gebhart/patrepeval huggingface dataset:
Application of Microwave Irradiation to the Synthesis of 14-Helical β-Peptides (2005)

[structure: see text] We have evaluated the effects of microwave irradiation on the solid-phase synthesis of beta-peptides. Sequences designed to adopt the 14-helix, especially those containing the structure-promoting residue trans-2-aminocyclohexanecarboxylic acid (ACHC), suffer from poor synthetic efficiency under standard SPPS conditions. A comparison of microwave and conventional heating shows that both provide excellent synthetic results for shorter sequences; however, we identify a clear benefit from microwave irradiation for longer beta-peptides.
Inhibiting Interleukin-4 and Interleukin-13 in Difficult-to-Control Asthma (2013)

One of the most challenging aspects of the clinical management of asthma is determining how to treat patients whose condition is poorly controlled despite the use of inhaled glucocorticoids and long-acting beta-agonists (LABAs). Although most patients have a response to these treatments, it is estimated that asthma remains poorly controlled in as many as 20% of patients who use combination therapy.1 Mainstays of the management of difficult-to-control asthma include increased adherence to treatment, avoidance of allergens and other exacerbating factors, and control of common coexisting conditions such as gastrointestinal reflux, postnasal drip, and sinusitis. Other adjuvant therapies currently available include . . .
Cosmic microwave background temperature and polarization anisotropy in Brans-Dicke cosmology (1999)

We develop a formalism for calculating cosmic microwave background (CMB) temperature and polarization anisotropies in cosmological models with Brans-Dicke gravity. We then modify publicly available Boltzmann codes to calculate numerically the temperature and polarization power spectra. Results are illustrated with a few representative models. Comparing with the general-relativistic model of the same cosmological parameters, both the amplitude and the width of the acoustic peaks are different in the Brans-Dicke models. We use a covariance-matrix calculation to investigate whether the effects of Brans-Dicke gravity are degenerate with those of variation in other cosmological parameters and to simultaneously determine whether forthcoming CMB maps might be able to distinguish Brans-Dicke and general-relativistic cosmology. Although the predicted power spectra for plausible Brans-Dicke models differ from those in general relativity only slightly, we find that MAP and/or the Planck Surveyor may in principle provide a test of Brans-Dicke theory that is competitive to solar-system tests. For example, if all other parameters except for the CMB normalization are fixed, a value of the Brans-Dicke parameter $\ensuremath{\omega}$ as large as 500 could be identified (at the 2\ensuremath{\sigma} level) with MAP, and for Planck, values as large as $\ensuremath{\omega}\ensuremath{\simeq}3000$ could be identified; these sensitivities are decreased roughly by a factor of 3 if we marginalize over the baryon density, Hubble constant, spectral index, and re-ionization optical depth. In more general scalar-tensor theories, $\ensuremath{\omega}$ may evolve with time, and in this case, the CMB probe would be complementary to that from solar-system tests.
Myoelectric control of gastrointestinal and biliary motility: a review. (1981)

The movement of ingested food and secretions through the gastrointestinal and its appendages depends on a highly integrated and coordinated response of the smooth muscle contained within the wall of the gut. This review will consider, in detail, the various myogenic factors that contribute to the usual aboral propulsion of the gastrointestinal contents. The role of myoelectrical complexes as represented by slow waves and spike potentials are emphasized, for they appear to play a central role in the initiation of sphincter function and gastrointestinal peristalsis. The myoelectric control of the sphincter of Oddi is discussed in relationship to gastroduodenal motility, since disturbances in this finely modulated sphincter may lead to biliary-pancreatic dysfunction and symptoms of upper gastrointestinal disease.
Vascular Endothelial Growth Factor-A Exerts Diverse Cellular Effects via Small G Proteins, Rho and Rap (2018)

Vascular endothelial growth factors (VEGFs) include five molecules (VEGF-A, -B, -C, -D, and placental growth factor), and have various roles that crucially regulate cellular functions in many kinds of cells and tissues. Intracellular signal transduction induced by VEGFs has been extensively studied and is usually initiated by their binding to two classes of transmembrane receptors: receptor tyrosine kinase VEGF receptors (VEGF receptor-1, -2 and -3) and neuropilins (NRP1 and NRP2). In addition to many established results reported by other research groups, we have previously identified small G proteins, especially Ras homologue gene (Rho) and Ras-related protein (Rap), as important mediators of VEGF-A-stimulated signaling in cancer cells as well as endothelial cells. This review article describes the VEGF-A-induced signaling pathways underlying diverse cellular functions, including cell proliferation, migration, and angiogenesis, and the involvement of Rho, Rap, and their related molecules in these pathways.
Lamellar polymer–LixMoO3 nanocomposites via encapsulative precipitation (1997)

With Li x MoO 3 (x=0.31–0.40) as a host material, a new family of polymer–molybdenum bronze nanocomposites has been synthesized using an exfoliation/encapsulation methodology. Nanocomposites with poly(ethylene oxide), poly(ethylene glycol), poly(propylene glycol), poly(vinylpyrrolidinone), methyl cellulose, polyacrylamide, and nylon-6 were prepared and characterized by thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), powder X-ray diffraction, FTIR spectroscopy, UV–VIS spectroscopy, variable-temperature 7 Li and 13 C solid-state NMR spectroscopy and magnetic susceptibility measurements. The electrical conductivity of these materials lies in the range from 10 -2 to 10 -7 S cm -1 , and decreases as the interlayer separation increases. The intercalated polymer imparts both mechanical strength and ease of processing to these materials. The water-soluble polymer–Li x MoO 3 nanocomposites can be cast into films and other shapes, which may provide opportunities for applications. Factors affecting the intercalation reaction and the structure of nanocomposites, such as variations in the preparation procedure, the polymer molecular mass and the annealing behaviour of the products are discussed.
Study of insertion task of a flexible wire into a hole by using visual tracking observed by stereo vision (2002)

Measuring the force on a flexible wire is difficult by using force/torque sensors when the flexural rigidity of the wire is small because the wire buckles and the force on the wire is smaller than the force that can be measured by a force/torque sensor. This paper presents a method of calculating the force on a wire from its shape observed by stereo vision. We propose a method of inserting the wire into a hole in a wall by using the estimated force. Three experiments have been successfully carried out.
Evaluation of anti-human leukocyte antigen-DR monoclonal antibody therapy in spontaneous canine lymphoma (2010)

A pilot study of anti-human leukocyte antigen (HLA)-DR monoclonal antibody (mAb) in dogs with lymphoma was undertaken to verify the suitability of a canine model to address therapeutically relevant endpoints prior to a full trial in dogs, and ultimately human investigation. In vitro studies demonstrated that L243, a murine IgG1 anti-HLA-DR, binds to normal and malignant canine lymphocytes and induces apoptosis in canine lymphoma cells. Moreover, L243 was administered safely to normal dogs and dogs with lymphoma, and bound to malignant cells in nodal tissue. Preliminary evidence of transient disease stabilization was observed in a subset of dogs with advanced-stage lymphoma following L243 immunotherapy. hL243γ4P (IMMU-114), a humanized IgG4 anti-HLA-DR, currently under evaluation preclinically for human trials, was also shown to bind malignant canine lymphocytes, and safety and pharmacokinetic data from the administration of IMMU-114 to normal dogs indicate similar behavior to L243 in these assessments. These findings provide a rationale for the use of dogs with lymphoma in safety and efficacy evaluations of anti-HLA-DR mAbs for both veterinary and human applications.
Waves and Fields in Inhomogeneous Media (1990)

Electrical Engineering/Electromagnetics Waves and Fields in Inhomogeneous Media A Volume in the IEEE Press Series on Electromagnetic Waves Donald G. Dudley, Series Editor ".it is one of the best wave propagation treatments to appear in many years." Gerardo G. Tango, CPG, Consulting Seismologist-Acoustician, Covington, LA This comprehensive text thoroughly covers fundamental wave propagation behaviors and computational techniques for waves in inhomogeneous media. The author describes powerful and sophisticated analytic and numerical methods to solve electromagnetic problems for complex media and geometry as well. Problems are presented as realistic models of actual situations which arise in the areas of optics, radio wave propagation, geophysical prospecting, nondestructive testing, biological sensing, and remote sensing.
Intraputamenal infusion of glial cell line–derived neurotrophic factor in PD: A two‐year outcome study (2005)

We have shown previously that intraparenchymal infusion of glial cell line-derived neurotrophic factor (GDNF) continuously into the posterior putamen in five Parkinson's disease patients is safe and may represent a new treatment option. Here, we report a continuation of this phase I study. After 2 years of continual GDNF infusion, there were no serious clinical side effects and no significant detrimental effects on cognition. Patients showed a 57% and 63% improvement in their off-medication motor and activities of daily living subscores of the Unified Parkinson's Disease Rating Scale, respectively, and health-related quality-of-life measures (Parkinson's Disease Questionnaire-39 and Short Form-36) showed general improvement over time.
Low-Voltage Tunnel Transistors for Beyond CMOS Logic (2010)

Steep subthreshold swing transistors based on interband tunneling are examined toward extending the performance of electronics systems. In particular, this review introduces and summarizes progress in the development of the tunnel field-effect transistors (TFETs) including its origin, current experimental and theoretical performance relative to the metal–oxide–semiconductor field-effect transistor (MOSFET), basic current-transport theory, design tradeoffs, and fundamental challenges. The promise of the TFET is in its ability to provide higher drive current than the MOSFET as supply voltages approach 0.1 V.
Relationship and probabilistic stratification of Eczema Area and Severity Index and objective Scoring Atopic Dermatitis severity scores for atopic dermatitis (2018)

The Harmonizing Outcome Measures for Eczema (HOME) recommended the Eczema Area and Severity Index (EASI) as the core outcome instrument for measuring the clinical signs of atopic dermatitis (AD). However, EASI may not have been used in previous clinical trials, and other scores, e.g. SCORAD (SCORing Atopic Dermatitis), the objective component of SCORAD (oSCORAD) and the Investigator Global Assessment (IGA), remain widely used. It is useful to establish a method to convert these scores into EASI to compare the results from different studies effectively. Indeed, EASI and oSCORAD have been found to be strongly correlated (rSpearman=0.92)7, suggesting a possibility to find a relationship between the two scores.
Does impairment of energy metabolism result in excitotoxic neuronal death in neurodegenerative illnesses? (1992)

The etiology of nerve cell death in neuronal degenerative disease is unknown, but it has been hypothesized that excitotoxic mechanisms may play a role. Such mechanisms may play a role in diseases such as Huntington's disease, Parkinson's disease, amyotropic lateral sclerosis, and Alzheimer's disease. In these illnesses, the slowly evolving neuronal death is unlikely to be due to a sudden release of glutamate, such as occurs in ischemia. One possibility, however, is that a defect in mitochondrial energy metabolism could secondarily lead to slow excitotoxic neuronal death, by making neurons more vulnerable to endogenous glutamate. With reduced oxidative metabolism and partial cell membrane depolarization, voltage-dependent N-methyl-D-aspartate (NMDA) receptor ion channels would be more easily activated. In addition, several other processes involved in buffering intracellular calcium may be impaired. Recent studies in experimental animals showed that mitochondrial toxins can result in a pattern of neuronal degeneration closely resembling that seen in Huntington's disease, which can be blocked with NMDA antagonists. NMDA antagonists also block neuronal degeneration induced by 1-methyl-4-phenylpyridium, which has been implicated in experimental models of Parkinson's disease. The delayed onset of neurodegenerative illnesses could be related to the progressive impairment of mitochondrial oxidative phosphorylation, which accompanies normal aging. If defective mitochondrial energy metabolism plays a role in cell death in neurodegenerative disorders, potential therapeutic strategies would be to use excitatory amino acid antagonists or agents to bypass bioenergetic defects.
Simultaneous inversion of pre‐stack seismic data (2005)

We present a new approach to the simultaneous pre‐stack inversion of and, optionally, angle gathers for the estimation of P‐impedance, S‐impedance and density. Our algorithm is based on three assumptions. The first is that the linearized approximation for reflectivity holds. The second is that and reflectivity as a function of angle can be given by the Aki‐Richards equations (Aki and Richards, 2002). The third is that there is a linear relationship between the logarithm of P‐impedance and both S‐impedance and density. Given these three assumptions, we show how a final estimate of P‐impedance, S‐impedance and density can be found by perturbing an initial P‐impedance model. After a description of the algorithm, we then apply our method to both model and real data sets.
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach (2016)

Targeted polypharmacology of kinases has emerged as a promising strategy to design efficient and safe therapeutics. Here, we perform a systematic study of kinase-ligand binding modes for the human structural kinome at scale (208 kinases, 1777 unique ligands, and their complexes) by integrating chemical genomics and structural genomics data and by introducing a functional site interaction fingerprint (Fs-IFP) method. New insights into kinase-ligand binding modes were obtained. We establish relationships between the features of binding modes, the ligands, and the binding pockets, respectively. We also drive the intrinsic binding specificity and which correlation with amino acid conservation. Third, we explore the landscape of the binding modes and highlight the regions of "selectivity pocket" and "selectivity entrance". Finally, we demonstrate that Fs-IFP similarity is directly correlated to the experimentally determined profile. These improve our understanding of kinase-ligand interactions and contribute to the design of novel polypharmacological therapies targeting kinases.
Oxidative Glycation and Free Radical Production: A Causal Mechanism of Diabetic Complications (1991)

Glucose may oxidise under physiological conditions and lead to the production of protein reactive ketoaldehydes, hydrogen peroxide and highly reactive oxidants. Glucose is thus able to modify proteins by the attachment of its oxidation derived aldehydes, leading to the development of novel protein fluorophores, as well as fragment protein via free radical mechanisms. The fragmentation of protein by glucose is inhibitable by metal chelators such as diethylenetriamine pentaacetic acid (DETAPAC) and free radical scavengers such as benzoic acid, and sorbitol. The enzymic antioxidant, catalase, also inhibits protein fragmentation. Protein glycation and protein oxidation are inextricably linked. Indeed, using boronate affinity chromatography to separate glycated from non-glycated material, we demonstrate that proteins which are glycated exhibit an enhanced tryptophan oxidation. Our observation that both glycation and oxidation occur simultaneously further supports the hypothesis that tissue damage associated with diabetes and ageing has an oxidative origin.
Human cytomegalovirus open reading frame US28 encodes a functional beta chemokine receptor. (1994)

Human cytomegalovirus infects epithelial, smooth muscle, and white blood cells in vivo causing acute, latent, and chronic infections. A data base search revealed that the amino acid sequence of the putative protein encoded by open reading frame US28 of human cytomegalovirus is approximately 30% identical to those of the mammalian leukocyte receptors for alpha and beta chemokines. This suggested that US28 was originally copied from a human chemokine receptor gene, perhaps to provide the virus with a selective advantage through molecular mimicry. Chemokines regulate the trafficking and activation of mammalian leukocytes and activate calcium-mobilizing, heptahelical, G protein-coupled receptors. We now show that US28 encodes a promiscuous calcium-mobilizing receptor for the beta chemokines RANTES (regulated upon activation, normal T expressed and secreted), macrophage inflammatory protein-1 alpha, and monocyte chemoattractant protein-1, but not for the alpha chemokines interleukin-8 or gamma IP10. The chemokine selectivity of the US28 product is distinct from that of known mammalian beta chemokine receptors. This finding suggests a role for beta chemokines in the pathogenesis of human cytomegalovirus infection by transmembrane signaling via the product of US28.
Mechanism of protein kinase C activation during the induction and maintenance of long-term potentiation probed using a selective peptide substrate. (1993)

Previous reports using various protein kinase inhibitors have suggested that protein kinase activity is necessary for both the induction and maintenance of hippocampal long-term potentiation (LTP), a cellular phenomenon likely to contribute to mammalian memory formation. We designed and characterized a selective peptide substrate for protein kinase C (PKC), corresponding to amino acids 28 to 43 of the neuronal protein neurogranin, and used the substrate to obtain direct biochemical evidence for activation of PKC in both the induction and maintenance phases of LTP. As the effect cannot be accounted for by either of two well-known mechanisms for persistent PKC activation, membrane insertion, or proteolysis, the persistent activation of PKC in the maintenance phase of LTP appears to occur via another mechanism. The maintenance phase of LTP is associated with decreased immunoreactivity of PKC, an effect that can be reversed with phosphatase treatment. Thus, PKC appears to be both phosphorylated and persistently activated in the maintenance phase of LTP.
Novel Oxa-di-π-methane and Norrish Type I Reactions in the S2 (π,π*) Excited State of a Series of β,γ-Unsaturated Ketones (2005)

[reaction: see text] Beta,gamma-unsaturated methyl ketones with electron-withdrawing groups at the gamma-position of the ene moiety undergo ODPM rearrangements and Norrish type I reactions on direct irradiation at 254 nm. The results are consistent with the involvement of alkene S(2) (pi,pi*) as reactive excited states in these processes.
Roles of Electrostatics and Conformation in Protein-Crystal Interactions (2010)

In vitro studies have shown that the phosphoprotein osteopontin (OPN) inhibits the nucleation and growth of hydroxyapatite (HA) and other biominerals. In vivo, OPN is believed to prevent the calcification of soft tissues. However, the nature of the interaction between OPN and HA is not understood. In the computational part of the present study, we used molecular dynamics simulations to predict the adsorption of 19 peptides, each 16 amino acids long and collectively covering the entire sequence of OPN, to the {100} face of HA. This analysis showed that there is an inverse relationship between predicted strength of adsorption and peptide isoelectric point (P<0.0001). Analysis of the OPN sequence by PONDR (Predictor of Naturally Disordered Regions) indicated that OPN sequences predicted to adsorb well to HA are highly disordered. In the experimental part of the study, we synthesized phosphorylated and non-phosphorylated peptides corresponding to OPN sequences 65-80 (pSHDHMDDDDDDDDDGD) and 220-235 (pSHEpSTEQSDAIDpSAEK). In agreement with the PONDR analysis, these were shown by circular dichroism spectroscopy to be largely disordered. A constant-composition/seeded growth assay was used to assess the HA-inhibiting potencies of the synthetic peptides. The phosphorylated versions of OPN65-80 (IC(50) = 1.93 microg/ml) and OPN220-235 (IC(50) = 1.48 microg/ml) are potent inhibitors of HA growth, as is the nonphosphorylated version of OPN65-80 (IC(50) = 2.97 microg/ml); the nonphosphorylated version of OPN220-235 has no measurable inhibitory activity. These findings suggest that the adsorption of acidic proteins to Ca2+-rich crystal faces of biominerals is governed by electrostatics and is facilitated by conformational flexibility of the polypeptide chain.
A NOVEL FLOW CYTOMETRY STIMULATION ASSAY USING CYTO-CHEX® BCT TUBES FOR USE IN CLINICAL TRIALS (2011)

from Streck Laboratories contain a priority fixative that stabilizes the blood at room temperature making flow cytometry analysis possible for up to one to two weeks after collection. This application has been advantageous for doctors and scientists in remote locations being able to transport specimens back to a testing lab that is not in close proximity to the draw site. These BCT tubes have also become very popular for use in clinical research trials for flow cytometry testing since humans are drawn from multiple sites and then the specimens are shipped to a central laboratory. One disadvantage of the tube is that since it contains a fixative, flow cytometry applications which require stimulation cannot be performed once the specimen is exposed to the fixative. In our laboratory we are working on ways to stimulate the specimen prior to placing in the Cyto-Chex® BCT tube. In one such method, we can measure the intracellular cytokine IL-17A expressed in T cells up to five days post-stimulation. This method can also be used to measure many phosphorylated proteins. These methods will greatly benefit the pharmaceutical and biotechnology industry in that whole blood specimens can be stimulated immediately after the draw, fixed and then shipped to a central testing facility. INTRODUCTION
A2E and Blue Light in the Retina: The Paradigm of Age-Related Macular Degeneration (2002)

The photoreceptors in the retina, designed to initiate the cascade of events which link the incoming light to the sensation of 'vision', are susceptible to damage by light, particularly blue light. The damage can lead to cell death and diseases. The turnover of retinal, an essential element of the visual process, is the basis of the events that lead to damage. Free retinal, absorbing in the blue region of the visible spectrum, is phototoxic, and is a precursor of the (photo)toxic compound A2E, which specifically targets cytochrome oxidase and thereby induces cell death by apoptosis. Cell death induced by A2E in the dark is prevented by negatively charged phospholipids. The blue light-filtering molecules lutein and zeaxanthin are tailor-made substances protecting the retina. In vitro, they protect cytochrome oxidase against the permanent damage caused by A2E in combination with light. These novel findings should enable us to prevent or cure the dry form of age-related macular degeneration, the leading cause of severe visual impairment in humans living in developed countries.