gebhart/patrepeval huggingface dataset:
Production of a non-functional nef protein in human immunodeficiency virus type 1-infected CEM cells (1990)

The nef gene product of the human immunodeficiency virus (HIV) is suggested to be a negative factor involved in down-regulating viral expression by a mechanism in which the correct conformation of the nef protein is essential. The nef protein expressed by vaccinia virus recombinants is phosphorylated by protein kinase C. We investigated the synthesis of the nef protein and its state of phosphorylation during HIV-1 infection of a T4 cell line (CEM cells). Maximum synthesis of viral proteins occurred 3 days after infection, when more than 90% of cells were producing viral proteins. The synthesis of the nef protein was detected in parallel with the env and gag proteins. As expected, the nef protein was myristylated but not phosphorylated, and its half-life was less than 1 h. By the use of the polymerase chain reaction technique, we isolated and sequenced the nef gene of this HIV-1 stock. Two significant mutations were observed. Firstly, threonine, at amino acid number 15, the site of phosphorylation by protein kinase C, was mutated into an alanine, and secondly aspartic acid of the tetrapeptide WRFD, which is probably involved in GTP binding, was mutated into an asparagine. The mutated nef gene was expressed in a vaccinia virus system, in which it was not phosphorylated and its half-life was dramatically reduced compared to the wild-type nef gene product. Furthermore, down-regulation of CD4 cell surface expression was no longer affected by the mutated nef gene. These results emphasize that phosphorylation of the nef protein provides an efficient test to monitor its biological activity.
Regional cerebral blood flow response to visual stimulation measured quantitatively with PET (1998)

Objectives: Regional cerebral blood flow (rCBF) was measured by positron emission tomography with bolus injections of 15 O-labeled water in order to learn the normal pattern of response of the occipital rCBF to flicker and video stimulation. Materials and methods: Six normal volunteers and a patient with partial cortical blindness were studied. They underwent quantitative rCBF measurement in the eye closed resting condition, under full-field stimulation with flickering light, and during video movie viewing, which contains form, color, and movement visual information. Stimulation-minus-rest subtraction PET images were overlaid onto the MRI images resliced parallel to the midline. Results: In normal subjects, the rCBF response to flickering stimuli and to the video in the posterior part of primary visual cortex was +30.5 and +34.5% of whole brain mean value, respectively. The rCBF increase in the association visual cortex was more pronounced by the video movie viewing (+27.5% of whole brain mean value) than by the flickering light stimulation (+6.5% of whole brain mean value). Activated areas in the primary visual cortex corresponded well to the stimulated visual field according to retinotopic organization. Poor activation in primary and in association visual cortex were seen in the patient with cortical blindness. Conclusion: Flickering light and video movie induced different activation patterns. More complicated visual stimuli, which require more extensive neuronal integration, caused greater activation of the higher visual cortex.
Patents on antifungal compounds effective against Candida species: 1999 ? 2002 (2003)

This review summarises patents from 1999 to 2002, claiming compounds and methods for antimicrobial agents effective against pathogenic fungi of the genus Candida. The majority of the patents described in this review will focus on modifications or novel compounds of the three major classes of antifungal agents currently approved for human use against Candida infections; polyenes, azoles and cell wall synthesis inhibitors. Novel compounds and approaches will also be considered. Since the correlation between antifungal effects in vitro and efficacy in vivo is often not strong with antifungal agents, emphasis will be placed on filings for which biological data in animal models has been disclosed.
Characterizing a fiber-based frequency comb with electro-optic modulator (2012)

We report on the characterization of a commercial- core fiber-based frequency comb equipped with an intracavity free-space electro-optic modulator (EOM). We investigate the relationship between the noise of the pump diode and the laser relative intensity noise (RIN) and demonstrate the use of a low-noise current supply to substantially reduce the laser RIN. By measuring several critical transfer functions, we evaluate the potential of the EOM for comb repetition rate stabilization. We also evaluate the coupling to other relevant parameters of the comb. From these measurements, we infer the capabilities of the femtosecond laser comb to generate very-low-phase-noise microwave signals when phase-locked to a high-spectral-purity ultra-stable laser.
Prevalence and clinical correlates of antinuclear antibody in patients with gastroparesis (2021)

The prevalence of a positive ANA in patients with gastroparesis was high at ~17% and did not differ significantly based on etiology. In idiopathic patients, ANA positivity was associated with rheumatoid arthritis, systemic sclerosis, and elevated ESR. ANA-positive gastroparesis represents a subset who often have other autoimmune symptoms or disorders, but less severe nausea and vomiting.
Vision Zero: on a Provable Method for Eliminating Roadway Accidents without Compromising Traffic Throughput (2018)

We propose an economical, viable, approach to eliminate almost all car accidents. Our method relies on a mathematical model of safety and can be applied to all modern cars at a mild cost.
High Proton Conduction in a Chiral Ferromagnetic Metal–Organic Quartz-like Framework (2011)

A complex-as-ligand strategy to get a multifunctional molecular material led to a metal-organic framework with the formula (NH(4))(4)[MnCr(2)(ox)(6)]·4H(2)O. Single-crystal X-ray diffraction revealed that the anionic bimetallic coordination network adopts a chiral three-dimensional quartz-like architecture. It hosts ammonium cations and water molecules in functionalized channels. In addition to ferromagnetic ordering below T(C) = 3.0 K related to the host network, the material exhibits a very high proton conductivity of 1.1 × 10(-3) S cm(-1) at room temperature due to the guest molecules.
Effect of additivs on the size reduction and modification by impact comminution. (1987)

The effects of organic additives on the finest comminution obtained by using an impact mill were studied. A commercial disintegrator (Jiyu-Mill M3, Nara Machinery) was modified by installing a recycling circuit and improved vanes. The additives used were triethanol amine (TEA), ethylene glycol (EG), acetic acid (AA) and others up to 5%. In a batch operation, the minimum attainable median particle size was significantly reduced, although the power consumption increased. Powders ground with additives were less edgy and showed smaller compressive strength and mold release resistance. The optimum concentration was between 0.5 and 5wt% which is much higher than that for a conventional ball mill. The characteristics of the mechanism of grinding aids were: (1) grinding energy was more efficiently transmitted on the powder particle by preventing the adhesion of the finest particles on the main parts of the grinding system, and (2) there was an increase in the effective solid concentration.
Structure of a chiral tricyclic phosphonamide (1991)

C 15 H 26 N 3 OPS 2 cristallise dans P3 1 21 avec a=b=9,778, c=34,214 A, Z=6, T=190 K; affinement jusqu'a R=0,046. La molecule contient deux cycles heterocycliques, un 1,3-diazaphosphole 2-oxyde et un 1,3-dithiolanylideneaminobutene lie a l'atome P qui est coordine tetraedriquement. Tous les cycles a 5 chainons sont dans une conformation demi chaise. Le cycle diaza est condense trans par rapport a un cyclohexane qui est dans la conformation chaise
Inhibitory Mechanisms by Which Suramin May Attenuate Neointimal Formation After Balloon Angioplasty (1999)

Restenotic neointimal lesions, a major limitation to coronary angioplasty, develop in response to diverse signals and depend on three properties of activated arterial smooth muscle cells (SMCs): proliferation, migration, and abnormal production of extracellular matrix. Most of the pharmacologic approaches targeting specific pathogenic factors facilitating development of restenosis have failed in clinical trials. Our results indicate that the polysulfonated naphthylurea suramin, a "non-specific drug" that interferes with multiple cellular proteins, inhibits neointimal formation in rabbit iliac arteries after balloon-catheter injury administered throughout the critical period of several weeks after the procedure. In vitro studies aimed at dissecting the mechanism(s) underlying the suramin-dependent effect demonstrated that, in addition to an inhibitory effect on SMC proliferation, suramin inhibited fibronectin and elastin deposition and the migration of SMCs through elastin membranes and into scratch gaps of monolayer cultures. We also demonstrated that suramin causes cell-surface accumulation of the elastin binding protein, a receptor that not only anchors SMCs to the extracellular matrix, but also inhibits SMC response to interleukin-1beta (IL-1beta). We conclude that suramin acts as a multitarget inhibitor of SMC activation and has a therapeutic potential as an agent that may attenuate arterial restenosis after angioplasty.
A scalable manufacturing process for flexible active‐matrix e‐paper displays (2005)

Abstract— A scalable manufacturing process for fabricating active‐matrix backplanes on low‐cost flexible substrates, a key enabler for electronic‐paper displays, is presented. This process is based on solution processing, ink‐jet printing, and laser patterning. A multilayer architecture is employed to enable high aperture ratio and array performance. These backplanes were combined with E Ink electrophoretic media to create high‐performance displays that have high contrast, are bistable, and can be flexed repeatedly to a radius of curvature of 5 mm.
Maximum-likelihood sequence detector for dynamic mode high density probe storage (2010)

There is an increasing need for high density data storage devices driven by the increased demand of consumer electronics. In this work, we consider a data storage system that operates by encoding information as topographic profiles on a polymer medium. A cantilever probe with a sharp tip (few nm radius) is used to create and sense the presence of topographic profiles, resulting in a density of few Tb per in. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The prevalent mode of using the cantilever probe is the static mode that is harsh on the probe and the media. In this article, the high quality factor dynamic mode operation, that is less harsh on the media and the probe, is analyzed. The read operation is modeled as a communication channel which incorporates system memory due to inter-symbol interference and the cantilever state. We demonstrate an appropriate level of abstraction of this complex nanoscale system that obviates the need for an involved physical model. Next, a solution to the maximum likelihood sequence detection problem based on the Viterbi algorithm is devised. Experimental and simulation results demonstrate that the performance of this detector is several orders of magnitude better than the performance of other existing schemes.
A four-dimensional model-based method for assessing cardiac contractile dyssynchrony in mice (2008)

Four-dimensional (4D), or equivalently, 3D + time, analysis is useful for comprehensive assessment cardiac function, especially in the asymmetric left ventricle (LV) after myocardial infarction (MI). This paper presents a 4D-model-based method for ultrasound assessment of cardiac contractile function in mice. Echocardiographic image sequences were acquired at high frequency (30 MHz) from the hearts of C57Bl/6 mice. Image sequences were acquired at contiguous slice locations encompassing the entire 3D LV. In order to reconstruct continuous, dynamic 3D LVs from the images using a 4D mathematical cardiac model, endocardial and epicardial contours were segmented for all image slice locations through one cardiac cycle. In the 4D model, shape and continuity constraints were applied in order to normalize irregularities caused by noise or non-uniform distribution of image data. Root mean square error (RMSE) was calculated between the model-fitted 4D LV and the actual LV surface measured from image data. RMSE was 0.23 mm (~4.5% of epicardial diameter) for the epicardial surface, and 0.20 mm (6.4% of endocardial diameter) for the endocardial surface. 3D regional wall thickening was calculated from the 4D LV surface, and LV dyssynchrony was assessed by analyzing the time to peak strain (T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">peak</sub> ). This 3D analysis of contractile function in post-MI mouse hearts revealed >80% reduction of peak radial displacement, a 10-15 ms delay in Tpeak in the infarct zone, and a SD_T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">peak</sub> of 6-10 ms over the entire 3D LV. In summary, the 4D-model-based method was successfully used for analyzing cardiac dyssynchrony in the 3D murine LV, and it proved advantageous over conventional 2D methods because it was more comprehensive and noise-robust.
Suppression of “volcano” morphology and parasitic defect luminescence in AlGaN-based deep-UV light-emitting diode epitaxy (2019)

In this study we overcame several critical growth issues related to epitaxy in AlGaN deep-ultraviolet light-emitting diodes. Irregular-shaped pits with dislocation clusters were observed in micron-thick layers of AlGaN on AlN. The strain-induced morphology and defects were suppressed after the insertion of superlattice transition layers between the AlGaN and AlN layers. The defect luminescence in the active region was governed by radiative recombination through the oxygen shallow donors and deep acceptors related to III-vacancies. After optimization of the growth conditions and a decrease in growth interruption, the intensity of the parasitic blue-band emission was suppressed by up to 95%. Energy dispersive spectroscopy suggests that the desorption of gallium from the surface is the major source of the III-vacancies. Keywords: Defects, Line defects, Point defects, Surface structures, Metalorganic vapor phase epitaxy, Light-emitting diodes
Experiments in Active Diesel Particulate Filter Regeneration (2003)

&lt;div class="htmlview paragraph"&gt;Diesel particulate filters (DPFs) are a technology likely to be deployed to meet future stringent emission levels for heavy and light duty diesel powertrains in North America and Europe. This paper discusses experimental results in the active regeneration of DPFs. Attention is given to the system components, the information based on which regeneration is triggered, and the means to achieve a regeneration. The paper will report on successful regenerations under several extreme conditions.&lt;/div&gt;
Enzymatic Release and Macrolactonization of Cryptophycins from a Safety-Catch Solid Support This project was generously funded by the Swiss National Science Foundation (PBBS2-113008 to W.S.) and NIH CA076477 (to D.H.S.) (2007)

No Abstract
Structure of Robot Compliance (1993)

The structure of nonsingular robot compliance is investigated by applying screw theory to two eigenvalue problems. For the first problem the eigenscrews are demonstrated to be Ball’s (1990) principal screws of the potential. Several new propositions are presented characterizing compliance matrix eigenstructure. Using a novel formulation, the second eigenvalue problem generalizes the three wrench-compliant axes of Dimentberg (1965) to include three twist-compliant axes. These two types of compliant axes are shown to be reciprocal and define conjugate screw systems. The wrench- and twist-compliant axes are demonstrated to the general elements of a compliant axis hierarchy.
Targeted design of porous materials without strong, directional interactions (2022)

A porous molecular crystal (TSCl) was found to crystallise from dichloromethane and water during the synthesis of tetrakis(4-sulfophenylmethane). Crystal structure prediction (CSP) rationalises the driving force behind the formation of this porous TSCl phase and the intermolecular interactions that direct its formation. Gas sorption analysis showed that TSCl is permanently porous with selective adsorption of CO<sub>2</sub> over N<sub>2</sub>, H<sub>2</sub> and CH<sub>4</sub> and a maximum CO<sub>2</sub> uptake of 74 cm<sup>3</sup> g<sup>-1</sup> at 195 K. Calculations revealed that TSCl assembles <i>via</i> a combination of weak hydrogen bonds and strong dispersion interactions. This illustrates that CSP can underpin approaches to crystal engineering that do not involve more intuitive directional interactions, such as hydrogen bonding.
MASP-2 and MASP-3 inhibitors block complement activation, inflammation, and microvascular stasis in a murine model of vaso-occlusion in sickle cell disease (2022)

Patients with sickle cell disease (SCD) have ongoing hemolysis that promotes endothelial injury, complement activation, inflammation, vaso-occlusion, ischemia-reperfusion pathophysiology, and pain. Complement activation markers are increased in SCD in steady-state and further increased during vaso-occlusive crisis (VOC). However, the mechanisms driving complement activation in SCD have not been completely elucidated. Ischemia-reperfusion and heme released from hemoglobin during hemolysis, events that characterize SCD pathophysiology, can activate the lectin pathway (LP) and alternative pathway (AP), respectively. Here we evaluated the role of LP and AP in Townes sickle (SS) mice using inhibitory monoclonal antibodies (mAb) to mannose binding lectin (MBL)-associated serine protease (MASP)-2 or MASP-3, respectively. Townes SS mice were pretreated with MASP-2 mAb, MASP-3 mAb, isotype control mAb, or PBS before they were challenged with hypoxia-reoxygenation or hemoglobin. Pretreatment of SS mice with MASP-2 or MASP-3 mAb, markedly reduced Bb fragments, C4d and C5a in plasma and complement deposition in the liver, kidneys, and lungs collected 4 hours after challenge compared to control mAb-treated mice. Consistent with complement inhibition, hepatic inflammation markers NF-ĸB phospho-p65, VCAM-1, ICAM-1, and E-selectin were significantly reduced in SS mice pretreated with MASP-2 or MASP-3 mAb. Importantly, MASP-2 or MASP-3 mAb pretreatment significantly inhibited microvascular stasis (vaso-occlusion) induced by hypoxia-reoxygenation or hemoglobin. These studies suggest that the LP and the AP are both playing a role in promoting inflammation and vaso-occlusion in SCD. Inhibiting complement activation via the LP or the AP might inhibit inflammation and prevent VOC in SCD patients.
Fast algebraic reconstruction using subsets of PET data (2003)

Filtered backprojection (FBP) method for positron emission tomography (PET) produces artifacts in the reconstructed images when the measurement system has the shift-variant characteristics. On the other hand, the conventional algebraic reconstruction methods, such as the generalized analytic reconstruction from discrete samples (CARDS), the natural pixel decomposition (NPD) and the algebraic reconstruction technique (ART), can correct these characteristics, while these methods have computational burden. Here, the authors propose a fast image reconstruction method for PET using an algebraic technique. In this method, a reconstruction operator is given approximately using subsets of sensitivity functions. The subsets are designed by selecting the sensitivity functions that have high sensitivity to each point to be reconstructed and by keeping an accuracy of the reconstructed images. The proposed method was applied to simulated data for the scanner, ECAT EXACT HR+ (Siemens/CTI) working in the 2D mode. This result shows that the proposed method produces images with almost the same quality as the conventional algebraic methods do and has a similar computation time to FBP method.
Intrinsic Ion Transport Properties of Block Copolymer Electrolytes (2020)

Knowledge of intrinsic properties is of central importance for materials design and assessing suitability for specific applications. Self-assembling block copolymer electrolytes (BCEs) are of great interest for applications in solid-state energy storage devices. A fundamental understanding of ion transport properties, however, is hindered by the difficulty in deconvoluting extrinsic factors, such as defects, from intrinsic factors, such as the presence of interfaces between the domains. Here, we quantify the intrinsic ion transport properties of a model BCE system consisting of poly(styrene-<i>block</i>-ethylene oxide) (SEO) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt using a generalizable strategy of depositing thin films on interdigitated electrodes and self-assembling fully connected parallel lamellar structures throughout the films. Comparison between conductivity in homopolymer poly(ethylene oxide) (PEO)-LiTFSI electrolytes and the analogous conducting material in SEO over a range of salt concentrations (<i>r</i>, molar ratio of lithium ion to ethylene oxide repeat units) and temperatures reveals that between 20% and 50% of the PEO in SEO is inactive. Using mean-field theory calculations of the domain structure and monomer concentration profiles at domain interfaces-both of which vary substantially with salt concentration-the fraction of inactive PEO in the SEO, as derived from conductivity measurements, can be quantitatively reconciled with the fraction of PEO that is mixed with greater than a few volume percent of polystyrene. Despite the detrimental interfacial effects for ion transport in BCEs, the intrinsic conductivity of the SEO studied here (<i>ca</i>. 10<sup>-3</sup> S/cm at 90 °C, <i>r</i> = 0.085) is an order of magnitude higher than reported values from bulk samples of similar molecular weight SEO (<i>ca</i>. 10<sup>-4</sup> S/cm at 90 °C, <i>r</i> = 0.085). Overall, this work provides motivation and methods for pursuing improved BCE chemical design, interfacial engineering, and processing.
High-Sensitivity Sandwich ELISA for Plasma NT-proUcn2: Plasma Concentrations and Relationship to Mortality in Heart Failure (2016)

The validated ELISA measured human NT-proUcn2 in plasma and showed modest but significant increases in HF patients compared with controls. In HF, the unusual inverse relationship between plasma NT-proUcn2 and 2-year mortality portends potential prognostic value but requires further corroboration.
Correction: Fast, quantitative, murine cardiac 19F MRI/MRS of PFCE-labeled progenitor stem cells and macrophages at 9.4T (2019)

The images for Figs 5 and 6 are incorrectly switched. The image that appears as Fig 5 should be Fig 6, and the image that appears as Fig 6 should be Fig 5.