gebhart/patrepeval huggingface dataset:
Acoustic Speckle: Theory and Experimental Analysis (1979)

A theoretical and experimental study of speckle, as applied to ultrasonic imaging, is presented. The concept of laser speckle is briefly reviewed and is used as a starting point to explain the origin of acoustic speckle. The primary differences between these two phenomena are discussed and are confirmed by experiment. An experimental study of speckle reduction by summation of multiple images is also presented. Several techniques for generating independent speckle patterns for use in image summation schemes are proposed. A phased array, dynamically focused sector imaging system was used in all of the experimental studies reported.
Cache-oblivious streaming B-trees (2007)

A streaming B-tree is a dictionary that efficiently implements insertions and range queries. We present two cache-oblivious streaming B-trees, the shuttle tree, and the cache-oblivious lookahead array (COLA).
Imiquimod-induced regression of actinic keratosis is associated with infiltration by T lymphocytes and dendritic cells: a randomized controlled trial (2005)

Imiquimod stimulates a cutaneous immune response characterized by increases in activated dendritic cells and CD4+ and CD8+ T cells.
Targeted therapies in development for non-small cell lung cancer (2013)

The iterative discovery in various malignancies during the past decades that a number of aberrant tumorigenic processes and signal transduction pathways are mediated by "druggable" protein kinases has led to a revolutionary change in drug development. In non-small cell lung cancer (NSCLC), the ErbB family of receptors (e.g., EGFR [epidermal growth factor receptor], HER2 [human epidermal growth factor receptor 2]), RAS (rat sarcoma gene), BRAF (v-raf murine sarcoma viral oncogene homolog B1), MAPK (mitogen-activated protein kinase) c-MET (c-mesenchymal-epithelial transition), FGFR (fibroblast growth factor receptor), DDR2 (discoidin domain receptor 2), PIK3CA (phosphatidylinositol-4,5-bisphosphate3-kinase, catalytic subunit alpha)), PTEN (phosphatase and tensin homolog), AKT (protein kinase B), ALK (anaplastic lym phoma kinase), RET (rearranged during transfection), ROS1 (reactive oxygen species 1) and EPH (erythropoietin-producing hepatoma) are key targets of various agents currently in clinical development. These oncogenic targets exert their selective growth advantage through various intercommunicating pathways, such as through RAS/RAF/MEK, phosphoinositide 3-kinase/AKT/mammalian target of rapamycin and SRC-signal transduction and transcription signaling. The recent clinical studies, EGFR tyrosine kinase inhibitors and crizotinib were considered as strongly effective targeted therapies in metastatic NSCLC. Currently, five molecular targeted agents were approved for treatment of advanced NSCLC: Gefitinib, erlotinib and afatinib for positive EGFR mutation, crizotinib for positive echinoderm microtubule-associated protein-like 4 (EML4)-ALK translocation and bevacizumab. Moreover, oncogenic mutant proteins are subject to regulation by protein trafficking pathways, specifically through the heat shock protein 90 system. Drug combinations affecting various nodes in these signaling and intracellular processes are predicted and demonstrated to be synergistic and advantageous in overcoming treatment resistance compared with monotherapy approaches. Understanding the role of the tumor microenvironment in the development and maintenance of the malignant phenotype provided additional therapeutic approaches as well. More recently, improved knowledge on tumor immunology has set the stage for promising immunotherapies in NSCLC. This review will focus on the rationale for the development of targeted therapies in NSCLC and the various strategies employed in preventing or overcoming the inevitable occurrence of treatment resistance.
Population pharmacokinetics of farletuzumab, a humanized monoclonal antibody against folate receptor alpha, in epithelial ovarian cancer (2012)

The pharmacokinetic parameters of farletuzumab are similar to those of other IgG mAbs. The results support weight-based dosing of farletuzumab on a weekly or 3-weekly schedule.
Infliximab Treatment of Rheumatoid Arthritis and Crohn's Disease (2003)

Infliximab is an effective new agent for the treatment of CD and RA. Its apparent unique mechanism of action makes infliximab an important addition to therapy. Caution should be exercised when considering infliximab for individuals who have chronic or recurrent infections, mild congestive heart failure (New York Heart Association [NYHA] class I/II), nervous system disorders, or live or have lived in an area endemic for histoplasmosis. Infliximab is contraindicated for patients with a clinically important, active infection, moderate to severe congestive heart failure (NYHA class III/IV), or an allergy to mouse proteins or any of the ingredients in infliximab. Further long-term efficacy, safety, and economic data on infliximab are required. Also, for the treatment of RA, the burden of administering infliximab (as a 2-hour supervised infusion) has to be considered when choosing among anti-TNF-alpha medication (as the other 2 approved agents, etanercept and adalimumab, can be self-administered by subcutaneous injection).
Proline biosynthesis from L-ornithine in Clostridium sticklandii: purification of Δ1-pyrroline-5-carboxylate reductase, and sequence and expression of the encoding gene, proC (1999)

Clostridium sticklandii utilizes combinations of amino acids for growth by Stickland reactions. Proline is an efficient electron acceptor in these reactions and is reduced to 5-aminovalerate. Proline can be partly synthesized from ornithine by the action of ornithine aminotransferase and delta1-pyrroline-5-carboxylate (PCA) reductase. Both enzymes were present in crude extracts of C. sticklandii in sufficient activity of 0.93 nkat (mg protein)(-1) and 4.3 nkat (mg protein)(-1), respectively, whereas enzymes involved in proline biosynthesis from glutamate were not detected. PCA reductase was purified to homogeneity in a three-step procedure involving ammonium sulfate precipitation, affinity chromatography with Procion Red and gel filtration on Sephadex GF200. The homogeneous enzyme was most likely an octamer of 230 kDa with a subunit size of 25 kDa as obtained by SDS-PAGE and 28.9 kDa as calculated from the sequence. Apparent Km values for PCA and NADH were 0.19 mM and 0.025 mM, respectively. The enzyme also catalysed in vitro the reverse reaction, the oxidation of proline, at alkaline pH values above 8 and higher substrate concentrations (apparent Km values: 1.55 mM for proline and 10.5 mM for NAD at pH 10.0). Studies with growing cells of C. sticklandii and [15N]proline revealed that proline is not oxidized in vivo because 15N was solely detected by HPLC-MS in 5-aminovalerate as the product of proline reduction. The proC gene encoding PCA reductase of C. sticklandii was cloned, sequenced and heterologously expressed in Escherichia coli. The enzyme exhibited high homologies to PCA reductases from different sources. Thus, C. sticklandii is able to synthesize the electron acceptor proline from ornithine (a degradation product of arginine) by action of ornithine aminotransferase and PCA reductase.
Histidine 289 Is Essential for Hydrolysis of the Alkyl-enzyme Intermediate of Haloalkane Dehalogenase (1995)

Haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic cleavage of carbon-halogen bonds in a broad range of halogenated aliphatic compounds. Previous work has shown that Asp124, which is located close to the internal substrate-binding cavity, carries out a nucleophilic attack on the C-alpha of the alkylhalide, displacing the halogen. The resulting alkyl-enzyme intermediate is subsequently hydrolyzed. In order to study the role of His289 in the hydrolysis of the intermediate, a His289-->Gln mutant was constructed by site-directed mutagenesis. The purified mutant enzyme was not catalytically active with haloalkanes, but a halide burst stoichiometric to the amount of enzyme was observed with 1,2-dibromoethane. Using ion spray mass spectrometry, accumulation of the covalent alkyl-enzyme and binding of the alkyl moiety of the substrate to an Asp124-containing tryptic peptide were shown. Fluorescence-quenching experiments indicated that halide ions are strongly bound by the alkyl-enzyme but not by the substrate-free enzyme. The results show that His289 is the base catalyst for the dealkylation of the covalent intermediate, but that it is not essential for the initial nucleophilic attack of Asp124 on the C-1 atom of the haloalkane. Furthermore, the halide ion that is released in the first step probably leaves the active site only after hydrolysis of the alkyl-enzyme.
Membrane Association, Electrostatic Sequestration, and Cytotoxicity of Gly-Leu-Rich Peptide Orthologs with Differing Functions (2004)

The skins of closely related frog species produce Gly-Leu-rich peptide orthologs that have very similar sequences, hydrophobicities, and amphipathicities but differ markedly in their net charge and membrane-damaging properties. Cationic Gly-Leu-rich peptides are hemolytic and very potent against microorganisms. Peptides with no net charge have only hemolytic activity. We have used ancestral protein reconstruction and peptide analogue design to examine the roles of electrostatic and hydrophobic interactions in the biological activity and mode of action of functionally divergent Gly-Leu-rich peptides. The structure and interaction of the peptides with anionic and zwitterionic model membranes were investigated by circular dichroism with 2-dimyristoyl-sn-glycero-3-phosphatidylcholine or 1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol vesicles and surface plasmon resonance with immobilized bilayers. The results, combined with antimicrobial assays, the kinetics of bacterial killing, and membrane permeabilization assays, reveal that Gly, Val, Thr, and Ile can all be accommodated in an amphipathic alpha helix when the helix is in a membrane environment. Binding to anionic and zwitterionic membranes fitted to a 2-stage interaction model (adsorption to the membrane followed by membrane insertion). The first step is governed by hydrophobic interactions between the nonpolar surface of the peptide helix and the membranes. The strong binding of Gly-Leu-rich cationic peptides to anionic membranes is due to the second binding step and involves short-range Coulombic interactions that prolong the residence time of the membrane-inserted peptide. The data demonstrate that evolution has positively selected charge-altering nucleotide substitutions to generate an orthologous cationic variant of neutral hemolytic peptides that bind to and permeate bacterial cell membranes.
Extrusion of food proteins (1992)

Abstract Protein extrusion has frustrated earlier predictions regarding its impact in the development of food products. The main reason for this disappointing performance has been its failure to yield fabricated food products with textural quality close enough to that of natural products at competitive prices. Texturized soya protein by extrusion is presently the only commercial success in this area, being incorporated into several convenience products, increasing their protein content and quality and conferring them some desirable sensory properties. Technological and scientific gaps in the extrusion texturization are still to be bridged if this technique is to be applied for upgrading unconventional protein. The precise mechanisms responsible for protein texturization through extrusion are still unclear. Proteins show a very wide range of extrusion behavior that is probably related to large differences in their association properties. New peptide bonds, formed by free amino and carboxylic groups of the protein, were postulated as being responsible for the cross‐linking that takes place in protein extrusion. However, disulfide bonds and electrostatic and hydrophobic interactions are regarded presently as the texturization mechanism in this process. The recently suggested suspension (or filled “melt”) model for biopolymer extrusion offered a new framework for testing extrusion of novel proteins. According to this view, the large differences between the association properties of proteins produce different types of aggregates. Some of them can be insoluble under extrusion conditions and act as a dispersed phase within the melt phase. The extrusion performance of a protein will thus depend on the amount of insoluble aggregate produced inside the extruder and on protein‐protein interactions that occur after the superheated molten mass leaves it.
Treatment of Intermittent Claudication With Physical Training, Smoking Cessation, Pentoxifylline, or Nafronyl (1999)

Physical training increased pain-free and total walking distance in level 2 studies. Only level 3 studies support the usefulness of smoking cessation. In level 1 studies, pentoxifylline and nafronyl increased pain-free and total walking distance, but the average effects were relatively small.
Expression of human extracellular superoxide dismutase in Chinese hamster ovary cells and characterization of the product. (1987)

A complementary DNA clone from human placenta, encoding human extracellular superoxide dismutase (EC-SOD; superoxide:superoxide oxidoreductase, EC 1.15.1.1), has recently been isolated and characterized. An expression plasmid, based on the EC-SOD complementary DNA, was transfected into Chinese hamster ovary cells (CHO-K1). The transfected cells secreted human EC-SOD to the culture medium. The secreted recombinant (r) EC-SOD was isolated in high yield with a three-step procedure beginning with immobilized monoclonal anti-EC-SOD antibodies. The properties of the rEC-SOD were compared with native (n) EC-SOD isolated from human umbilical cords. The specific activities and amino-terminal amino acid sequences were identical. The amino acid compositions were virtually identical and very similar to the composition deduced from the complementary DNA sequence. Both rEC-SOD and nEC-SOD contained 4 Cu and 4 Zn atoms per molecule, and the presence of Zn in EC-SOD is thus now established. The rEC-SOD produced is type C, since its affinity for heparin-Sepharose was identical to that of nEC-SOD type C. Both enzymes bound to concanavalin A, lentil lectin, and wheat germ lectin and are thus glycoproteins. rEC-SOD and nEC-SOD seem to have the same subunit structure and composition as analyzed by polyacrylamide gel electrophoresis and gel chromatography.
Recommendations on size and position of surgically and gastrically implanted electronic tags in European silver eel (2013)

Information on European silver eel Anguilla anguilla anatomy was collected to gain information on limitations on size and placement of electronic tags. To reduce the eel’s ability to bite its own sutures, it may be an advantage to make surgical incisions close to the head, but this increases the risk of cutting the liver. Recommended placement of an incision was slightly further from the head than one-fourth of the fish’s body length (L T) to avoid damaging the liver. Long, flexible tags comprising various components can be adjusted to the narrow body cavity and undulating movements of eels. There was space for surgically implanting a 100 mm long tag (11 mm in diameter) in the body cavity of eels with L T ≥380 mm. During gastric tagging, tag length is limited by stomach length. Silver eels with L T 380 to 998 mm had stomach lengths of 47 to 185 mm, indicating that there was space for short gastric tags in the smallest eels, but that there was space for relatively long tags in larger eels. The distance from the snout to the start of the stomach constituted 15 to 23% of L T, indicating how far the transmitter should be inserted during tagging. This information aids the development of tags and tagging methods that consider the unique morphological and behavioral features of eels.
Real-time imaging of renal clearance using multispectral optoacoustic tomography (2012)

Multi-Spectral Optoacoustic Tomography (MSOT) offers real time imaging that simultaneously exploits high ultrasound resolutions and strong optical contrast. It allows visualizing absorbers in tissue by using their distinct spectral absorption profiles. This work presents a non-invasive in vivo study of kinetics involved in the clearance of carboxylated dye in mouse kidneys. The distinctio
The pathophysiology of skeletal muscle ischemia and the reperfusion syndrome: a review (2002)

There are two components to the reperfusion syndrome, which follows extremity ischemia. The local response, which follows reperfusion, consists of limb swelling with its potential for aggravating tissue injury and the systemic response, which results in multiple organ failure and death. It is apparent that skeletal muscle is the predominant tissue in the limb but also the tissue that is most vulnerable to ischemia. Physiological and anatomical studies show that irreversible muscle cell damage starts after 3 h of ischemia and is nearly complete at 6 h. These muscle changes are paralleled by progressive microvascular damage. Microvascular changes appear to follow rather than precede skeletal muscle damage as the tolerance of capillaries to ischemia vary with the tissue being reperfused. The more severe the cellular damage the greater the microvascular changes and with death of tissue microvascular flow ceases within a few hours-the no reflow phenomenon. At this point tissue swelling ceases. The inflammatory responses following reperfusion varies greatly. When muscle tissue death is uniform, as would follow tourniquet ischemia or limb replantation, little inflammatory response results. In most instances of reperfusion, which follows thrombotic or embolic occlusion, there will be a variable degree of ischemic damage in the zone where collateral blood flow is possible. The extent of this region will determine the magnitude of the inflammatory response, whether local or systemic. Only in this region will therapy be of any benefit, whether fasciotomy to prevent pressure occlusion of the microcirculation, or anticoagulation to prevent further microvascular thrombosis. Since many of the inflammatory mediators are generated by the act of clotting, anticoagulation will have additional benefit by decreasing the inflammatory response. In instances in which the process involves the bulk of the lower extremity, amputation rather than attempts at revascularization may be the most prudent course to prevent the toxic product in the ischemic limb from entering the systemic circulation.
Elevated glycated haemoglobin in non-diabetic patients is associated with an increased mortality in myocardial infarction (1998)

Diabetes is associated with increased mortality following acute myocardial infarction compared to the general population. Elevated glycated haemoglobin (HbA1c) in diabetic patients is also associated with increased mortality following acute myocardial infarction, while mild elevation in HbA1c are associated with impaired glucose tolerance. The aim of this study was to determine the influence of HbA1c on outcome of acute myocardial infarction in 253 non-diabetic patients, 46 of whom died in one year. In univariate analysis, risk factors for death included smoking, glucose, cholesterol and HbA1c. In logistic regression analysis HbA1c was an independent risk factor for death. Over one-third of the fatality group had an HbA1c in the highest quartile, compared to one-fifth of the surviving group (p = 0.02). Elevated HbA1c is a risk marker for short-term mortality following acute myocardial infarction in non-diabetic subjects.
A Note on the Brewster Angle in Lossy Dielectric Media (2010)

Abstract : In electromagnetism, the Brewster angle is the angle of incidence at which there is no reflection of the parallel (i.e. vertical) polarized wave from a planar interface between materials with differing permittivity. That is, the reflection coefficient goes to zero at this angle and all of the incident power is transmitted into the dielectric medium. The reflection coefficient is a function of the constitutive parameters permittivity and permeability of the two media forming the interface as well as the angle of incidence. For media with the Brewster angle is commonly expressed where the r subscript denotes the relative constitutive parameter, the i subscript denotes the parameter of the medium in which the incident wave is propagating, and the t subscript denotes parameter of the medium into which the wave is transmitted. We assume the incident medium is free space and the transmitted medium is soil for the purposes of ground penetrating radar (GPR). For perpendicularly polarized waves, no real incident angle exists that will reduce the reflection coefficient to zero.
False data injection attacks against state estimation in electric power grids (2011)

A power grid is a complex system connecting electric power generators to consumers through power transmission and distribution networks across a large geographical area. System monitoring is necessary to ensure the reliable operation of power grids, and state estimation is used in system monitoring to best estimate the power grid state through analysis of meter measurements and power system models. Various techniques have been developed to detect and identify bad measurements, including interacting bad measurements introduced by arbitrary, nonrandom causes. At first glance, it seems that these techniques can also defeat malicious measurements injected by attackers. In this article, we expose an unknown vulnerability of existing bad measurement detection algorithms by presenting and analyzing a new class of attacks, called false data injection attacks , against state estimation in electric power grids. Under the assumption that the attacker can access the current power system configuration information and manipulate the measurements of meters at physically protected locations such as substations, such attacks can introduce arbitrary errors into certain state variables without being detected by existing algorithms. Moreover, we look at two scenarios, where the attacker is either constrained to specific meters or limited in the resources required to compromise meters. We show that the attacker can systematically and efficiently construct attack vectors in both scenarios to change the results of state estimation in arbitrary ways. We also extend these attacks to generalized false data injection attacks , which can further increase the impact by exploiting measurement errors typically tolerated in state estimation. We demonstrate the success of these attacks through simulation using IEEE test systems, and also discuss the practicality of these attacks and the real-world constraints that limit their effectiveness.