gebhart/patrepeval huggingface dataset:
Detection of Superoxide in Vascular Tissue (2002)

During the past decade, it has become apparent that reactive oxygen species play a critical role in the genesis of many vascular diseases. The superoxide anion is among the most important of these, not only because of its rapid reaction with NO but also because it serves as a progenitor for many other reactive oxygen species. Although there are many approaches to detecting and quantifying superoxide in chemical systems, its detection in intact tissues is more difficult. The validity of the most popular and frequently used assay for this purpose, lucigenin-enhanced chemiluminescence, has been recently questioned. It has been suggested that lucigenin itself, especially at high concentrations (>50 micromol/L), may act as a source for superoxide via redox cycling. Lower lucigenin concentrations (5 micromol/L) do not participate in redox cycling to an important extent in intact tissues and, therefore, provide an accurate assessment of the rate of superoxide production in such samples. Other useful assays for superoxide include those using the fluorescent dye dihydroethidine, 2-methyl-6-phenyl-3,7-dihydroimidazo(1,2-alpha)pyrazin-3-one (CLA), and 2-(p-hydroxybenzyl)-6-(p-hydroxyphenyl) 8-benzylimidazo[1,2-alpha]pyrazin-3-one (coelenterazine). The chemiluminescent compound 5-amino-2,3-dihydroxy-1,4-phthalayineidone (luminol) may also be used to detect various reactive oxygen species and may be made specific for various oxidants, such as hydrogen peroxide, superoxide, and peroxynitrite, by altering the experimental conditions. Although each of these methods may be associated with potential artifacts, the use of > or =2 different techniques that yield similar results provides a reliable approach for the study of reactive oxygen species in intact vascular tissues.
Assessment tools for adult bipolar disorder. (2009)

This article reviews the current state of the literature on the assessment of bipolar disorder in adults. Research on reliable and valid measures for bipolar disorder has unfortunately lagged behind assessment research for other disorders, such as major depression. We review diagnostic tools, self-report measures to facilitate screening for bipolar diagnoses, and symptom severity measures. We briefly review other assessment domains, including measures designed to facilitate self-monitoring of symptoms. We highlight particular gaps in the field, including an absence of research on the reliable diagnosis of bipolar II and milder forms of disorder, a lack of empirical data on the best ways to integrate data from multiple domains, and a shortage of measures targeting a broader set of illness-related constructs relevant to bipolar disorder.
Scalable Photonic Interconnection Network With Multiple-Layer Configuration for Warehouse-Scale Networks (2011)

A scalable and flexible photonic interconnection network architecture suitable for warehouse-scale networks is proposed. The architecture comprises three functional layers: physical, optical, and logical layers. The network topologies achieved at the layers are tree in the physical layer; hypercube in the optical layer; and relatively lower dimensional topologies like two-dimensional mesh, tree, and ring in the logical layer. The application of the appropriate network configuration in each layer by making good use of wavelength division multiplexing technology realizes a truly scalable and flexible network. Evaluation of the physical link requirements reveals the scalability of the proposed network architecture.
Orbital Angular Momentum Mode-Group Beamforming System Based on An Integrated Optical True Time Delay Line Chip (2021)

An orbital angular momentum (OAM) mode-group beamforming system based on an integrated optical true time delay line (OTTDL) chip is presented in this paper. Spatial field digital modulation (SFDM) can be realized by this system. This system operating at 10.2 GHz can achieve no-distortion beam scanning, and three directions (0°, ±90°) are shown in the paper. Besides, the speed of beam scanning is measured as 1.2 kHz.
Systematic identification of regulatory proteins critical for T-cell activation (2003)

This study identified important signal regulators in T-cell activation. It also demonstrated a highly efficient strategy for discovering many components of signal transduction pathways and validating them in physiological settings.
Stability of low-temperature amorphous silicon thin film transistors formed on glass and transparent plastic substrates (2000)

This article describes the formation of amorphous silicon thin film transistors (TFTs) on glass and flexible transparent plastic substrates using rf plasma enhanced chemical vapor deposition and a maximum processing temperature of 110 °C. Silane diluted with hydrogen was used for the preparation of the amorphous silicon, and SiH4/NH3/N2 or SiH4/NH3/N2/H2 mixtures were used for the deposition of the silicon nitride gate dielectric. The amorphous silicon nitride layers were characterized by transmission infrared spectroscopy and current-voltage measurements; the plastic substrates were 10 mil thick (0.25 mm) polyethylene terephthalate sheets. Transistors formed using the same process on glass and plastic showed linear mobilities ranging from 0.1 to 0.5 cm2/V s with ION/IOFF ratios⩾107. To characterize the stability of the transistors on glass, n- and p-channel transconductances were measured before and after bias stressing. Devices formed at 110 °C show evidence of charge trapping near the a-Si/SiNx interface and the creation of dangling-bond defects. The defect dynamics are consistent with the defect pool model. Under +10 and +25 V bias stress, the rates of creation of low energy defects are only moderately larger than those for high temperature devices; the devices show markedly higher rates of defect creation under higher positive bias. Current-voltage analysis of low temperature dielectrics shows very low leakage, but positive bias stress shows a significantly higher electron trapping rate near the a-Si:H/SiNx interface, indicating problems with low temperature dielectric formation. The magnitude of the rates of defect creation and trapping in these nonoptimized devices suggests that amorphous silicon TFTs with stability approaching that of typical large area active matrix electronic devices could be formed at low temperatures compatible with transparent flexible polymeric substrates.
Carboxylation of alkali metal phenoxide with carbon dioxide at terrestrial temperature (2000)

The reaction between potassium (or sodium) phenoxide and carbon dioxide at room temperature forms salicylic acid and p-hydroxybenzoic acid at the same time besides the complex, [alkali metal phenoxide·CO2]. The complex had been thought an intermediate of the Kolbe–Schmitt reaction but is found inactive to the carboxy-lation at terrestrial temperatures. Copyright © 2000 John Wiley & Sons, Ltd.
The database language GEM (1983)

GEM (an acronym for General Entity Manipulator) is a general-purpose query and update language for the DSIS data model, which is a semantic data model of the Entity-Relationship type. GEM is designed as an easy-to-use extension of the relational language QUEL, providing support for the notions of entities with surrogates, aggregation, generalization, null values, and set-valued attributes.
Patterning of Polymeric/Inorganic Nanocomposite and Nanoparticle Layers (2002)

Polymeric/inorganic nanocomposite dishes of hydrolyzed poly(styrene-alt-maleic anhydride) (HSMA) and TiO2 were patterned on substrates by microcontact printing (μCP) of the dispersions of nanosized TiO2 colloidal particles in HSMA solutions; the structure formation with respect to the μCP process was discussed. The orderly arranged HSMA/TiO2 dishes are homogeneous in size. After removal of the polymer in the printed composite dishes by calcination, well-defined nanostructured TiO2 layers are formed in the regions where the composite dishes appear. The printed composite dishes come from the dishlike composite aggregates transferred onto a substrate from a stamp surface. The drying of the dispersion droplets formed in a topographically controlled de-wetting of the dispersion on the stamp surface results in the dishlike aggregates, for which the pinning of the droplet contact line is of key importance. The diameter of the printed dishes is mainly determined by the stamp geometry, and not influenced remarkably by HSMA and/or TiO2 concentrations. The component fractions mainly influence the heights of the dish rim and plate, the width of the dish rim, and the continuity of the plate within the rim.
Transforming growth factor-beta complexes with thrombospondin. (1992)

Thrombospondin (TSP) was demonstrated to inhibit the growth of bovine aortic endothelial cells, an activity that was not neutralized by antibodies to TSP or by other agents that block TSP-cell interactions but that partially was reversed by a neutralizing antibody to transforming growth factor-beta (TGF-beta). Similar to TGF-beta, TSP supported the growth of NRK-49F colonies in soft agar in a dose-dependent manner, which required epidermal growth factor and was neutralized by anti-TGF-beta antibody. Chromatography of a TSP preparation did not separate the TGF-beta-like NRK colony-forming activity from high molecular weight protein. However, when chromatography was performed at pH 11, this activity was dissociated from TSP. These results suggest that at least some growth modulating activities of TSP are due to TGF-beta associated with TSP by strong non-covalent forces. Most of the active TGF-beta released from platelets after degranulation was associated with TSP, as demonstrated by anti-TSP immunoaffinity and gel permeation chromatography. 125I-TGF-beta binds to purified TSP in an interaction that is specific in the sense that bound TGF-beta could be displaced by TGF-depleted TSP but not significantly by native TSP, heparin, decorin, alpha 2-macroglobulin, fibronectin, or albumin. Hence, TGF-beta can bind to TSP, and the complex forms under physiological conditions. Furthermore, TSP-associated TGF-beta is biologically active, and the binding of TGF-beta to TSP may protect TGF-beta from extracellular inactivators.
Determining 3-D Relative Transformations for Any Combination of Range and Bearing Measurements (2012)

In this paper, we address the problem of motion-induced 3-D robot-to-robot extrinsic calibration that is based on ego-motion estimates and combinations of interrobot measurements (i.e., distance and/or bearing observations from either or both of the two robots, recorded across multiple time steps). In particular, we focus on solving minimal problems, where the unknown 6-degree-of-freedom (DOF) transformation between the two robots is determined based on the minimum number of measurements necessary to find a finite set of solutions. In order to address the very large number of possible combinations of interrobot observations, we identify symmetries in the measurement sequence and use them to prove that any extrinsic robot-to-robot calibration problem can be solved based on the solutions of only 14 (base) minimal problems. Moreover, we provide algebraic (closed-form) and efficient symbolic-numerical (analytical) solution methods to these minimal problems. Finally, we evaluate the performance of our proposed solvers through extensive simulations and experiments.
E. coli -Based In Vitro Transcription/Translation: In Vivo-Specific Synthesis Rates and High Yields in a Batch System (1998)

A highly efficient Escherichia coli-based, batch in vitro protein synthesis system using circular plasmid DNA is described. Compared to a presently available commercial kit, this improved system produced several hundredfold greater yields of the rDNA human protein thrombopoietin (ca. 450 micrograms/mL). The system is capable of obtaining specific synthesis rates similar to those in vivo, approximately a 1000-fold increase compared to the original methods previously described. It compares favorably in rates and yields to the recently published semicontinuous methods but with the convenience of a true batch system.
Photoacoustic study of surface plasmons in metals (1982)

A photoacoustic technique was used to observe the nonradiative decay of surface plasmons in evaporated thin films of silver. The signal amplitudes from an attenuated total reflection photon-plasmon coupler were measured as a function of the angle of incidence and the chopping frequency of p-polarized 1.96-eV photons. A 1-D analysis was made on the photoacoustic data in conjunction with simultaneously measured absorptance data. Such an analysis allowed us to separate the nonradiative and the roughness-assisted radiative relaxations of the plasmons and determine their relative probabilities.
Purification of recombinant human pepsinogens and their application as immunoassay standards (1998)

Human pepsinogen (PG) A and C were cloned in Escherichia coli, but the levels of expression were low and unstable. When there were fused to maltose-binding protein (MBP), the fusion proteins (MBP-PGA and MBP-PGC) were expressed as the major products. Although these fused products were almost totally recovered from the insoluble fraction, the renaturation and purification procedures were easy and simple. MBP-PGA and the PGA segment obtained by factor Xa digestion (designated as r-PGA) possessed proteolytic activities equivalent to native PGA purified from gastric tissue (t-PGA). For PGCs (MBP-PGC, r-PGC and t-PGC) also, the specific activities were almost the same. However, the activities of PGCs were about 3- to 4-hold higher than those of PGAs. In PGA and PGC immunoassay systems, r-PGs (r-PGA and r-PGC) and the EIA kit standard PGs (gastric mucosal PGs) exhibited a good correlation. From these results, r-PGs would seem to be applicable as assay standards without compromising the sensitivity of the immunoassay systems.
The ecology and evolution of Aspergillus spp. fungal parasites in honey bees (2013)

Evolution of virulence in parasites has profound effects on both host-parasite co-evolution and ecology and is influenced by environmental factors and the genotypes involved. Many parasite infections consist of multiple strains or species that are predicted to result in the evolution of more virulent strains that exploit the host less prudently. In opportunistic parasites, the dynamics and evolution of virulence are poorly understood as traditional epidemiological models do not adequately describe parasites capable of persisting outside of the host. In addition, as microbial pathogenicity may shift from opportunistic to obligatory strategies with time, knowledge of the evolutionary dynamics of opportunistic pathogens is crucial for predicting and understanding disease emergence. Aspergillus species of fungi have a ubiquitous distribution and are the etiological agents of stonebrood disease in honey bees. It is generally considered that stonebrood occurs rarely in honey bees, but the epidemiology and predisposing conditions for the disease are almost entirely unknown. In this study, I examine the occurrence, pathogenicity and competitive ability of Aspergillus spp. when infecting honey bees, as well as the effect of nutrition on host susceptibility and the adaptation of the fungi over the course of experimental evolution. A high prevalence and diversity of Aspergillus spp. isolates were identified following the screening of an apiary, and the pathogenicity of three species (A. flavus, A. nomius and A. phoenicis) was established. Further, in laboratory-reared larvae a nutritionally limited diet increased susceptibility to A. fumigatus. In a series of single-generation interspecific competition experiments between Aspergillus spp. and the obligate pathogen chalkbrood (Ascophaera apis), the virulence and fitness of dual infections were influenced by complex within-host interactions depending on the species involved, which ranged from synergistic to inhibitory effects. Finally, following serial passage of A. flavus and A. phoenicis in the honey bee larval hosts to determine the evolution of virulence and fitness, no evidence of host adaptation was observed, revealing the unpredictability of these asexually reproducing opportunistic pathogens. These findings illustrate a complex relationship between Aspergillus spp. and honey bees and emphasises the significant influence these ubiquitous organisms can have on the ecology and evolution of honey bees.
Cooperation between Fibroblast Growth Factor Receptor-4 and ErbB2 in Regulation of Cyclin D1 Translation (2004)

Alterations in ErbB2 or fibroblast growth factor receptor-4 (FGFR-4) expression and activity occur in a significant fraction of breast cancers. Because signaling molecules and pathways cooperate to drive cancer progression, simultaneous targeting of multiple pathways is an appealing therapeutic strategy. With this in mind, we examined breast tumor cells for their sensitivity to the ErbB2 and FGFR inhibitors, PKI166 and PD173074, respectively. Simultaneous blocking of ErbB2 and FGFR-4 in MDA-MB-453 tumor cells had a stronger anti-proliferative effect than treatment with individual inhibitors. Examination of cell cycle regulators revealed a novel translation-mediated mechanism whereby ErbB2 and FGFR-4 cooperate to regulate cyclin D1 levels. Our results showed that FGFR-4 and ErbB2 via the MAPK and the phosphatidylinositol 3-kinase/protein kinase B pathways, respectively, both contribute to the maintenance of constitutive activity of the mammalian target of rapamycin translational pathway. Dual inhibition of these receptors strongly blocked S6 kinase 1 (S6K1) activity and cyclin D1 translation, as attested by a decrease in cyclin D1 mRNA association with polysomes. Ectopic expression of active protein kinase B or active S6K1 abrogated the dual inhibitor-mediated down-regulation of cyclin D1 expression, demonstrating the importance of these FGFR-4/ErbB2 signaling targets in regulating cyclin D1 translation. S6K1 has the central role in this process, since small interfering RNA-targeted S6K1 depletion led to a decrease in cellular S6K1 activity and, as a consequence, repression of cyclin D1 expression. Thus, we propose a novel mechanism for controlling cyclin D1 expression downstream of combined activity of ErbB2 and FGFR-4 that involves S6K1-mediated translation.
Compact and low loss 90° optical hybrid on a silicon-on-insulator platform (2017)

We present a compact and low loss 90° optical hybrid on a silicon-on-insulator (SOI) platform for coherent receiving systems. Our 90° optical hybrid uses a novel topology, comprising one Y-junction and three 2x2 multimode interference (MMI) couplers. The geometry of the 90° optical hybrid is fully optimized using particle swarm optimization (PSO). The fabricated 90° optical hybrid has a compact footprint of 21.6 μm x 27.9 μm, with an insertion loss less than 0.5 dB, a common mode rejection ratio (CMRR) larger than 30 dB, and phase error smaller than 3° in the C-band across 22 reticles on one wafer. The measured phase error (< 3°) in a packaged coherent receiver further confirms the excellent performance of the 90° optical hybrid.
Two-Phase Computed Tomography Study of Warthin Tumor of Parotid Gland (2013)

The enhancement pattern of early fill-in and early washout is the typical finding of WTs on 2-phase CT scans, which may be attributed pathologically to abundant blood vessel and extensive capillary network.
Determination of Free Energies of N-Capping in .alpha.-Helixes by Modification of the Lifson-Roig Helix-Coil Theory To Include N- and C-Capping (1994)

We have previously shown that varying the N-terminal amino acid in alpha-helical peptides can cause large variations in helix content (Chakrabartty et al., 1993a). The Lifson-Roig theory for the helix-coil transition predicts, however, that substitutions at the N-terminus in an unacetylated peptide should have no effect on alpha-helix stability. We have therefore modified the theory to include these N-capping effects by assigning a statistical weight (the "n-value") to the amino acid immediately preceding a stretch of helical residues. The n-value measures the N-capping propensity of an amino acid, and like the helix propensity (w-value), it is independent of neighboring residues or positions in sequence. The new theory was used, with the experimental data for these substitutions, to calculate n-values and, hence, free energies for N-capping for the amino acids Gln, Ala, Val, Met, Pro, Ile, Leu, Thr, Gly, Ser, and Asn as well as for the acetyl group, which is commonly used to cap peptides. The free energies vary by approximately 1 kcal mol-1 from Gln (worst) to Asn (best), and the acetyl group is nearly as effective as Asn. N-Capping free energies were also found for Leu, Thr, Gly, Ser, and Asn when the N-terminus is charged at pH 5. The unfavorable effect of protonation of the N-terminus in an alpha-helix was found to be approximately 0.5 kcal mol-1. Our results agree well with a survey of N-capping preferences from protein crystal structures and are compared to results from site-directed mutagenesis of N-caps in proteins.
Pompe disease gene therapy (2011)

Pompe disease is an autosomal recessive metabolic myopathy caused by the deficiency of the lysosomal enzyme acid alpha-glucosidase and results in cellular lysosomal and cytoplasmic glycogen accumulation. A wide spectrum of disease exists from hypotonia and severe cardiac hypertrophy in the first few months of life due to severe mutations to a milder form with the onset of symptoms in adulthood. In either condition, the involvement of several systems leads to progressive weakness and disability. In early-onset severe cases, the natural history is characteristically cardiorespiratory failure and death in the first year of life. Since the advent of enzyme replacement therapy (ERT), the clinical outcomes have improved. However, it has become apparent that a new natural history is being defined in which some patients have substantial improvement following ERT, while others develop chronic disability reminiscent of the late-onset disease. In order to improve on the current clinical outcomes in Pompe patients with diminished clinical response to ERT, we sought to address the cause and potential for the treatment of disease manifestations which are not amenable to ERT. In this review, we will focus on the preclinical studies that are relevant to the development of a gene therapy strategy for Pompe disease, and have led to the first clinical trial of recombinant adeno-associated virus-mediated gene-based therapy for Pompe disease. We will cover the preliminary laboratory studies and rationale for a clinical trial, which is based on the treatment of the high rate of respiratory failure in the early-onset patients receiving ERT.