gebhart/patrepeval huggingface dataset:
A 2‐oxoglutarate‐dependent dioxygenase from <i>Ruta graveolens</i> L. exhibits <i>p‐</i>coumaroyl CoA 2′‐hydroxylase activity (C2′H): a missing step in the synthesis of umbelliferone in plants (2011)

Coumarins are important compounds that contribute to the adaptation of plants to biotic or abiotic stresses. Among coumarins, umbelliferone occupies a pivotal position in the plant phenylpropanoid network. Previous studies indicated that umbelliferone is derived from the ortho-hydroxylation of p-coumaric acid by an unknown biochemical step to yield 2,4-dihydroxycinnamic acid, which then undergoes spontaneous lactonization. Based on a recent report of a gene encoding a 2-oxoglutarate-dependent dioxygenase from Arabidopsis thaliana that exhibited feruloyl CoA 6'-hydroxylase activity (Bourgaud et al., 2006), we combined a bioinformatic approach and a cDNA library screen to identify an orthologous ORF (Genbank accession number JF799117) from Ruta graveolens L. This ORF shares 59% amino acid identity with feruloyl CoA 6'-hydroxylase, was functionally expressed in Escherichia coli, and converted feruloyl CoA into scopoletin and p-coumaroyl CoA into umbelliferone with equal activity. Its bi-functionality was further confirmed in planta: transient expression of JF799117 in Nicotiana benthamiana yielded plants with leaves containing high levels of umbelliferone and scopoletin when compared to control plants, which contained barely detectable traces of these compounds. The expression of JF799117 was also tightly correlated to the amount of umbelliferone that was found in UV-elicited R. graveolens leaves. Therefore, JF799117 encodes a p-coumaroyl CoA 2'-hydroxylase in R. graveolens, which represents a previously uncharacterized step in the synthesis of umbelliferone in plants. Psoralen, which is an important furanocoumarin in R. graveolens, was found to be a competitive inhibitor of the enzyme, and it may exert this effect through negative feedback on the enzyme at an upstream position in the pathway.
Charge inversion by multivalent ions: Dependence on dielectric constant and surface-charge density (2005)

Charge inversion occurs when the effective charge of a surface exposed to solution reverses polarity due to an excess of counterions accumulating in the immediate vicinity of the surface. Using atomic force spectroscopy, we have directly measured the effect on charge inversion of changing the dielectric constant of the solvent and the surface-charge density. Both decreasing the dielectric constant and increasing the bare surface-charge density lower the charge-inversion concentration. These observations are consistent with the theoretical proposal that spatial correlations between ions are the dominant driving mechanism for charge inversion.
Asymmetric gradient boosting with application to spam filtering (2007)

In this paper, we propose a new asymmetric boosting method, Boosting with Different Costs. Traditional boosting methods assume the same cost for misclassified instances from different classes, and in this way focus on good performance with respect to overall accuracy. Our method is more generic, and is designed to be more suitable for problems where the major concern is a low false positive (or negative) rate, such as spam filtering. Experimental results on a large scale email spam data set demonstrate the superiority of our method over state-of-the-art techniques. 1.
Ring-fusion as a perylenediimide dimer design concept for high-performance non-fullerene organic photovoltaic acceptors (2016)

A series of perylenediimide (PDI) dimers are evaluated as acceptors for organic photovoltaic (OPV) cells. The materials are characterized using a wide variety of physical and computational techniques. These dimers are first linked at the bay position of each PDI molecule <i>via</i> an aromatic spacer; subsequent photocyclization affords ring-fused dimers. Thus, photocyclization of the thiophene-linked dimer 2,5-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1-yl]-thiophene (<b>T1</b>) affords the twisted acceptor [2,3-<i>b</i>:2',3'-<i>d</i>]-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1,12-yl]-thiophene (<b>T2</b>), while photocyclization of the thienothiophene-linked dimer, 2,5-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1-yl]-thienothiophene (<b>TT1</b>) affords the planar acceptor [2,3-<i>b</i>:2',3'-<i>d</i>]-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1,12-yl]-thienothiophene (<b>TT2</b>). Furthermore, a dimer linked by a phenylene group, 1,4-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1-yl]-benzene (<b>Ph1</b>), can be selectively photocyclized to form either the twisted dimer, [1,2:3,4]-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1,12-yl]-benzene (<b>Ph1a</b>) or the planar dimer [1,2:4,5]-bis-[<i>N</i>,<i>N</i>'-bis-perylenediimide-1,12-yl]-benzene (<b>Ph2b</b>). Ring-fusion results in increased electronic coupling between the PDI units, and increased space-charge limited thin film electron mobility. While charge transport is efficient in bulk-heterojunction blends of each dimer with the polymeric donor <b>PBDTT-FTTE</b>, in the case of the twisted dimers ring fusion leads to a significant decrease in geminate recombination, hence increased OPV photocurrent density and power conversion efficiency. This effect is not observed in planar dimers where ring fusion leads to increased crystallinity and excimer formation, decreased photocurrent density, and decreased power conversion efficiency. These results argue that ring fusion is an effective approach to increasing OPV bulk-heterojunction charge carrier generation efficiency in PDI dimers as long as they remain relatively amorphous, thereby suppressing excimer formation and coulombically trapped charge transfer states.
<scp>l</scp>-Arginine infusion increases glucose clearance during prolonged exercise in humans (2005)

Nitric oxide synthase (NOS) inhibition has been shown in humans to attenuate exercise-induced increases in muscle glucose uptake. We examined the effect of infusing the NO precursor L-arginine (L-Arg) on glucose kinetics during exercise in humans. Nine endurance-trained males cycled for 120 min at 72+/-1% Vo(2 peak) followed immediately by a 15-min "all-out" cycling performance bout. A [6,6-(2)H]glucose tracer was infused throughout exercise, and either saline alone (Control, CON) or saline containing L-Arg HCL (L-Arg, 30 g at 0.5 g/min) was confused in a double-blind, randomized order during the last 60 min of exercise. L-Arg augmented the increases in glucose rate of appearance, glucose rate of disappearance, and glucose clearance rate (L-Arg: 16.1+/-1.8 ml.min(-1).kg(-1); CON: 11.9+/- 0.7 ml.min(-1).kg(-1) at 120 min, P<0.05) during exercise, with a net effect of reducing plasma glucose concentration during exercise. L-Arg infusion had no significant effect on plasma insulin concentration but attenuated the increase in nonesterified fatty acid and glycerol concentrations during exercise. L-Arg infusion had no effect on cycling exercise performance. In conclusion, L-Arg infusion during exercise significantly increases skeletal muscle glucose clearance in humans. Because plasma insulin concentration was unaffected by L-Arg infusion, greater NO production may have been responsible for this effect.
Analysis of Signalling Pathways by Western Blotting and Immunoprecipitation (2011)

This chapter describes the analysis of signaling pathways in bone cells by the use of western blotting and immunoprecipitation, including a step-by-step guide to cell culture techniques, cellular and subcellular fractionation, protein isolation, purification, measurement, electrophoretic transfer, and detection.
Phenalenones. IV. Heterocycles from 3‐hydroxyphenalenone (I) (1981)

Abstract 3‐Hydroxyphenalenone reacts with o ‐disubstituted benzenes (substituents: NH 2 , OH, CH 2 OH and SH), aliphatic and aromatic aldehydes to give the various heterocyclic compounds which are fused with phenalene ring. These reactions resemble those of 1,3‐cyclohexanediones in many respects.
Optical decoherence and spectral diffusion at<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mn>1.5</mml:mn><mml:mspace width="0.3em"/><mml:mi>μ</mml:mi><mml:mi mathvariant="normal">m</mml:mi></mml:mrow></mml:math>in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mi>Er</mml:mi><mml:mrow><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup><mml:mo>:</mml:mo><mml:msub><mml:mi mathvariant="normal">Y</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi>SiO</mml:mi><mml:mn>5</mml:mn></mml:msub></mml:mrow></mml:math>versus magnetic field, temperature, and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mi>Er</mml:mi><mml:mrow><mml:mn>3</mml:mn><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>concentration (2006)

The mechanisms and effects of spectral diffusion for optical transitions of paramagnetic ions have been explored using the inhomogeneously broadened 1536 nm $^{4}\mathrm{I}_{15∕2}\ensuremath{\rightarrow}^{4}\mathrm{I}_{13∕2}$ transition in ${\mathrm{Er}}^{3+}:{\mathrm{Y}}_{2}{\mathrm{SiO}}_{5}$. Using photon echo spectroscopy, spectral diffusion was measured by observing the evolution of the effective coherence lifetimes over time scales from $1\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{s}$ to 20 ms for magnetic-field strengths from 0.3 to 6.0 T, temperatures from 1.6 to 6.5 K, and nominal ${\mathrm{Er}}^{3+}$ concentrations of 0.0015%, 0.005%, and 0.02%. To understand the effect of spectral diffusion on material decoherence for different environmental conditions and material compositions, data and models were compared to identify spectral diffusion mechanisms and microscopic spin dynamics. Observations were successfully modeled by ${\mathrm{Er}}^{3+}\ensuremath{-}{\mathrm{Er}}^{3+}$ magnetic dipole interactions and ${\mathrm{Er}}^{3+}$ electron spin flips driven by the one-phonon direct process. At temperatures of 4.2 K and higher, spectral diffusion due to $^{89}\mathrm{Y}$ nuclear spin flips was also observed. The success in describing our extensive experimental results using simple models provides an important capability for exploring larger parameter spaces, accelerating the design and optimization of materials for spatial-spectral holography, and spectral hole-burning devices. The broad insight into spectral diffusion mechanisms and dynamics is applicable to other paramagnetic materials, such as those containing ${\mathrm{Yb}}^{3+}$ or ${\mathrm{Nd}}^{3+}$.
A technique for micro-rollback self-recovery synthesis (1995)

The problem and efficient solution of automated synthesis of a self-recovery chip using micro-rollback and checkpoint insertion techniques are proposed and discussed. An efficient design of micro-rollback and checkpoint insertion can be achieved by considering them during the scheduling and allocation steps. The rollback and recovery scheme is designed to satisfy the constraints on the number of registers available and the maximum allowable recovery time. The proposed checkpointing (rollback point) algorithm will allow the system to recover from most transient faults.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A ZigBee honeypot to assess IoT cyberattack behaviour (2017)

Wireless Personal Area Networks (WPAN) allow for the implementation of applications such as home automation, remote control services, near-field technologies and personal health care management. Security is a critical requirement of the standards and protocols for these environments. One suite of layered protocols within WPAN is ZigBee. ZigBee is a low bit rate protocol utilised in Wireless Sensor Networks (WSN). Attacks such as physical, crypto key interception, injection and replay are perpetrated on ZigBee networks. These attacks can be instigated and controlled within the physical ZigBee WSN location or via a gateway. This paper creates a honeypot that simulates a ZigBee gateway. It is designed to assess the presence of ZigBee attack intelligence on a SSH attack vector. It captures all attack traffic for retrospective analysis. It sandboxes attacks of interest to determine if any attempts are targeting ZigBee specifically. Finally it concludes that all captured mass attacks are mainstream DDoS and bot malware, whereas individual attackers where attracted to and interacted with the ZigBee simulated Honeypot.
A comparison of methods for mammogram registration (2003)

Mammogram registration is an important technique to optimize the display of cases on a digital viewing station, and to find corresponding regions in temporal pairs of mammograms for computer-aided diagnosis algorithms. Four methods for mammogram registration were tested and results were compared. The performance of all registration methods was measured by comparing the distance between annotations of abnormalities in the previous and current view before and after registration. Registration by mutual information outperformed alignment based on nipple location, alignment based on center of mass of breast tissue, and warping.
Theory of order statistic filters and their relationship to linear FIR filters (1989)

Necessary and/or sufficient conditions on both the filter coefficients and the signal process are derived in order that nonrecursive order statistic (OS) and linear filtering are equivalent operations. The results indicate that an understanding of OS filters hinges on a better understanding of the properties of signals containing logically monotonic components. The results extend a number of previous theories characterizing the well-known median and ranked-order filters to a broader class of filters and input signals.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Some cortical spiking neuron models using CNN (2002)

In this paper we show cellular neural network (CNN) models of some basic types of cells characterised by diverse spiking patterns. After showing some preliminary models (ion channels, neurons), CNN models of the action potential generation are given followed by an analysis of the rate coding capabilities of the models. Furthermore, CNN models of neurons with diverse intrinsic firing patterns are presented followed by some conclusions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Broad‐host range expression vectors containing manipulated <i>meta</i>‐cleavage pathway regulatory elements of the TOL plasmid (1988)

The construction of pERD20 and pERD21, two broad-host range expression vectors, is described. The vectors contain the Pm promoter of the meta-cleavage pathway operon of the TOL plasmid pWWO; this promoter is present within a polylinker which provides a number of downstream cloning sites close to the transcription initiation site. Transcription from the Pm promoter in these vectors is controlled not by the natural positive regulator of Pm, the Xy1S protein, but by an Xy1S mutant analogue, Xy1S2tr6, which inhibits an altered effector specificity and can mediate a 3-8-fold higher level of transcription than can Xy1S in a wide range of temperatures. Controlled expression of cloned genes can be achieved in a broad spectrum of Gram negative bacteria grown at a wide range of temperatures.
Multi-channel OSNR monitoring for WDM networks (2002)

The advantages of adding polarization analysis to the conventional methods for monitoring the performance of WDM systems are discussed. Measurements on a 600 km commercial WDM system performed with a wavelength selective polarimeter are presented
Well-Test Optimization and Automation (2006)

Abstract Much can be done to improve the Well Testing through effective use of minimal electronic instrumentation on the well head and the test separator. The purpose of this paper is to describe Shell tools and experiences using the resulting real time data to enable well test optimization and automation.
Artificial Intelligence (2010)

Recent decades have witnessed the emergence of artificial intelligence as a serious science and engineering discipline. This textbook, aimed at junior to senior undergraduate students and first-year graduate students, presents artificial intelligence (AI) using a coherent framework to study the design of intelligent computational agents. By showing how basic approaches fit into a multidimensional design space, readers can learn the fundamentals without losing sight of the bigger picture. The book balances theory and experiment, showing how to link them intimately together, and develops the science of AI together with its engineering applications. Although structured as a textbook, the book's straightforward, self-contained style will also appeal to a wide audience of professionals, researchers, and independent learners. AI is a rapidly developing field: this book encapsulates the latest results without being exhaustive and encyclopedic. The text is supported by an online learning environment, AIspace, http://aispace.org, so that students can experiment with the main AI algorithms plus problems, animations, lecture slides, and a knowledge representation system, AIlog, for experimentation and problem solving.
Diode lasers emitting near 3.44 µm in continuous-wave regime at 300K (2010)

A continuous-wave, room temperature operation of type-I quantum well diode lasers was extended above 3.4 µm. The laser heterostructure, optimised for minimum threshold carrier concentration, was pseudomorphically grown by solid source molecular beam epitaxy on GaSb. Multimode lasers generate 29 mW of output power at 17 °C.
Network QoS Management in Cyber-Physical Systems (2008)

Technical advances in ubiquitous sensing, embedded computing, and wireless communication are leading to a new generation of engineered systems called cyber-physical systems (CPS). CPS promises to transform the way we interact with the physical world just as the Internet transformed how we interact with one another. Before this vision becomes a reality, however, a large number of challenges have to be addressed. Network quality of service (QoS) management in this new realm is among those issues that deserve extensive research efforts. It is envisioned that wireless sensor/actuator networks (WSANs) will play an essential role in CPS. This paper examines the main characteristics of WSANs and the requirements of QoS provisioning in the context of cyber-physical computing. Several research topics and challenges are identified. As a sample solution, a feedback scheduling framework is proposed to tackle some of the identified challenges. A simple example is also presented that illustrates the effectiveness of the proposed solution.
Evaluation of the Firmness Measurement of Fruit by Using a Non–contact Ultrasonic Technique (2013)

In this study, we investigated the feasibility of using a novel non-contact ultrasonic technique to measure fruit firmness. The intensity of the reflected ultrasonic signal that bounces back from the fruit surface is dependent on the firmness of the fruit surface. However, differences in fruit size cause the reflected intensity to change with the distance separating the non-contact ultrasonic transducer and fruit surface. Therefore, it is necessary to eliminate the effect of fruit size on signal intensity to accurately predict fruit firmness when using a reflected ultrasonic signal. In this study, we developed and evaluated distance correction factors, which may reduce the size effects of fruit on the reflected ultrasonic signal. The distance correction factors were proposed using a combination of ultrasonic parameters obtained from the first and second reflected ultrasonic signals in the time and frequency domain. Fruit firmness parameters, such as bioyield strength and apparent elastic modulus, were measured and correlated with the distance corrected non-contact ultrasonic parameters. Multiple linear regression models to predict fruit firmness using ultrasonic parameters were assessed. The results demonstrated the potential utility of the distance corrected non-contact ultrasonic technique for the non-destructive measurement of fruit firmness.
Mitochondrial autophagy by Bnip3 involves Drp1-mediated mitochondrial fission and recruitment of Parkin in cardiac myocytes (2011)

The Bcl2/adenovirus E1B 19-kDa interacting protein 3 (Bnip3) is an atypical BH3-only protein that is associated with mitochondrial dysfunction and cell death. Bnip3 is also a potent inducer of mitochondrial autophagy, and in this study we have investigated the mechanisms by which Bnip3 induces autophagy in cardiac myocytes. We found that Bnip3 induced mitochondrial translocation of dynamin-related protein 1 (Drp1), a protein involved in mitochondrial fission in adult myocytes. Drp1-mediated mitochondrial fission correlated with increased autophagy, and inhibition of Drp1 reduced Bnip3-mediated autophagy. Overexpression of Drp1K38E, a dominant negative of Drp1, or mitofusin 1 prevented mitochondrial fission and autophagy by Bnip3. Also, inhibition of mitochondrial fission or autophagy resulted in increased death of myocytes overexpressing Bnip3. Moreover, Bnip3 promoted translocation of the E3 ubiquitin ligase Parkin to mitochondria, which was prevented in the presence of a Drp1 inhibitor. Interestingly, induction of autophagy by Bnip3 was reduced in Parkin-deficient myocytes. Thus our data suggest that induction of autophagy in response to Bnip3 is a protective response activated by the cell that involves Drp1-mediated mitochondrial fission and recruitment of Parkin.
Partitioning of Hydrophobic Organic Compounds to Sorbed Surfactants. 2. Model Development/Predictions for Surfactant-Enhanced Remediation Applications (1998)

A one-dimensional numerical model was developed to simulate the performance of surfactant-enhanced remediation (SER) applications for saturated subsurface systems containing adsorbed hydrophobic organic compounds (HOCs). The model incorporates temporally and spatially dependent HOC and surfactant mass balance equations to compute distributions in the aqueous, micellar, sorbed surfactant, and subsurface solid phases. In particular, the model accounts for losses of surfactant by sorption to the subsurface media and for the subsequent partitioning of HOCs to sorbed surfactant. Parameter values for the model were estimated from experimental rate and equilibrium data from the literature, and sensitivity analysis was conducted to evaluate the model performance and potential SER applications. Simulation results show that the relative affinity of HOCs and surfactants for the immobile subsurface solid phase (i.e., the respective retardation factors) is critical for determining whether contaminant desorption can be enhanced by surfactants. For example, under the conditions simulated here, removal of phenanthrene and naphthalene from a representative sandy (i.e., low organic carbon) aquifer is actually hindered by flushing with surfactant solutions, whereas for more hydrophobic contaminants (e.g., pyrene) surfactant addition can enhance HOC removal. Likewise, an increase in the organic carbon content of the subsurface solid phase increases the effectiveness of SER processes. The important rate and equilibrium model parameters evaluated in this study provide useful guidelines for the design and application of SER processes for contaminated subsurface systems and for interpreting SER-related studies.