starts to emerge from the ribosome, competition for the protein between different targeting factors begins. After recognition and binding, the targeting factor delivers the protein to the translocation sites at the cytoplasmic membrane. Only by means of a specific interaction between the targeting component and its receptor is the cargo released for further processing and translocation. This mechanism ensures the high-fidelity targeting of premembrane and membrane proteins to the translocation site.
Positron Tomography and Nuclear Magnetic Resonance Imaging (1982)

Noninvasive imaging methods for medical diagnosis and biological investigations, have evolved from qualitative radiological techniques to quantitative methods of measuring biochemical and physiological processes in human body. In particular, new developments in emission tomography, nuclear magnetic resonance imaging, and in vivo spectroscopy offer new horizons for medical research and clinical activities. These methods and their potentials are reviewed and contrasted.
Effect of Endothelin-1 on Blood Pressure and Bronchopulmonary System of the Guinea Pig (1989)

The bronchopulmonary and pressor effects of endothelin-1 (ET-1), a newly described vasoconstrictor peptide produced by endothelial cells, were investigated in the guinea pig. Intravenous injection of ET-1 (1 nmol/kg) induced an increase in pulmonary inflation pressure (PIP) as well as an important and sustained increase in arterial blood pressure (BP). Pretreatment of these animals with propranolol (1 mg/kg i.v.), provoked a significant enhancement of the ET-1-induced increase in PIP, accompanied by a dramatic and significant decrease of BP. When administered by aerosol for 1 min, ET-1 (1, 5, or 10 micrograms/ml) induced a dose-dependent increase in PIP that was maximal by 4-5 min, but no significant change of BP. Pretreatment of guinea pigs with propranolol (1 mg/kg), mepyramine (1 mg/kg i.v.), nifedipine (50 mg/kg i.p.), or verapamil (0.3 mg/kg i.v.) did not inhibit the bronchopulmonary response evoked by aerosol administration of 10 micrograms/ml of ET-1. In contrast, pretreatment of the animals with indomethacin (10 mg/kg i.v.) or BN 52021 (10 mg/kg i.v.) significantly reduced the bronchopulmonary response of ET-1 given by aerosol. Injection of ET-1 (0.1, 0.3, and 1 micrograms) into isolated guinea pig lungs caused significant increases in PIP that were accompanied by the release of TxB2 but not histamine. These results demonstrate that ET-1 induces bronchopulmonary alterations in the guinea pig that appear to be dissociated from the systemic vascular effects of the peptide.
Devices for particle handling by an AC electric field (2005)

Devices for particle handling using an AC electric field are proposed and experimentally validated. With the application of balanced multi- phase high voltage in the 200Vptp to 2kVptp range to a series of encased parallel electrodes with a cen- ter-to-center pitch length of 400pm, particles on a thin protecting and insulating film become charged and are conveyed by the created traveling field. Devices with various novel transportation and ma- nipulation features, utilizing multi-phase AC electric fields that instantly generate particle driving forces, have been designed and produced. Their features include newly developed methods for particle con- veyance smoothing, grouping, and sorting, as well as two-dimensional handling. Particle conveyance char- aderistics have been studied under the influence of three different voltage profiles and in diverse envi- ronments. Various particle materials with a 5pm to 400pm diameter range have been examined in ex- periments; Fe, AZ, glass, and plastic spheres showed the best performances.
A Toolbox Approach to High-Throughput TR-FRET-Based SUMOylation and DeSUMOylation Assays (2009)

The posttranslational modification of target substrates by the ubiquitin-like proteins, specifically the small ubiquitin-like modifier (SUMO), has emerged as an essential mechanism to regulate protein function and control intracellular trafficking. Traditional methods for monitoring either the attachment or removal of SUMO, such as gel electrophoresis or western blot, are effective but typically suffer from a lack of throughput. Here, we report the development and application of time-resolved Förster resonance energy transfer (TR-FRET)-based assays capable of detecting SUMOylation or deSUMOylation in a high-throughput screening (HTS) format. Using Ran GTPase-activating protein (RanGAP1) as a model target substrate, we have demonstrated that the SUMOylation of this protein can be detected using LanthaScreen (Invitrogen, Carlsbad, CA) TR-FRET technology. Additionally, we have generated reagents useful for assessing the deSUMOylation activity of a sentrin-specific protease. All assays are performed in 384-well format and display excellent statistical data (Z' > 0.7) with high signal-to-background levels. Together, this collection of tools can be utilized in a modular approach to develop HTS assays for inhibitors of SUMOylation or deSUMOylation.
The Role of Steady Phosphodiesterase Activity in the Kinetics and Sensitivity of the Light-Adapted Salamander Rod Photoresponse (2000)

We investigated the kinetics and sensitivity of photocurrent responses of salamander rods, both in darkness and during adaptation to steady backgrounds producing 20-3,000 photoisomerizations per second, using suction pipet recordings. The most intense backgrounds suppressed 80% of the circulating dark current and decreased the flash sensitivity approximately 30-fold. To investigate the underlying transduction mechanism, we expressed the responses as a fraction of the steady level of cGMP-activated current recorded in the background. The fractional responses to flashes of any fixed intensity began rising along a common trajectory, regardless of background intensity. We interpret these invariant initial trajectories to indicate that, at these background intensities, light adaptation does not alter the gain of any of the amplifying steps of phototransduction. For subsaturating flashes of fixed intensity, the fractional responses obtained on backgrounds of different intensity were found to "peel off" from their common initial trajectory in a background-dependent manner: the more intense the background, the earlier the time of peeling off. This behavior is consistent with a background-induced reduction in the effective lifetime of at least one of the three major integrating steps in phototransduction; i.e., an acceleration of one or more of the following: (1) the inactivation of activated rhodopsin (R*); (2) the inactivation of activated phosphodiesterase (E*, representing the complex G(alpha)-PDE of phosphodiesterase with the transducin alpha-subunit); or (3) the hydrolysis of cGMP, with rate constant beta. Our measurements show that, over the range of background intensities we used, beta increased on average to approximately 20 times its dark-adapted value; and our theoretical analysis indicates that this increase in beta is the primary mechanism underlying the measured shortening of time-to-peak of the dim-flash response and the decrease in sensitivity of the fractional response.
A Role for the Cytoplasmic Tail of the Pre-T Cell Receptor (TCR) α Chain in Promoting Constitutive Internalization and Degradation of the Pre-TCR (2003)

Engagement of the alpha beta T cell receptor (TCR) by its ligand results in the down-modulation of TCR cell surface expression, which is thought to be a central event in T cell activation. On the other hand, pre-TCR signaling is a key process in alpha beta T cell development, which appears to proceed in a constitutive and ligand-independent manner. Here, comparative analyses on the dynamics of pre-TCR and TCR cell surface expression show that unligated pre-TCR complexes expressed on human pre-T cells behave as engaged TCR complexes, i.e. they are rapidly internalized and degraded in lysosomes and proteasomes but do not recycle back to the cell surface. Thus, pre-TCR down-regulation takes place constitutively without the need for extracellular ligation. By using TCR alpha/p Tau alpha chain chimeras, we demonstrate that prevention of recycling and induction of degradation are unique pre-TCR properties conferred by the cytoplasmic domain of the pT alpha chain. Finally, we show that pre-TCR internalization is a protein kinase C-independent process that involves the combination of src kinase-dependent and -independent pathways. These data suggest that constitutive pre-TCR down-modulation regulates pre-TCR surface expression levels and hence the extent of ligand-independent signaling through the pre-TCR.
Digital Predistortion of Envelope Tracking Amplifiers driven by slew-rate limited envelopes (2011)

This paper presents a new Digital Predistorter (DPD) to compensate for nonlinear distortion that arises in Envelope Tracking (ET) Power Amplifiers (PAs) driven by slew-rate limited versions of the real signal's envelope. The slower version of the transmitted signal's envelope is used to cope with the slew-rate and bandwidth limitations of Envelope Amplifiers (EAs). Unfortunately, the use of slower versions of the real signal's envelope as the drain modulator generates a special kind of nonlinear memory effects. This paper shows experimental results that prove that is possible to compensate for these nonlinear memory effects that appear when exciting the supply of a RF linear PA with a slew-rate limited version of the envelope.