gebhart/patrepeval huggingface dataset:
LEUKOTRIENES (1983)

The leukotrienes are a family of biologically active molecules, formed by leukocytes, mastocytoma cells, macrophages, and other tissues and cells in response to immunological and nonimmunological stimuli. They exhibit a number of biological effects such as contraction of bronchial smooth muscles, stimulation of vascular permeability, and attraction and activation of leukocytes. Compared to histamine, which causes constriction of airways and edema formation, the leukotrienes are three to four orders of magnitude more potent and the effects have longer duration. The leukotrienes were discovered in 1938 as a smooth muscle-contracting factor in lung perfusates. It was referred to as "slow reacting substance" (SRS) or "slow reacting substance of anaphylaxis" (SRS-A) until 1979 when its structure was reported. The term "leukotriene" was introduced at that time as a trivial name for the new type of compound. Leukotrienes C4 and D4 are glutathione and cysteinylglycine conjugates, respectively, of arachidonic acid. After hydrolytic release from phospholipids of the cell membrane, arachidonic acid is oxygenated by a lipoxygenase to 5-hydroperoxy-6,8,11,14-eicosatetraenoic acid. This product is further converted to leukotrienes by elimination of the 10-pro-R hydrogen and OH from the hydroperoxy group to give 5,6-oxido-7,9,11, 14-eicosatetraenoic acid (leukotriene A4). Nucleophilic opening of the epoxide at C-6 by the sulfhydryl group of glutathione gives leukotriene C4, which is metabolized to leukotrienes D4 and E4 by sequential elimination of glutamic acid and glycine. The latter reactions are catalyzed by gamma-glutamyl transpeptidase and a particulate dipeptidase from kidney. Alternatively, water may add at C-12 of leukotriene A4, leading also to opening of the epoxide at C-6 with formation of 5,12-dihydroxy-6,8,10,14-eicosatetraenoic acid (leukotriene B4). Leukotriene B4 is metabolized by omega-hydroxylation to 20-hydroxy and 20-carboxy leukotriene B4. Leukotrienes are also formed from eicosatrienoic acid (n-9) and eicosapentaenoic acid (n-3) after oxygenation at C-5 and from eicosatrienoic acid (n-6) and arachidonic acid after oxygenation at C-8 (eicosatrienoic acid) and C-12 or C-15 (arachidonic acid). Although they are formed from the same and additional fatty acids as prostaglandins and thromboxanes [reviewed in this series in (1)], the structures and the reactions involved in biosynthesis and catabolism of leukotrienes are completely separate from those required for prostaglandin formation and metabolism. The leukotrienes seem to provide a new system of biological regulators that are important in many diseases involving inflammatory or immediate hypersensitivity reactions.
Soluble intercellular cell adhesion molecule-1 and L-selectin plasma concentrations and response to surfactant in preterm infants (2002)

In preterm infants with respiratory distress, a poor response to surfactant within 6 hrs of administration is associated with elevated circulating ICAM-1 concentrations at 24 hrs of age. Low plasma L-selectin at 24 hrs of age predicts prolonged requirement for supplemental oxygen.
Remediation of cut slopes and retaining structures in Huis River Pass : geotechnical engineering (2009)

The Huis River Pass has a long history and a geological beauty that was first opened to the public in 1897 by the Divisional Councils of Ladismith and Calitzdorp. As with most of South Africa's older mountain passes, the cut rock slopes have deteriorated with time, increasing the frequency of rockfalls and the need for road closures.
In the early 1960s, a new surfaced pass was designed by Kantey & Templer Consulting Engineers. Mr Basil Kantey, one of the founding members of the firm, played an integral part in the selection of four areas along the route where reinforced concrete retaining structures were constructed.
Interaction of calf skin collagen with glycerol: linked function analysis (1986)

Glycerol stabilizes the triple-helical structure of solubilized calf skin collagen. The equilibrium melting temperature of the protein increased linearly from 38.0 degrees C in AS buffer (0.01 M NaOAc and 0.02 M NaCl, pH 4.0) to 43.0 degrees C in AS and 6 M glycerol buffer. To understand the thermodynamic basis of this effect on the equilibrium melting temperature and the glycerol inhibition of collagen self-association, the preferential interactions of native and denatured calf skin collagens in AS buffer containing 1.5, 3, and 4.5 M glycerol were measured with a precision densimeter. The results indicated that native collagen binds glycerol preferentially whereas denatured collagen neither binds nor repels glycerol. The preferential binding of glycerol by native collagen, when interpreted in terms of the three-component solution thermodynamics, suggests that the surface interaction of native collagen with glycerol is energetically more favorable than its interaction with water. By use of the Wyman linked function, the negative chemical potential change of collagen derived from its preferential binding of glycerol can account for both the glycerol stabilization of the triple-helical structure of collagen and the inhibition of in vitro self-association of monomers into fibrils.
Style-based reuse for software architectures (2002)

Although numerous mechanisms for promoting software reuse have been proposed and implemented over the years, most have focused on the reuse of implementation code. There is much conjecture and some empirical evidence, however, that the most effective forms of reuse are generally found at more abstract levels of software design. We discuss software reuse at the architectural level of design. Specifically, we argue that the concept of "architectural style" is useful for supporting the classification, storage, and retrieval of reusable architectural design elements. We briefly describe the Aesop system's Software Shelf (D. Garlan et al., 1994), a tool that assists designers in selecting appropriate design elements and patterns based on stylistic information and design constraints.
Molecules isoelectronic with 2,2,2-triphenylethanol: multiple hydrogen-bonding modes in the structures of O-tritylhydroxylamine, Ph3CONH2, and triphenylmethanesulfenamide, Ph3CSNH2 (1994)

O-Tritylhydroxylamine, C 19 H 17 NO (IV), forms dimers in the solid state which are made up from two different molecules; these dimers exhibit three type of hydrogen bond, intermolecular N-H...N and N-H...π(arene), and intramolecular (aryl)C-H...O. Triphenylmethanesulfenamide, C 19 H 17 NS (V), forms centrosymmetric dimers in the solid state in which N-H...S hydrogen bonds are the sole type observed
Anti-immunoglobulin augments the B-cell antigen-presentation function independently of internalization of receptor-antigen complex. (1985)

All mouse splenic B cells, including small resting B cells, process and present the native globular protein antigens, pigeon and tobacco hornworm moth cytochromes c, to a cytochrome c-specific T-cell hybrid in a major histocompatibility complex-restricted fashion, in the micromolar to nanomolar antigen-concentration range. As is the case for macrophages, treatment with paraformaldehyde or the lysosomotropic agents chloroquine and ammonium chloride blocked processing of the native pigeon protein but did not affect the presentation of a carboxyl-terminal peptide fragment of pigeon cytochrome c (residues 81-104) which contained the T-cell antigenic determinant. However, in contrast to macrophages, whose antigen-processing and -presentation functions are insensitive to radiation, radiation blocked the processing of the native protein but not the presentation of the peptide fragment. The processing and presentation function of the B cells was augmented by F(ab')2 of rabbit anti-mouse Ig antibodies, in that 1/10th to 1/30th as many cells and 1/10th as much antigen were required to maximally activate the T-cell hybrid. This augmentation did not appear to be due to either crosslinking of the Ig receptors or to B-cell activation, as monovalent Fab fragments were nearly as effective as the bivalent reagent, and the concentrations of F(ab')2 anti-Ig used did not induce measurable proliferative responses. Furthermore, enhancement can occur in the absence of cytochrome c binding and internalization, since B cells that were fixed with paraformaldehyde after treatment with F(ab')2 anti-Ig were more effective in presenting the carboxyl-terminal peptide than were untreated fixed cells. The same phenomenon followed the binding of an irrelevant antigen (carboxydinitrophenylated bovine serum albumin) by antigen-binding B cells, resulting in enhanced processing and/or presentation of native pigeon cytochrome c. Thus, nonspecific enhancement of antigen processing and presentation can be obtained by either antigen or anti-Ig binding to the B-cell antigen receptor, both treatments presumably delivering the same signal without requiring internalization of the specifically bound antigen for subsequent processing.
&lt;title&gt;VVD: VCR operations for video on demand&lt;/title&gt; (1999)

Current Video on Demand (VoD) systems do not provide for interactive VCR-like scan operations such as rewind or fast- forward. Pre-storing the entire movie on a set-top box for implementation of such operations is currently neither practical nor feasible. Other approaches to VCR-like controls are either computationally complex or the server or consume large amounts of bandwidth during the operation. This paper proposes a novel technique, VVD, for real-time implementation of VCR-like operations, supporting multiple scan speeds, for Video on Demand with low latency and overhead. VVD uses multi-level compression of movie files to encode the same movie at a hierarchy of playout rates. Depending on the rate at which a scan operation is requested, the corresponding compressed movie file is transmitted. Frame dropping and repetition are used to provide smooth speed transitions among the multiple levels. The overhead of this scheme can be controlled to be less than 100% of the movie storage size.
Immunosuppression for Membranous Nephropathy (2013)

Alkylating agents plus corticosteroids had long-term and short-term benefits for adult IMN, but resulted in more withdrawals or hospitalizations.
Phosphorylation-dependent Regulation of Cardiac Na+/Ca2+ Exchanger via Protein Kinase C (1996)

The cardiac Na+/Ca2+ exchanger (NCX1) plays a major role in the extrusion of Ca2+ from cardiomyocytes. We studied the role of protein phosphorylation in the regulation of cardiac NCX1 using CCL39 stably overexpressing the canine cardiac NCX1 and rat neonatal cardiomyocytes. In both cell types, the NCX1 protein immunoprecipitated with a chicken anti-NCX1 antibody exhibited a significant basal phosphorylation that was further enhanced by treatment with endothelin-1, acidic fibroblast growth factor, phorbol 12-myristate 13-acetate, or okadaic acid. In contrast, calphostin C, K252a, or EGTA inhibited the phosphorylation. The phosphorylation occurred on two major tryptic phosphopeptides (P1 and P2) exclusively on serine residues. Evidence is presented suggesting that P2 was derived from an N-terminal half (amino acids 240-475) of the central cytoplasmic domain of NCX1 and was phosphorylated directly by protein kinase C (PKC). The agents that increased NCX1 phosphorylation significantly enhanced both the forward and reverse modes of Na+/Ca2+ exchange. This exchange activation exhibited a very good correlation with the NCX1 phosphorylation. In NCX1-transfected cells, PKC down-regulation following prolonged exposure to phorbol 12-myristate 13-acetate abolished the acidic fibroblast growth factor-induced activation of exchange activity. On the other hand, cell ATP depletion reduced the exchange activity and abolished the effects of the above agents on exchange activity. These results indicate that the cardiac NCX1 is up-regulated by PKC-catalyzed phosphorylation. The cardiac NCX1 thus could play an important role in the previously reported negative inotropic actions of phorbol esters and other PKC-activating agents.
Aerosol Therapy in Mechanically Ventilated Patients: Recent Advances and New Techniques (2000)

Therapeutic aerosols are commonly used in mechanically ventilated patients, yet information regarding their efficacy and optimal technique of administration has been limited. The advantages of aerosol therapy include a smaller dose, efficacy comparable with that observed with systemic administration of the drug, and a rapid onset of action. Inhaled drugs are delivered directly to the respiratory tract, their systemic absorption is limited, and systemic side effects are minimized. Inhaled bronchodilators are routinely used with mechanically ventilated patients in the intensive care unit, but a variety of drugs ranging from antibiotics to surfactants has been administered. Nebulizers and metered-dose inhalers (MDIs) are commonly used aerosol generators because they produce respirable particles with a mass median aerodynamic diameter (MMAD) between 1 and 5 mum. Due to the limitation of available formulations, MDIs are chiefly used to deliver bronchodilators and steroids, whereas nebulizers have greater versatility and can be used to administer bronchodilators, antibiotics, surfactant, mucokinetic agents, and other drugs. The delivery of inhaled drugs in mechanically ventilated patients differs from that in ambulatory patients in several respects. Until recently, the consensus of opinion was that the efficiency of aerosol delivery to the lower respiratory tract in mechanically ventilated patients was much lower that that in ambulatory patients. Data suggest that this might be overly pessimistic and that the endotracheal tube may actually facilitate greater aerosol delivery compared with the normal airway when a variety of variables effecting aerosol delivery during mechanical ventilation are optimized.
The Role of Regulatory T Cells in Chronic and Acute Viral Infections (2008)

Regulatory T cells, a subset of CD4(+) T lymphocytes, play a pivotal role in the maintenance of the balance between the tissue-damaging and protective effects of the immune response. These cells have immunosuppressive function and have been intensely studied in the context of autoimmunity, cancer, allergies, asthma, and infectious diseases. Their role in chronic and persistent viral infections is well appreciated. In acute viral infections, the function of these cells is still unclear. The host and pathogen factors that control the generation and activity of regulatory T cells and the role of these cells in modulating expansion, contraction, and development of immune memory in acute respiratory virus infection need to be further elucidated.
Mechanisms of rejection induced by tumor cell-targeted gene transfer of interleukin 2, interleukin 4, interleukin 7, tumor necrosis factor, or interferon gamma. (1993)

Interleukin (IL)-2, IL-4, IL-7, tumor necrosis factor (TNF), or interferon-gamma (IFN-gamma) has been shown to be able to induce tumor rejection if produced locally by the tumor cells after gene transfer. To analyze whether the cellular rejection mechanisms are different or redundant we have expressed the cytokines in the same tumor cell line (J558L). Cell depletion experiments revealed that all cytokines required CD8+ T cells for complete long-term tumor eradication, although effective but transient host-dependent tumor suppression was also observed in the complete absence of CD8+ T cells. The transient tumor suppression induced by IL-2, IL-4, TNF, or IFN-gamma was also operative in nude and severe combined immunodeficient mice, whereas only tumor suppression induced by IL-7 was dependent on the presence of CD4+ T cells and was not evident in nude mice. The T-cell-independent effector arm of IL-2 and IFN-gamma but not IL-4 and TNF was mediated in part by natural killer cells. The transience of tumor suppression in the absence of T cells reflected loss of cytokine production in the case of TNF, IL-2, and IL-4 but not IFN-gamma. Immunohistologic analysis revealed all cytokine-producing tumors to be heavily infiltrated by macrophages. IL-4 and IL-7 tumors additionally contained eosinophils. The infiltration by T cells did not necessarily reflect their contribution to tumor rejection. Thus, the different cytokines activate heterogeneous transient tumor-suppressive mechanisms but always require CD8+ T cells for complete tumor rejection.
Development of a heme protein structure electrochemical function database (2007)

Proteins containing heme, iron(protoporphyrin IX) and its variants, continue to be one of the most-studied classes of biomolecules due to their diverse range of biological functions. The literature is abundant with reports of structural and functional characterization of individual heme proteins which demonstrate that heme protein reduction potential values, E(m), span the range from -550 mV to +450 mV versus SHE. In order to unite these data for the purposes of global analysis, a new web-based resource of heme protein structure-function relationships is presented: the Heme Protein Database (HPD). This database is the first of its kind to combine heme protein structural classifications including protein fold, heme type and heme axial ligands, with heme protein reduction potential values in a web-searchable format. The HPD is located at http://heme.chem.columbia.edu/heme.php. The data illustrate that heme protein E(m) values are modulated over a 300 mV range by the type of global protein fold, a 600 mV range by the type of porphyrin and an 800 mV range by the axial ligands. Thus, the 1 V range observed in heme protein reduction potential values in biological systems arises from subtle combinations of these various factors.
A flexible, multi-mode of operation, high-resolution survey platform for surface and underwater operations (2009)

This paper describes the ROVLATIS , a multi-mode of operation flexible platform for high-resolution near-seabed survey from shallow inshore waters to depths beyond 1000m. The paper further describes the operation modes of the vehicle. Special system features include: deployment flexibility for both small inshore boats and larger research vessel; fault tolerant controls; onboard computer control enabling real-time disturbance reaction, autopilot functionality and autonomous underwater vehicle (AUV) experimentation; and topside augmented reality operations support, simulation for remotely operated vehicle (ROV) pilot and sonar operator/hydrographer training. Vehicle and control development using the University of Limerick (UL) virtual underwater laboratory/simulation tools and hardware-in-the-loop testing is described. The paper includes test results from the March 2009 offshore sea trials with the ROVLATIS
Determination of bile acids in biological fluids by liquid chromatography-electrospray tandem mass spectrometry (2001)

A simple, sensitive, and specific liquid chromatography-electrospray tandem mass spectrometry (LC-MS/MS) method for the determination of bile acids in human bile has been developed. The bile acids were extracted with a C(18) (octadecyl) reversed-phase column and identified and quantified by simultaneous monitoring of their parent and daughter ions, using the multiple reaction monitoring mode. Identification and quantification of conjugated bile acids in bile was achieved in 5 min. The detection limit was 1 ng, and the determination was linear for concentrations up to 100 ng. The percent recovery of standards made of single conjugated (glycine and taurine) bile acid or of mixture of glycine- or taurine-conjugated cholic acid, chenodeoxycholic acid, deoxycholic acid, ursodeoxycholic acid, and lithocholic acid averaged 71.73% to 95.92%. The percent recovery of the same standard bile acids was also determined by gas chromatography-mass spectrometry (GC-MS), using the selected ion monitoring mode, and averaged 66% to 96%. A biliary bile acid profile of human gallbladder bile was obtained by LC-MS/MS and GC-MS. The results showed a good correlation between the two techniques and no significant differences between the two methods were observed. The LC-MS/MS method was also used for the analysis of serum, urine, and fecal bile acids. In conclusion, LC-MS/MS is a simple, sensitive, and rapid technique for the analysis of conjugated bile acids in bile and other biological samples. - Perwaiz, S., B. Tuchweber, D. Mignault, T. Gilat, and I. M. Yousef. Determination of bile acids in biological fluids by liquid chromatography-electrospray tandem mass spectrometry. J. Lipid Res. 2001. 42: 114;-119.
Maleimide Cross‐Linked Bioactive PEG Hydrogel Exhibits Improved Reaction Kinetics and Cross‐Linking for Cell Encapsulation and In Situ Delivery (2011)

Engineered polyethylene glycol-maleimide matrices for regenerative medicine exhibit improved reaction efficiency and a wider range of Young's moduli by utilizing maleimide cross-linking chemistry. This hydrogel chemistry is advantageous for cell delivery due to the mild reaction that occurs rapidly enough for in situ delivery, while easily lending itself to “plug-and-play” design variations such as incorporation of enzyme-cleavable cross-links and cell-adhesion peptides. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Processing remote sensing images using the 2-D FFT; noise reduction and other applications (1993)

Abstract With the development of faster and less expensive computers, it is now practical to employ algorithms for processing remote sensing images that were only feasible on large mainframe computers a short time ago. The two-dimensional (2-D) fast Fourier transform (FFT) is a powerful means for removing noise because it can be used to design and implement efficient filters based on the observed spatial or frequency patterns of the noise. Illustrations of transforms of image points and lines in various configurations and periodic patterns are used as a tutorial to identify and reduce a variety of noise patterns of increasing complexity from an assortment of spacecraft and aircraft systems. A general strategy for filtering developed from this study involves: filtering only derived products (not original images), initially removing noise evident in the transform, and applying a 'minimum' filter to reduce residual noise. The 2-D FFT is also applied to mosaicking, enlargement, registration, and extraction of albedo and slope information.
Functional Specialization of the Axon Initial Segment by Isoform-Specific Sodium Channel Targeting (2003)

Voltage-dependent sodium channels cluster at high density at axon initial segments, where propagating action potentials are thought to arise, and at nodes of Ranvier. Here, we show that the sodium channel Na v 1.6 is precisely localized at initial segments of retinal ganglion cells (RGCs), whereas a different isoform, Na v 1.2, is found in the neighboring unmyelinated axon. During development, initial segments first expressed Na v 1.2, and Na v 1.6 appeared later, approximately in parallel with the onset of repetitive RGC firing. In Shiverer mice, Na v 1.6 localization at the initial segment was unaffected, although Na v 1.6 expression was severely disrupted in the aberrantly myelinated optic nerve. Targeting or retention of Na v 1.6 requires molecular interactions that normally occur only at initial segments and nodes of Ranvier. Expression at nodes but not initial segments exhibits an additional requirement for intact myelination. Because of their high density at the initial segment, Na v 1.6 channels may be crucial in determining neuronal firing properties.