gebhart/patrepeval huggingface dataset:
Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design (2013)

The hepatitis C virus (HCV) RNA polymerase, NS5B, is a leading target for novel and selective HCV drug design. The enzyme has been the subject of intensive drug discovery aimed at developing direct acting antiviral (DAA) agents that inhibit its activity and hence prevent the virus from replicating its genome. In this study, we focus on one class of NS5B inhibitors, namely nucleos(t)ide mimetics. Forty-one distinct nucleotide structures have been modeled within the active site of NS5B for the six major HCV genotypes. Our comprehensive modeling protocol employed 287 different molecular dynamics simulations combined with the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) methodology to rank and analyze these structures for all genotypes. The binding interactions of the individual compounds have been investigated and reduced to the atomic level. The present study significantly refines our understanding of the mode of action of NS5B-nucleotide-inhibitors, identifies the key structural elements necessary for their activity, and implements the tools for ranking the potential of additional much needed novel inhibitors of NS5B.
Process window OPC verification: dry versus immersion lithography for the 65nm node (2006)

Ensuring robust patterning after OPC is becoming more and more difficult due to the continuous reduction of layout dimensions and diminishing process windows associated with each successive lithographic generation. Lithographers must guarantee high imaging fidelity throughout the entire range of normal process variations. To verify the printability of a design across process window, compact optical models similar to those used for standard OPC are used. These models are calibrated from experimental data measured at the limits of the process window. They are then applied to the design to predict potential printing failures. This approach has been widely used for dry lithography. With the emergence of immersion lithography in production in the IC industry, the predictability of this approach has to be validated on this new lithographic process. In this paper, a comparison between the dry lithography process model and the immersion lithography process model is presented for the Poly layer at 65 nm node patterning. Examples of specific failure predictions obtained separately with the two processes are compared with experimental results. A comparison in terms of process performance will also be a part of this study.
Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling (2018)

Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2<sup>T202/Y204</sup> protein levels at higher compound concentrations.
Impulsive noise reduction using Auto-Gating technique (2011)

This paper presents the design and simulation of an Auto-Gating technique for impulsive noise reduction in communication systems. The Auto-Gating process applies an adaptive approach in order to reduce the impact of impulsive noise. An AWGN system model that uses both 16-QAM and QPSK were implemented. The BER performance for the proposed technique under AWGN and impulsive noise was compared with different impulsive noise reduction techniques such as Fixed-Gating. The results showed that the proposed technique offered clear improvement over conventional techniques.
CMOS smart pixel for free-space optical communication (2001)

Fully integrated imaging receivers present a method of low power free-space optical communication with advantages over radio frequency and single element optical communication for a variety of network scenarios. This paper discusses the theoretical performance of such receivers and the design of a single 'smart pixel' for use in a 2.5 Mbps integrated CMOS imaging receiver. The receiver has a simulated input referred noise power of -51 dBm and a dynamic range greater than 30 dB when operating at 2.5 Mbps. Power consumption is less than 50 (mu) W and the pixel fits on a 150 micrometers pitch in a standard 0.35 micrometers digital CMOS process, readily allowing fabrication of inexpensive imaging arrays as large as 64 by 64 pixels. Th receiver presented covers all aspects of reception from optical detection through A/D conversion. An asynchronous digital serial receiver could decode the resulting data stream from this receiver. A low overhead architecture for communicating decoded data packets form any pixel in the imaging array to the edge of the chip is briefly described.
Human Glial Cell Line-derived Neurotrophic Factor Receptor α4 Is the Receptor for Persephin and Is Predominantly Expressed in Normal and Malignant Thyroid Medullary Cells (2001)

Glial cell line-derived neurotrophic factor (GDNF) family ligands signal through receptor complex consisting of a glycosylphosphatidylinositol-linked GDNF family receptor (GFR) alpha subunit and the transmembrane receptor tyrosine kinase RET. The inherited cancer syndrome multiple endocrine neoplasia type 2 (MEN2), associated with different mutations in RET, is characterized by medullary thyroid carcinoma. GDNF signals via GFRalpha1, neurturin via GFRalpha2, artemin via GFRalpha3, whereas the mammalian GFRalpha receptor for persephin (PSPN) is unknown. Here we characterize the human GFRalpha4 as the ligand-binding subunit required together with RET for PSPN signaling. Human and mouse GFRalpha4 lack the first Cys-rich domain characteristic of other GFRalpha receptors. Unlabeled PSPN displaces (125)I-PSPN from GFRA4-transfected cells, which express endogenous Ret. PSPN can be specifically cross-linked to mammalian GFRalpha4 and Ret, and is able to promote autophosphorylation of Ret in GFRA4-transfected cells. PSPN, but not other GDNF family ligands, promotes the survival of cultured sympathetic neurons microinjected with GFRA4. We identified different splice forms of human GFRA4 mRNA encoding for two glycosylphosphatidylinositol-linked and one putative soluble isoform that were predominantly expressed in the thyroid gland. Overlapping expression of RET and GFRA4 but not other GFRA mRNAs in normal and malignant thyroid medullary cells suggests that GFRalpha4 may restrict the MEN2 syndrome to these cells.
Multiple-description wavelet based image coding (2002)

We consider the problem of image coding for communication systems that use diversity to overcome channel impairments. We focus on the special case in which there are two channels of equal capacity between a transmitter and a receiver. Our designs are based on a combination of techniques successfully applied to the construction of some of the most efficient wavelet based image coding algorithms, with multiple description scalar quantizers (MDSQs). For a given image, we produce two bitstreams, to be transmitted over each channel. Should one of the channels fail, each individual description guarantees a minimum image quality specified by the user. However, if both descriptions arrive at destination, they are combined to produce a higher quality image than that achievable based on individual descriptions. We formulate a discrete optimization problem, whose solution gives parameters of the proposed encoder yielding optimal performance in an operational sense. Simulation results are presented.
Shelding analysis for a manned Mars rover powered by an Sp-100 type reactor (1991)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Nicholas J. Morley, Mohamed S. El‐Genk; Shelding analysis for a manned Mars rover powered by an Sp‐100 type reactor. AIP Conf. Proc. 1 January 1991; 217 (1): 347–354. https://doi.org/10.1063/1.40007 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
IgA Immunodeficiency Leads to Inadequate Th Cell Priming and Increased Susceptibility to Influenza Virus Infection (2001)

IgA is considered to be the principal Ab involved in defense against pathogens in the mucosal compartment. Using mice with a targeted disruption in IgA gene expression (IgA(-/-) mice), we have examined the precise role of IgA in protective anti-influenza responses after intranasal vaccination. IgA(-/-) mice immunized intranasally with soluble hemagglutinin (hemagglutinin subtype 1) and neuraminidase (neuraminidase subtype 1) vaccine in the absence of adjuvant were found to be more susceptible to influenza virus infection than IgA(+/+) mice (13 vs 75% survival after virus challenge). Inclusion of IL-12 during immunization restored the protective efficacy of the vaccine to that seen in IgA(+/+) animals. IgA(-/-) mice had no detectable IgA expression, but displayed enhanced serum and pulmonary IgM and IgG Ab levels after IL-12 treatment. Assessment of T cell function revealed markedly depressed splenic lymphoproliferative responses to PHA in IgA(-/-) animals compared with IgA(+/+) mice. Furthermore, IgA(-/-) animals displayed impaired T cell priming to the H1N1 subunit vaccine, with concomitant reduction in recall memory responses due to a defect in APC function. Collectively, these results provide evidence that a major role of IgA is to facilitate presentation of Ag to mucosal T cells. IL-12 treatment can overcome IgA deficiency by providing adequate T cell priming during vaccination.
Tetramethylpyrazine Ameliorated Hypoxia-Induced Myocardial Cell Apoptosis via HIF-1α/JNK/p38 and IGFBP3/BNIP3 Inhibition to Upregulate PI3K/Akt Survival Signaling (2015)

Our results strongly suggest that TMP could be used to restore hypoxia-induced myocardial cell apoptosis and cardiac hypoxic damage.
Supplementary Methods from <i>PIK3CA</i> Mutations and Copy Number Gains in Human Lung Cancers (2023)

Supplementary Methods from &lt;i&gt;PIK3CA&lt;/i&gt; Mutations and Copy Number Gains in Human Lung Cancers
A multiagent architecture for protection engineering diagnostic assistance (2003)

Protection engineers use data from a range of monitoring devices to perform post-fault disturbance diagnosis. In the past, heterogeneous intelligent systems have been developed to interpret the data and provide information to engineers to assist with the disturbance diagnosis task. The majority of these systems remain standalone due to the problems associated with systems integration. This paper proposes the use of multiagent systems for providing a flexible and scalable alternative to existing integration approaches. A novel multiagent system (MAS) has been developed entitled protection engineering diagnostic agents (PEDAs) which integrates a legacy SCADA interpretation system with new systems for digital fault recorder (DFR) record interpretation and for enhancing fault record retrieval from remote DFRs. The use of MAS technology provides a flexible and scalable architecture open to the introduction of new data interpretation systems. The paper discusses the benefits of a multiagent approach and the design and implementation of PEDA.
Wireless Channels that Exhibit "Worse than Rayleigh" Fading: Analytical and Measurement Results (2006)

We describe several disparate practical settings in which cases of severe, or "worse than Rayleigh," fading have been encountered. To explain this behavior, we present two physical models. The first model employs a statistically non-stationary random process that switches between two distributions, akin to the multi-state models proposed for land mobile satellite channels. The other model we propose is a multiplicative model of two small scale fading processes. We also describe the analytical pdf for such a multiplicative model using two Weibull random variables as the underlying small scale fading distributions. Measured data is used to corroborate these models, and our computer simulations confirm the ability to replicate the statistics of these severe fading processes. These proposed models can be used by researchers investigating communication system designs in severe fading environments.
Stereochemistry of Phellinsin A: A Concise Synthesis of α‐Arylidene‐γ‐Lactones (2005)

Abstract Phellinsin A (1a) was prepared in a concise way, thereby elucidating the relative stereochemistry of the aryl and carboxylic acid groups in 1a. The synthesis employed selective monohydrolysis of the dilactones derived from oxidative dimerization of cinnamic acid derivatives. This approach provided a practical synthetic route to α‐arylidene‐γ‐lactones.
Defect mitigation and root cause studies in IMEC's 14nm half-pitch chemo-epitaxy DSA flow (2015)

High defect density in thermodynamics driven DSA flows has been a major cause of concern for a while and several questions have been raised about the relevance of DSA in high volume manufacturing. The major questions raised in this regard are: 1. What is the intrinsic level of DSA-induced defects, 2. Can we isolate the DSA-induced defects from the other processes-induced defects, 3. How much do the DSA materials contribute to the final defectivity and can this be controlled, 4. How can we understand the root causes of the DSA-induced defects, their kinetics of annihilation and finally, 5. Can we have block co-polymer anneal durations that are compatible with standard CMOS fabrication techniques (in the range of minutes) with low defect levels. This manuscript addresses these important questions and identifies the issues and the level of control needed to achieve a stable DSA defect performance.
A vapor pressure thermometer for use in muscle microcalorimetry (2011)

Measurement of the energy consumption of isolated cardiac trabeculae requires highly sensitive temperature sensors. In this paper we describe and characterize an initial prototype of a vapor pressure thermometer being designed and built for application to muscle microcalorimetry. The device exploits the change in vapor pressure with temperature of a solvent and the change in pressure with volume of a gas. The sensor achieves a sensitivity of 86 μm/K and a resolution of 3.6 μK. Predictions from a finite element model of the expected displacement compare favorably with the tests performed.
Gap Analysis for Operating IPv6-Only MPLS Networks (2015)

This document reviews the Multiprotocol Label Switching (MPLS)
protocol suite in the context of IPv6 and identifies gaps that must be
addressed in order to allow MPLS-related protocols and applications to
be used with IPv6-only networks. This document is intended to focus on
gaps in the standards defining the MPLS suite, and is not intended to
highlight particular vendor implementations (or lack thereof) in the
context of IPv6-only MPLS functionality. In the data plane, MPLS
fully supports IPv6, and MPLS labeled packets can be carried over IPv6
packets in a variety of encapsulations. However, support for IPv6
among MPLS control-plane protocols, MPLS applications, MPLS
Operations, Administration, and Maintenance (OAM), and MIB modules is
mixed, with some protocols having major gaps. For most major gaps,
work is in progress to upgrade the relevant protocols.
ChemInform Abstract: Structure and Dynamic Behavior in Solution of Binuclear Nickel(II) Face‐to‐Face Complexes with Bis(cyclidene) Ligands. (1986)

Abstract NMR studies of the dinickel(II) complexes (I) with macrocyclic bis(cyclidene) ligands reveal a dynamic molecular motion in solution.
Back Cover: A Highly‐Ordered 3D Covalent Fullerene Framework (Angew. Chem. Int. Ed. 26/2015) (2015)

A 3D covalent fullerene framework with a structure based on hexafunctionalized fullerene building blocks with octahedral symmetry is reported by T. Bein et al. in their Communication on page 7577 ff. Each fullerene in the highly ordered framework is separated from the next by six functional groups, and the mesoporosity is controlled by template-directed, evaporation-induced self-assembly with a block copolymer. The TEM images in the background show the periodic porous fullerene framework.
Fluence-based dosimetry of proton and heavier ion beams using single track detectors (2016)

Due to their superior spatial resolution, small and biocompatible fluorescent nuclear track detectors (FNTDs) open up the possibility of characterizing swift heavy charged particle fields on a single track level. Permanently stored spectroscopic information such as energy deposition and particle field composition is of particular importance in heavy ion radiotherapy, since radiation quality is one of the decisive predictors for clinical outcome. Findings presented within this paper aim towards single track reconstruction and fluence-based dosimetry of proton and heavier ion fields. Three-dimensional information on individual ion trajectories through the detector volume is obtained using fully automated image processing software. Angular distributions of multidirectional fields can be measured accurately within ±2° uncertainty. This translates into less than 5% overall fluence deviation from the chosen irradiation reference. The combination of single ion tracking with an improved energy loss calibration curve based on 90 FNTD irradiations with protons as well as helium, carbon and oxygen ions enables spectroscopic analysis of a detector irradiated in Bragg peak proximity of a 270 MeV u(-1) carbon ion field. Fluence-based dosimetry results agree with treatment planning software reference.
Ad Hoc Routing Modeling and Mathematical Analysis (2012)

This chapter analyzes the performance of existing ad hoc routing protocols using simulations and a test bed. It also analyzes the use of a hybrid routing approach for ad hoc networks based on the results. The chapter briefly describes the ad hoc on-demand distance vector, dynamic source routing, and the temporally ordered routing algorithm as the most widely used reactive ad hoc routing protocols. It introduces the destination sequenced distance vector routing and the optimized link state routing as the most representative proactive ad hoc routing protocols. The chapter includes the results from a large set of simulations, and provides the measurements obtained from our test bed to seek confirmation of the accuracy of our propositions. It presents simulation results justifying the advantages and disadvantages of the reactive and proactive ad hoc routing protocols. The reactive routing protocols under analysis have clear drawbacks such as the excessive flooding traffic in the route discovery and the route acquisition delay.
Scheduling in Multi-Channel Wireless Networks: Rate Function Optimality in the Small-Buffer Regime (2014)

The problem of designing scheduling algorithms for a multichannel (e.g., orthogonal frequency division multiplexing-based) wireless downlink network is considered. The classic MaxWeight algorithm, although throughput-optimal, results in a very poor per-user delay performance in such systems. Hence, an alternate class of algorithms called iterated longest queues first (iLQF) is proposed for overcoming this issue. The iLQF-class algorithms are analyzed in a number of different system configurations. A particular algorithm in this class, called iLQF with pullup, is shown to be rate function optimal for the problem in an appropriate large deviations setting, and is shown to result in a strictly positive value of the rate function for a number of modifications to the basic system model. Thus, the proposed algorithm yields provable performance guarantees. The analytic results are confirmed through simulations.
Characterization of the Salmonella paratyphi C Vi polysaccharide (1989)

The Vi capsular polysaccharide (Vi) is both a virulence factor and a protective antigen of Salmonella typhi; its pathogenic role for Salmonella paratyphi C is less well understood. We found no differences between the antigenic and immunogenic properties and the structure of the Vi from representative strains of S. paratyphi C, S. typhi, and Citrobacter freundii. There were, however, differences in both the amount produced per cell and the degree of association with the cell among the Vi from the three species of Enterobacteriaceae. S. paratyphi C produced less Vi than both the wild-type S. typhi and C. freundii did, and it showed the fastest release of Vi into the media. These findings may provide an explanation for the inability of the Vi to inhibit completely the agglutination of S. paratyphi C by anti-O sera. In an outbreak of enteric fever caused by S. paratyphi C, 66 of 78 isolates (85%) were Vi positive.
Approximate minimum spanning tree clustering in high-dimensional space (2009)

Minimum spanning tree (MST ) clustering sequentially inserts the nearest points in the ℜ d space into a list which is then divided into clusters by using desired criteria. This insertion order, however, can be relaxed provided approximately nearby po
Multi-directional Greedy Stereo Matching (2008)

In this paper, we propose a new stereo matching method to reduce a memory size and handle an large image such as satellite images while its performance satisfies speed and accuracy. Our new method is based on a Multidirectional Greedy algorithm and RANSAC. First, we obtain a depth image along multi-directioanl scanlines using the Greedy algorithm. Then, we find reliable areas from the distribution of several depth images using RANSAC. Finally, we extend the reliable areas by iterating the Greedy algorithm and RANSAC several times starting with the previously obtained reliable areas and decide a final depth image. Experimental results show that our algorithm proves the possibility of stereo matching for an enormous image using low memory size while satisfying the performance from the view point of speed and accuracy.
Robust Experiment Design for Virtual Reference Feedback Tuning (2018)

This paper deals with robust experiment design for the Virtual Reference Feedback Tuning (VRFT) approach, a non-iterative control design method aimed to tune fixed-order controllers directly from experimental data, without the need for a model of the plant. In a previous contribution, it has been shown that the spectrum of the optimal input depends on the frequency response of the controller achieving the desired performance. In this work, a robust input design procedure is proposed, which requires only mild prior knowledge about the optimal controller. The solution is obtained analytically via constrained min-max optimization. Simulation results on a benchmark case study for digital control systems show the effectiveness of the proposed approach.
A More Comprehensive NDE: PCRT for Ceramic Components (2010)

This chapter contains sections titled: Introduction Process Compensated Resonance Testing (PCRT) Applications of PCRT