gebhart/patrepeval huggingface dataset:
Time-Resolved Imaging of VLSI Circuits Using a Single-Point Single-Photon Detector and a Scanning Head (2019)

Abstract In this paper, we present the first prototype of a Scanning Time-Resolved Emission (STRE) system consisting of a high-sensitivity, low-noise, and low-jitter single-point Superconducting Single-Photon Detector (SSPD) combined with a specialized scanning head of a Laser Scanning Microscope (LSM). This idea was first proposed in late 2006 [1] but required the right combination of detector, customization, and collaboration with a tool vendor to get to fruition. It should be understood that this is still a prototype system under development and significant improvements in acquisition time, resolutions, and performance are expected in the near future. In this paper, we will also present the first preliminary results acquired using a test chip fabricated in 32 nm SOI.
An intravenous (i.v.) route-compatible formulation of FL118, a survivin, Mcl-1, XIAP, and cIAP2 selective inhibitor, improves FL118 antitumor efficacy and therapeutic index (TI). (2013)

We recently reported a novel anticancer small molecule, designated FL118, which was discovered via high throughput screening (HTS), and followed by hit-lead in vitro and in vivo analysis. FL118 selectively inhibits the expression of four major cancer survival-associated gene products (survivin, Mcl-1, XIAP, and cIAP2) and shows promising antitumor activity in animal models of human cancers when administered using a weekly x 4 schedule (Ling et al., PLOS ONE. 2012, 7: e45571). Here, we compared the antitumor efficacy and therapeutic index (TI) of FL118 in a newly developed Tween 80-free formulation that can be delivered intravenously (i.v.) and intraperitoneally (i.p.) against the previous Tween 80-containing formulation that can only be delivered via an i.p. route. We found that the maximum tolerated dose (MTD) for FL118 in the i.v. formulation increases 3-7 fold in comparison with the MTD of FL118 in the i.p. formulation. FL118 in the i.v. recipe was able to eliminate human tumor xenografts in all three major schedules tested (daily x 5, q2 x 5 and weekly x 5). In contrast, FL118 was able to eliminate human tumor xenografts in the i.p. formulation only with the weekly x 4 schedule previously reported. The TI of FL118 in the i.v. formulation reached 5-6 in the most effective schedule, while the TI of FL118 in the i.p. formulation was only 1.3 - 2. These findings overcome several clinical challenges including FL118 formulation to realize clinically compatible drug administration routes, and expanding effective treatment schedules. The striking improvement of the TI makes FL118 a much safer drug for further development toward clinical trials.
Micromachined infrared sensors using tunneling displacement transducers (1996)

Uncooled infrared sensors are important for a number of technological and scientific measurements. We have designed, built, and tested a new uncooled infrared sensor which is made by silicon micromachining. This infrared sensor uses a tunneling displacement transducer to detect the thermal expansion of a small volume of trapped gas. Prototype devices based on this design have been operated with NEP better than 3×10−10 W/√Hz at 25 Hz, which is competitive with the best comparably sized uncooled sensors available. This article will describe the design, fabrication, and operation of all elements of this sensor.
Current Mode Image Sensor With Two Transistors per Pixel (2009)

A linear current mode active pixel sensor for low fixed-pattern noise imaging is presented. The photo pixel is composed of a photodiode, a reset transistor, and a transconductance amplifier transistor. The address switch transistor is placed outside the pixel. The increased linearity of the pixel current coupled with current mode difference double sampling greatly reduces spatial variations across the image sensor array. The fabricated image sensor is composed of an array of 50 × 128 pixels and consumes 5 mW at 30 fps. Column fixed pattern noise of 0.1% from the saturated current and signal to noise ratio of 43.3 dB is achieved.
DNA protecting and genotoxic effects of olive oil related components in cells exposed to hydrogen peroxide (2005)

In search for compounds, able to protect nuclear DNA in cells exposed to oxidative stress, extracts from olive leaves, olive fruits, olive oil and olive mill waste water were tested by using the "single cell gel electrophoresis" methodology (comet assay). Jurkat cells in culture were exposed to continuously generated hydrogen peroxide (11.8+/-1.5 microM per min) by direct addition into the growth medium of the appropriate amount of the enzyme "glucose oxidase" in the presence or absence of the tested total extracts. The protective effects of the tested extracts or isolated compounds were evaluated from their ability to decrease hydrogen peroxide-induced formation of single strand breaks in the nuclear DNA, while the toxic effects were estimated from the increase of DNA damage when the extracts or isolated compounds were incubated directly with the cells. Significant protection was observed in extracts from olive oil and olive mill waste water. However, above a concentration of 100 microg/ml olive oil extracts exerted DNA damaging effects by themselves in the absence of any H2O2. Extracts from olive leaves and olive fruits although protective, were also able to induce DNA damage by themselves. Main compounds isolated from the above described total extracts, like oleuropein glucoside, tyrosol, hydroxytyrosol and caffeic acid, were tested in the same experimental system and found to exert cytotoxic (oleuropein glucoside), no effect (tyrosol) or protective effects (hydroxytyrosol and caffeic acid). In conclusion, cytoprotective as well as cytotoxic compounds with potential pharmaceutical properties were detected in extracts from olive oil related sources by using the comet assay methodology.
A Power–Frequency Controller for Bidirectional Inductive Power Transfer Systems (2011)

Inductive power transfer (IPT) technology is a well-recognized technique for supplying power to a wide range of applications with no physical contacts. With the emergence of applications such as electric vehicles and vehicle-to-grid systems, IPT systems with bidirectional power flow have become a recent focus. In contrast to simple unidirectional IPT systems, bidirectional systems are complex in nature and essentially require more sophisticated and robust control strategies. This paper proposes a new controller, which is based on power-frequency droop characteristics of IPT systems, to regulate its power flow in both directions without a dedicated communication link. The proposed controller is applicable to unidirectional as well as bidirectional IPT systems with either single or multiple loads and ensures that power intake by the load side is always kept within the capability of the supply side. Analysis, together with both experimental and simulated results, of a 1-kW single-load bidirectional IPT system is presented with discussions to show that the proposed droop controller can successfully be used to regulate the two-way power flow.
Transmembrane Topology of Glucose-6-Phosphatase (1998)

Deficiency of microsomal glucose-6-phosphatase (G6Pase), the key enzyme in glucose homeostasis, causes glycogen storage disease type 1a, an autosomal recessive disorder. Characterization of the transmembrane topology of G6Pase should facilitate the identification of amino acid residues contributing to the active site and broaden our understanding of the effects of mutations that cause glycogen storage disease type 1a. Using N- and C-terminal tagged G6Pase, we show that in intact microsomes, the N terminus is resistant to protease digestion, whereas the C terminus is sensitive to such treatment. Our results demonstrate that G6Pase possesses an odd number of transmembrane helices, with its N and C termini facing the endoplasmic reticulum lumen and the cytoplasm, respectively. During catalysis, a phosphoryl-enzyme intermediate is formed, and the phosphoryl acceptor in G6Pase is a His residue. Sequence alignment suggests that mammalian G6Pases, lipid phosphatases, acid phosphatases, and a vanadium-containing chloroperoxidase (whose tertiary structure is known) share a conserved phosphatase motif. Active-site alignment of the vanadium-containing chloroperoxidase and G6Pases predicts that Arg-83, His-119, and His-176 in G6Pase contribute to the active site and that His-176 is the residue that covalently binds the phosphoryl moiety during catalysis. This alignment also predicts that Arg-83, His-119, and His-176 reside on the same side of the endoplasmic reticulum membrane, which is supported by the recently predicted nine-transmembrane helical model for G6Pase. We have previously shown that Arg-83 is involved in positioning the phosphate during catalysis and that His-119 is essential for G6Pase activity. Here we demonstrate that substitution of His-176 with structurally similar or dissimilar amino acids inactivates the enzyme, suggesting that His-176 could be the phosphoryl acceptor in G6Pase during catalysis.
Edge effects on PN code chip time tracking loop with smart antenna (2003)

This paper employs a smart antenna algorithm to improve pseudonoise (PN) code chip time tracking loop (PNCTL), and analyzes its root-mean-square-chip-time-jitter (RMS) for a third generation (3G) wideband code division multiple access wireless communications system (W-CDMA). The edge effect may happen frequently in a mobile environment and causes a sudden change in the direction of arrival angle (DOA) at a receiver when a transmitter moves around a building corner. The objective of this paper is to analyze the edge effect on the RMS performance of the PNCTL with a smart antenna. This paper concludes that the smart antenna can still significantly improve the PNCTL performance even under realistic edge effect and mobile fading environments.
Joint inter-intra prediction based on mode-variant and edge-directed weighting approaches in video coding (2014)

Most modern video compression codecs, like VP9, HEVC and H.264, encode square or rectangular blocks either by inter prediction or intra prediction. A joint inter-intra predictor that combines motion compensation and intra extrapolation by two novel weighting schemes is proposed to improve compression quality. Prior work on joint prediction employs inter-intra weights that only rely on the pixel locations. As an enhancement, we design a weighting approach by also considering the angle of intra prediction, which is the actual direction that the intra prediction errors evolve. Moreover, our second approach, inspired by prior work on geometric-partition-based motion compensation, breaks the limitation of traditional quad-tree partition by jointly using different predictors that implies soft step weighting functions for new and existing objects co-occurring around irregular motion edges. The proposed joint prediction approaches deliver consistent coding gains, as shown by extensive experiments on the experimental branch of VP9, Google's open source video compression tool.
NASA PS400: A New Temperature Solid Lubricant Coating for High Temperature Wear Applications (2009)

A new solid lubricant coating, NASA PS400, has been developed for high temperature tribological applications. This plasma sprayed coating is a variant of the patented PS304 coating and has been formulated to provide higher density, smoother surface finish and better dimensional stability than PS304. PS400 is comprised of a nickel-molybdenum binder that provides strength, creep resistance and extreme oxidative and dimensional stability. Chromium oxide, silver and barium-calcium fluoride eutectic are added to the binder to form PS400.Tribological properties were evaluated with a pin-on-disk test rig in sliding contact to 650 C. Coating material samples were exposed to air, argon and vacuum at 760 C followed by cross section microscopic analysis to assess microstructure stability. Oil-Free microturbine engine hot section foil bearing tests were undertaken to assess PS400 s suitability for hot foil gas bearing applications. The preliminary results indicate that PS400 exhibits tribological characteristics comparable to the PS304 coating but with enhanced creep resistance and dimensional stability suitable for demanding, dynamic applications.
Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors (2015)

Tankyrase activity has been linked to the regulation of intracellular axin levels, which have been shown to be crucial for the Wnt pathway. Deregulated Wnt signaling is important for the genesis of many diseases including cancer. We describe herein the discovery and development of a new series of tankyrase inhibitors. These pyranopyridones are highly active in various cell-based assays. A fragment/structure based optimization strategy led to a compound with good pharmacokinetic properties that is suitable for in vivo studies and further development.
Synthesis of a Specified, Silica Molecular Sieve by Using Computationally Predicted Organic Structure‐Directing Agents (2014)

Abstract Crystalline molecular sieves are used in numerous applications, where the properties exploited for each technology are the direct consequence of structural features. New materials are typically discovered by trial and error, and in many cases, organic structure‐directing agents (OSDAs) are used to direct their formation. Here, we report the first successful synthesis of a specified molecular sieve through the use of an OSDA that was predicted from a recently developed computational method that constructs chemically synthesizable OSDAs. Pentamethylimidazolium is computationally predicted to have the largest stabilization energy in the STW framework, and is experimentally shown to strongly direct the synthesis of pure‐silica STW. Other OSDAs with lower stabilization energies did not form STW. The general method demonstrated here to create STW may lead to new, simpler OSDAs for existing frameworks and provide a way to predict OSDAs for desired, theoretical frameworks.
Relational time series forecasting (2018)

Abstract Networks encode dependencies between entities (people, computers, proteins) and allow us to study phenomena across social, technological, and biological domains. These networks naturally evolve over time by the addition, deletion, and changing of links, nodes, and attributes. Despite the importance of modeling these dynamics, existing work in relational machine learning has ignored relational time series data . Relational time series learning lies at the intersection of traditional time series analysis and statistical relational learning, and bridges the gap between these two fundamentally important problems. This paper formulates the relational time series learning problem, and a general framework and taxonomy for representation discovery tasks of both nodes and links including predicting their existence, label, and weight (importance), as well as systematically constructing features. We also reinterpret the prediction task leading to the proposal of two important relational time series forecasting tasks consisting of (i) relational time series classification (predicts a future class or label of an entity), and (ii) relational time series regression (predicts a future real-valued attribute or weight). Relational time series models are designed to leverage both relational and temporal dependencies to minimize forecasting error for both relational time series classification and regression. Finally, we discuss challenges and open problems that remain to be addressed.
Signal classification in digital telephone networks (2002)

This paper considers the problem of classifying voice-band data, facsimile, and speech signals, using discriminant functions that are extensions of those described by Benvenuto (see IEEE Trans. on Commun., vol.41, no.4, p.539, 1993). Both the central second-order moment of the rectified signal, and the low order lags of the estimated autocorrelation sequence are computed. These discriminants are used to perform classification in 128 ms. with 0% misclassification for most signal types considered. Algorithm enhancements improve classification performance, reduce computational complexity, and extend the voice-band data subclassification abilities.
Highly Conformal Thin Films of Tungsten Nitride Prepared by Atomic Layer Deposition from a Novel Precursor (2003)

Highly uniform, smooth, and conformal coatings of tungsten nitride were synthesized by atomic layer deposition (ALD) from vapors of a novel precursor, bis(tert-butylimido)-bis(dimethylamido)tungsten, (tBuN)2(Me2N)2W, and ammonia at low substrate temperatures (250−350 °C). This tungsten precursor is a low-viscosity, noncorrosive liquid with sufficient volatility at room temperature to be a vapor source for ALD. These vapors were alternately pulsed into a heated reactor, yielding up to 0.1 nm of tungsten nitride film for every cycle, with no initial delay or induction period. The films were uniform in thickness along the 20-cm length of the deposition zone, as determined by scanning electron microscopy. Successful depositions were carried out on all substrates tested, including silicon, glass, quartz, glassy carbon, stainless steel, aluminum, gold, and copper. The films are shiny, silver-colored, and electrically conducting. All of the films showed good adhesion to the substrates, were acid-resistant, and did not oxidize over time. The stoichiometry of the WN films was determined to be 1:1 by Rutherford backscattering spectrometry. The films were amorphous as-deposited, as shown by X-ray diffraction and high-resolution transmission electron microscopy. 100% step coverage was obtained inside holes with aspect ratios greater than 200:1. Annealing for 30 min at temperatures above 725 °C converted the WN to pure, polycrystalline tungsten metal. WN films as thin as 1.5 nm proved to be good barriers to diffusion of copper for temperatures up to 600 °C. ALD of copper onto the surface of the WN produced strongly adherent copper films that could be used as “seed” layers for chemical vapor deposition (CVD) or electrodeposition of thicker copper coatings.
Hierarchical Distributed Voltage Regulation in Networked Autonomous Grids (2018)

We propose a novel algorithm to solve optimal power flow (OPF) that aims at dispatching controllable distributed energy resources (DERs) for voltage regulation at minimum cost. The proposed algorithm features unprecedented scalability to large distribution networks by utilizing an information structure based on networked autonomous grids (AGs). Specifically, each AG is a subtree of a large distribution network that has a tree topology. The topology and line parameters of each AG are known only to a regional coordinator (RC) that is responsible for communicating with and dispatching the DERs within this AG. The reduced network, where each AG is treated as a node, is managed by a central coordinator (CC), which knows the topology and line parameters of the reduced network only and communicates with all the RCs. We jointly explore this information structure and the structure of the linearized distribution power flow (LinDistFlow) model to derive a hierarchical, distributed implementation of the primal-dual gradient algorithm that solves the OPF. The proposed implementation significantly reduces the computation burden compared to the centrally coordinated implementation of the primal-dual algorithm. Numerical results on a 4,521-node test feeder show that the proposed hierarchical distributed algorithm can achieve an improvement of more than tenfold in the speed of convergence compared to the centrally coordinated primal-dual algorithm.
<title>Novel methods of analyzing radio-frequency echo signals for the purpose of imaging brachytherapy seeds used to treat prostate cancer</title> (2002)

Brachytherapy using small implanted radioactive seeds is becoming an increasingly popular method for treating prostate cancer. Seeds are inserted into the prostate transperineally using ultrasound guidance. Dosimetry software determines the optimal placement of seeds for achieving the prescribed dose based on ultrasonic determination of the gland boundaries. However, because of prostate movement after planning images are acquired and during the implantation procedure, seeds commonly are not placed in the desired locations and the delivered dose may differ from the prescribed dose. Current methods of ultrasonic imaging do not adequately display implanted seeds for the purpose of correcting the delivered dose. We are investigating new methods of ultrasonic imaging that overcome limitations of conventional ultrasound. These methods include resonance, modified elastographic, and signature techniques. Each method shows promise for enhancing the visibility of seeds in ultrasound images. Combining the information provided by each method may reduce ambiguities in determining where seeds are present or absent. If successful, these novel imaging methods will enable correction of seed-misplacement errors during the implantation procedure, and hence will improve the therapeutic radiation dose delivered to target tissues.
MEC: Memory-efficient Convolution for Deep Neural Network. (2017)

Convolution is a critical component in modern deep neural networks, thus several algorithms for convolution have been developed. Direct convolution is simple but suffers from poor performance. As an alternative, multiple indirect methods have been proposed including im2col-based convolution, FFT-based convolution, or Winograd-based algorithm. However, all these indirect methods have high memory-overhead, which creates performance degradation and offers a poor trade-off between performance and memory consumption. In this work, we propose a memory-efficient convolution or MEC with compact lowering, which reduces memory-overhead substantially and accelerates convolution process. MEC lowers the input matrix in a simple yet efficient/compact way (i.e., much less memory-overhead), and then executes multiple small matrix multiplications in parallel to get convolution completed. Additionally, the reduced memory footprint improves memory sub-system efficiency, improving performance. Our experimental results show that MEC reduces memory consumption significantly with good speedup on both mobile and server platforms, compared with other indirect convolution algorithms.
Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6 (2016)

There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50-70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.