gebhart/patrepeval huggingface dataset:
Botulinum Toxin A in Anal Fissure: Why Does It Work? (2004)

Diseases of the Colon & Rectum: February 2004 - Volume 47 - Issue 2 - p 257-258 doi: 10.1007/s10350-003-0021-x
Sandstone Acidizing Using A New Class of Chelating Agents (2011)

Abstract The objective of stimulation of sandstone reservoirs is to remove the damage caused to the production zone during drilling or completion operations. Many problems may occur during sandstone acidizing with HCl/HF mud acid. Among these problems: decomposition of clays in HCl acids, precipitation of fluosilicates, the presence of carbonates can cause the precipitation of calcium fluorides, silica-gel filming, colloidal silica-gel precipitation. In this study, a recently introduced chelating agent, glutami-N, N-diacetic acid(GLDA), was used to stimulate sandstone cores. Berea sandstone cores with 8 wt% clays content were used in this study. Different GLDA solution pH values (1.7 - 13) were used in the coreflood experiments. The sandstone cores were scanned before and after the treatment to investigate the effect of GLDA on the core. The effluent samples were analyzed for calcium, magnesium, aluminum, and iron using the ICP to assess the ability of GLDA on the complexation of these ions. Coreflood experiments were run at temperatures of 200 to 300°F and the concentration of GLDA was determined after the treatment. The effects of injection rate, volume of GLDA, temperature, and GLDA initial pH value were investigated on the Berea sandstone cores in the coreflood experiments. Different correlations were used to determine the core permeability after the treatment, and the correlation that gave the minimum error was determined. GLDA showed a strong ability in chelating calcium, iron, magnesium, and it chelated small amounts of aluminum ions from the sandstone cores. At 300°F, GLDA at different pH values was able to enhance the core permeability. Decreasing the injection rate from 5 to 2 cm3/min increased the contact time between the fluid and the rock and increased the amount of dissolved ions. X-ray CT scan showed a porosity increase after the treatments at different conditions. The concentration of GLDA after the coreflood experiment was almost the same before the treatment showing a high thermal stability up to 300°F in the coreflood experiment. Labrid was found to be the best correlation to predict for the core permeability after treating Berea sandstone cores by 20 wt% GLDA solutions.
Late onset neurological phenotype of the X-ALD gene inactivation in mice: a mouse model for adrenomyeloneuropathy (2002)

Adrenomyeloneuropathy (AMN) and cerebral childhood adrenoleukodystrophy (CCALD) are the main phenotypic variants of an X-linked inherited metabolic disorder causing demyelination, X-linked adrenoleukodystrophy (X-ALD). It is caused by mutations in the ABCD1 (ALD) gene encoding a peroxisomal ABC transporter. Inactivation of the murine ALD gene does not lead to a detectable clinical phenotype in mice up to 6 months, and no cerebral pathology resembling the childhood form (CCALD) was observed. In this work, we show that older ALD-deficient mice exhibit an abnormal neurological and behavioral phenotype, starting at around 15 months. This is correlated with slower nerve conduction, and with myelin and axonal anomalies detectable in the spinal cord and sciatic nerve, but not in brain. The phenotype of ALD-deficient mice mimics features of human AMN, thus providing a model for investigating the pathogenesis of this disease.
A protein corona-enabled blood test for early cancer detection (2016)

Pancreatic cancer is a very aggressive malignancy that is often diagnosed in the advanced stages, with the implication that long-term survivors are extremely rare. Thus, developing new methods for the early detection of pancreatic cancer is an urgent task for current research. To date, nanotechnology offers unprecedented opportunities for cancer therapeutics and diagnosis. The aim of this study is the development of a new pancreatic cancer diagnostic technology based on the exploitation of the nano-bio-interactions between nanoparticles and blood samples. In this study, blood samples from 20 pancreatic cancer patients and 5 patients without malignancy were allowed to interact with designed lipid nanoparticles, leading to the formation of a hard "protein corona" at the nanoparticle surface. After isolation, the protein patterns were characterized by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS PAGE). We found that the protein corona of pancreatic cancer patients was much more enriched than that of healthy individuals. Statistical analysis of SDS-PAGE results allowed us to discriminate between healthy and pancreatic cancer patients with a total discriminate correctness rate of 88%.
On the ‘wave momentum’ myth (1981)

Controversies over ‘the momentum’ of waves have repeatedly wasted the time of physicists for over half a century. The persistence of the controversies is surprising, since regardless of whether classical or quantum dynamics is used the facts of the matter are simple and unequivocal, are well checked by laboratory experiment, are clearly explained in several published papers, and on the theoretical side can easily be verified by straightforward calculations. They are illustrated here by some simple, classical examples involving acoustic and gravity waves.
Solution and Interface Aggregation States of Crotalus atrox Venom Phospholipase A2 by Two-Photon Excitation Fluorescence Correlation Spectroscopy (2001)

The dimeric Crotalus atrox venom PLA2 is part of the secreted phospholipase A2 (PLA2) enzyme family that interacts at the lipid-solution interface to hydrolyze the sn-2 acyl ester bond of phospholipids. We have employed fluorescence correlation spectroscopy (FCS) to study the monomer-dimer equilibrium of the C. atrox venom PLA2 in solution, in the presence of urea, and in the presence of monomeric and micellar n-dodecylphosphocholine (C12-PN), a phosphatidylcholine analogue. Dilution experiments show that PLA2 is an extremely tight dimer, Kd < or = 0.01 nM, in solution. Urea was introduced to weaken the subunit's association, and an estimate for the PLA(2) dimer dissociation constant in buffer was obtained by linear extrapolation. The derived dissociation constant was at least several orders of magnitude greater than that suggested from the dilution experiments, indicating a complex interaction between urea and the PLA2 dimer. FCS data indicate that the PLA2 dimer begins to dissociate at 10 mM C12-PN in 10 mM Ca2+ and at 5 mM C12-PN in 1 mM EDTA. The PLA2 tryptophan fluorescence displayed spectral shifts and intensity changes upon interacting with C12-PN. On the basis of the FCS and tryptophan fluorescence results, we postulate an intermediate state where the two monomers are in loose interaction within a protein-lipid comicelle. As the concentration of C12-PN was increased, complete dissociation of the dimer was observed, inferred from the doubling of the particle number, and the average diffusion constant decreased to approximately 60 microm2/s, consistent with PLA2 associated with a C12-PN micelle. The presence of Ca2+ makes the comicelle intermediate more stable, retarding the separation of the monomers in the micellar suspension. Our data clearly indicate that PLA2, though a strong dimer in the absence of lipids, is dissociated by micellar C12-PN and supports the monomer hypothesis for PLA2 action.
Interaction of a high-power laser beam with low-density porous media (1997)

We have experimentally investigated the processes of laser light absorption and energy transfer in porous targets made of “agar-agar” (C14H18O7) with an average density of 1–4 mg/cm3 illuminated by the focused beam of a neodymium laser with an intensity of 1014 W/cm2 within a pulse of duration 2.5 ns. Many important scientific and technical problems, e.g., inertial-confinement thermonuclear fusion, the creation of lasers in the x-ray regime, and the modeling of astrophysical phenomena under laboratory conditions, can be successfully addressed by using low-density porous media as components of such targets. In our experiments with porous targets of variable density and thickness we used optical and x-ray diagnostic methods, which ensured that our measurements were made with high temporal and spatial resolution. We show that a region forms within the porous target consisting of a dense high-temperature plasma which effectively absorbs the laser radiation. Energy is transferred from the absorption region to the surrounding layer of porous material at up to 2×107 cm/s. Experimental data are in good agreement with the predictions of our theoretical model, which takes into account the specific features of absorption of laser radiation in a porous material and is based on representing the energy transfer within the material as a hydrothermal wave.
Resolving T-cell receptor clonality in two and genotype in four multiplex polymerase chain reactions. (2005)

Clonality can be accurately determined in nodal T-cell lymphoma with two single-tube multiplex PCR targeting TCRG and TCRD. TCRB analysis should be considered in equivocal cases in which a polyclonal background may obscure clonal TCRD, but clonal incomplete TCRB rearrangement alone is insufficient for presuming T-cell lineage. In the absence of objective evidence of B-cell neoplasia, multiplex PCR of T-cell receptor genes may be used early in the diagnostic work-up, including for fine needle aspirates.
Modelling of biological neurons by artificial neural networks (2002)

A general approach for modeling biological neurons by means of ANNs is presented. This approach does not require any a-priori information about the system dynamics. A close-loop neural network architecture based on a multilayer feed forward network, is used as an alternative approach to standard system identification. The model can be employed to simulate the behavior of complex networks.
Physical Interaction between GATA-5 and Hepatocyte Nuclear Factor-1α Results in Synergistic Activation of the Human Lactase-Phlorizin Hydrolase Promoter (2002)

GATA-4, -5, and -6 zinc finger and hepatocyte nuclear factor-1alpha (HNF-1alpha) homeodomain transcription factors are expressed in the intestinal epithelium and synergistically activate the promoter of intestinal genes. Here, we demonstrate that GATA-5 and HNF-1alpha physically associate both in vivo and in vitro and that this interaction is necessary for cooperative activation of the lactase-phlorizin hydrolase promoter. Furthermore, physical association is mediated by the C-terminal zinc finger of GATA factors and the homeodomain of HNF-1alpha. Deletion of HNF-1alpha activation domains or interruption of HNF-1-binding sites in the lactase-phlorizin hydrolase promoter resulted in a complete loss of cooperativity, whereas deletion of GATA-5 activation domains or interruption of GATA-binding sites resulted in a reduction, but not an elimination, of cooperativity. We hypothesize that GATA/HNF-1alpha cooperativity is mediated by HNF-1alpha through its activation domains, which are oriented for high levels of activation through binding to DNA and physical association with GATA factors. These data suggest a paradigm whereby intestine-specific gene expression is regulated by unique interactions among tissue-restricted transcription factors coexpressed in the intestine. Parallel mechanisms in other tissues as well as in Drosophila suggest that zinc finger/homeodomain interactions are an efficient pathway of cooperative activation of gene transcription that has been conserved throughout evolution.
Colorimetric Detection of Pb2+ Using Glutathione Functionalized Gold Nanoparticles (2010)

A facile, cost-effective and sensitive colorimetric detection method for Pb(2+) has been developed by using glutathione functionalized gold nanoparticles (GSH-GNPs). The sensitivity and selectivity of detection were investigated in detail. The GSH-GNPs could be induced to aggregate immediately in the presence of Pb(2+), especially after the addition of 1 M NaCl aqueous solution. The Pb(2+) could be detected by colorimetric response of GNPs that could be monitored by a UV-vis spectrophotometer or even naked eyes, and the detection limit could reach 100 nM. The GSH-GNPs bound by Pb(2+) showed excellent selectivity compared to other metal ions (Hg(2+), Mg(2+), Zn(2+), Ni(2+), Cu(2+), Co(2+), Ca(2+), Mn(2+), Fe(2+), Cd(2+), Ba(2+), and Cr(3+)), which led to prominent color change. This provided a simple and effective colorimetric sensor (no enzyme or DNA) for on-site and real-time detection of Pb(2+). Most importantly, this probe was also applied to determine the Pb(2+) in the lake samples with low interference and high sensitivity.
IgG Subclasses and Antibody Response to Pneumococcal Capsular Polysaccharides in Children with Severe Sinopulmonary Infections and Asthma (1991)

A prospective open study was carried out on 30 pediatric patients with most severe chest disease whose serum immunoglobulin levels were normal. The patients entered into the study had had two or more documented episodes of pneumonia, and/or six episodes of bronchitis with fever within a year, and/or severe asthma (steroid-dependent), and/or hospitalization for chest disease for more than 30 days within the year preceding the study. Eleven patients had sinopulmonary infections, 19 had asthma. Twenty patients had low levels of one or two IgG subclasses: 11 were deficient in IgG3, three in IgG4, three in IgG3 + IgG4, and three in IgG2 + IgG4. Patients with low IgG subclass levels were distributed throughout the different clinical entities. These children had significantly longer periods of hospitalization than the patients in whom all IgG subclasses were within the normal range. They suffered more often from sinopulmonary infections. Asthmatic children with low levels of an IgG subclass reported more days with wheezing and needed more steroids than the children without subclass deficiencies.
Myofibroblast Differentiation by Transforming Growth Factor-1 Is Dependent on Cell Adhesion and Integrin Signaling via Focal Adhesion Kinase (2003)

Myofibroblast differentiation and activation by transforming growth factor-beta1 (TGF-beta1) is a critical event in the pathogenesis of human fibrotic diseases, but regulatory mechanisms for this effect are unclear. In this report, we demonstrate that stable expression of the myofibroblast phenotype requires both TGF-beta1 and adhesion-dependent signals. TGF-beta1-induced myofibroblast differentiation of lung fibroblasts is blocked in non-adherent cells despite the preservation of TGF-beta receptor(s)-mediated signaling of Smad2 phosphorylation. TGF-beta1 induces tyrosine phosphorylation of focal adhesion kinase (FAK) including that of its autophosphorylation site, Tyr-397, an effect that is dependent on cell adhesion and is delayed relative to early Smad signaling. Pharmacologic inhibition of FAK or expression of kinase-deficient FAK, mutated by substituting Tyr-397 with Phe, inhibit TGF-beta1-induced alpha-smooth muscle actin expression, stress fiber formation, and cellular hypertrophy. Basal expression of alpha-smooth muscle actin is elevated in cells grown on fibronectin-coated dishes but is decreased on laminin and poly-d-lysine, a non-integrin binding polypeptide. TGF-beta1 up-regulates expression of integrins and fibronectin, an effect that is associated with autophosphorylation/activation of FAK. Thus, a safer and more effective therapeutic strategy for fibrotic diseases characterized by persistent myofibroblast activation may be to target this integrin/FAK pathway while not interfering with tumor-suppressive functions of TGF-beta1/Smad signaling.
The Ullmann Condensation Reaction of Haloanthraquinone Derivatives with Amines in Aprotic Solvents. IV. Kinetic Studies of the Condensation with Ethylenediamine (1979)

Abstract In the Ullmann condensation of bromoanthraquinones (AQBr) with ethylenediamine using copper(I) bromide as a catalyst, the reaction rate decreased with time which has been interpreted in terms of the formation of the ineffective copper(II) species. The kinetic investigation showed the reaction rate to be first order both for the copper(I) species and AQBr. After prolonged reaction the copper(I) species was quantitatively converted to the copper(II) species, the copper(II) species appearing to have little catalytic activity due to strong coordination with ethylenediamine. The reactivities of the haloanthraquinones were dependent on the ease of coordination with Cu(I) and the rate of Cu(II) formation. The mechanism, including the reaction between CuI(AQBr) and ethylenediamine, has been proposed and discussed.
Integrin-Mediated Signal Transduction in Human Endothelial Cells: Analysis of Tyrosine Phosphorylation Events (1994)

Adhesion of human umbilical endothelial cells to fibronectin resulted in increased tyrosine phosphorylation of a group of proteins with molecular mass ranging from 100 to 130 kDa and of a 70 kDa protein. This pattern of tyrosine phosphorylation was also observed when endothelial cells adhered to vitronectin, collagen IV, collagen I and laminin or to culture dishes coated with antibodies directed to either beta 1, alpha 3, alpha 5, alpha 6 or beta 3 integrin subunits. Increased phosphorylation of the 100-130 kDa proteins was detectable as early as 30 sec after adhesion, reached maximal level after 15 min, and remained high as long as the cells adhere to culture dishes. The 70 kDa protein was phosphorylated with a slower kinetics and its phosphorylation increased over a period of 3 h. Using specific monoclonal antibodies, the major component of the 100-130 kDa complex was identified as the focal adhesion tyrosine kinase p125FAK. The phosphorylation of the p125FAK was also observed by inducing beta 1 integrin clustering in non adherent HEC, indicating that this is a primary signalling event induced by integrins. Using tyrosine kinase inhibitors, we show a direct correlation between integrin-stimulated tyrosine kinases and assembly of focal adhesions and actin fibres.
Effects of Deformability, Uneven Surface Charge Distributions, and Multipole Moments on Biocolloid Electrophoretic Migration (2005)

Liposomes have been widely used as cellular and bioparticle mimics due to their lipid bilayer structure and relative ease of production and manipulation. Such biocolloids are frequently characterized by capillary electrophoresis (CE), which promises a wealth of information about such properties as surface charge, composition, and rigidity. The applicability of this information is somewhat limited, however, since it is interpreted with colloidal theories that do not account for the unique properties of biocolloids. In this work, the effects of deformability, mobile surface charges, intrinsic polarizability, and uneven surface charge distributions are incorporated into colloidal theories in order to better model the electrophoretic behaviors of liposomes.
Introduction of site-specific mutations into the genome of influenza virus. (1990)

We succeeded in rescuing infectious influenza virus by transfecting cells with RNAs derived from specific recombinant DNAs. RNA corresponding to the neuraminidase (NA) gene of influenza A/WSN/33 (WSN) virus was transcribed in vitro from plasmid DNA and, following the addition of purified influenza virus RNA polymerase complex, was transfected into MDBK cells. Superinfection with helper virus lacking the WSN NA gene resulted in the release of virus containing the WSN NA gene. We then introduced five point mutations into the WSN NA gene by cassette mutagenesis of the plasmid DNA. Sequence analysis of the rescued virus revealed that the genome contained all five mutations present in the mutated plasmid. The ability to create viruses with site-specific mutations will allow the engineering of influenza viruses with defined biological properties.
Parathyroid hormone: past and present (2005)

Research on parathyroid hormone (PTH) has undergone four rather distinctive phases, beginning just before the turn of the 20th century. Early debates about the function of the parathyroids were resolved by 1925, when understanding the role of PTH led to comprehending the action of the glands in calcium physiology. Elucidation of the pathophysiology of hormone excess (severe bone loss) and deficiency (hypocalcemia) continued over the following decades. With the advent of advances in chemical and molecular biology, the structure of PTH and its principal receptor (PTHrP-receptor [PTHR1]) were established. Tests with purified hormonal peptide in humans led to the surprising, even paradoxical, finding that PTH can be used pharmacologically to build bone, providing a dramatic therapeutic impact on osteoporosis. These developments have stimulated the field of calcium and bone biology and posed new questions about the role of PTH as well as possible new directions in therapy.
Elevated Tissue Factor and Tissue Factor Pathway Inhibitor Circulating Levels in Ischaemic Heart Disease Patients (1998)

Several studies have shown that thrombosis and inflammation play an important role in the pathogenesis of Ischaemic Heart Disease (IHD). In particular, Tissue Factor (TF) is responsible for the thrombogenicity of the atherosclerotic plaque and plays a key role in triggering thrombin generation. The aim of this study was to evaluate the TF/Tissue Factor Pathway Inhibitor (TFPI) system in patients with IHD. We have studied 55 patients with IHD and not on heparin [18 with unstable angina (UA), 24 with effort angina (EA) and 13 with previous myocardial infarction (MI)] and 48 sex- and age-matched healthy volunteers, by measuring plasma levels of TF, TFPI, Prothrombin Fragment 1-2 (F1+2), and Thrombin Antithrombin Complexes (TAT). TF plasma levels in IHD patients (median 215.4 pg/ml; range 72.6 to 834.3 pg/ml) were significantly (p<0.001) higher than those found in control subjects (median 142.5 pg/ml; range 28.0-255.3 pg/ml). Similarly, TFPI plasma levels in IHD patients were significantly higher (median 129.0 ng/ml; range 30.3-316.8 ng/ml; p<0.001) than those found in control subjects (median 60.4 ng/ml; range 20.8-151.3 ng/ml). UA patients showed higher amounts of TF and TFPI plasma levels (TF median 255.6 pg/ml; range 148.8-834.3 pg/ml; TFPI median 137.7 ng/ml; range 38.3-316.8 ng/ml) than patients with EA (TF median 182.0 pg/ml; range 72.6-380.0 pg/ml; TFPI median 115.2 ng/ml; range 47.0-196.8 ng/ml) and MI (TF median 213.9 pg/ml; range 125.0 to 341.9 pg/ml; TFPI median 130.5 ng/ml; range 94.0-207.8 ng/ml). Similar levels of TF and TFPI were found in patients with mono- or bivasal coronary lesions. A positive correlation was observed between TF and TFPI plasma levels (r = 0.57, p<0.001). Excess thrombin formation in patients with IHD was documented by TAT (median 5.2 microg/l; range 1.7-21.0 microg/l) and F1+2 levels (median 1.4 nmol/l; range 0.6 to 6.2 nmol/l) both significantly higher (p<0.001) than those found in control subjects (TAT median 2.3 microg/l; range 1.4-4.2 microg/l; F1+2 median 0.7 nmol/l; range 0.3-1.3 nmol/l). As in other conditions associated with cell-mediated clotting activation (cancer and DIC), also in IHD high levels of circulating TF are present. Endothelial cells and monocytes are the possible common source of TF and TFPI. The blood clotting activation observed in these patients may be related to elevated TF circulating levels not sufficiently inhibited by the elevated TFPI plasma levels present.
Regulatory T cells in inflammatory bowel disease (2008)

Tregs are important for the maintenance of intestinal self-tolerance and will likely prove to be an important avenue for therapeutic manipulation in IBD.