gebhart/patrepeval huggingface dataset:
Development of Gram Stain Scoring System Based on Pro-Inflammatory Cytokines in the Sheep Model for Testing Toxicity of Vaginal Products (2021)

<b>Background:</b> Development of safe, effective products to prevent the sexual transmission of HIV remains a priority. Prior to clinical testing, the products must undergo strict safety evaluations to avoid mucosal drug toxicity, inflammation, and vaginal microbiome (VMB) shifts. Based on the Food and Drug Administration (FDA) guidance, we designed a study to measure the inflammatory markers and VMB changes after intravaginal treatment with products that have been associated with toxicity, with the objective to develop a Gram stain slide scoring system, similar to Nugent scoring, correlated with the proinflammatory cytokines in sheep. <b>Methods:</b> Non-pregnant Dorset ewes (<i>n</i> = 34) were randomized to receive 5 ml intravaginal 4% nonoxynol-9 (N9) contraceptive gel, positive control (0.2% benzalkonium chloride), placebo control [hydroxethyl cellulose (HEC)], or no application daily for 10 days, with 11-day post-treatment follow-up. The vaginal swabs were collected for the cytokines, VMB, and Gram-stained slides. An enzyme-linked immunosorbent assay (ELISA) analysis of cytokines interleukin (IL)-1β, IL-8, CXCL10, and tumor necrosis factor-α (TNF-α) was used to determine inflammatory state of the sample. Vaginal microbiome community types (CT) were utilized to create five equivalent slide subsets for iterative development of a Gram-stained slide scoring system with comparisons with inflammatory state based on the cytokine levels. <b>Results:</b> Digital images of the Gram-stained slides were scored based on Gram staining and morphology of bacteria, presence of sheep epithelial cells, and immune cells. The scoring system was modified in an iterative fashion with weighting based on cytokine categorization of inflamed samples, with three of four cytokine values above the mean indicating that the sample was inflamed. The parameters in the final version of the scoring system included mature epithelial cells, Gram-negative rods, and Gram-positive diplococci indicating normal and immune cells indicating inflammation. The area under the receiver operator characteristic curve (ROC AUC) was 0.725 (ROC AUCs range between 0.5 and 1.0) with a greater area indicating higher diagnostic ability of a test with a binary outcome: inflamed or normal. <b>Conclusion:</b> The scoring system, derived from the advanced VMB and cytokine analyses, provides a validated, practical method for quantification of Gram-stained slides that can be performed in most laboratories, increasing the potential for standardization. The training plan can assist laboratories to determine the safety of intravaginal products in their sheep studies or the methodological approach can be applied to other animal models where such data are also needed.
Coronary Endothelial Function Is Preserved With Chronic Endothelin Receptor Antagonism in Experimental Hypercholesterolemia In Vitro (1999)

Hypercholesterolemia is associated with increased circulating and tissue endothelin-1 immunoreactivity, decreased nitric oxide (NO) activity, and altered endothelial function. We tested the hypothesis that chronic endothelin receptor antagonism preserves endothelial function and increases NO in experimental porcine hypercholesterolemia. Pigs were randomized to 3 groups: Group 1, a 2% high-cholesterol (HC) diet alone (n=7); group 2, RO-48-5695, a combined endothelin receptor antagonist, and an HC diet (n=8); and group 3, ABT-627, a selective endothelin-A receptor antagonist, and an HC diet (n=8). Coronary epicardial and arteriolar endothelial function was determined by a dose-response relaxation to bradykinin (10(-11) to 10(-6) mol/L), in all groups and in pigs maintained on a normal diet. Plasma total oxidized products of NO (NO(x)) were determined by chemiluminescence at baseline and after 12 weeks. Bradykinin-stimulated coronary epicardial and arteriolar relaxation in group 1 was attenuated compared with normal-diet controls. This relaxation was normalized with endothelin receptor antagonism. Plasma NO(x) decreased after 12 weeks in group 1 (-74.8+/-5.5%). This decrease was attenuated in the endothelin receptor antagonist groups (group 2, -28.2+/-15.0%; group 3, -38.9+/-20.6%). Chronic endothelin receptor antagonism preserves coronary endothelial function and increases NO in hypercholesterolemia. This study supports a role of endothelin-1 in the regulation of NO activity and suggests a possible therapeutic role for endothelin receptor antagonists in hypercholesterolemia.
Spectral Proper Orthogonal Decomposition Downstream of a Vortex Tube Separator Array (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-2354.vid Vortex tube separator (VTS) arrays are frequently used to filter foreign particles, such as sand, from helicopter engine intakes. While studies have been conducted on singular separators, these devices are implemented in array configurations of dozens or hundreds of separators, to which little research is devoted. VTS arrays surround all separators with a common plenum known as the “scavenge chamber” that allows them to aerodynamically interact, potentially increasing the complexity of the flow. In the current study, experimental particle image velocimetry (PIV) measurements are conducted downstream of a VTS array model to identify array-specific phenomena that do not necessarily appear in single-VTS configurations. Mean flow data reveals the rapid development of a recirculation zone just 0.23DVTS downstream of the central outlet in the array (where �������� is the inlet tube diameter of each separator), which likely leads to axial flow gradients in the associated separator. This behavior was not seen in single-VTS configurations. Spectral proper orthogonal decomposition reveals high-energy tonal modes at very low Strouhal numbers of 9.8 × 10−3, 1.8 × 10−2, and 2.6 × 10−2 that depict back-and-forth pumping motions at the center of the duct. These motions appear to comprise the central recirculation zone, which appears as merely stagnant in the mean flow. Additional high-energy precession motions are observed at a Strouhal number of 1.5 × 10−1, which appear to represent the rotation of a spanwise vortex within the central recirculation zone. Studies of precession in similar cyclone separators have concluded that such behaviors can resonate with low-frequency oscillations and negatively affect filtration performance.
Meso-scale controlled motion for a microfluidic drop ejector. (2004)

The objective of this LDRD was to develop a uniquely capable, novel droplet solution based manufacturing system built around a new MEMS drop ejector. The development all the working subsystems required was completed, leaving the integration of these subsystems into a working prototype still left to accomplish. This LDRD report will focus on the three main subsystems: (1) MEMS drop ejector--the MEMS ''sideshooter'' effectively ejected 0.25 pl drops at 10 m/s, (2) packaging--a compact ejector package based on a modified EMDIP (Electro-Microfluidic Dual In-line Package--SAND2002-1941) was fabricated, and (3) a vision/stage system allowing precise ejector package positioning in 3 dimensions above a target was developed.
Free energy dependence of the rate of long-range electron transfer in proteins. Reorganization energy in ruthenium-modified myoglobin (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree energy dependence of the rate of long-range electron transfer in proteins. Reorganization energy in ruthenium-modified myoglobinJennifer L. Karas, Charles M. Lieber, and Harry B. GrayCite this: J. Am. Chem. Soc. 1988, 110, 2, 599–600Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/ja00210a048https://doi.org/10.1021/ja00210a048research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Decreased accumulation of [14c]carboplatin in human cisplatin-resistant cells results from reduced energy-dependent uptake (2000)

We have isolated cisplatin-resistant human liver carcinoma (7404-CP20) cells with reduced accumulation of cisplatin and other drugs (methotrexate, arsenate, and arsenite) to which these cells are cross-resistant. To determine whether the reduction of drug accumulation in cisplatin-resistant cells results from impaired uptake or from active efflux, [(14)C]carboplatin was used for kinetic analysis of drug uptake and efflux. We demonstrate here that the uptake of [(14)C]carboplatin in 7404 parental cells is time, temperature, and energy dependent, and that the rate of uptake is reduced in 7404-CP20 cells. Efflux of [(14)C]carboplatin in cisplatin-resistant cells was comparable to efflux in the parental cisplatin-sensitive cells. There was little effect of temperature (between 37 degrees C and 4 degrees C) on efflux in cisplatin-resistant cells. Immunoblotting with specific antibodies directed to MRP1 and MRP2 (cMOAT) also showed that expression of these two ABC transporter genes was considerably reduced in 7404-CP20 cells and another cisplatin-resistant cell line KB-CP20, in contradistinction to previous studies suggesting that MRP might be responsible for cisplatin efflux. To rule out a generalized defect in uptake of small molecules, fluorescence-activated cell sorter (FACS) analysis of rhodamine 123 uptake showed that there was no difference between cisplatin-sensitive and -resistant cells. The presence of a pleiotropic defect in uptake of [(14)C]carboplatin, [(3)H]methotrexate, [(73)As]arsenate, and [(73)As]arsenite in cisplatin-resistant cells, in association with reduced expression of related cell surface proteins as demonstrated in our previous work, suggests a novel mechanism for acquisition of resistance to cisplatin associated with reduced activity of many different specific uptake systems.
New Low-Density Lipoprotein Receptor Upregulators Acting via a Novel Mechanism (1996)

The synthesis and biological activity of a new series of benzamides and related compounds that upregulate the expression of the low-density lipoprotein (LDL) receptor in human hepatocytes (HepG2 cells) by a novel mechanism are described. The lead compound, N-[5-[(3-cyclohexylpropionyl)amino]-2-methylphenyl]-4-hydroxybe nzamide (1, RPR102359), increased the expression of the LDL receptors in HepG2 cells by 80% when tested at a concentration of 3 microM. Mevinolin (lovastatin) was found to increase the LDL receptor expression by 70% at the same concentration. In contrast to mevinolin, 1 was found to have no effect on cholesterol biosynthesis in liver homogenates or in HepG2 cells at doses where substantial upregulation of the LDL receptor was observed and thus stimulated LDL receptor expression by a novel mechanism.
Zonal-Progressive Design: New Multifocal Ophthalmic Lens to Correct Presbyopia (1992)

Optical design of a multifocal intraocular lens is limited to the simultaneous vision principle which features two or more lens powers within the pupillary area at the same time. The principle is applied as well to contact lenses though some design requirements are different due to contact lens fitting constrains, wearer's residual accommodation and IOL's safety considerations. The simultaneous principle can be divided into two basic designs: Bifocal lens specified by two levels of diopter powers and Progressive Aspheric with continuous range of diopter powers (Charman and Saunders, 1990; Morrison, 1986; Freeman and Stones, 1987; Charm et al., 1987; Charman and Walsh, 1988; Evans and Morrison, 1983; Evans, 1983; Charman and Walsh, 1986; Erickson et al., 1988).
Filter Diagonalization (1997)

Filter-Diagonalization was introduced in 1990 (D. Neuhauser, J. Chem. Phys. 93, 2611) as a general approach for extracting high-energy eigenstates. The method combines simultaneous calculation of a rough Filter at many energies with a subsequent small-matrix diagonalization stage. The hybrid method combines the advantages of the pure-matrix and the diagonalization approaches, without their deficiencies. Recently, we have been able to reformulate the method so that it can extract frequencies and eigenfunctions at any energy range from a fixed set of residues, without large storage requirements. Given the residues, repetitive calculations of spectra and eigenfunctions at arbitrary multiple energy ranges are trivial. We review the achievements of the approach, as well as a a new feature of it, the ability to extract frequencies from a short-time segment of any signal, even if the signal is not due to a quantum correlation function. Introduction A general problem in chemistry and other fields
Modulation of Hexadecyl‐LPA‐Mediated Activation of Mast Cells and Microglia by a Chemical Probe for LPA5 (2016)

Mast cells and microglia play a critical role in innate immunity and inflammation and can be activated by a wide range of endogenous and exogenous stimuli. Lysophosphatidic acid (LPA) has recently been reported to activate mast cells and microglia. Using the human mast cell line HMC-1 and the mouse microglia cell line BV-2, we show that LPA-mediated activation can be prevented by blockade of the LPA receptor 5 (LPA5) in both cell lines. The identification of new LPA5-specific antagonists as tool compounds to probe and modulate the LPA5/LPA axis in relevant in vitro and in vivo assays should contribute to better understanding of the underlying role of LPAs in the development and progression of (neuro-) inflammatory diseases.
Message from the SDIM 2018 Workshop Organizers (2018)

Presents the introductory welcome message from the conference proceedings. May include the conference officers' congratulations to all involved with the conference event and publication of the proceedings record.
Solution of master equations for small bistable systems (1987)

The master equations for bistability in the bad cavity limit in an atomic system is solved when the number of atoms N is not more than 45. A detailed comparison is made of results from Fokker-Planck equations and from the master equation. The validity of the decorrelation approximation for the master equation is examined.
Optical and electrical Barkhausen noise induced by recording ferroelectric domain holograms (1995)

Ferroelectric domain gratings with periods of the order of an optical wavelength are induced in strontium barium niobate by photorefractive space-charge fields. We measure the Barkhausen noise in current and diffraction efficiency while optically recording domain gratings and show that the two are strongly correlated in time. Significant random depolarization occurs under high-intensity illumination. We deduce the kinetics of the domain inversion process from the shape of the current transients.
Enhanced Efficacy of Bleomycin in Bladder Cancer Cells by Photochemical Internalization (2014)

Bleomycin is a cytotoxic chemotherapeutic agent widely used in cancer treatment. However, its efficacy in different cancers is low, possibly due to limited cellular internalization. In this study, a novel approach known as photochemical internalization (PCI) was explored to enhance bleomycin delivery in bladder cancer cells (human T24 and rat AY-27), as bladder cancer is a potential indication for use of PCI with bleomycin. The PCI technique was mediated by the amphiphilic photosensitizer disulfonated tetraphenyl chlorin (TPCS(2a)) and blue light (435 nm). Two additional strategies were explored to further enhance the cytotoxicity of bleomycin; a novel peptide drug ATX-101 which is known to impair DNA damage responses, and the protease inhibitor E-64 which may reduce bleomycin degradation by inhibition of bleomycin hydrolase. Our results demonstrate that the PCI technique enhances the bleomycin effect under appropriate conditions, and importantly we show that PCI-bleomycin treatment leads to increased levels of DNA damage supporting that the observed effect is due to increased bleomycin uptake. Impairing the DNA damage responses by ATX-101 further enhances the efficacy of the PCI-bleomycin treatment, while inhibiting the bleomycin hydrolase does not.
Computation-Guided Design of Interface Engineering in All-Solid-State Li-Ion Batteries: A First Principles Study (2016)

All-solid-state Li-ion battery based on solid electrolyte materials is a promising next-generation Li-ion battery technology with intrinsic safety, high energy density, and enhanced cyclability. The key problem in enabling this new battery technology is the high interfacial resistance and interfacial degradation at the solid electrolyte-electrode interfaces. In this presentation, I will show how we use computational modeling to provide unique insights into the fundamental mechanisms at these buried interfaces, which are difficult to access in experiments. I will first demonstrate using first principles computation to predict various materials properties of the solid electrolyte materials with little experimental input. In addition, we systematically investigate and compare the electrochemical stability and chemical stability of the solid electrolyte-electrode interfaces, and study how these interfaces affect the interfacial resistance, low cyclability, and mechanical failure in all-solid-state Li-ion batteries. Our computation results suggest the formation of decomposition interphase layers in all-solid-state Li-ion batteries and the significant effects of the interphase layers on the electrochemical performance of the all-solid-state Li-ion batteries. Different interfaces between solid electrolyte and electrode materials may have different problems at the interfaces, which require different interfacial engineering strategies to resolve. The mechanisms of artificial layers to improve the interfacial properties are revealed by our computation. This computational study provides novel insights and general guidance for interfacial engineering in all-solid-state Li-ion batteries.
Electromagnetic properties and electronic structure of the iron-based layered superconductor LaFePO (2008)

Structural, electronic, and magnetic properties of undoped and aliovalent-ion (Ca, F)-doped LaFePO, which undergo superconducting transitions at transition temperatures $({T}_{c})$ 4--7 K [Y. Kamihara et al., J. Am. Chem. Soc. 128, 10012 (2006)], were investigated. ${T}_{c}$ of the samples varied from 2.4 to 5.5 K in the undoped samples and was increased up to $\ensuremath{\sim}7\text{ }\text{K}$ by Ca and $F$ doping. The ${T}_{c}$ increases are correlated with a decrease in the lattice volume. LaFePO exhibits paramagnetism in the normal conducting state. Photoemission spectroscopy combined with first-principle band calculations clarified that Fe $\text{Fe}\text{ }3d$ $({d}_{z2}+({d}_{xz},{d}_{yz}))$ orbitals hybridized with $\text{P}\text{ }3p$ to form a Fermi surface. The band calculations also suggest that the $3d$ electron of the Fe in LaFePO is basically in the low-spin configuration, and that the spin moment of LaFePO is almost quenched, leading to the paramagnetism of the itinerant electrons.
(Invited) Ultrafast Studies of Plasmonic and Photonic Structures for Energy Conversion Applications (2020)

Hybrid materials with plasmonic and/or photonic components are of great interest for enhancing the efficiency of light harvesting and energy conversion processes. Those processes that occur on an ultrafast timescale can be very impactful on overall efficiencies of conversion, and therefore are important to understand. These processes can be, for example, the dynamics of hot plasmonic electron decay or the rate of excitonic migration within materials. In this talk, I describe studies of ultrafast spectroscopy and imaging in several types of plasmonic and photonic structures. These include the ultrafast plasmonic behavior of refractory metals and also gap plasmon metamaterials. Efforts to understand how to create greater numbers of energetic carriers, and how to monitor for their presence spectroscopically, are described. Also described are studies of exciton transport in biomimetic materials, particularly to understand how the concentration and orientation of chromophores impact the efficiency of exciton migration. Also described are metal-organic-frameworks and their relevance to supporting photoinduced exciton transport, with ultrafast photoluminescence used to characterize transport in optically scattering media. Finally I briefly describe the user science capabilities of the Center for Nanoscale Materials. This work was performed, in part, at the Center for Nanoscale Materials, a U.S. Department of Energy Office of Science User Facility, and supported by the U.S. Department of Energy, Office of Science, under Contract No. DE-AC02-06CH11357.
Fully-integrated CMOS phase-locked loop with 15 to 240 MHz locking range and ±50 ps jitter (2002)

Phase-locked loops (PLL) are widely used for clock-phase synchronization, frequency synthesis and clock distribution. It is highly desirable that the standard digital CMOS process be used in the PLL design because process modifications increase product cost. Other desirable features include insensitivity to noise and a fully integrated design. The PLL design reported in this paper has all the above features. A standard digital CMOS process is used to produce a fully differential structure that is immune to substrate and supply noise. The PLL function includes multiplication of frequency and synchronization of input and output clock phases. The architecture is unique because resistors are not needed for PLL loop stabilization.
Fundamentals of the Use of Performance Reference Compounds (PRCs) in Passive Samplers (2005)

James N. Huckins1, Kees Booij2, Walter L. Cranor1, David A. Alvarez1, Robert W. Gale1, Michael E. Bartkow3, Gary L. Robertson4, Randal C. Clark1 and Roger E. Stewart5 1USGS, CERC, Columbia, MO, USA; 2Royal Netherlands Institute for Sea Research, Texel, The Netherlands; 3National Research Centre for Environmental Toxicology, Coopers Plains, Queensland, Australia; 4US EPA, NERL, Las Vegas, NV, USA; 5Virginia Department of Environmental Quality, Richmond, VA, USA