gebhart/patrepeval huggingface dataset:
Handbook of synthetic substrates : for the coagulation and fibrinolytic system (1983)

I. Basic enzymology.- I. 1. Introduction.- I. 2. Maximal velocity.- I. 3. Michaelis constant.- I. 4. Low substrate concentration the efficiency of an enzyme.- I. 5. High substrate concentration the saturation curve.- I. 6. The characteristic parameters of an enzymatic reaction.- I. 7. Enzyme inhibition.- I. 8. Rate-constants and enzymatic mechanism.- I. 9. The reaction mechanism of serine proteases.- 1.10. Transient state kinetics.- 1.11. Data from a reaction going to completion.- 1.12. Active site titration.- 1.13. Simultaneous reactions in complicated reaction mixtures.- II. Measuring the conversion of a chromogenic substrate.- II. 1. Photometric assays.- II. 2. Absorption spectrophotometry.- II. 3. Choice of wavelength and absorbancy range.- II. 4. Temperature.- II. 5. The reaction medium.- II. 6. Substrate solution.- II. 7. Methodology.- II. 8. Execution of the experiment.- II. 9. Fluorescence.- II.10. Electrochemical determinations.- III. Substrates.- III.1. Specificity in serine proteases.- III.2. Substrate selectivity and sensitivity.- III.3. Inhibition by artificial substrates.- III.4. Data on commercially available substrates.- III.5. Fluorogenic substrates.- III.6. General principles of fluorogenic peptide substrates with 7-amino-4-methylcoumarine (MCA) as a leaving group.- III.7. Thioesters.- III.8. Substrates for electrochemical determinations.- III.9. Luminogenic substrates.- IV. Determinations that can be carried out with chromogenic substrates.- IV. 1. Thrombin and derived determinations.- 1.1. thrombin.- 1.2. prothrombin.- 1.3. antithrombin III and heparin cofactor.- 1.4. prothrombinase, factor V, platelet factor 3.- 1.4.1. prothrombinase.- 1.4.2. factor V.- 1.4.3. platelet factor 3.- IV.2. Factor Xa and derived determinations.- 2.1. factor Xa.- 2.2. factor X.- 2.3. antifactor Xa (antithrombin III, heparin cofactor).- 2.4. heparin.- 2.5. platelet factor 4 and other antiheparins.- 2.6. factor X activating enzymes.- 2.6.1. factor VIII.- 2.6.2. factor IX.- 2.6.3. platelet factor 3.- 2.6.4. factor VII and tissue thromboplastin.- IV.3. Determination of fibrinolytic pathway components in plasma.- 3.1. plasminogen.- 3.2. plasminogen activator.- 3.3. 'free' protease activity.- 3.4. plasmin generation rates.- 3.5. ?2-plasmin inhibitor.- IV.4. The contact activation system.- 4.1. plasma prekallikrein.- 4.2. factor XII.- 4.3. activated factor XI.- IV.5. Miscellaneous determinations.- 5.1. glandular kallikrein.- 5.2. brinase and brinase inhibitors.- 5.3. bacterial endotoxins.- Bibliography of synthetic substrates (as available Fall 1982).- Index of subjects.
Measurement of NOS Activity by Conversion of Radiolabeled Arginine to Citrulline Using Ion-Exchange Separation (2003)

Nitric oxide synthase (NOS) catalyzes a complex reaction utilizing L-arginine, nicotinamide adenine dinucleotide phosphate (NADPH) and oxygen to synthesize NO, and with citrulline and NADP+ being produced as co-products (reviewed in ref. ). This chapter describes the measurement of NOS-functional activity by determining the NOS inhibitor-sensitive conversion of radiolabeled (14C or 3H) arginine to citrulline, with separation of the labeled product from substrate by ion-exchange techniques. The earliest forms of this assay used rather slow and labor-intensive separations, e.g., on an amino-acid analysis ion-exchange column (). However, a simple method of separating arginine from citrulline using the Na+ form of the strongly acidic-cation exchanger Dowex 50 (which has sulphonic-acid functional groups) was described by Gopalakrishna and Nagarajan (), and this technique was applied by Bredt and Snyder () to assays of purified NOS. We have subsequently modified this assay (, , ) to simplify it further and to make it suitable for the study of NOS activity in a wide variety of settings.
Interleukin‐1 regulation of hematopoietic growth factor production by human stromal fibroblasts (1988)

The human stromal fibroblastoid cell strain designated ST-1 represents a normal population of cells capable of supporting hematopoiesis in vitro. These cells constitutively elaborate hematopoietic growth factor activity into the medium and the level of production of this activity dramatically increases following stimulation of the cells with IL-1. This enhanced production is due at least in part to increased expression of the genes for GM-CSF, G-CSF, and IL-6, but not IL-3. The IL-1 treatment had little effect on the expression of M-CSF, a factor made constitutively by the cells. These results are consistent with the model that hematopoiesis is regulated at least in part by constant short-range interactions of humoral factors produced by stromal cells both with other types of stromal cells and with the hematopoietic progenitors.
Rare earth metal initiated polymerizations of polar and nonpolar monomers to give high molecular weight polymers with extremely narrow molecular weight distribution (1995)

Abstract Organolanthanide (III) initiated polymerizations of alkyl methacrylates and alkyl acrylates proceed in a living fashion and yield high molecular weight polymers with extremely narrow molecular weight distribution at high conversion. Random and block copolymerizations of alkyl acrylates are carried out successfully to give almost “monodisperse” polymers. Rare earth metal initiated polymerizations of lactones such as ε‐caprolactone and δ‐valerolactone produce again high molecular weight polymers with narrow molecular weight distribution. Bulky divalent and trivalent rare earth metal complexes catalyze the living polymerization of ethylene and α‐olefins and the Sm (OR) 3 /AIR 3 H 2 O initiator system catalyzes the polymerization of propylene oxide to give polymers with narrow molecular weight distribution.
Maculatin 1.1, an anti‐microbial peptide from the Australian tree frog, <i>Litoria genimaculata</i> (2000)

The dorsal glands of Australian tree frogs from the Litoria species contain a diversity of antibiotic peptides that forms part of the defence system of the animal. Here, the antibiotic activity and structure of maculatin 1.1, a 21 amino acid peptide from Litoria genimaculata, are compared. The activity data on maculatin 1.1 and a series of its analogues imply that the mechanism of action of maculatin 1.1 involves binding to, and subsequent lysis of, the bacterial cell membrane. The structure of maculatin 1.1 was determined using NMR spectroscopy in a trifluoroethanol/water mixture and when incorporated into dodecylphosphocholine micelles. Under both conditions, the peptide adopts a very similar conformation, i.e. a helical structure with a central kink in the vicinity of Pro15. The kink allows the peptide to adopt a well-defined amphipathic conformation along its entire length. The similar structures determined under both solvent conditions imply that structures of membrane-interacting peptides in trifluoroethanol/water mixtures are representative of those adopted in a membrane environment, e.g. when incorporated into micelles. The synthetic Ala15 analogue of maculatin 1.1 has markedly reduced activity and its NMR-derived structure is a well-defined helix, which lacks the central kink and flexibility of the parent molecule. It is concluded that the kink is important for full biological activity of the peptide, probably because it allows maximum amphipathicity of the peptide to facilitate interaction with the membrane. The structure of maculatin 1.1 is compared with a related peptide, caerin 1.1 [Wong, H., Bowie, J.H. and Carver, J.A. (1997) Eur. J. Biochem. 247, 545-557], which has an additional central proline residue and enhanced central flexibility compared with maculatin 1.1. The role of central flexibility within antibiotic peptides in their interaction with bacterial membranes is discussed.
Anxiogenic activity of intraventricularly administered bradykinin in rats (1995)

The anxiogenic action of bradykinin was investigated in rats and compared with that of yohimbine, a known anxiogenic agent. Bradykinin (0.5, 1 and 2 μg/rat) was administered intracerebroventricularly (i.c.v.), whereas yohimbine (2 mg/kg) was administered i.p. The experimental methods used were the open- field, elevated plus-maze, social interaction and novelty suppressed feeding latency tests, and estimation of brain tribulin activity in terms of endogenous monoamine oxidase (MAO) A and MAO B inhibition. The behavioural and biochemical effects induced by bradykinin were qualitatively similar to those of yohimbine. Thus, both the drugs reduced ambulation and rears, and increased immobility and defecation, in the open-field test. They decreased the number of entries and time spent on the open arms of the elevated plus-maze, reduced social interaction in paired rats and increased the feeding latency in an unfamiliar environment in 48 h food-deprived rats. These effects are known to be associated with anxiety in animals. Bradykinin and yohimbine increased rat brain tribulin activity, the effect on the MAO A inhibitor component being more marked than that on the MAO B inhibitor component. The MAO A inhibitor component has been postulated to be the major anxiogenic moiety of tribulin. Lorazepam, a well known benzodiazepine anxiolytic agent, attenuated the anxiogenic effects of bradykinin and yohimbine, which may not be a functional effect. The investigation indicates that, like cholecystokinin (CCK), bradykinin may function as an endogenous anxiogenic peptide.
An open‐label, single‐dose bioavailability study of the pharmacokinetics of CAT‐354 after subcutaneous and intravenous administration in healthy males (2010)

CAT-354 exhibited bioavailability of approximately 60% when given s.c. to healthy male subjects.
Plate Heights below 50 nm for Protein Electrochromatography Using Silica Colloidal Crystals (2010)

Silica colloidal crystals formed from 330 nm nonporous silica spheres inside of 75 μm i.d. fused silica capillaries were evaluated for the efficiency of capillary electrochromatography of proteins. Three proteins, ribonuclease A, cytochrome C, and lysozyme, each covalently labeled with fluorophor, were well separated over a distance of 1 cm by isocratic electromigration, using 40:60 acetonitrile/water with 0.1% formic acid. A van Deemter plot showed that the plate height for lysozyme, which was the purest of the three proteins, was diffusion-limited for electric fields ranging from 400 to 1400 V/cm. The plate height for lysozyme was below 50 nm at almost all of the migration velocities, and it approached 10 nm at the highest velocity. Eddy diffusion was negligible. Lysozyme migrated over a 12 mm separation length with more than 10(6) plates in 1.5 min. These results indicate that silica colloidal crystals are well suited for electrically driven separations of large, highly charged analytes such as proteins. The 10(6) plates observed for a separation length of barely more than a centimeter means they are potentially valuable for miniaturized separations in microchip and lab-on-a-chip devices.
Panax ginseng Administration in the Rat Prevents Myocardial Ischemia-Reperfusion Damage Induced by Hyperbaric Oxygen: Evidence for an Antioxidant Intervention (1999)

The aim of this work was to investigate in the rat the protective effect of an oral administration (one week) of Panax ginseng (PG) extract (10 mg/ml in drinking water; 1.6 g/kg/day) on myocardial post-ischemic damage induced by hyperbaric oxygen (HBO) and on the loss in functionality of the endothelium in aorta ring preparations. The hearts from control rats (no-HBO and no-HBO-PG), and from rats exposed to HBO and to HBO after PG treatment were isolated and subjected to mild ischemia and then reperfused. HBO greatly worsens the post-ischemic damage in controls, as demonstrated by the rise of left ventricular end diastolic pressure (LVEDP) and coronary perfusion pressure (CPP). PG significantly restrained the increase of LVEDP and CPP in respect to HBO-untreated rats, as well as that of CPP induced by injection of angiotensin II during pre-ischemia. In HBO control rats the reduction of the vasorelaxant effect of acetylcholine on norepinephrine precontracted aortic rings, was markedly recovered by PG; a similar trend was observed in aortic rings challenged with the nitric oxide synthase inhibitor NG-monomethyl-L-arginine (56% recovery). These results strongly indicate that PG prevents the myocardial ischemia/reperfusion damage and the impairment of endothelial functionality induced by reactive oxygen species arising from HBO exposure, through an antioxidant intervention. The in vitro radical scavenging activity of PG seems to be too weak (0.05-0.5 mg/ml) to explain by itself the cardiac and extra-cardiac protective effects, and this suggests a role also for an indirect antioxidant action of the drug (endothelial nitric oxide synthase stimulation).
Self-Sensing Ionic Polymer Actuators: A Review (2015)

Ionic electromechanically active polymers (IEAP) are laminar composites that can be considered attractive candidates for soft actuators. Their outstanding properties such as low operating voltage, easy miniaturization, and noiseless operation are, however, marred by issues related to the repeatability in the production and operation of these materials. Implementing closed-loop control for IEAP actuators is a viable option for overcoming these issues. Since IEAP laminates also behave as mechanoelectrical sensors, it is advantageous to combine the actuating and sensing functionalities of a single device to create a so-called self-sensing actuator. This review article systematizes the state of the art in producing self-sensing ionic polymer actuators. The IEAPs discussed in this paper are conducting (or conjugated) polymers actuators (CPA), ionic polymer-metal composite (IPMC), and carbonaceous polymer laminates.
Surface plasmon resonance : methods and protocols (2010)

1. Surface Plasmon Resonance: A General Introduction Nico J. de Mol and Marcel J.E. Fischer 2. The Role of Mass Transport Limitation and Surface Heterogeneity in the Biophysical Characterization of Macromolecular Binding Processes by SPR Biosensing Peter Schuck and Huaying Zhao 3. Amine Coupling Through EDC/NHS: A Practical Approach Marcel J.E. Fischer 4. High Affinity Immobilization of Proteins Using Biotin- and GST-based Coupling Strategies Stephanie Q. Hutsell, Randall J. Kimple, David P. Siderovski, Francis S. Willard, and Adam J. Kimple 5. A Capture Coupling Method for the Covalent Immobilization of Hexahistidine Tagged Proteins for Surface Plasmon Resonance Adam J. Kimple, Robin E. Muller, David P. Siderovski, and Francis S. Willard 6. Affinity Constants for Small Molecules from SPR Competition Experiments Nico J. de Mol 7. Surface Plasmon Resonance Signal Enhancement for Immunoassay of Small Molecules John S. Mitchell and Yinqiu Wu 8. High-Throughput Kinase Assay Based on Surface Plasmon Resonance Hiroyuki Takeda, Naoki Goshima, and Nobuo Nomura 9. SPR Biosensor as a Tool for Screening Prion Protein Binders as Potential Antiprion Leads Beining Chen 10. Carbohydrate-Lectin Interactions Assayed by SPR Eric Duverger, Nathalie Lamerant-Fayel, Natacha Frison, and Michel Monsigny 11. DNA Sensors Based on Mixed Self-Assembled DNA/Alkanethiol Films Sara Peeters and Tim Stakenborg 12. Preparation of Lipid Membrane Surfaces for Molecular Interaction Studies by Surface Plasmon Resonance Biosensors Mojca Podlesnik Besenicar and Gregor Anderluh 13. Capture of Intact Liposomes on Biacore Sensor Chips for Protein-Membrane Interaction Studies Vesna Hodnik and Gregor Anderluh 14. Surface Plasmon Resonance Spectroscopy for Studying the Membrane Binding of Antimicrobial Peptides Kristopher Hall and Marie-Isabel Aguilar 15. Surface Plasmon Resonance Spectroscopy in Determination of the Interactions between Amyloid ss Proteins (Ass) and Lipid Membranes Xu Hou, David H. Small, and Marie-Isabel Aguilar 16. Incorporation of a Transmembrane Protein into a Supported 3D-Matrix of Liposomes for SPR Studies Annette Graneli 17. Application of Surface Plasmon Resonance Spectroscopy to Study G-Protein Coupled Receptor Signalling Konstantin E. Komolov and Karl-Wilhelm Koch 18. Integration of SPR Biosensors with Mass Spectrometry (SPR-MS) Dobrin Nedelkov 19. SPR/MS: Recovery from Sensorchips for Protein Identification by MALDI-TOF Mass Spectrometry Jonas Borch and Peter Roepstorff
Ray-tracing polymorphic multidomain spectral/hp elements for isosurface rendering (2006)

The purpose of this paper is to present a ray-tracing isosurface rendering algorithm for spectral/hp (high-order finite) element methods in which the visualization error is both quantified and minimized. Determination of the ray-isosurface intersection is accomplished by classic polynomial root-finding applied to a polynomial approximation obtained by projecting the finite element solution over element-partitioned segments along the ray. Combining the smoothness properties of spectral/hp elements with classic orthogonal polynomial approximation theory, we devise an adaptive scheme which allows the polynomial approximation along a ray-segment to be arbitrarily close to the true solution. The resulting images converge toward a pixel-exact image at a rate far faster than sampling the spectral/hp element solution and applying classic low-order visualization techniques such as marching cubes.
Optimim design for a broadband microstrip balun (1977)

The letter reports calculations of Marchand balun performance which show that bandwidths approaching 50:1 (for a V.S.W.I.≤2:1) should be achievable with overlaid microstrip structures. The bandwidth limits (≲8:1) reported by previous writers appear to reflect only the inaccessibility of the true optimum to the semiempirical design methods used and the limitations of fabrication on single-thickness card. Preliminary experimental results confirm the theoretical indications.
Quasi-partitioning: a new paradigm for transaction execution in partitioned distributed database systems (2003)

The quasi-partitioning paradigm of operation for partitioned database systems is discussed in which a broken main link between two partitions can be replaced by a much slower backup link (e.g. a dial-up telephone connection). The paradigm solves the problem of preparation for network partitioning. The quasi-partitioning mode of operation has two primitive operations: creeping retrieval and creeping merge. Creeping retrieval increases data availability by crossing partition boundaries (over backup links) to read foreign data. Similarly, creeping merge improves the degree of partition-consistency by crossing partition boundaries to perform merge actions. A quasi-partitioning protocol consists of an adaptation protocol and a merge protocol. Taxonomies are shown for quasi-partitioning adaptation protocols and for quasi-partitioning merge protocols (for restoring partition-consistency after system reconnection). Since merge protocols and adaptation protocols are interdependent, it is indicated here how these protocols should be paired.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Condensation of dimethyl malonate with benzal-4-acetylanilines: A chemoselective reaction (2009)

Dimethyl malonate has reacted chemoselectively with carbon-nitrogen double bond of benzal-4-acetylanilines (1-8) leaving thc carbon-oxygen double bond, considered to be more reactive, intact under reaction conditions, leading to the formation of mono addition-elimination products rather than bis attack at both the double bonds, even when the reaction has been carried out with two moles of dimethyl malonate.
Developmental Neurobiology of the Stress Response: Multilevel Regulation of Corticotropin‐Releasing Hormone Function<sup>a</sup> (1997)

The ability to respond to adverse environmental cues is present in the neonatal and infant rat, although in an immature form: A number of laboratories have demonstrated stress-induced elevations of plasma glucocorticoids during the first two postnatal weeks. The limbic and hypothalamic mechanisms controlling the hormonal stress-response during this period are not fully understood and are, therefore, the focus of this report. Both hypothalamic corticotropin-releasing hormone (CRH) and vasopressin contribute to the release of ACTH from the pituitary in the adult. The relative roles of these two peptides during the neonatal (first week) and infant (second week) developmental period, are controversial. Evidence is presented that argues strongly for a major role for CRH. Up-regulation of hypothalamic CRH synthesis is a major component in the mature stress response. CRH-mRNA levels in the hypothalamic PVN are increased with cold stress by ninth postnatal day, but not during the first postnatal week. Further, down-regulation of CRH gene expression by glucocorticoids (GC) constitutes a critical "shut-down" mechanism for the hormonal stress response. In vivo and in vitro experiments supporting the "immaturity" of GC feedback on CRH synthesis during the first postnatal week are described. CRH-mediated neurotransmission, in both the endocrine and neuronal effector arms of the response to stress may be modulated via alteration of receptor number. The first member of the CRH receptor family, CRF1, probably mediates the neuroendocrine effects of CRH. The developmental profile of CRF1-mRNA reveals several distinctive spatial and temporal patterns. In the hippocampal CA1, CA2, and CA3a peak (300-600% adult values) CRF1-mRNA is found on postnatal day 6. In the amygdala, CRH receptor mRNA levels are maximal on the ninth postnatal day (at 180% of adult values). In cortex, a steady decline from high postnatal day 2 levels results in adult levels by 12. These findings demonstrate distinct, regional, age-specific control of the synthesis of CRF1. Receptor expression profile may provide important information regarding modulation of the age-specific roles of CRH in different regions. For example, a high ratio of hippocampus/amygdala receptors may preferentially activate negative hippocampal input to the hypothalamus during the neonatal period. Additionally, increased CRH receptor mRNA in the infant compared with the adult provides a mechanism for enhanced excitatory effect of the peptide at this age. In conclusion, increasing evidence exists for multiple control points of the early postnatal response and adaptation to stress. CRH synthesis in hypothalamus and amygdala, its sensitivity to GC feedback, and the abundance and distribution of at least two distinct CRH receptors in the limbic central nervous system and the pituitary are developmentally regulated. All serve as control points permitting an effective endocrine, autonomic, and behavioral response to stressful environmental cues.
A vertically reciprocating NbTi solenoid used in a regenerative magnetic refrigerator (1991)

An 8.2T-NbTi superconducting solenoid used for periodic magnetization by vertical motion along a bed of magnetocaloric material in a regenerative magnetic refrigerator using all active magnetic regenerator (AMR) has been designed, fabricated, and tested. The magnet design had two primary requirements: field uniformity and minimum stray flux. The magnet is charged with demountable leads and switched into persistent mode. Wheels and tracks guide the magnet in a liquid-helium dewar which is part of a larger environment cooled by a gas cycle refrigerator. Positioning of the magnet is determined by a computer-driven, PI-controlled linear actuator servo. design, test configuration, and test results of the solenoid systems are described.