gebhart/patrepeval huggingface dataset:
Optical Fiber Sensors Based on Nanoparticle-Embedded Coatings (2015)

The use of nanoparticles (NPs) in scientific applications has attracted the attention of many researchers in the last few years. The use of NPs can help researchers to tune the physical characteristics of the sensing coating (thickness, roughness, specific area, refractive index, etc.) leading to enhanced sensors with response time or sensitivity better than traditional sensing coatings. Additionally, NPs also offer other special properties that depend on their nanometric size, and this is also a source of new sensing applications. This review focuses on the current status of research in the use of NPs within coatings in optical fiber sensing. Most used sensing principles in fiber optics are briefly described and classified into several groups: absorbance-based sensors, interferometric sensors, fluorescence-based sensors, fiber grating sensors, and resonance-based sensors, among others. For each sensor group, specific examples of the utilization of NP-embedded coatings in their sensing structure are reported.
Site-directed mutagenesis of the hinge peptide from the hemagglutinin protein: enhancement of the pH-responsive conformational change (2008)

Environmentally responsive proteins and peptides are increasingly finding utility in various engineered systems due to their ability to respond to the presentation of external stimuli. A classic example of this behavior is the influenza hemagglutinin (HA) fusion protein. At neutral pH, HA exists in a non-fusogenic state, but upon exposure to low pH, the conformation of the structure changes to expose a fusogenic peptide. During this structural change, massive rearrangements occur in a subunit of HA (HA2). Crystallography data has shown that a loop of 28 amino acids (residues 54-81) undergoes a dramatic transition from a random coil to an alpha-helix. This segment connects to two flanking helical regions (short and long) to form a long, continuous helix. Here, we report the results of site-directed mutagenesis study on LOOP-36 to further understand the mechanism of this important stimulus-responsive peptide. The conformational transition of a bacterially expressed LOOP-36 was found to be less dramatic than has been previously reported. The systematic mutation of glutamate and histidine residues in the peptide to glutamines (glutamine scanning) did not impact the conformational behavior of the peptide, but the substitution of the glycine residue at position 22 with alanine resulted in significant pH-responsive behavior. Therefore this mutant stimulus-responsive peptide may be more valuable for future protein engineering and bionanotechnology efforts.
Catalytic Enantioselective meso-Epoxide Ring Opening Reaction with Phenolic Oxygen Nucleophile Promoted by Gallium Heterobimetallic Multifunctional Complexes (2000)

The catalytic enantioselective meso-epoxide ring opening reaction with phenolic oxygen nucleophile (4-methoxyphenol) is described for the first time herein. This reaction was first found to be promoted by (R)-GaLB (Ga = gallium, L = lithium, B = (R)-BINOL), giving a variety of epoxide opening products in good to high ee (67−93% ee). However, chemical yield was only modest (yield 31−75%), despite the use of more than 20 mol % GaLB. This was due to the undesired ligand exchange between BINOL and 4-methoxyphenol, which resulted in the decomplexation of GaLB. Application of various known chiral ligands such as 6,6‘-bis((triethylsilyl)ethynyl)-BINOL and H8-BINOL were examined, but satisfactory results were not obtained. To overcome this problem a novel linked-BINOL containing coordinative oxygen atom in the linker has been developed. By linking two BINOL units in GaLB, the stability of the Ga-complex was greatly improved. Using 3−10 mol % (R,R)-Ga-Li-linked-BINOL complex, a variety of epoxide opening reactions were found to proceed smoothly, affording products in analogous ee (66−96% ee) and in much higher yield (yield 67−94%) compared to (R)-GaLB. The structure of the LiCl free Ga-Li-linked-BINOL complex was elucidated by X-ray analysis. This is the first X-ray data for an asymmetric catalyst containing gallium. The possible mechanism of the entitled reaction is also discussed, based on the X-ray structure of the Ga-complex.
Photophysical Studies on Binding of Curcumin to Bovine Serum Albumin¶ (2003)

The excited-state photophysical properties of curcumin in the presence of bovine serum albumin (BSA) have been studied. The absorption and fluorescence changes in curcumin on binding to BSA have been followed at varying concentrations of either curcumin or BSA to determine the binding constant, which has been found to be approximately 10(4) to 10(5) M(-1). Stopped-flow kinetics studies suggested at least two distinct kinetic steps for the binding of curcumin to BSA. The photophysical properties of the singlet-excited state of the curcumin-BSA complex have also been studied. Whereas the absorption spectrum of curcumin is redshifted, the fluorescence spectrum of curcumin was blueshifted in the presence of BSA. The fluorescence quantum yield of curcumin on complexing with BSA was approximately 0.05. Steady-state fluorescence anisotropy studies showed a significant increase in the anisotropy value of 0.37 in BSA-bound curcumin. The fluorescence decay of the curcumin-BSA complex followed a biexponential decay with fluorescence lifetimes of 413 ps (33%) and 120 ps (67%). On the basis of these complementary results, it has been concluded that curcumin shows very high binding to BSA, probably at the hydrophobic cavities inside the protein.
Sustaining Neovascularization of a Scaffold Through Staged Release of Vascular Endothelial Growth Factor-A and Platelet-Derived Growth Factor-BB (2011)

Tissue regeneration into a three-dimensional scaffold requires the stimulation of blood vessel ingrowth. We have employed a freely interconnecting porous scaffold developed by us to determine the utility of a covalently bound heparin surface coating for the delivery of vascular endothelial growth factor (VEGF) and platelet-derived growth factor BB (PDGF-BB) in vivo. The heparin surface was shown to release VEGF far more rapidly than PDGF-BB in vitro (VEGF: 75 ng/h for 24 h; PDGF-BB: 86 pg/h for >7 days). In rat subcutaneous implants, at 10 days the heparin surface alone increased vessel ingrowth substantially (p<0.05 vs. unmodified scaffold), release of VEGF resulted in a further increase (p<0.05 vs. heparinized scaffold), whereas PDGF-BB had no additional effect. The increase induced by the combination of growth factors was similar to VEGF alone. After 2 months, PDGF-BB, but not VEGF delivery, resulted in a substantial increase in vascularization above that induced by heparin (p<0.05). At the longer time point the combination of growth factors was similar to PDGF-BB. However, only the combination of growth factors significantly elevated the number of ingrowing arterioles (p<0.05 vs. heparinized scaffold). Thus, the covalent modification of a porous scaffold with heparin allows for the differential release of VEGF and PDGF-BB that results in both a rapid and sustained increase in scaffold vascularization.
Monomeric bovine IgG2 is a potent stimulus for bovine neutrophils (1995)

Bovine plasma contains factors that can stimulate bovine neutrophils. Bovine plasma at 1:1,000,000-1:1,000 dilution induced a dose-dependent superoxide production in bovine neutrophils. When bovine plasma was fractionated with a protein G column, only the IgG fraction contained induction activity. At similar concentrations purified IgG induced a much stronger response than that of plasma IgG. Purified monomeric bovine IgG induced a dose-dependent increase in superoxide production. The maximum induction can be achieved at 100 micrograms/ml of bovine IgG. When subclasses of bovine IgG were examined, monomeric bovine IgG2 potently stimulated bovine polymorphonuclear leukocytes. In contrast, bovine IgG 1 failed to induce a response at similar concentrations, and neither bovine IgG F(ab')2 and Fc were effective. Both recombinant bovine granulocyte-macrophage colony-stimulating factor (r-BoGM-CSF) and recombinant bovine granulocyte colony-stimulating factor (r-BoG-CSF) primed bovine neutrophils for superoxide production induced by bovine IgG. The above results suggest that: (1) bovine plasma contain factors that can activate bovine neutrophils; (2) bovine plasma IgG is the major component that is responsible for bovine neutrophil activation; (3) bovine plasma contains factors that can inhibit the effect of bovine IgG; (4) monomeric bovine IgG2, but not IgG1, can activate bovine neutrophils directly without Fc receptor cross-linkage; (5) the integrity of bovine IgG is important in bovine polymorphonuclear leukocyte activation; and (6) bovine neutrophil activation induced by bovine IgG can be primed by r-BoGM-CSF or r-BoG-CSF.
The aquatic vertebrate embryo as a sentinel for toxins: zebrafish embryo dechorionation and perivitelline space microinjection (1997)

Pollution of aquatic ecosystems poses a serious threat to aquatic organisms and ultimately the entire ecosystem. Understanding how a toxin affects embryonic development is key to determining the risk a pollutant represents to the environment. Extraembryonic membranes, such as the chorion of fish eggs, provide a protective barrier between the embryo and the environment. Although the fish chorion excludes many chemical pollutants, some noxious agents can still gain access to the aquatic embryo. Therefore a monitoring system that tests the effects directly upon the embryo must be established. Although exposure to a single toxin in the laboratory can determine the concentration at which a pollutant becomes a health or environmental hazard, embryos and adults in nature are not merely affected by a single chemical, but are exposed to mixtures of different pollutants. Zebrafish (Danio rerio) and medaka (Oryzias latipes) embryos were employed for the rapid observation of the effects of single chemicals and chemical mixtures on development. Using dechorionation and a perivitelline space microinjection system, the embryos were effective sentinels for low concentrations of aquatic pollutants. The developmental effects of small quantities of toxins were observed. Embryos treated during the late gastrula stage of development with hexachlorobenzene (HCB); 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD); toluene; benzene; or mixtures of these chemicals developed cardiovascular abnormalities. The zebrafish dechorionation exposure technique, Micro Intrachorionic Zebrafish Embryo Live Laboratory test, was especially effective in testing the pollutant mixtures. Combinations of both TCDD and benzene (as well as the toluene and benzene combinations) were tested and the mixtures acted synergistically; the combinations were more toxic than either chemical by itself. Hexachlorobenzene- and TCDD-treated embryos tested positively for expression of cytochrome P450 1A indicating that the cytochrome metabolic pathways were already functional in these early embryos, and suggested that a product of the cytochrome system may be involved in HCB and TCDD pollution associated cardiovascular defects.
Beyond the clause: extraction of phosphorylation information from medline abstracts (2005)

Motivation: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed and implemented to connect and merge pieces of information about phosphorylation mentioned in different sentences in the text. The effectiveness and accuracy of the system as a whole as well as that of the methods for extraction beyond a clause/sentence is evaluated using an independently annotated dataset, the Phospho.ELM database. The new methods developed to merge pieces of information from different sentences are shown to be effective in significantly raising the recall without much difference in precision. Contact:vijay@cis.udel.edu
Roles of porphyrins and host iron transport proteins in regulation of growth of Porphyromonas gingivalis W50 (1991)

Porphyromonas gingivalis (Bacteroides gingivalis) requires iron in the form of hemin for growth and virulence in vitro, but the contributions of the porphyrin ring structure, porphyrin-associated iron, host hemin-sequestering molecules, and host iron-withholding proteins to its survival are unknown. Therefore, the effects of various porphyrins, host iron transport proteins, and inorganic iron sources on the growth of P. gingivalis W50 were examined to delineate the various types of iron molecules used for cellular metabolism. Cell envelope-associated hemin and iron stores contributed to the growth of P. gingivalis in hemin-free culture, and depletion of these endogenous reserves required eight serial transfers into hemin-free medium for total suppression of growth. Comparable growth of P. gingivalis was observed with 7.7 microM equivalents of hemin as hemoglobin (HGB), methemoglobin, myoglobin, hemin-saturated serum albumin, lactoperoxidase, cytochrome c, and catalase. Unrestricted growth was recorded in the presence of haptoglobin-HGB and hemopexin-hemin complexes, indicating that these host defense proteins do not sequester HGB and hemin from P. gingivalis. The iron chelator 2,2'-bipyridyl functionally chelated hemin-associated iron, resulting in dose-dependent inhibition of growth in hemin-restricted cultures at 1 to 25 microM 2,2'-bipyridyl concentrations. In the absence of an exogenous iron source, protoporphyrin IX did not support P. gingivalis growth. These findings suggest that the iron atom in the hemin molecule is the critical constituent for growth and that the tetrapyrrole porphyrin ring structure may represent an important vehicle for delivery of iron into the P. gingivalis cell. P. gingivalis does not have a strict requirement for porphyrins, since growth occurred with nonhemin iron sources, including high concentrations (200 muM) of ferric, ferrous, and nitrogenous inorganic iron, and P. gingivalis exhibited unrestricted growth in the presence of host transferrin, lactoferrin, and serum albumin. The diversity of iron substrates utilized by P. gingivalis and the observation that growth was not affected by the bacteriostatic effects of host iron-withholding proteins, which it may encounter in the periodontal pocket, may explain why P. gingivalis is such a formidable pathogen in the periodontal disease process.
The Structural and Ideological Contradictions of Britain's Post-War Reconstruction (1994)

Hay's essay offers a critique of both liberal and Marxist historiographies, providing an alternative theoretical-informed account of Britain's post-war reconstruction which suggests the existence of twin domestic post-war settlements.
A pilot clinical trial of a recombinant ricin vaccine in normal humans (2006)

Ricin, a highly potent toxin produced by castor beans, is classified by the Centers for Disease Control and Prevention as a level B biothreat because it is easily produced, readily available, and highly stable. There have been >750 cases of documented ricin intoxication in humans. There is no approved vaccine for ricin. Ricin contains a lectin-binding B chain and a ribotoxic A chain (RTA). In addition to its ribotoxic site, we have identified a separate site on RTA that is responsible for inducing vascular leak syndrome (VLS) in humans. We have generated a recombinant RTA with two amino acid substitutions that disrupt its ribotoxic site (Y80A) and its VLS-inducing site (V76M). This mutant recombinant RTA (named RiVax) was expressed and produced in Escherichia coli and purified. When RiVax was injected i.m. into mice it protected them against a ricin challenge of 10 LD50s. Preclinical studies in both mice and rabbits demonstrated that RiVax was safe. Based on these results, we have now conducted a pilot clinical trial in humans under an investigational new drug application submitted to the Food and Drug Administration. In this study, three groups of five normal volunteers were injected three times at monthly intervals with 10, 33, or 100 mug of RiVax. The vaccine was safe and elicited ricin-neutralizing Abs in one of five individuals in the low-dose group, four of five in the intermediate-dose group, and five of five in the high-dose group. These results justify further development of the vaccine.
Production of conjugated linoleic acid by dairy starter cultures (1998)

Nineteen different strains of lactobacilli, lactococci, streptococci and propionibacteria commonly used as dairy starter cultures were tested for their ability to produce conjugated linoleic acid (CLA) from free linoleic acid in vitro. Two strains of Propionibacterium freudenreichii ssp. freudenreichii and one strain of P. freudenreichii ssp. sheramnii were found to be capable of converting free linoleic acid to extracellular CLA. The highest level of CLA formed in the media was 265 micrograms ml-1. Of the different isomers, cis- and trans-9,11-octadecadienoic acid represented more than 70% of the total CLA formed. The inhibitory effect of linoleic acid on the growth of the bacteria and its conversion to CLA in different media by propionibacteria are discussed.
A new approach to high impedance fault detection using wavelet packet analysis (2002)

The paper presents a new approach to high impedance fault detection based on wavelet packet analysis. The nature and dynamics of the arc phenomenon related to high impedance faults are analyzed. A background is reported about wavelet transform and wavelet packet decomposition. Then, detecting criteria are proposed and assessing parameters calculated. Finally, in order to evaluate the procedure, the approach is applied to power system signals in normal conditions.
Chemoradiotherapy versus radiotherapy in patients with advanced nasopharyngeal cancer: phase III randomized Intergroup study 0099. (1998)

We conclude that chemoradiotherapy is superior to radiotherapy alone for patients with advanced nasopharyngeal cancers with respect to PFS and overall survival.
3-Year Suppression of HIV Viremia with Indinavir, Zidovudine, and Lamivudine (2000)

A three-drug regimen of indinavir, zidovudine, and lamivudine suppressed viremia in two thirds of patients for at least 3 years.
Predict Personal Continuous Route (2008)

In the daily life, people often repeat regular routes in certain periods. Predicting personal future routes using this information helps to achieve many goals, including improving the quality of intelligent transportation systems (ITSs) and location-based services (LBSs) for individuals. In this paper, a novel system is developed to predict the personal future routes based on the continuous route patterns extracted in advance. The proposed approach predicts a person's future route through the use of a probabilistic tree model built from his / her route patterns. The route patterns are extracted from personal history of movement using a new mining algorithm, continuous route pattern mining (CRPM), which based on PrefixSpan. Furthermore, the separated system architecture guarantees the safety of personal privacy while greatly reducing the computational load on mobile devices. An evaluation using a corpus of real routes from 17 persons demonstrates the effectiveness of the system. Using only a month recorded trips data, our system can get an average correct rate of about 74.3% in one step predicting. In route prediction, the average Levenshtein distance between the real trips and predicting results produced by our system is about 30% shorter than that produced by the basic Markov method.
Is the small intestinal epithelium truly "tight" to inulin permeation? (1991)

In this study, we evaluated the "leakiness" of intestinal epithelium through examination of small intestinal absorption of inulin in vivo by perfusing rat jejunum with 10 microM inulin. In physiological conditions, we found significant absorption of inulin at a rate of 44.6 nmol.100 cm-1.h-1 or absorption of 14.7%.100 cm-1.h-1 of the amount perfused. Increasing water flux by changing the luminal osmolarity resulted in linear (y = 31.1 + 2.4x, r = 0.97) increase in absorption of inulin, indicating a significant convective component of inulin absorption. There was large permeation of inulin at net water secretion and at zero net water fluxes (31.1 nmol.100 cm-1.h-1), indicating significant absorption of inulin by diffusive movement as well. The small intestinal tissue retention of inulin occurred rapidly within the first 15 min of perfusion, and the total tissue retention remained unchanged thereafter at approximately 10.8 nmol/100 cm. 16,16-Dimethylprostaglandin E2 decreased water flux, whereas cyclooxygenase inhibitors, indomethacin and acetylsalicylate, increased water flux. Inulin absorption closely paralleled changes in water flux induced by these agents. Taurocholate also caused parallel decrease in water and inulin absorption. Varying the resistance of unstirred water layer with changing luminal flow rate, the addition of mucolytic agent acetylcysteine, or alterations of luminal pH did not affect water or inulin absorption. We conclude that inulin permeates the small intestinal epithelium in significant amounts under normal physiological conditions, presumably through the paracellular pathways utilizing aqueous channels.
Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome (2012)

The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have been affected by the revised annotation.
Cutting Edge: Evidence for a Dynamically Driven T Cell Signaling Mechanism (2012)

T cells use the αβ TCR to bind peptides presented by MHC proteins (pMHC) on APCs. Formation of a TCR-pMHC complex initiates T cell signaling via a poorly understood process, potentially involving changes in oligomeric state, altered interactions with CD3 subunits, and mechanical stress. These mechanisms could be facilitated by binding-induced changes in the TCR, but the nature and extent of any such alterations are unclear. Using hydrogen/deuterium exchange, we demonstrate that ligation globally rigidifies the TCR, which via entropic and packing effects will promote associations with neighboring proteins and enhance the stability of existing complexes. TCR regions implicated in lateral associations and signaling are particularly affected. Computational modeling demonstrated a high degree of dynamic coupling between the TCR constant and variable domains that is dampened upon ligation. These results raise the possibility that TCR triggering could involve a dynamically driven, allosteric mechanism.