gebhart/patrepeval huggingface dataset:
Dual Mechanisms Regulating AMPK Kinase Action in the Ischemic Heart (2005)

AMP-activated protein kinase (AMPK) is emerging as an important signaling protein during myocardial ischemia. AMPK is a heterotrimeric complex containing an alpha catalytic subunit and beta and gamma regulatory subunits. Phosphorylation of Thr172 in the activation loop of the alpha subunit by upstream AMPK kinase(s) (AMPKK) is a critical determinant of AMPK activity. However, the mechanisms regulating AMPK phosphorylation in the ischemic heart remain uncertain and were therefore investigated. In the isolated working rat heart, low-flow ischemia rapidly activated AMPKK activity when measured using recombinant AMPK (rAMPK) as substrate. The addition of AMP (10 to 200 micromol/L) augmented the ability of heterotrimeric alpha1beta1gamma1 or alpha2beta1gamma1 rAMPK to be phosphorylated by heart AMPKK in vitro, whereas physiologic concentrations of ATP inhibited rAMPK phosphorylation. However, neither AMP nor ATP directly influenced AMPKK activity: they had no effect on AMPKK-mediated phosphorylation of rAMPK substrates lacking normal AMP-binding gamma subunits (isolated truncated alpha1(1-312) or alpha1beta1gamma1 rAMPK containing an R70Q mutation in the gamma1 AMP-binding site). Regional ischemia in vivo also increased AMPKK activity and AMPK phosphorylation in the rat heart. AMPK phosphorylation could also be induced in vivo without activating AMPKK: AICAR infusion increased AMPK phosphorylation without activating AMPKK; however, the AMP-mimetic AICAR metabolite ZMP enhanced the ability of heterotrimeric rAMPK to be phosphorylated by AMPKK. Thus, heart AMPKK activity is increased by ischemia and its ability to phosphorylate AMPK is highly modulated by the interaction of AMP and ATP with the heterotrimeric AMPK complex, indicating that dual mechanisms regulate AMPKK action in the ischemic heart.
Extracellular recombinant protein production from an <i>Escherichia coli lpp</i> deletion mutant (2008)

E. coli is one of the most commonly used host strains for recombinant protein production. However, recombinant proteins are usually found intracellularly, in either cytoplasm or periplasmic space. Inadequate secretion to the extracellular environment is one of its limitations. This study addresses the outer membrane barrier for the translocation of recombinant protein directed to the periplasmic space. Specifically, using recombinant maltose binding protein (MalE), xylanase, and cellulase as model proteins, we investigated whether the lpp deletion could render the outer membrane permeable enough to allow extracellular protein production. In each case, significantly higher excretion of recombinant protein was observed with the lpp deletion mutant. Up to 90% of the recombinant xylanase activity and 70% of recombinant cellulase activity were found in the culture medium with the deletion mutant, whereas only 40-50% of the xylanase and cellulase activities were extracellular for the control strain. Despite the weakened outer membrane in the mutant strain, cell lysis did not occur, and increased excretion of periplasmic protein was not due to cell lysis. The lpp deletion is a simple method to generate an E. coli strain to effect significant extracellular protein production. The phenotype of extracellular protein production without cell lysis is useful in many biotechnological applications, such as bioremediation and plant biomass conversion.
CLASS IDENTIFICATION OF BIO-MOLECULES BASED ON MULTI-COLOR NATIVE FLUORESCENCE SPECTROSCOPY (2007)

Laser-induced native fluorescence is measured on a set of bio-molecules from different classes (bacteria, proteins, fungi) for excitation at 266nm and 355nm. A method of preprocessing the spectra to obtain an inherently normalized set of data is described. Class identification on the normalized data set is demonstrated.
Determination of the transcriptome of <i>Vibrio cholerae</i> during intraintestinal growth and midexponential phase <i>in vitro</i> (2003)

Vibrio cholerae is the etiologic bacterial agent of cholera, a severe diarrheal disease endemic in much of the developing world. The V. cholerae genome contains 3,890 genes distributed between a large and a small chromosome. Although the large chromosome encodes the majority of recognizable gene products and virulence determinants, the small chromosome carries a disproportionate number of hypothetical genes. Thus, little is known about the role of the small chromosome in the biology of this organism or other Vibrio species. We have used the rabbit ileal loop model of V. cholerae infection to obtain in vivo-grown cells under near midexponential conditions in the small-intestinal environment. We compared the global transcriptional pattern of these in vivo-grown cells to those grown to midexponential phase in rich medium under aerobic conditions. Under both conditions, the genes showing the highest levels of expression reside primarily on the large chromosome. However, a shift occurs in vivo that results in many more small chromosomal genes being expressed during growth in the intestine. Our analysis further suggests that nutrient limitation (particularly iron) and anaerobiosis are major stresses experienced by V. cholerae during growth in the rabbit upper intestine. Finally, relative to in vitro growth, the intestinal environment significantly enhanced expression of several virulence genes, including those involved in phenotypes such as motility, chemotaxis, intestinal colonization, and toxin production.
Anti-glycation defences in yeast (2003)

Saccharomyces cerevisiae is an outstanding cellular model for metabolic studies in glycation. Due to its high glycolytic activity, it produces methylglyoxal, a highly reactive intracellular glycation agent, at a rate of approx. 0.1% of the glycolytic flux. We investigated methylglyoxal metabolism in Saccharomyces cerevisiae cells, using haploid null mutants. Growth studies showed that the most sensitive strains to 2-oxoaldehydes were the null mutants for GSH1 and GLO1, coding for glutathione synthase I and glyoxalase I respectively. The GRE3 null mutant, lacking aldose reductase activity, is as sensitive as the control strain. Kinetic modelling and computer simulation of this type of experiment were also performed, and we concluded that the most important parameters for controlling the intracellular concentration of methylglyoxal are the activity of glyoxalase I and the GSH concentration. Moreover, our model predicts an intracellular steady-state concentration of methylglyoxal of approx. 2 microM. Our results show that the glyoxalase pathway is the main detoxification pathway for 2-oxoaldehydes in yeast, and is likely to be the key enzymatic anti-glycation agent in these cells.
Dynamics of Pulsed Atmospheric pressure Plasma Streams generated by a Plasma Gun (2012)

A specific plasma jet device named Plasma Gun has been developed in GREMI for biomedical applications. Recent studies using this device concerned plasma antitumoral effect and potential endoscopic treatments. The plasma gun is based on dielectric barrier discharge (DBD) flushed with rare gases at low flow rates (10-1000 sccm), and powered by a pulsed generator. It allows Pulsed Atmospheric- pressure Plasma Streams (PAPS) generation at high velocities (108 cm.s-1). PAPS can propagate over long distances in dielectric capillaries (from few tens of cm to m). At the capillary outlet, a plasma plume is generated in ambient air, leading to production of reactive species which participate to the plasma treatment. In order to optimize plasma target exposition, it is necessary to better understand the mechanisms of generation and propagation of the PAPS in the dielectric capillary and at its outlet.
In this work, generation and propagation mechanisms were investigated mainly by means of ICCD imaging. Fast ionization wave (FIW) velocity measurements are obtained using a bunch of optical fibers, connected to a PMT, placed along the PAPS propagation path. Two propagation modes have been highlighted: Wall hugging PAPS (Wh-PAPS) and Homogeneous PAPS (H-PAPS). PAPS propagation is dependent on the voltage pulse shape and, to a lesser extent, on the pulse repetition rate and the gas flow rate. It appears that the photo-ionization plays a minor role, but the PAPS propagation mechanisms are clearly dependent on the plasma tail characteristics (namely impedance) [1] that connects the higher intensity zone (corresponding to the FIW front) to the DBD reactor. Indeed, the PAPS propagation is sustained by the high electric field induced by the ionization front. Even at long distances, if the local electric field is high enough in the vicinity of the FIW, a secondary PAPS can be generated in another capillary close to the initial one through the dielectric wall. A recent study based on a numerical model developed by Z. Xiong and M.J. Kushner at the University of Michigan, has investigated mechanisms of PAPS propagation, splitting and mixing. It has been shown that the PAPS splitting is symmetric, in terms of electron density ne and electron temperature Te [2] as can be a priori estimated from experiments performed in T-branched capillary. Even if there are still discrepancies between calculated and measured velocities, both simulation and experimental data emphasize the key role of the plasma tail between FIW and initial discharge volume on the final characteristics of the plasma created at the capillary outlet.
This work was supported by ANR ”PAMPA” and by Region Centre through the APR program “Plasmed”. V.S. was financially supported by Conseil General du Loiret.
References
[1] E. Robert, V. Sarron, D. Ries, S. Dozias, M. Vandamme, J.M. Pouvesle Plasma Sources Sci Technol in press.
[2] Z. Xiong, E. Robert, V. Sarron, J.M. Pouvesle and M.J. Kushner J. Phys. D. (submitted 2012)
Film Growth Kinetics of Chemical Vapor Deposition of Copper from Cu (  HFA  ) 2 (1993)

Copper films have been grown by chemical vapor deposition (CVD) from copper (II) hexafluoroacetylacetonate,, in a cold wall, vertical flow reactor with pure hydrogen and a mixture of hydrogen (75%)/argon (25%). The quantitatively measured operating conditions were 10 Torr total pressure, 300 to 400°C substrate temperature, and 70 to 85°C precursor temperature. Film growth rates were between 100 to 1000 Å/min depending on processing conditions. The copper film growth rate was 0.5 order in both precursor and hydrogen concentration. A deposition temperature of about 300°C was needed to obtain significant film growth. Only surface impurities were detected in copper film. Any impurities below the surface were under the detection limits of Auger electron spectroscopy analysis. Resistivities of 2.0–3.0 μΩ cm were routinely obtained. Two mechanisms are proposed for the growth of copper films by CVD using which are consistent with our experimental observations and those in the literature.
Laser etching of LiNbO3 in a Cl2 atmosphere (1988)

Single-crystal LiNbO3 is etched in an atmosphere of 500-Torr Cl2 by focusing a 257-nm, frequency-doubled CW argon-ion laser beam onto the surface. The observed laser intensity threshold for etching is consistent with a process involving surface melting of the crystal. A single laser scan forms a shallow depression with marked ripples transverse to the direction of laser polarization, while repeated scans give a groove with a nearly triangular cross section. During laser etching, reacted material is redeposited on the crystal surface. This material is subsequently analyzed for chemical composition. The LiNbO3 surface is partially depleted of Li and O both at the etched grooves and at significant distances away from the grooves. Studies at low light intensities suggest that photochemical generation of gas-phase Cl radicals is responsible for the O depletion and part of the Li depletion. In addition, a dark reaction between Cl2 and LiNbO3 depletes only Li.
A multi-stage approach for the thermal generator maintenance scheduling problem (2003)

The thermal generator maintenance scheduling problem has been tackled by a variety of traditional optimisation techniques over the years. While these methods can give an optimal solution to small scale problems, they are often inefficient and impractical when applied to larger problems. We employ a multi-stage approach where the problem is decomposed into smaller sub-problems, each of which can be solved much more efficiently by existing algorithms. After each part of the problem has been solved, the results are then recombined to form the solution to the whole problem. Both tabu search and a memetic algorithm have been observed to produce very good results but they take a significant amount of time to run. We utilise both techniques to form the basis of a multi-stage approach to solve the thermal generator maintenance scheduling problem. The results demonstrate that the multi-stage methodology is just as effective for this problem while achieving a significant reduction in run-time.
A digitally enhanced 1.8-V 15-bit 40-MSample/s CMOS pipelined ADC (2004)

A 1.8-V 15-bit 40-MSample/s CMOS pipelined analog-to-digital converter with 90-dB spurious-free dynamic range (SFDR) and 72-dB peak signal-to-noise ratio (SNR) over the full Nyquist band is presented. Its differential and integral nonlinearities are 0.25 LSB and 1.5 LSB, respectively, and its power consumption is 400 mW. This performance is enabled by digital background calibration of internal digital-to-analog converter (DAC) noise and interstage gain errors. The calibration achieves improvements of better than 12 dB in signal-to-noise plus distortion ratio and 20 dB in SFDR relative to the case where calibration is disabled. Other enabling features of the prototype integrated circuit (IC) include a low-latency, segmented, dynamic element-matching DAC, distributed passive input signal sampling, and asymmetric clocking to maximize the time available for the first-stage residue amplifier to settle. The IC is realized in a 0.18-/spl mu/m mixed-signal CMOS process and has a die size of 4mm/spl times/5 mm.
Improving the MVA Vaccine Potential by Deleting the Viral Gene Coding for the IL-18 Binding Protein (2012)

This study demonstrates the relevance of IL-18 bp contribution in the immune response evasion during MVA infection. Our findings clearly show that the deletion of the viral IL-18 bp gene is an effective approach to increase MVA vaccine efficacy, as immunogenicity improvements were observed against vector antigens and more importantly to HIV antigens.
A study of prefix hijacking and interception in the internet (2007)

There have been many incidents of prefix hijacking in the Internet. The hijacking AS can blackhole the hijacked traffic. Alternatively, it can transparently intercept the hijacked traffic by forwarding it onto the owner. This paper presents a study of such prefix hijacking and interception with the following contributions: (1). We present a methodology for prefix interception, (2). We estimate the fraction of traffic to any prefix that can be hijacked and intercepted in the Internet today, (3). The interception methodology is implemented and used to intercept real traffic to our prefix, (4). We conduct a detailed study to detect ongoing prefix interception.
Cyclic Numerical Time Integration in Variational Non-Rigid Image Registration based on Quadratic Regularisation (2012)

In the present work, a novel computational framework for variational non-rigid image registration is discussed. The fundamental aim is to provide an alternative to approximate approaches based on successive convolution, which have gained great popularity in recent years, due to their linear complexity and ease of implementation. An optimise-then-discretise framework is considered. The corresponding Euler-Lagrange equations (ELEs), which arise from calculus of variation, constitute a necessary condition for a minimiser of the variational optimisation problem. The conventional, semi-implicit (SI) time integration for the solution of the ELEs is replaced by an explicit approach rendering the implementation straightforward. Since explicit methods are subject to a restrictive stability requirement on the maximal admissible time step size, they are in general inefficient and prone to get stuck in local minima. As a remedy, we take advantage of methods based on cyclic explicit numerical time integration. With this the strong stability requirement on each individual time step can be replaced by a relaxed stability requirement. This in turn results in an unconditionally stable method, which is as efficient as SI approaches. As a basis of comparison, SI methods are considered. Generalisability is demonstrated within a generic variational framework based on quadratic regularisation. Qualitative and quantitative analysis of numerical experiments based on synthetic test data demonstrates accuracy and efficiency.
Improved impulse detection in power line communication systems (2008)

Impulse noise is generated by many house hold appliances that are attached to the electrical network. Its presence is often detrimental to the performance of a power line communication system, causing PHY throughput degradation in the order of 30°50%. The goal of impulse noise mitigation is to improve the SNR of the received signal by means of signal processing tools. In this work we focus on optimizing the detection of impulsive noises. A new method is developed for the setting of the detection threshold, that is both efficiently computed (in an iterative manner), and performs well in various impulsive noise conditions. Once impulses are detected they are removed from the received waveform by applying simple windowing mechanisms. To evaluate different impulse detection algorithms we test them against real life (impulsive) noise waveforms that have been captured on the power line. The selected algorithm is further validated on the power line against realtime captures of impulse noise impeded signals.
Total Synthesis of Serofendic Acids A and B Employing Tin-Free Homoallyl−Homoallyl Radical Rearrangement (2005)

Total syntheses of serofendic acids A (1a) and B (1b) are described. The key strategic element of the approach involves the novel tin-free homoallyl-homoallyl radical rearrangement of 5 for the construction of bicyclo[2.2.2]octane ring system 4. In addition, the conversion of methyl atisirenoate 2 to serofendic acids A (1a) and B (1b) was achieved on the basis of the Michael reaction of sodium thiomethoxide.[reaction: see text]
Execution Support to Long Running Workflows (2014)

Workflows have been widely adopted in enterprise environments to allow the formalization and automation of business processes through the execution of activities implemented by computational services. Some of these workflows, namely long running workflows, take a long time (e.g., Hours or even days and weeks) to complete their work and produce the expected results. The long execution time is inherent to the nature of some business processes, e.g., To buy a book in a bookstore using the Internet. These workflows are usually deployed at operational environments that explicitly deal with the particularities of their executions, e.g., The long time running, possibility of changes in the business rules, need of resource provisioning, security and so on. To build this kind of environment is a complex task due to the aforementioned characteristics of long running workflows. In this context, this paper presents the architecture, design and implementation of an environment specially conceived to support long running workflows. In order to evaluate the proposed environment, we carried out a performance evaluation.
VLASIC: A Catastrophic Fault Yield Simulator for Integrated Circuits (1986)

This paper describes the yield simulator VLASIC (VLSI Layout Simulation for Integrated Circuits). VLASIC is a Monte Carlo simulator that uses defect models and statistics to place random catastrophic point defects on a chip layout and determine what circuit faults, if any, have occurred. The defect models are described in tables, and so are readily extended to new processes or defect types. The defect statistical model is based on actual fabrication line data, and has not appeared before in the literature. The circuit fault information generated by VLASIC can be used to predict yield, optimize design rules, generate test vectors, evaluate redundancy, etc. A redundancy analysis system which uses these data is described, and an example of its use given.
Traceless Ligation of Cysteine Peptides Using Selective Deselenization (2010)

Selective deselenization: Native chemical ligation at selenocysteine is followed by selective deselenization of the selenocysteine to alanine, in the presence of cysteine residues without protecting groups (see scheme). This selectivity is achieved by using the water-soluble tris(2-carboxyethyl)phosphine (TCEP) in the absence of a radical initiator. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Low complexity approximate maximum throughput scheduling for LTE (2010)

In this paper we address the challenge of multiuser scheduling in the downlink of 3GPP UMTS/LTE. Long Term Evolution (LTE) imposes the constraint of using the same code rate, modulation order and transmit power for all resources a User Equipment (UE) is scheduled onto. This, in addition to the lack of channel knowledge, prohibits theoretical concepts such as capacity maximization to be applied for resource allocation. Based on the Channel Quality Indicator (CQI) feedback we derive a linearized model for multiuser scheduling. In contrast to other proposals we use Mutual Information Effective SNR Mapping (MIESM) to calculate an average CQI value for all UE resources. This enables a rate increase while still guaranteeing an imposed Block Error Ratio (BLER) constraint. The proposed framework can also be applied to implement other scheduling strategies. This is demonstrated by comparing different standard schedulers in terms of achieved throughput and fairness.
U.S. technology policy in the information age (1996)

article Free Access Share on U.S. technology policy in the information age Author: Hal Berghel Computer Science at the University of Arkansas Computer Science at the University of ArkansasView Profile Authors Info & Claims Communications of the ACMVolume 39Issue 6June 1996 pp 15–18https://doi.org/10.1145/228503.228506Published:01 June 1996Publication History 3citation6,797DownloadsMetricsTotal Citations3Total Downloads6,797Last 12 Months8Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF