gebhart/patrepeval huggingface dataset:
Hydrophilic Anilinogeranyl Diphosphate Prenyl Analogues Are Ras Function Inhibitors (2006)

Sequential processing of H-Ras by protein farnesyl transferase (FTase), Ras converting enzyme (Rce1), and protein-S-isoprenylcysteine O-methyltransferase (Icmt) to give H-Ras C-terminal farnesyl-S-cysteine methyl ester is required for appropriate H-Ras membrane localization and function, including activation of the mitogen-activated protein kinase (MAPK) cascade. We employed a Xenopus laevis oocyte whole-cell model system to examine whether anilinogeranyl diphosphate analogues of similar shape and size, but with a hydrophobicity different from that of the FTase substrate farnesyl diphosphate (FPP), could ablate biological function of H-Ras. Analysis of oocyte maturation kinetics following microinjection of in vitro analogue-modified H-Ras into isoprenoid-depleted oocytes revealed that analogues with a hydrophobicity near that of FPP supported H-Ras biological function, while the analogues p-nitroanilinogeranyl diphosphate (p-NO2-AGPP), p-cyanoanilinogeranyl diphosphate (p-CN-AGPP), and isoxazolaminogeranyl diphosphate (Isox-GPP) with hydrophobicities 2−5 orders of magnitude lower than that of FPP did not. We found that although H-Ras modified with FPP analogues p-NO2-AGPP, p-CN-AGPP, and Isox-GPP was an efficient substrate for C-terminal postprenylation processing by Rce1 and Icmt, co-injection of H-Ras with analogues p-NO2-AGPP, p-CN-AGPP, or Isox-GPP could not activate MAPK. We propose that H-Ras biological function requires a minimum lipophilicity of the prenyl group to allow important interactions downstream of the C-terminal processed H-Ras protein. The hydrophilic FPP analogues p-NO2-AGPP, p-CN-AGPP, and Isox-GPP are H-Ras function inhibitors (RFIs) and serve as lead compounds for a unique class of potential anticancer therapeutics.
Nonimaging solar concentrator with uniform irradiance (2004)

We report results of a study our group has undertaken under NREL/DOE auspices to design a solar concentrator with uniform irradiance on a planar target. This attribute is especially important for photovoltaic concentrators.
Multiple access in ultra-wideband communications using multiple pulses and the use of least squares filters (2004)

Multiple access (MA) in UWB communication has recently been studied in the context of multiple transmitted-reference short duration chirp pulses in the presence of additive white Gaussian noise (AWGN). The transmitted-reference (TR) receiver was extended in previous studies using multiple orthogonal pulses. Improved performance was observed in simulations by sampling the receiver autocorrelation function (ACF) at both zero- and non-zero lags. Sampling of non-zero ACF lags of orthogonal pulses is a novel approach. Method of using least squares filtering techniques for further tolerance against noise and interference for the TR method is proposed.
Ranking Causal Anomalies by Modeling Local Propagations on Networked Systems (2017)

Complex systems are prevalent in many fields such as finance, security and industry. A fundamental problem in system management is to perform diagnosis in case of system failure such that the causal anomalies, i.e., root causes, can be identified for system debugging and repair. Recently, invariant network has proven a powerful tool in characterizing complex system behaviors. In an invariant network, a node represents a system component, and an edge indicates a stable interaction between two components. Recent approaches have shown that by modeling fault propagation in the invariant network, causal anomalies can be effectively discovered. Despite their success, the existing methods have a major limitation: they typically assume there is only a single and global fault propagation in the entire network. However, in real-world large-scale complex systems, it's more common for multiple fault propagations to grow simultaneously and locally within different node clusters and jointly define the system failure status. Inspired by this key observation, we propose a two-phase framework to identify and rank causal anomalies. In the first phase, a probabilistic clustering is performed to uncover impaired node clusters in the invariant network. Then, in the second phase, a low-rank network diffusion model is designed to backtrack causal anomalies in different impaired clusters. Extensive experimental results on real-life datasets demonstrate the effectiveness of our method.
Data from Two Novel ALK Mutations Mediate Acquired Resistance to the Next-Generation ALK Inhibitor Alectinib (2023)

<div>Abstract<p><b>Purpose:</b> The first-generation ALK tyrosine kinase inhibitor (TKI) crizotinib is a standard therapy for patients with <i>ALK</i>-rearranged non–small cell lung cancer (NSCLC). Several next-generation ALK-TKIs have entered the clinic and have shown promising activity in crizotinib-resistant patients. As patients still relapse even on these next-generation ALK-TKIs, we examined mechanisms of resistance to the next-generation ALK-TKI alectinib and potential strategies to overcome this resistance.</p><p><b>Experimental Design:</b> We established a cell line model of alectinib resistance, and analyzed a resistant tumor specimen from a patient who had relapsed on alectinib. We developed Ba/F3 models harboring alectinib-resistant ALK mutations and evaluated the potency of other next-generation ALK-TKIs in these models. We tested the antitumor activity of the next-generation ALK-TKI ceritinib in the patient with acquired resistance to alectinib. To elucidate structure–activity relationships of ALK mutations, we performed computational thermodynamic simulation with MP-CAFEE.</p><p><b>Results:</b> We identified a novel V1180L gatekeeper mutation from the cell line model and a second novel I1171T mutation from the patient who developed resistance to alectinib. Both ALK mutations conferred resistance to alectinib as well as to crizotinib, but were sensitive to ceritinib and other next-generation ALK-TKIs. Treatment of the patient with ceritinib led to a marked response. Thermodynamics simulation suggests that both mutations lead to distinct structural alterations that decrease the binding affinity with alectinib.</p><p><b>Conclusions:</b> We have identified two novel ALK mutations arising after alectinib exposure that are sensitive to other next-generation ALK-TKIs. The ability of ceritinib to overcome alectinib-resistance mutations suggests a potential role for sequential therapy with multiple next-generation ALK-TKIs. <i>Clin Cancer Res; 20(22); 5686–96. ©2014 AACR</i>.</p></div>
Video-QoE aware resource management at network core (2014)

We address the problem of video-aware multiuser resource management in modern wireless networks such as 3GPP Long Term Evolution (LTE) in the context of video delivery systems like HTTP Adaptive Streaming (HAS). HAS is a client driven video rate adaptation and delivery framework that is becoming popular due to its inherent advantages over existing video delivery solutions. Quality of Experience (QoE) is the prime performance criterion for adaptive video streaming and wireless resource management is a critical part in providing a target QoE for video delivery over wireless systems. However modifying resource management functionality to be video-aware at the network edge is rather difficult in practical networks. In this paper, we propose an alternative architecture to enhance video QoE in QoS (Quality of Service)-aware networks wherein the intelligence for video aware resource management resides at the network-core rather than at the network edge. In this new architecture, a "Video Aware Controller" (VAC) is placed at the network core. The VAC periodically receives HAS-related feedback from adaptive streaming clients/servers which it converts to QoS parameters for each user. Further, we propose an algorithm to dynamically compute the Maximum Bit Rate (MBR) for each streaming user based on media buffer feedback. Our simulation results on an LTE system level simulator demonstrate significant reduction in re-buffering percentage and enhanced QoE-outage capacity compared to existing schemes.
Self-Reported Effectiveness and Safety of Trokie® Lozenges: A Standardized Formulation for the Buccal Delivery of Cannabis Extracts (2018)

Therapeutic use of cannabinoids, the main active ingredients of <i>Cannabis</i><i>sativa</i> L., is often hindered by their limited bioavailability and undesirable psychoactivity. We conducted an observational study in December 2016 and another one in February 2018 to investigate respectively: (i) the effectiveness of Trokie<sup>®</sup> lozenges, a standardized formulation containing cannabis extracts, to deliver cannabinoids via buccal absorption and (ii) its long-term safety. Participants were members of the Palliative Care Corporation health clinic, registered California cannabis patients, and had a diagnosis of chronic non-cancer pain. For the effectiveness study, 49 participants were asked to self-report pain perception before and after 1-12 weeks of taking Trokie<sup>®</sup> lozenges, using an 11-point pain intensity numeric rating scale (PI-NRS). A mean reduction in PI-NRS score of 4.9 ± 2.0 points was observed. Onset of analgesia typically varied between 5 and 40 min, which seems consistent with, at least partial, buccal absorption. In the safety study, 35 participants were asked to complete a questionnaire about adverse events (AEs) associated with Trokie<sup>®</sup> lozenges. AEs were reported by 16 subjects (46%), the most common being dizziness/unsteadiness (<i>N</i> = 7), bad taste (<i>N</i> = 5), and throat irritation/dry mouth (<i>N</i> = 4). None of the self-reported AEs resulted in a serious medical situation and most of them had limited impact on daily functions. Despite the AEs, 90% of participants reported being "satisfied" or "very satisfied" with the product. These observations suggest that buccal administration of standardized extracts via Trokie<sup>®</sup> lozenges may represent an efficacious and safe approach to cannabis administration.
Spatial mapping of the biomechanical properties of rabbit cornea after cross-linking using optical coherence elastography (2015)

Keratoconus, a structural degeneration of the cornea, is often treated with UV-induced collagen cross-linking (CXL) to increase tissue resistance to further deformation and degeneration. Optimal treatment would be customized to the individual and consider pre-existing biomechanical properties as well as the effects induced by CXL. This requires the capability to noninvasively measure corneal mechanical properties. In this study, we demonstrate the use of phase-stabilized swept source optical coherence elastography (PhS-SSOCE) to assess the relaxation rate of a deformation which was induced by a focused air-pulse in tissue-mimicking gelatin phantoms of various concentration and partially cross-linked rabbit corneas. The temporal relaxation process was utilized to estimate the Young’s modulus from a newly developed model based elasticity reconstruction method. Due to the high spatial sensitivity of PhS-SSOCE, the deformation was only a few microns. The results show that the relaxation process was successfully used to differentiate the untreated (UT) and CXL region of the cornea. The results also indicate that the CXL regions had faster relaxation rates and greater Young’s moduli than the UT regions. Therefore, this method can be used to spatially assess the stiffness of the cornea. This non-contact and noninvasive measurement technique utilizes minimal force for excitation and can be potentially used to study the biomechanical properties of ocular and other sensitive tissues.
Synthesis of Novel Imidazo[1,2-<i>a</i>]pyridines with Potent Activity against Herpesviruses (2003)

[reaction: see text] Synthesis of a novel imidazopyridine with potent activity against herpes simplex viruses is presented. Several synthetic approaches that describe the introduction of a C-3 pyrimidine substituent on the imidazopyridine core via construction of the pyrimidine or Stille coupling are outlined. Methodology for efficient installation of C-8 amine substituents was developed. The outlined strategies provide a high-yielding, scalable route that is amenable to rapid analogue synthesis.
A 64 Channel Multiplexer with Frequency Discrimination Characteristics (1989)

This paper describes a new class of multiplexing filter structure that has both the properties of channelized filtering and channelized linear frequency discrimination. The channelized filter-discriminator is intended for use as part of a microwave receiving system possessing a high probability of intercept for incoming signals. The selective properties of the band pass filters provide an interference-reduction capability while the discriminator property provides for instantaneous frequency measurement. The paper describes a design procedure for achieving a very high degree of discriminator linearity in association with a reasonable selectivity comparable to a maximally flat filter. The theoretical design data are provided in a normalized table generated by computer optimization. The hardware realization of a 64 channel multiplexer-discriminator is described. Measured data is presented that agrees very closely with the theoretical predictions.
<title>Recording characteristics of a magneto-optical super-resolution disk</title> (1994)

To reduce recording magnetic field of a magneto-optical super-resolution disk which uses an in-plane magnetization readout layer, we developed a new disk structure. By preparing a DyFeCo intermediate layer between the readout layer and the recording layer, the recording magnetic field was greatly reduced and then both super-resolution readout and mark-edge recording by a magnetic field modulation method were achieved. By using the new triple-layered disk for super-resolution readout, a carrier to noise ratio of 45 dB at a 0.4 micrometers mark length was obtained and the recording magnetic field became 15 kA/m.
Design and synthesis of N-(N-((S)-1-ethoxycarbonyl-3-phenylpropyl)-L-alanyl)-N-(indan-2-yl)glycine (CV-3317), a new, potent angiotensin converting enzyme inhibitor. (1986)

A new angiotensin converting enzyme (ACE) inhibitor, N-[N-[(S)-1-ethoxycarbonyl-3-phenylpropyl]-L-alanyl]-N-(indan-2-yl)glycine (9a), was found as a result of extensive studies on the structural requisites for the C-terminal amino acid moiety in ACE inhibitors. The synthesis and the determination of the absolute configuration of 9a are described.
High-Power-Density GaN-Based Single-Phase Online Uninterruptible Power Supply (2019)

This paper introduces a new topology suitable for a high-power-density single-phase online uninterruptible power supply (UPS) with a common neutral between its input and output ac ports while avoiding a split dc bus. The proposed topology enables high power density by utilizing half-bridge switch structures compatible with MHz-frequency operation. High efficiency is maintained in this converter by achieving soft-switching in rectifier stage with a boundary conduction mode control strategy. A comprehensive design methodology is developed to optimize the design of this converter. A 1-kVA prototype online UPS based on the proposed topology that utilizes GaN transistors and operates at switching frequencies up to 2 MHz is built and tested. The prototyped UPS achieves a power density of 26.4 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Nautilus (2017)

Natural images often exhibit symmetries that should be taken into account when editing them. In this paper we present Nautilus --- a method for automatically identifying symmetric regions in an image along with their corresponding symmetry transformations. We compute dense local similarity symmetry transformations using a novel variant of the Generalised PatchMatch algorithm that uses Metropolis-Hastings sampling. We combine and refine these local symmetries using an extended Lucas-Kanade algorithm to compute regional transformations and their spatial extents. Our approach produces dense estimates of complex symmetries that are combinations of translation, rotation, scale, and reflection under perspective distortion. This enables a number of automatic symmetry-aware image editing applications including inpainting, rectification, beautification, and segmentation, and we demonstrate state-of-the-art applications for each of them.
Identification of Chondroitin Sulfate Glucuronyltransferase as Chondroitin Synthase-3 Involved in Chondroitin Polymerization (2008)

Recently, we demonstrated that chondroitin polymerization is achieved by any two combinations of human chondroitin synthase-1 (ChSy-1), ChSy-2 (chondroitin sulfate synthase 3, CSS3), and chondroitin-polymerizing factor (ChPF). Although an additional ChSy family member, called chondroitin sulfate glucuronyltransferase (CSGlcA-T), has been identified, its involvement in chondroitin polymerization remains unclear because it possesses only glucuronyltransferase II activity responsible for the elongation of chondroitin sulfate (CS) chains. Herein, we report that CSGlcA-T exhibits polymerization activity on alpha-thrombomodulin bearing the truncated linkage region tetrasaccharide through its interaction with ChSy-1, ChSy-2 (CSS3), or ChPF, and the chain length of chondroitin formed by the co-expressed proteins in various combinations is different. In addition, ChSy family members co-expressed in various combinations exhibited distinct but overlapping acceptor substrate specificities toward the two synthetic acceptor substrates, GlcUAbeta1-3Galbeta1-O-naphthalenemethanol and GlcUAbeta1-3Galbeta1-O-C(2)H(4)NH-benzyloxycarbonyl, both of which share the disaccharide sequence with the glycosaminoglycan-protein linkage region tetrasaccharide. Moreover, overexpression of CSGlcA-T increased the amount of CS in HeLa cells, whereas the RNA interference of CSGlcA-T resulted in a reduction of the amount of CS in the cells. Furthermore, the analysis using the CSGlcA-T mutant that lacks any glycosyltransferase activity but interacts with other ChSy family members showed that the glycosyltransferase activity of CSGlcA-T plays an important role in chondroitin polymerization. Overall, these results suggest that chondroitin polymerization is achieved by multiple combinations of ChSy-1, ChSy-2, CSGlcA-T, and ChPF and that each combination may play a unique role in the biosynthesis of CS. Based on these results, we renamed CSGlcA-T chondroitin synthase-3 (ChSy-3).
Mechanism and kinetics of dithiobenzoate‐mediated RAFT polymerization. I. The current situation (2006)

Abstract Investigations into the kinetics and mechanism of dithiobenzoate‐mediated Reversible Addition–Fragmentation Chain Transfer (RAFT) polymerizations, which exhibit nonideal kinetic behavior, such as induction periods and rate retardation, are comprehensively reviewed. The appreciable uncertainty in the rate coefficients associated with the RAFT equilibrium is discussed and methods for obtaining RAFT‐specific rate coefficients are detailed. In addition, mechanistic studies are presented, which target the elucidation of the fundamental cause of rate retarding effects. The experimental and theoretical data existing in the literature are critically evaluated and apparent discrepancies between the results of different studies into the kinetics of RAFT polymerizations are discussed. Finally, recommendations for further work are given. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5809–5831, 2006
Micro Feature Enhanced Sinter Bonding of Metal Injection Molded (MIM) Parts to Solid Substrate (2011)

In MIM, fine metal powders are mixed with a binder and injected into molds, similar to plastic injection molding. After molding, the binder is removed from the part, and the compact is sintered to almost full density. The obstacle to sinter bonding a MIM part to a conventional (solid) substrate lies in the sinter shrinkage of the MIM part, which can be up to 20%, meaning that the MIM part shrinks during sintering, while the conventional substrate maintains its dimensions. This behavior would typically inhibit bonding and/or cause cracking and deformation of the MIM part. A structure of micro features molded onto the surface of the MIM part allows for shrinkage while bonding to the substrate. The micro features tolerate certain plastic deformation to permit the shrinkage without causing cracks after the initial bonds are established. In a first series of tests, bond strengths of up to 80% of that of resistance welds have been achieved. This paper describes how the authors developed their proposed method of sinter bonding and how they accomplished effective sinter bonds between MIM parts and solid substrates.
Voice conversion by combining frequency warping with unit selection (2008)

In this paper, we propose a novel voice conversion method by combining frequency warping and unit selection to improve the similarity to target speaker. We use frequency warping to get the warped source spectrum, which will be used as estimated target for later unit selection of the target speaker's spectrum. Such estimated target can preserve the natural transition of human's speech. Then, part of the warped source spectrum is replaced by the selected target speaker's real spectrum before reconstructing the converted speech to reduce the difference in detailed spectrum. TC- STAR 2007 voice conversion evaluation results show that the proposed method can achieve about 20% improvement in similarity score compared to only frequency warping.
Long-Range Emergency Preemption of Traffic Lights (2005)

A forwarding system could prove beneficial as an addition to an electronic communication-and-control system that automatically modifies the switching of traffic lights to give priority to emergency vehicles. A system to which the forwarding system could be added could be any of a variety of emergency traffic-signal-preemption systems: these include systems now used in some municipalities as well as advanced developmental systems described in several NASA Tech Briefs articles in recent years. Because of a variety of physical and design limitations, emergency traffic-signal- preemption systems now in use are often limited in range to only one intersection at a time: in a typical system, only the next, closest intersection is preempted for an emergency vehicle. Simulations of gridlock have shown that such systems offer minimal advantages and can even cause additional delays. In analogy to what happens in fluid dynamics, the forwarding system insures that flow at a given location is sustained by guaranteeing downstream flow along the predicted route (typically a main artery) and intersecting routes (typically, side streets). In simplest terms, the forwarding system starts by taking note of any preemption issued by the preemption system to which it has been added. The forwarding system predicts which other intersections could be encountered by the emergency vehicle downstream of the newly preempted intersection. The system then forwards preemption triggers to those intersections. Beyond affording a right of way for the emergency vehicle at every intersection that lies ahead along any likely route from the current position of the vehicle, the forwarding system also affords the benefit of clearing congested roads far ahead of the vehicle. In a metropolitan environment with heavy road traffic, forwarding of preemption triggers could greatly enhance the performance of a pre-existing preemption system.
Square-lattice large-pitch hollow-core photonic crystal fiber (2008)

Large pitch square-lattice hollow core photonic crystal fibers have been fabricated. Measurements show that the fiber exhibits similar optical linear properties to the Kagome fiber.