gebhart/patrepeval huggingface dataset:
Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach (2019)

Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.
A Direct and Versatile Assay Measuring Membrane Penetration of Adenovirus in Single Cells (2013)

Endocytosis is the most prevalent entry port for viruses into cells, but viruses must escape from the lumen of endosomes to ensure that viral genomes reach a site for replication and progeny formation. Endosomal escape also helps viruses bypass endolysosomal degradation and presentation to certain Toll-like intrinsic immunity receptors. The mechanisms for cytosolic delivery of nonenveloped viruses or nucleocapsids from enveloped viruses are poorly understood, in part because no quantitative assays are readily available which directly measure the penetration of viruses into the cytosol. Following uptake by clathrin-mediated endocytosis or macropinocytosis, the nonenveloped adenoviruses penetrate from endosomes to the cytosol, and they traffic with cellular motors on microtubules to the nucleus for replication. In this report, we present a novel single-cell imaging assay which quantitatively measures individual cytosolic viruses and distinguishes them from endosomal viruses or viruses at the plasma membrane. Using this assay, we showed that the penetration of human adenoviruses of the species C and B occurs rapidly after virus uptake. Efficient penetration does not require acidic pH in endosomes. This assay is versatile and can be adapted to other adenoviruses and members of other nonenveloped and enveloped virus families.
Ring Opening of 4-Chloroquinazoline into 2-Arylmethyleneaminobenzonitrile by Grignard Reaction (1994)

The treatment of 4-chloroquinazoline (1) with arylmagnesium bromide (3) in tetrahydrofuran (THF) resulted in the formation of 2-arylme- thyleneaminobenzonitrile (2). Continued reaction of ring opening of (1) and subsequent hydrolysis of the products (2) afforded the corresponding arenecarbaldehydes (4)
Mathematical Modeling of the Limiting Current Density from Diffusion-Reaction Systems (2022)

The limiting current density is one of to the most important indicators in electroplating for the maximal current density from which a metal can be deposited effectively from an electrolyte. Hence, it is an indicator of the maximal deposition speed and the homogeneity of the thickness of the deposited metal layer. For these reasons, a major interest in the limiting current density is given in practical applications. Usually, the limiting current density is determined via measurements. In this article, a simple model to compute the limiting current density is presented, basing on a system of diffusion–reaction equations in one spatial dimension. Although the model formulations need many assumptions, it is of special interest for screenings, as well as for comparative work, and could easily be adjusted to measurements.
Algorithm animation of neural networks (1996)

Article Free Access Share on Algorithm animation of neural networks Authors: David Jackson Department of Computer Science, University of Liverpool, PO Box 147, Liverpool L69 3BX, United Kingdom Department of Computer Science, University of Liverpool, PO Box 147, Liverpool L69 3BX, United KingdomView Profile , Ian G. Morton Department of Computer Science, University of Liverpool, PO Box 147, Liverpool L69 3BX, United Kingdom Department of Computer Science, University of Liverpool, PO Box 147, Liverpool L69 3BX, United KingdomView Profile Authors Info & Claims ITiCSE '96: Proceedings of the 1st conference on Integrating technology into computer science educationJune 1996 Pages 39–41https://doi.org/10.1145/237466.237522Published:01 January 1996Publication History 5citation411DownloadsMetricsTotal Citations5Total Downloads411Last 12 Months27Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Formalization of VT Codes and Their Single-Deletion Correcting Property in Lean (2020)

This manuscript reports on our project on formalization for deletion codes in Lean theorem prover: the definition of Varshamov-Tenengolts (VT) codes and their single-deletion error-correcting property are formalized. It also reports progress on our attempt to resolve an open problem of VT codes in Lean.
Mobile Application and Device Power Usage Measurements (2012)

Reducing power consumption has become a crucial design tenet for both mobile and other small computing devices that are not constantly connected to a power source. However, unlike devices that have a limited and predefined set of functionality, recent mobile smart phone devices have a very rich set of components and can handle multiple general purpose programs that are not a-priori known or profiled. In this paper, we present a general methodology for collecting measurements and modelling power usage on smart phones. Our goal is to characterize the device subsystems and perform accurate power measurements. We implemented a system that effectively accounts for the power usage of all of the primary hardware subsystems on the phone: CPU, display, graphics, GPS, audio, microphone, and Wi-Fi. To achieve that, we make use of the per-subsystem time shares reported by the operating system's power-management module. We present the models capability to further calculate the power consumption of individual applications given measurements, and also the feasibility of our model to operate in real-time and without significant impact in the power footprint of the devices we monitor.
Enhanced Rank Based Cooperative Game (ERBCG) strategy for IEEE 802.11s Mesh WLAN power management (2013)

IEEE 802.11s Mesh WLAN is a promising access network standard launched for the aim of enhancing channels' utilization, coverage extension with simple and cheap network deployment. Mesh WLAN faces challenges in power management, channel assignment, traffic forwarding, admission control, security and coexistence with other technologies. The main objective of this paper is to increase the mesh WLAN throughput by adjusting the mesh nodes' transmission power. Increasing the node's transmission power increases its users' bit rate but in the same time increases the interference on the neighboring nodes, hence decreasing their bit rates and the overall throughput. Power management also controls the users and mesh nodes connectivity, the number of hops to the gateway and traffic forwarding. This paper proposes a new power management algorithm; Enhanced Rank Based Cooperative Game (ERBCG) algorithm, as an enhancement for the Rank-based algorithm in the literature to optimize the average users' data rates and minimize the algorithm iterations. The Rank-based algorithm showed better performance than the non-cooperative game Nash equilibriums and a comparable result with the optimum power assignment. Results of the ERBCG algorithm proves that the proposed algorithm significantly increases the uplink and downlink average user's data rates and thus enhancing the overall network throughput while significantly decreasing the number of power management iterations to less than half the number consumed by the Rank-based algorithm, which results in less overhead and reduced latency in mesh nodes power adjustment.
Interfacial roughening during solid phase epitaxy: Interaction of dopant, stress, and anisotropy effects (2004)

The effects of externally applied stress and rate-enhancing dopants on interfacial roughness during the solid phase epitaxial growth of ion-implantation-doped Si are investigated using cross-sectional transmission electron microscopy and time-resolved reflectivity. We find long-wavelength roughness in the absence of an applied stress that arises solely from the dopant-gradient. With the addition of a compressive stress, the interface roughens further with an enhanced magnitude and a dramatically reduced wavelength. We discuss the experimental results in the context of a simulation that includes our current understanding of stress, dopant-gradient, and interface anisotropy effects. We find a rich interplay between these effects in determining growth morphology evolution, and demonstrate the successes and current limitations of the model.
Action Image Representation: Learning Scalable Deep Grasping Policies with Zero Real World Data (2020)

This paper introduces Action Image, a new grasp proposal representation that allows learning an end-to-end deep-grasping policy. Our model achieves 84% grasp success on 172 real world objects while being trained only in simulation on 48 objects with just naive domain randomization. Similar to computer vision problems, such as object detection, Action Image builds on the idea that object features are invariant to translation in image space. Therefore, grasp quality is invariant when evaluating the object-gripper relationship; a successful grasp for an object depends on its local context, but is independent of the surrounding environment. Action Image represents a grasp proposal as an image and uses a deep convolutional network to infer grasp quality. We show that by using an Action Image representation, trained networks are able to extract local, salient features of grasping tasks that generalize across different objects and environments. We show that this representation works on a variety of inputs, including color images (RGB), depth images (D), and combined color-depth (RGB-D). Our experimental results demonstrate that networks utilizing an Action Image representation exhibit strong domain transfer between training on simulated data and inference on real-world sensor streams. Finally, our experiments show that a network trained with Action Image improves grasp success (84% vs. 53%) over a baseline model with the same structure, but using actions encoded as vectors.
A Method for Integration of Knowledge Using Fuzzy Structure (2007)

This paper presents an approach for knowledge integration using fuzzy structure. For this aim knowledge elements being integrated are assumed to be fuzzy sets, and the distance functions between fuzzy sets are defined. Next postulates for integration are specified and algorithms for integration are proposed.
Image Restoration Via Iterative Improvement Of The Wiener Filter (1988)

The Wiener filter has often been employed as a means for solving the signal/image restoration problem. Unfortunately, the information that is required as input for the realization of this filter is, in many practical situations, not available. In particular, when only one degraded, noisy observation of the signal is presented as data, the spectral density function for the signal to be recovered will generally not be known. A typical &apos;fix&apos; to this dilemma has been to assume that the ratio of noise to signal spectral densities is constant with frequency. The value of this constant that makes the best reconstruction is then determined via trial-and-error by a human. In this paper we present an alternative to this over-simplified version of the Wiener filter (K-filter). Specifically, we demonstrate that an estimate of the signal spectral density can be made via an iterative procedure from the data. This results in reconstructions that are generally superior to any output that the simplified Wiener filter can provide. We show simulated results for the case of one-dimensional degradations of image data.
Interrelationship of voltage and temperature dependence of oxide breakdown for ultrathin oxides (2000)

We report that voltage acceleration of time- or charge-to-breakdown is insensitive to temperature variations over a wide range of temperature (30 to 200/spl deg/C) for oxides below 3 nm, regardless of oxide process, injection polarity or device type (NFET, PFET). Based on this observation, an essentially universal, non-Arrhenius temperature dependence for ultrathin oxide is obtained by a natural normalization scheme. The consequences of these findings for reliability projection are discussed.
Structure of the Mesophases Formed by a Perfluoroalkyl/Biphenyl Compound. Amphiphilic andSteric Effects (1996)

We describe the synthesis and mesomorphic behaviour of 4-(1H,1H-perfluorooctyloxy)- 4'-methoxy biphenyl. Two mesophases of smectic E and smectic A types were observed. X-ray diffraction study of the smectic E phase indicates a herringbone arrangement of the biphenyl cores, the perfluoroalkyl chains being in a molten state. The SE ↦SA transition is related to the melting of the biphenyl sublattice. In both phases, the flexibility of perfluoroalkyl chains permits the area matching between the two segregated sublayers.
Morphology study of freeze-drying mononuclear cells of human cord blood. (2005)

The research on haematopoietic stem cells of human cord blood has become more important recently. At present, cord blood is mainly preserved at ultra-low temperatures. In the former study, we compared the effects of preserving mononuclear cells (MNC) and whole human cord blood by freeze-drying. This time, a further study was conducted on freeze-drying mononuclear cells. Samples in the presence of PVP, sucrose, mannitol and FBS were firstly frozen to -38 degrees C. Afterwards, they were vacuum-dried at a selected shelf temperature of -30 degrees C for the main drying stage, and then vacuum-dried at 15 degrees C for the second drying stage. The entire time of freeze-drying process was 41 hours. Samples were stored at room temperature for 7 days prior to evaluation. Subsequently, the dried samples were resuspended in an isotonic phosphate-buffered saline solution. The residual moisture content was 6.5 +/- 0.87%. The recovery of the cells was tested by a haemacytometer, and the numerical cell count recovery of rehydrated MNC increased by 8%. Morphology of the fresh and rehydrated MNC was analyzed respectively using standard light microscopy, scanning electron microscope and transmission electron microscope. The results showed that karyons changed and cytoplasm decreased after rehydration, but it is still unknown that whether these changes will influence the proliferative ability of the stem cells.
Effect of Residual Oxygenated Functional Groups on the Behavior of Alternative Jet Fuel Properties (Project 31B) (2018)

The goal of this project is the identification of the nature and the content of the oxygenated compounds present in alternative jet fuels and to develop methods for the fast identification of these oxygenated compounds. The chemical composition and fuel properties of nine alternative jet fuels (named as AJF 1-9) and three commercial jet fuels (named as CJF 1, 2 and 3) were studied. The fuels were characterized by gas chromatography–mass spectrometry (GC/MS), SEP-GC/MS (for quantification of oxygenated molecules), viscosity, density, water content, water solubility at 0 °C, carbonyl content, total acid number, elemental composition, calorific value, flash point, differential scanning calorimetry, and surface tension. The content of oxygenated compounds measured was in all the cases very low and comparable with the amount found in commercial jet fuels. Phenols are the most common trace oxygenated compounds found in aviation fuels. A new method based on the identification of extracted phenolic compounds by UV-fluorescence was developed. This method is much faster to identify the presence of phenols but does not allow to quantify them and still requires SPE of phenols. In order to avoid the extraction step, fluorescence quenching with Rhodamine-B in jet fuel was studied. Rhodamine-B show fluorescence quenching in the presence of phenols. A new method is proposed for the fast identification of phenols in jet fuels at operational field conditions.\n
Monitoring of Nozzle Wear during Plasma Spray (1997)

Abstract Presented in this paper are the results of preliminary experiments carried out for monitoring of plasma nozzle wear. The experiment system consists of two microphones, one accelerometer and voltage measurement. In the experiment, three nozzles were tested, new, used and worn. The test results show clearly the difference in acoustic characteristics with wear in the nozzle. Some observations obtained from the experiment include: 1) the microphone mounted at 45° may be the best choice for nozzle wear monitoring; 2) voltage signal could be used with the 45° microphone as an indicator for severe nozzle wear; 3) vibration signal is not as sensitive to nozzle wear as 45° microphone and voltage signal; and 4) the 90° microphone is insensitive to nozzle wear.
A natural modal expansion for the flexible robot arm problem via a self-adjoint formulation (1990)

The equations of motion of a flexible robot arm consist of a coupled partial differential equation describing the arm's transverse vibrations and an ordinary differential equation describing the hub's rigid motion. Many researchers obtained a solution using a modal expansion based on the arm's equation alone, which has erroneous eigenfunctions and eigenvalues. A novel method is presented for obtaining an equivalent but self-adjoint form for the problem. This self-adjoint form leads to a natural modal expansion, where the equations decouple. This method is used to show that the effect of the hub-arm model coupling depends exclusively on the hub-inertia-to-arm-mass ratio. The need for a self-adjoint form arises in many control applications. This is because, typically, the control design is based on approximate models, and in order to guarantee robust performance, a prior estimate of the approximation error is required. When a self-adjoint form is available, obtaining approximate modes and the associated error bounds becomes an easy task.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Impaired Expression of Glycogen Synthase mRNA in Skeletal Muscle of NIDDM Patients (1991)

Based on recent studies of the abnormal physiology and biochemistry of the glycogen synthesis in skeletal muscle of non-insulin-dependent diabetes mellitus (NIDDM) patients and their first-degree relatives, the key enzyme of this pathway, glycogen synthase (GS), is considered a candidate gene in the pathogenesis of insulin resistance. Comparing matched groups of 14 NIDDM patients with 14 control subjects, we found that impaired insulin-stimulated nonoxidative glucose metabolism of peripheral tissue (P less than 0.02) and reduced total GS activity (P less than 0.05) of vastus lateralis muscle from patients with NIDDM were accompanied by a 39% reduction (P less than 0.02) in the steady state level of GS mRNA per microgram DNA of muscle. In both diabetic and control subjects, the mRNA expression of GS was unaffected after euglycemic-hyperinsulinemic clamp for 4 h. With single-stranded conformation polymorphism analysis of the entire coding sequence of the GS gene, we were unable to detect any genetic variants in a subset of eight NIDDM patients. We conclude that abnormal pretranslational regulation of the GS gene may contribute to impaired glycogen synthesis of muscle in NIDDM. Our studies give no evidence for structural changes in the coding region of the GS gene, and it is unknown if the decreased mRNA expression is due to impaired transcription or accelerated degradation of the transcript.
Antioxidant Potential of Gallocatechins. A Pulse Radiolysis and Laser Photolysis Study (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntioxidant Potential of Gallocatechins. A Pulse Radiolysis and Laser Photolysis StudySlobodan V. Jovanovic, Yukihiko Hara, Steen Steenken, and Michael G. SimicCite this: J. Am. Chem. Soc. 1995, 117, 39, 9881–9888Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ja00144a014https://doi.org/10.1021/ja00144a014research-articleACS PublicationsRequest reuse permissionsArticle Views1043Altmetric-Citations228LEARN 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
Preference of glucokinase for the alpha anomer of hexose: relation to alpha-anomer preference in hexose-induced insulin release by pancreatic islets. (1983)

The alpha anomers of glucose and mannose were more rapidly phosphorylated than the beta anomers by rat liver glucokinase, whose chromatographic and kinetic properties are known to be quite similar to those of pancreatic islet glucokinase. This result may explain our previous findings of the alpha-anomeric preference in glucose- and mannose-stimulated insulin release, and therefore suggests to support the hypothesis that glucokinase in islets functions as a crucial hexose sensing enzyme for insulin release induced by glucose and mannose.