gebhart/patrepeval huggingface dataset:
Luminescence Properties of Eu2+-Activated Alkaline-Earth Silicon-Oxynitride MSi2O2-δN2+2/3δ (M = Ca, Sr, Ba):  A Promising Class of Novel LED Conversion Phosphors (2005)

The luminescence properties of Eu2+-activated alkaline-earth silicon-oxynitrides have been studied. In the BaO−SiO2−Si3N4 system, a new BaSi2O2N2 compound was obtained having the monoclinic structure with lattice parameters a = 14.070(4) Å, b = 7.276(2) Å, c = 13.181(3) Å, β = 107.74(6)°. All MSi2O2-δN2+2/3δ:Eu2+ (M = Ca, Sr, Ba) materials can be efficiently excited in the UV to visible region (370−460 nm), making them attractive as conversion phosphors for LED applications. A blue-green emission at 490−500 is observed for BaSi2O2N2:Eu2+, yellow emission at 560 nm for CaSi2O2-δN2+2/3δ:Eu2+ (δ ≈ 0), and a green-yellow emission peaking from 530 to 570 nm for SrSi2O2-δN2+2/3δ:Eu2+ (δ ≈ 1), the position depending on the exact value of δ. BaSi2O2N2:Eu2+ is the most promising conversion phosphor for white-light LEDs due to its high conversion efficiency for blue light from InGaN-based LEDs related to its very small Stokes shift.
Phenomenological models of synaptic plasticity based on spike timing (2008)

Synaptic plasticity is considered to be the biological substrate of learning and memory. In this document we review phenomenological models of short-term and long-term synaptic plasticity, in particular spike-timing dependent plasticity (STDP). The aim of the document is to provide a framework for classifying and evaluating different models of plasticity. We focus on phenomenological synaptic models that are compatible with integrate-and-fire type neuron models where each neuron is described by a small number of variables. This implies that synaptic update rules for short-term or long-term plasticity can only depend on spike timing and, potentially, on membrane potential, as well as on the value of the synaptic weight, or on low-pass filtered (temporally averaged) versions of the above variables. We examine the ability of the models to account for experimental data and to fulfill expectations derived from theoretical considerations. We further discuss their relations to teacher-based rules (supervised learning) and reward-based rules (reinforcement learning). All models discussed in this paper are suitable for large-scale network simulations.
Early T Cell Activation: Integrating Biochemical, Structural, and Biophysical Cues (2015)

T cells carry out the formidable task of identifying small numbers of foreign antigenic peptides rapidly and specifically against a very noisy environmental background of endogenous self-peptides. Early steps in T cell activation have thus fascinated biologists and are among the best-studied models of cell stimulation. This remarkable process, critical in adaptive immune responses, approaches and even seems to exceed the limitations set by the physical laws ruling molecular behavior. Despite the enormous amount of information concerning the nature of molecules involved in the T cell antigen receptor (TCR) signal transduction network, and the description of the nanoscale organization and real-time analysis of T cell responses, the general principles of information gathering and processing remain incompletely understood. Here we review currently accepted key data on TCR function, discuss the limitations of current research strategies, and suggest a novel model of TCR triggering and a few promising ways of going further into the integration of available data.
Multi-Robot System for Artistic Pattern Formation (2011)

This paper describes work on multi-robot pattern formation.Arbitrary target patterns are represented with an optimal robot deployment, using a method that is independent of the number of robots.Furthermore, the trajectories are visually appealing in the sense of being smooth, oscillation free, and showing fast convergence.A distributed controller guarantees collision free trajectories while taking into account the kinematics of differentially driven robots.Experimental results are provided for a representative set of patterns, for a swarm of up to ten physical robots, and for fifty virtual robots in simulation.
Generative Adversarial Nets from a Density Ratio Estimation Perspective (2016)

Generative adversarial networks (GANs) are successful deep generative models. GANs are based on a two-player minimax game. However, the objective function derived in the original motivation is changed to obtain stronger gradients when learning the generator. We propose a novel algorithm that repeats the density ratio estimation and f-divergence minimization. Our algorithm offers a new perspective toward the understanding of GANs and is able to make use of multiple viewpoints obtained in the research of density ratio estimation, e.g. what divergence is stable and relative density ratio is useful.
A novel mammalian cell (Vero) derived influenza virus vaccine: development, characterization and industrial scale production. (1999)

Influenza virus for vaccine production are presently produced in embryonated chicken eggs. This conventional standard methodology is extremely cumbersome; it requires a huge amount of eggs and an extensive purification to reduce the amount of contaminating egg proteins and to minimize the risk of allergies against egg albumin. The shortage of eggs in a pandemic situation, the selection of egg-adapted variants and the presence of adventitious viruses has emphasized the necessity for production of influenza vaccines on a well characterized stable cell line. Our established Vero cell technology has been successfully adapted to large scale production of a variety of influenza virus strains. The production in 1200 litre fermenter cultures under serum-free conditions gave antigen yields comparable to the conventional embryonated egg technology. The development of a rapid and efficient purification scheme resulted in a safe high purity vaccine which was at least as immunogenic as conventional egg-derived vaccines in a mouse model. This vaccine has been shown to be safe and highly immunogenic in chimpanzees and to be capable of protecting ferrets against challenge with live virus. Clinical trials have now been initiated in the UK and Austria.
Thermodynamic and kinetic processes involved in the growth of epitaxial GaN thin films (1993)

Our experimental results using reactive magnetron sputtering, combined with earlier literature, are used to understand the thermodynamic and kinetic processes involved in GaN film growth and the limiting factors involved in the incorporation of nitrogen during the growth process. We show that GaN films fabricated with low pressure growth techniques (&amp;lt;0.1 Torr) such as sputtering and molecular beam epitaxy are formed under metastable conditions with a nonequilibrium kinetically limited reaction. For these methods, the growth process is controlled by a competition between the forward reaction, which depends on the arrival of activated nitrogen species at the growing surface, and the reverse reaction whose rate is limited by the unusually large kinetic barrier of decomposition of GaN. In practice, the thermally activated rate of decomposition sets an upper bound to the growth temperature.
Immunodominant protein epitopes II. The primary antibody response to hen egg white lysozyme requires and focuses upon a unique N‐terminal epitope (1984)

The antibody response to a defined protein antigen, hen egg white lysozyme (HEL) has been investigated using an aminopeptidase-treated HEL molecule, des-1,2,3-HEL (AP-HEL). Surprisingly, removal of these three N-terminal residues eliminates an epitope which is a dominant B cell determinant recognized in the primary antibody response to HEL. Thus, the initial antibody response focuses on a very small region of the molecule. Even more striking is the observation that removal of this epitope markedly reduces the immunogenicity of HEL. Therefore, the epitope is not only the focus of the primary antibody response, but is essential for the initiation of the response. This report demonstrates that a selective mechanism must be activated during the response to this protein antigen. Of the multitude of B cell determinants present on HEL, only a limited number are focused upon by the immune system.
Curcumin blocks cytokine-mediated NF-kappa B activation and proinflammatory gene expression by inhibiting inhibitory factor I-kappa B kinase activity. (1999)

NF-kappa B plays a critical role in the transcriptional regulation of proinflammatory gene expression in various cells. Cytokine-mediated activation of NF-kappa B requires activation of various kinases, which ultimately leads to the phosphorylation and degradation of I kappa B, the NF-kappa B cytoplasmic inhibitor. The food derivative curcumin has been shown to inhibit NF-kappa B activity in some cell types. In this report we investigate the mechanism of action of curcumin on cytokine-induced proinflammatory gene expression using intestinal epithelial cells (IEC). Curcumin inhibited IL-1 beta-mediated ICAM-1 and IL-8 gene expression in IEC-6, HT-29, and Caco-2 cells. Cytokine-induced NF-kappa B DNA binding activity, RelA nuclear translocation, I kappa B alpha degradation, I kappa B serine 32 phosphorylation, and I kappa B kinase (IKK) activity were blocked by curcumin treatment. Wound-induced p38 phosphorylation was not inhibited by curcumin treatment. In addition, mitogen-activated protein kinase/ERK kinase kinase-1-induced IL-8 gene expression and 12-O-tetraphorbol 12-myristate 13-acetate-responsive element-driven luciferase expression were inhibited by curcumin. However, I kappa B alpha degradation induced by ectopically expressed NF-kappa B-inducing kinase or IKK was not inhibited by curcumin treatment. Therefore, curcumin blocks a signal upstream of NF-kappa B-inducing kinase and IKK. We conclude that curcumin potently inhibits cytokine-mediated NF-kappa B activation by blocking a signal leading to IKK activity.
A molecular mechanism of complement resistance of human melanoma cells. (1986)

The susceptibility of human melanoma cells to lysis by human complement after sensitization with the R24 murine IgG3 monoclonal antibody to the GD3 ganglioside antigen was investigated. It was found that the melanoma cell lines were either susceptible (greater than or equal to 70% cytotoxicity) or resistant (less than or equal to 30% cytotoxicity) to complement-mediated killing. We determined the kinetics of binding of C3 to and its subsequent fate on the melanoma cells. We found that on susceptible cell lines, maximal binding of C3 occurred within 10 min of incubation. At that time, approximately 90% of the bound C3 was in the form of C3b. During the subsequent incubation, the C3b was slowly inactivated, apparently generating the physiologic degradation products iC3b, C3dg, and C3d. However, this degradation of C3b could be inhibited without affecting the final degree of cytotoxicity, indicating that it is of no apparent consequence for the killing of susceptible melanoma cells. Very different results were obtained with resistant melanoma cells. Bound C3b was rapidly inactivated, and C3d was the predominant form of C3 on resistant cells throughout the incubation. Therefore, rapid inactivation of C3b was identified as a protective mechanism of human melanoma cells against complement attack. In addition, we found that resistance to complement is not an inherent property of the cells but depends on the antibody used for sensitization, because the resistant cell lines could be lysed after sensitization with polyclonal antiserum.
Molecular dynamics study of a gelsolin‐derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5‐bisphosphate (2003)

Gelsolin is an actin-severing protein whose action is initiated by Ca(2+) and inhibited by binding to phosphorylated inositol lipid or phosphoinositides. The regions of gelsolin responsible for phosphoinositide binding are comprised of residues 150-169 (G150-169) and 135-142 (G135-142). The corresponding peptides possess similar binding potency as native gelsolin. Their common feature is the presence of arginine and lysine residues that can bind to negatively charged phosphate groups of phosphoinositides. In this work the binding of the G150-169 peptide to a phosphatidylinositol 4,5-bisphosphate (PIP2) cluster in a lipid membrane model was investigated by molecular dynamics calculations (MD) with the AMBER 4.1 force field, taking into account explicit solvent molecules. Initially the structure of G150-169 was simulated by using the electrostatically driven Monte Carlo (EDMC) and MD methods, and the resulting structure agreed within 3.7 A backbone-atom root mean square deviation with the corresponding experimentally derived structure (PDB code: 1SOL). Using this model for the peptide, a subsequent MD simulation of G150-169 in a periodic box containing a model of dimyristoyl-phosphatidylcholine (DMPC) lipids with a cluster of four PIP2 molecules was carried out. During the simulation G150-169 interacted strongly with PIP2 molecules, initially by formation of salt bridges between its N-terminal basic groups and the phosphate groups of PIP2, followed by formation of hydrophobic bonds between the hydrophobic side chains of the peptide and the fatty acid tail of the lipid. As a result of the formation of hydrophobic bonds, the PIP2 molecules were pulled out from the lipid bilayer. This mode of binding differs from those of other PIP2-binding protein motifs such as PH domains that interact solely with the hydrophilic head group of PIP2. These results suggest that dissociation of gelsolin from actin by PIP2 lipids may involve entering of the PIP2 molecules to the gelsolin-actin interface, thereby weakening the interactions between these proteins.
Fibrinogen binding to ICAM-1 promotes EGFR-dependent mucin production in human airway epithelial cells (2009)

Mucous hypersecretion is a serious feature of chronic airway diseases such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Although mucins are produced via activation of an EGF receptor (EGFR) signaling cascade, the mechanisms leading to exaggerated mucin production in mucous hypersecretory diseases are unknown. Because expression of ICAM-1 and of the ICAM-1 ligand fibrinogen is increased in the airways of subjects with mucous hypersecretory diseases, we hypothesized that fibrinogen binding to ICAM-1 could increase EGFR-dependent mucin production in human airway (NCI-H292) epithelial cells. Consistent with this hypothesis, we found that an ICAM-1 neutralizing antibody and an ICAM-1(8-22) peptide that binds fibrinogen decreased mucin production induced by the EGFR ligand transforming growth factor (TGF)-alpha dose-dependently. Exogenous fibrinogen and a fibrinogen(117-133) peptide that binds ICAM-1 rescued mucin production in cells treated with the ICAM-1(8-22) peptide. Surprisingly, the ICAM-1(8-22) peptide increased EGFR phosphotyrosine and phospho-ERK1/2 in cells treated with TGF-alpha. The ICAM-1(8-22) peptide-induced increases in EGFR phosphotyrosine and phospho-ERK1/2 were prevented by exogenous fibrinogen, by the fibrinogen(117-133) peptide, and by selective inhibitors of phospholipase C (PLC), protein kinase C (PKC)-alpha/beta, and metalloproteases. These results suggest that fibrinogen binding to ICAM-1 promotes mucin production by decreasing TGF-alpha-induced EGFR and ERK1/2 activation and that the fibrinogen-ICAM-1-dependent decrease in EGFR and ERK1/2 activation occurs via inhibition of an early positive feedback pathway involving PLC- and PKC-alpha/beta-dependent metalloprotease activation and subsequent metalloprotease-dependent EGFR reactivation.
The Gator Tech Smart House: a programmable pervasive space (2005)

Research groups in both academia and industry have developed prototype systems to demonstrate the benefits of pervasive computing in various application domains. Unfortunately, many first-generation pervasive computing systems lack the ability to evolve as new technologies emerge or as an application domain matures. To address this limitation, the University of Florida's Mobile and Pervasive Computing Laboratory is developing programmable pervasive spaces in which a smart space exists as both a runtime environment and a software library. Service discovery and gateway protocols automatically integrate system components using generic middleware that maintains a service definition for each sensor and actuator in the space. The Gator Tech Smart House in Gainesville, Florida, is the culmination of more than five years of research in pervasive and mobile computing. The project's goal is to create assistive environments such as homes that can sense themselves and their residents and enact mappings between the physical world and remote monitoring and intervention services.
Characterization of Amplifiable, Circulating RNA in Plasma and Its Potential as a Tool for Cancer Diagnostics (2004)

Extracellular RNA is most likely protected within protein or lipid vesicles, possibly apoptotic bodies, which can be disrupted by detergents. Despite optimizing many aspects of plasma RNA detection, we were unable to reproducibly detect cancer-related transcripts. Our data suggest that measurement of circulating RNA may not be a good approach to early cancer diagnosis.
Plasma cholesterol metabolism in end-stage renal disease. Difference between treatment by hemodialysis or peritoneal dialysis. (1986)

Plasma cholesterol metabolism was investigated in normotriglyceridemic patients with end-stage renal disease treated by hemo- or continuous ambulatory peritoneal dialysis (CAPD), and compared with that in a control group with normal renal function. A reversed net transport of free cholesterol from plasma to cultured fibroblasts, as well as greatly reduced levels of plasma cholesterol esterification and cholesterol ester transfer rates to low and very low density lipoproteins (LDL and VLDL), was found in the hemodialysis group compared to the controls. The LDL and VLDL contained increased amounts of free cholesterol and inhibited cholesterol ester transfer when recombined with control plasma. The LDL triglyceride content was doubled in the hemodialysis group, whereas cholesterol esters were decreased. Patients treated by CAPD, in marked contrast, had cholesterol metabolic rates that were within the normal range, as well as normal lipoprotein composition.
Policy-based authentication and authorization: secure access to the network infrastructure (2002)

A gaping hole in many of today's networks is the weak security surrounding the network devices themselves-the routers, the switches and the access servers. In all public networks and in some private networks, the network devices are shared virtually among different user communities. Access to the configuration schemes and command lines is most often an "all or nothing" proposition-the network administrator gets either read-only privileges or read/write privileges. In this case, authentication equals authorization. Herein lies the problem. Security policies may mandate that certain administrators have read-only capabilities for all device parameters and read/write capabilities for a certain subset of commands. Each administrator may have a unique access profile. Authentication verifies identity; authorization verifies privileges. This paper addresses the value of using a centralized, provisioned management structure that disseminates network policies and administration privileges to all the devices that make up the network infrastructure.
Design and optimization of 2.5 dimension porous media micromodel for nanosensor flow experiments (2012)

Micromodels are used to visualize and study pore-scale phenomena such as immiscible displacements in porous media, foam flow behavior, and CO2 flooding. The understanding gained from these experiments can be used to develop models to predict future behavior of the reservoir. Most micromodels are constructed using lithography techniques that are restricted to 2D patterns that require artificial generation or manipulation of images to develop connected micromodels. Characteristics innate to the original rock structure are often lost or skewed in developing micromodels that bear little resemblance to the original media. Alternative microfabrication techniques using a micromilling tool have allowed us to vary the floor height in a micromodel, thus giving some variation in the third dimension. We refer to these structures (with varying floor height and fixed ceiling, and which cannot have passages on top of one another) as 2.5D micromodels. Using a technique called depth averaging, in which we take a section of a 3D voxel image of porous media and project the solid voxels down while simultaneously pushing the void space above, we generate micromodels that may allow for more accurate representations of the pore structure in 3D rock. The design of the etched pattern requires the selection of a specific depth (or number of XMCT image slice) over which to average the image data. The 2.5-D pattern was obtained by optimizing a series of parameters to ensure the structure and flow patterns matched as closely as possible to the equivalent 3D structure and flow as can be accommodated given the restricted dimensionality. Parameters considered include flow-based parameters, common statistical correlations, and a host of topological parameters obtained by network model generation techniques. For a Boise sandstone core sample imaged at 5.07 µm/pixel, an optimized depth of 115 µm gave the most accurate measures across the range of parameters. However, due to constraints regarding the resolution of the micromilling process, a second series of flow simulations were conducted in the originally optimized region of interest (100-150 µm) for a lower resolution image that resulted in the selection of 130 µm to depth average. This design was then used to fabricate a brass mold insert. The process of developing the microchips for nanosensor experiments is currently in the stage of assembling the PMMA chips.
A switched-current sample-and-hold circuit (2002)

A switched-current sample-and-hold circuit is reported. The circuit was fabricated in a 0.8 /spl mu/m BiCMOS process. Measurements indicate a sampling frequency of 57 MHz with 10 bits linearity and suggests that operation at sampling frequencies beyond 80 MHz is feasible. Comparisons of this circuit with other switched-current sample-and-hold circuits are given to highlight the strengths and weaknesses of the circuit. The feasibility of the sample-and-hold circuit as a under-sampler intended for the Canadian CT2Plus personal communication system is also presented.
N<sup>ε</sup>-(carboxymethyl)lysine (CML) as a Biomarker of Oxidative Stress in Long-Lived Tissue Proteins (2003)

Glycoxidation products are a subset of advanced glycation endproducts (AGEs) that are formed by the nonenzymatic glycation and subsequent irreversible oxidation of proteins (1,2). Nε-(carboxymethyl)lysine (CML) is a well-characterized glycoxidation product that accumulates in tissues with age, and its rate of accumulation is accelerated in diabetes (1–4). CML is now known to be formed from the oxidation of both carbohydrates and lipids, making it a biomarker of general oxidative stress (5–7). Oxidative stress and resultant protein modification have been implicated in the pathogenesis of the chronic complications of diabetes, including nephropathy and atherosclerosis (1,4,5,8). The accumulation of CML in long-lived tissue such as skin collagen reflects oxidative stress over an extended period of the life-span, and has been shown to be greater in patients with diabetic complications than those without complications (8,9).