gebhart/patrepeval huggingface dataset:
Small Peptide Inhibitors Disrupt a High-Affinity Interaction between Cytoplasmic Dynein and a Viral Cargo Protein (2010)

Several viruses target the microtubular motor system in early stages of the viral life cycle. African swine fever virus (ASFV) protein p54 hijacks the microtubule-dependent transport by interaction with a dynein light chain (DYNLL1/DLC8). This was shown to be a high-affinity interaction, and the residues gradually disappearing were mapped on DLC8 to define a putative p54 binding surface by nuclear magnetic resonance (NMR) spectroscopy. The potential of short peptides targeting the binding domain to disrupt this high-affinity protein-protein interaction was assayed, and a short peptide sequence was shown to bind and compete with viral protein binding to dynein. Given the complexity and number of proteins involved in cellular transport, the prevention of this viral-DLC8 interaction might not be relevant for successful viral infection. Thus, we tested the capacity of these peptides to interfere with viral infection by disrupting dynein interaction with viral p54. Using this approach, we report on short peptides that inhibit viral growth.
Identification of a distinct low-affinity receptor for human interleukin-4 on pre-B cells (1993)

Biotinylated interleukin-4 (IL-4) was used to examine IL-4 receptor (IL-4R) expression on a range of human B-cell lines by flow cytometry. Using high concentrations of biotinylated IL-4, we have identified a novel low-affinity IL-4 receptor expressed at high levels on pre-B lines. Expression of this low-affinity receptor did not correlate with detected mRNA levels for the previously cloned receptor or with reactivity of two anti-human IL-4R monoclonal antibodies (MoAb). Radiolabeled IL-4 cross-linking studies using pre-B lines showed a doublet of 65 to 75 Kd in contrast to the 110- to 130-Kd molecule detected on cells expressing the cloned IL-4R. A soluble IL-4 binding protein (IL-4bp) was purified from the supernatants of three pre-B lines expressing the low-affinity receptor on their surface. IL-4bp could block both IL-4-mediated CD23 induction on tonsil B cells and IL-4-induced inhibition of proliferation of the pre-B line JM1. Partial N-terminal amino acid sequence was obtained from purified IL-4bp that confirmed this protein to be novel. A 12 amino acid peptide based on the IL-4bp sequence was used to produce a polyclonal antiserum that was reactive with purified IL-4bp, and also bound to the surface of pre-B cells but not to murine CTLL cells transfected with the human IL-4R. Blocking MoAb against the previously characterized high-affinity receptor inhibited IL-4-mediated proliferation of hIL-4R+ CTLL cells but had no effect on IL-4-induced inhibition of JM1 cell proliferation, and only partially inhibited IL-4-mediated CD23 and sIgM induction and proliferation of tonsil B cells. The data presented here provide evidence for a novel cell-surface expressed low-affinity IL-4R that also exists as a biologically active soluble IL-4 binding protein.
Hiding the Long Latency of Persist Barriers Using Speculative Execution (2017)

Byte-addressable non-volatile memory technology is emerging as an alternative for DRAM for main memory. This new Non-Volatile Main Memory (NVMM) allows programmers to store important data in data structures in memory instead of serializing it to the file system, thereby providing a substantial performance boost. However, modern systems reorder memory operations and utilize volatile caches for better performance, making it difficult to ensure a consistent state in NVMM. Intel recently announced a new set of persistence instructions, clflushopt, clwb, and pcommit. These new instructions make it possible to implement fail-safe code on NVMM, but few workloads have been written or characterized using these new instructions.
Indolinyl-Thiazole Based Inhibitors of Scavenger Receptor-BI (SR-BI)-Mediated Lipid Transport (2015)

A potent class of indolinyl-thiazole based inhibitors of cellular lipid uptake mediated by scavenger receptor, class B, type I (SR-BI) was identified via a high-throughput screen of the National Institutes of Health Molecular Libraries Small Molecule Repository (NIH MLSMR) in an assay measuring the uptake of the fluorescent lipid DiI from HDL particles. This class of compounds is represented by ML278 (17–11), a potent (average IC50 = 6 nM) and reversible inhibitor of lipid uptake via SR-BI. ML278 is a plasma-stable, noncytotoxic probe that exhibits moderate metabolic stability, thus displaying improved properties for in vitro and in vivo studies. Strikingly, ML278 and previously described inhibitors of lipid transport share the property of increasing the binding of HDL to SR-BI, rather than blocking it, suggesting there may be similarities in their mechanisms of action.
Effectiveness of Bone Suppression Imaging in the Detection of Lung Nodules on Chest Radiographs (2017)

The use of BSI software improved the performance in lung-nodule detection on CXRs regardless of observer's experience and was more effective for observers with limited experience.
Quantitative Methods Based on Twisted Nematic Liquid Crystals for Mapping Surfaces Patterned with Bio/Chemical Functionality Relevant to Bioanalytical Assays (2008)

We report methods for the acquisition and analysis of optical images formed by thin films of twisted nematic liquid crystals (LCs) placed into contact with surfaces patterned with bio/chemical functionality relevant to surface-based assays. The methods are simple to implement and are shown to provide easily interpreted maps of chemical transformations on surfaces that are widely exploited in the preparation of analytic devices. The methods involve acquisition of multiple images of the LC as a function of the orientation of a polarizer; data analysis condenses the information present in the stack of images into a spatial map of the twist angle of the LC on the analytic surface. The potential utility of the methods is illustrated by mapping (i) the displacement of a monolayer formed from one alkanethiol on a gold film by a second thiol in solution, (ii) coadsorption of mixtures of amine-terminated and ethylene glycol-terminated alkanethiols on gold films, which leads to a type of mixed monolayer that is widely exploited for immobilization of proteins on analytic surfaces, and (iii) patterns of antibodies printed onto surfaces. These results show that maps of the twist angle of the LC constructed from families of optical images can be used to reveal surface features that are not apparent in a single image of the LC film. Furthermore, the twist angles of the LC can be used to quantify the energy of interaction of the LC with the surface with a spatial resolution of <10 microm. When combined, the results described in this paper suggest nondestructive methods to monitor and validate chemical transformations on surfaces of the type that are routinely employed in the preparation of surface-based analytic technologies.
Hybrid organic-inorganic GaN LED based color downconversion for displays (2002)

The availability of small short wavelength III-N light sources have opened up new possibilities for applications involving color conversion. As a new application, we consider the hybrid organic-inorganic structure which consists of a GaN based LED emitting in the blue to uv coupled with an organic thin film with high fluorescence efficiency. Upon operation, the organic film absorbs the electroluminescence and emits in the green to red, resulting in color down conversion. Such a hybrid device is simple and has potential application as units for small full color pixelated displays for mobile applications. An array of identical GaN light emitters may be used as a substrate for deposition and patterning of appropriate emissive organic layers to form a full color display. Advantages over fully organic displays is that the electrical transport is confined to the robust GaN part, since organic films have poor electrical transport properties and degrade under electrical operation due to moisture. Advantages over fully semiconductor based displays is that different LEDs emitting different wavelengths do not have to be pieced together: the GaN LED is used as a skeleton to which an appropriate organic layer is simply added for the desired color. We demonstrate the operation of such hybrid LED units and discuss applicability for displays.
Highly sensitive ultraviolet PIN photodiodes of ZnSSe n<sup>+</sup>–i–p structure/p<sup>+</sup>‐GaAs substrate grown by MBE (2006)

Abstract Highly sensitive and stable ultraviolet PIN photodiodes of ZnSSe junction structure on p + ‐GaAs substrates are developed by molecular beam epitaxy (MBE) growth. The short‐wavelength photodiodes are grown on p‐type (100)GaAs by MBE utilizing an optimized “hetero‐interface super‐lattice (SLE) buffer” consisting of a ZnTe–ZnSe multiple quantum well, by which a large energy barrier (>1 eV) for hole ohmic conduction is overcome. ZnSSe n + –i–p photodiodes with a thin interface SLE are grown in a complete lattice‐matched condition (S = 6%). High sensitivities of 0.30 A/W (external quantum efficiency: η = 83.6%) in the blue (450 nm), 0.24 A/W ( η = 75.8%) in the blue–violet (400 nm: for BlueRay and HD‐DVD systems) and 0.12 A/W ( η = 50.9%) in the ultraviolet (300 nm) regions are obtained with an extremely low dark leakage current (∼sub pA/mm 2 ) under high reverse bias (20 V) at 300 K. Because of the low dark current, a very low noise equivalent power value below 10 –14 W $ \sqrt {{\rm Hz/cm}^{-2}} $ (450 nm) is proved in the blue–violet region. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Better Field Development Decisions from Multi-Scenario, Interdependent Reservoir, Well, and Facility Simulations (2003)

Abstract Making better decisions, which take into account uncertainty in all the components of an exploration and production (E&P) asset's value chain, continues to be a significant challenge for the industry. The literature of the last few years has emphasized the importance of workflows that integrate and include formal quantification of uncertainties across subsurface, well locations, well configurations and operations, surface interconnections, and economics. Much of the effort has focused on scenario and probabilistic analysis decision support techniques. The industry continues to make many field development decisions from flow simulation ‘sensitivity cases’ or from simplified models, which can have the effect of underestimating the full uncertainty and adding unnecessary constraints. This paper presents an integrated system that can assist field development decisions. The complex relationships between the earth models, the development strategy and the economics are retained in the development decision process. A full-physics reservoir simulator is used to maintain high fidelity to the physics of both the subsurface and surface components. The interdependencies of underlying uncertainties can affect the choices to be made. The system described can be implemented for project decisions at any stage within an asset's life cycle. In this paper, we illustrate the application of the system on a single, significant reservoir unit, taken through a development-planning exercise. The exercise includes coupled well and facility scenarios and evaluates economic outputs that are fully coupled with the flow simulation outputs. The reservoir is a faulted structure covering about 30 square miles and has around a 450 feet thick oil column. Uncertainties in the earth model were present in the static properties, faulting, and fluid-rock dynamic properties. Uncertainties included both distinct scenarios and continuous distributions. multiple choices around well placement, drainage strategies with and without injection, and scheduling are included. Ultimate recoveries, profiles, and ultimate economics for the range of possibilities are evaluated.
An Intelligent Recovery Progress Evaluation System for ACL Reconstructed Subjects Using Integrated 3-D Kinematics and EMG Features (2014)

An intelligent recovery evaluation system is presented for objective assessment and performance monitoring of anterior cruciate ligament reconstructed (ACL-R) subjects. The system acquires 3-D kinematics of tibiofemoral joint and electromyography (EMG) data from surrounding muscles during various ambulatory and balance testing activities through wireless body-mounted inertial and EMG sensors, respectively. An integrated feature set is generated based on different features extracted from data collected for each activity. The fuzzy clustering and adaptive neuro-fuzzy inference techniques are applied to these integrated feature sets in order to provide different recovery progress assessment indicators (e.g., current stage of recovery, percentage of recovery progress as compared to healthy group, etc.) for ACL-R subjects. The system was trained and tested on data collected from a group of healthy and ACL-R subjects. For recovery stage identification, the average testing accuracy of the system was found above 95% (95-99%) for ambulatory activities and above 80% (80-84%) for balance testing activities. The overall recovery evaluation performed by the proposed system was found consistent with the assessment made by the physiotherapists using standard subjective/objective scores. The validated system can potentially be used as a decision supporting tool by physiatrists, physiotherapists, and clinicians for quantitative rehabilitation analysis of ACL-R subjects in conjunction with the existing recovery monitoring systems.
Preparation of Efficient Carbon Monoxide Adsorbent from Iron(II) Chloride, Copper(II) Chloride, and Active Carbon (1987)

Abstract An adsorbent for carbon monoxide is prepared from 30.0 mmol of copper(II) chloride, 30.0 mmol of iron(II) chloride, and 20.0 g of active carbon. The adsorbing capacity (28.4 mmol) of the adsorbent is 2.1 times as large as the sum (13.7 mmol) of the capacity (11.8 mmol) of the active carbon-supported copper(II) chloride and that (1.9 mmol) of the active carbon-supported iron(II) chloride.
Identification of a New Chondropsin Class of Antitumor Compound That Selectively Inhibits V-ATPases (2003)

We identify a new naturally occurring class of inhibitor of vacuolar H+-ATPases (V-ATPases) isolated from vacuolar membranes of Neurospora crassa and from chromaffin granule membranes of Bos taurus. To date, the new class includes six chondropsins and poecillastrin A, large polyketide-derived macrolide lactams with 33-37 membered rings. In the National Cancer Institute's 60-cell screen the chondropsin class showed a tumor cell growth inhibitory fingerprint essentially indistinguishable from that of the bafilomycin/concanamycin and the salicylihalamide/lobatamide classes of well-established V-ATPase inhibitors. Half-maximal inhibition of V-ATPase activity in vitro occurred at 0.04-0.7 microM for the fungal vacuolar V-ATPase and at 0.4 to >10 microM for the chromaffin granule V-ATPase. Thus, the new inhibitors are somewhat less potent than the other two classes, which typically have Ki values of <10 nM for V-ATPases, and the new inhibitors differ from the other two classes in their specificity. The bafilomycin class inhibits all eucaryotic V-ATPases, the salicylihalamide class inhibits mammalian V-ATPases but not fungal V-ATPases, and the new chondropsin class inhibits the N. crassa V-ATPase better than the chromaffin granule V-ATPase. Two mutations in the N. crassa V-ATPase that affect the binding of bafilomycin had small but reproducible effects on the affinity of chondropsins for the V-ATPase, suggesting the possibility of a similar mechanism of inhibition.
The robot intelligence Kernel (2006)

The Robot Intelligence Kernel (RIK) is a portable, reconfig-urable suite of perceptual, behavioral, and cognitive capabili-ties that can be used across many different platforms, environ-ments, and tasks. The RIK coupled with a virtual 3D interface have been shown to dramatically improve human-robot inter-actions across a variety of navigation and exploration tasks. The Robot Intelligence Kernel is a portable, reconfig-urable suite of perceptual, behavioral, and cognitive capa-bilities that can be used across many different platforms, en-vironments, and tasks. The RIK integrates algorithms and hardware for perception, world-modeling, adaptive commu-nication, dynamic tasking, and autonomous behaviors in navigation, search, and detection tasks. The integration of software algorithms and hardware takes place over four lev-
Unsaturated aldehydes induce CCK secretion via TRPA1 in STC‐1 cells (2013)

Unsaturated Alds are potent aliphatic stimulants for CCK secretion through the activation of TRPA1.
Acoustic waves in pressurized boreholes: A finite difference formulation (1996)

A velocity‐stress, finite difference formulation of acoustic waves in a fluid‐filled, pressurized borehole yields synthetic waveforms for monopole or dipole sources before and after borehole pressurization. Processing of these waveforms using a variation of Prony's procedure isolates dominant arrivals in the full wave field. Differences between the slownesses of individual arrivals before and after pressurization provide stress‐induced changes in propagation characteristics that are of importance in estimating mechanical properties of the formation. The borehole pressurization in an isotropic formation produces insignificant changes in the compressional head wave slownesses; and small changes in the shear head wave slownesses. The most significant changes occur in the Stoneley and flexural slownesses at relatively higher frequencies in the range of 5–10 kHz for a borehole of diameter 20.32 cm (8 inches). These differences in the Stoneley and flexural slowness dispersions for a known increase in the borehole pressure can be used to calculate the acoustoelastic coefficients of the formation. These coefficients are measures of nonlinear elastic parameters of the formation that are generally larger for poorly consolidated slow formations than those of tightly consolidated fast formations.
Novel high resolution scanning thermal probe (2001)

Scanning thermal microscopy is a scanning proximal probe technique, which can be used for mapping spatial variation of thermal properties of a surface such as temperature, thermal conductivity, and thermal diffusivity. The sensor presented here is a resistance based probe consisting of a nanometer-sized filament formed at the end of a piezoresistive atomic force microscope type cantilever. The freestanding filament is deposited by focused electron beam deposition using methylcyclopentadienyl trimethyl platinum as a precursor gas. The filament height is in the range of 2–5 μm, with typical “wire” diameters between 30 and 100 nm. Typical deposition times are between 2 and 5 min, and might be further shortened by optimizing the precursor gas flux. Because of its small size, the new probe has a high spatial resolution (&lt;20 nm tip end radius) and, due to the low thermal mass, a high thermal sensitivity and fast response time. In this article, experiments designed to characterize the mechanical stability and electrical and thermal properties of the nanometer-sized probe are presented.
Polyphenolic Extract from Maple Syrup Potentiates Antibiotic Susceptibility and Reduces Biofilm Formation of Pathogenic Bacteria (2015)

Phenolic compounds are believed to be promising candidates as complementary therapeutics. Maple syrup, prepared by concentrating the sap from the North American maple tree, is a rich source of natural and process-derived phenolic compounds. In this work, we report the antimicrobial activity of a phenolic-rich maple syrup extract (PRMSE). PRMSE exhibited antimicrobial activity as well as strong synergistic interaction with selected antibiotics against Gram-negative clinical strains of Escherichia coli, Proteus mirabilis, and Pseudomonas aeruginosa. Among the phenolic constituents of PRMSE, catechol exhibited strong synergy with antibiotics as well as with other phenolic components of PRMSE against bacterial growth. At sublethal concentrations, PRMSE and catechol efficiently reduced biofilm formation and increased the susceptibility of bacterial biofilms to antibiotics. In an effort to elucidate the mechanism for the observed synergy with antibiotics, PRMSE was found to increase outer membrane permeability of all bacterial strains and effectively inhibit efflux pump activity. Furthermore, transcriptome analysis revealed that PRMSE significantly repressed multiple-drug resistance genes as well as genes associated with motility, adhesion, biofilm formation, and virulence. Overall, this study provides a proof of concept and starting point for investigating the molecular mechanism of the reported increase in bacterial antibiotic susceptibility in the presence of PRMSE.
Molecular-Based Diagnosis of Multiple Sclerosis and Its Progressive Stages (P4.395) (2017)

To determine on an example of multiple sclerosis (MS) if cerebrospinal fluid (CSF) signatures of complex neurological diseases allow their reliable differentiation from conditions that have overlapping clinical or imaging features or share common pathophysiology.
An Enzyme-Linked Immunosorbent Assay (ELISA) for the Measurement of Activated Factor XII (Hageman Factor) in Human Plasma (1996)

A direct enzyme-linked immunosorbent assay (ELISA) employing 2/215 mouse monoclonal hybridoma antibody is described. The assay is capable of detecting activated factor XII in human plasma and can be used to assess early detection of the intrinsic blood coagulation pathway. No cross reactivity with human factor XII zymogen has been found. The assay was used to assess activation of factor XII in patients with renal failure, pregnancy and diabetes compared to a control group.
Generalization of Phase-Encoded NMR Chemical Shift Imaging (1986)

An echo-time encoding NMR chemical shift imaging proposed by Dixon is generalized to be applicable to multiline chemical shift imaging. The method utilizes the phase differences among nuclei encoded by shifting the position of the rf pulse in the spin echo sequence to resolve chemical shift images. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom images measured under the same conditions as the actual measurements. The minimum number of encodings can be reduced to half the number of chemical shifts without sacrificing spatial resolution. The experiments were carried out for 3-line 1H chemical shifts using benzene, water, and acetone at 0.5 T. All the chemical shift images could be clearly resolved with only two scans when the field inhomogeneity was larger than the maximum chemical shift difference.
(2,6-Methano-3-benzazocin-11.beta.-yl)alkanones. 1. Alkylalkanones: a new series of N-methyl derivatives with novel opiate activity profiles (1979)

A general stereospecific synthesis of (N-methyl-2,6-methano-3-benzazocin-11 beta-yl)alkanones is described and applied to the preparation of a series of alkyl ketones wherein the alkyl group is a straight or terminally branched chain containing from one to six carbon atoms. Several compounds with methoxy groups in the aromatic ring are in the morphine range of potency; they are uniformly inactive as phenazocine antagonists. Phenolic analogues range up to 100 times as potent as morphine. Those containing five or six carbon atoms in the alkyl group exhibit phenazocine antagonist activity, in one case equivalent to naloxone. This compound (3e) is selective for phenazocine in its antagonist action.