gebhart/patrepeval huggingface dataset:
The Lack of Mitochondrial Thioredoxin TRXo1 Affects In Vivo Alternative Oxidase Activity and Carbon Metabolism under Different Light Conditions (2019)

The alternative oxidase (AOX) constitutes a nonphosphorylating pathway of electron transport in the mitochondrial respiratory chain that provides flexibility to energy and carbon primary metabolism. Its activity is regulated in vitro by the mitochondrial thioredoxin (TRX) system which reduces conserved cysteines residues of AOX. However, in vivo evidence for redox regulation of the AOX activity is still scarce. In the present study, the redox state, protein levels and in vivo activity of the AOX in parallel to photosynthetic parameters were determined in Arabidopsis knockout mutants lacking mitochondrial trxo1 under moderate (ML) and high light (HL) conditions, known to induce in vivo AOX activity. In addition, 13C- and 14C-labeling experiments together with metabolite profiling were performed to better understand the metabolic coordination between energy and carbon metabolism in the trxo1 mutants. Our results show that the in vivo AOX activity is higher in the trxo1 mutants at ML while the AOX redox state is apparently unaltered. These results suggest that mitochondrial thiol redox systems are responsible for maintaining AOX in its reduced form rather than regulating its activity in vivo. Moreover, the negative regulation of the tricarboxylic acid cycle by the TRX system is coordinated with the increased input of electrons into the AOX pathway. Under HL conditions, while AOX and photosynthesis displayed similar patterns in the mutants, photorespiration is restricted at the level of glycine decarboxylation most likely as a consequence of redox imbalance.
Time-Stamping of Ultrafast Electron Probes Using Terahertz Radiation (2022)

We show a method for detection and correction of the time-of-arrival jitter of electron bunches generated from an rf photoeinjector through Terahertz time-stamping, subsequently improving the temporal resolution of pump-probe UED measurements.
Josephson weak links: shunted-junction and mechanical-model results (1972)

We have investigated two models of a superconducting weak link which give physical insight into the behavior of many Josephson-effect devices. The first of these is a low-inductance oxide-barrier Josephson tunnel junction with an external resistive shunt; the second is a mechanical analog—a driven damped pendulum. The externally shunted junction acts as a generalized weak link in that, by adjusting its shunt resistance or critical supercurrent, it exactly replicates the dc electrical characteristics of many widely different weak links. In fact, we can readily alter its characteristic while the junction is immersed in liquid helium simply by applying a small external magnetic field of 1 Oe or less to decrease the critical current. The mechanical analog, by enabling us to observe the instantaneous behavior of the phase, gives new insight into the nonlinear properties of such weak links. The behavior of both models is governed by the second-order nonlinear differential equation independently proposed by Stewart and McCumber. These models not only verify the computer-generated solutions for weak links in detail, they give new physical insight into the underlying nonlinear behavior.
Policy and charging control in the evolved packet system (2009)

Policy and charging control provides operators with advanced tools for service-aware QoS and charging control. PCC for the evolved packet system, defined as part of the 3 GPP Release 8 specifications, has evolved significantly from previous releases to support multiple-access technologies, roaming, and mobility. Within the PCC framework, a number of protocols have been specified to implement these functions. This article describes key PCC concepts and explains additional amendments to support PCC in the EPS.
Discriminative vs. generative approaches in semantic role labeling (2008)

This paper describes the two algorithms we developed for the CoNLL 2008 Shared Task "Joint learning of syntactic and semantic dependencies". Both algorithms start parsing the sentence using the same syntactic parser. The first algorithm uses machine learning methods to identify the semantic dependencies in four stages: identification and labeling of predicates, identification and labeling of arguments. The second algorithm uses a generative probabilistic model, choosing the semantic dependencies that maximize the probability with respect to the model. A hybrid algorithm combining the best stages of the two algorithms attains 86.62% labeled syntactic attachment accuracy, 73.24% labeled semantic dependency F1 and 79.93% labeled macro F1 score for the combined WSJ and Brown test sets.
Asynchronous network-on-chips (NoCs) for resource efficient many core architectures (2019)

In this chapter, different GALS approaches for the implementation of embedded NoC architectures were presented. The GALS approach allows for the reduction of the resource requirements at an increased scalability of the NoC without sacrificing performance. The three approaches of synchronous, mesochronous, and asynchronous NoCs were compared. For the mesochronous NoC special synchronizers between the links were implemented. For the asynchronous NoC, the routers were completely realized as an asynchronous circuits. The results have shown that modern design methods (CCOpt design fl ow) allow a good scaling of MPSoCs even for synchronous NoCs. Nevertheless, the asynchronous NoC showed lower area and energy requirement compared to the mesochronous and synchronous implementation, while still providing a comparable performance. When comparing a place and route of an MPSoC, the asynchronous NoC leads to 3.1% less area requirements. The power consumption of an asynchronous router is only 22.4% (0.94 mW in idle state) or 53% (3.94 mW during communication) of the power consumption of a clock -based router. In the last section of the chapter, the global clock tree for an MPSoC with 256 CPUs was examined. The synchronous and mesochronous NoC show almost the same power consumption of about 7.7 mW. Using the asynchronous NoC reduces the power consumption by about 25% (5.78 mW). In addition, the mesochronous and asynchronous variants achieve a 2.6% higher clock frequency.
An Improved Spectrophotometric Method for Toluene‐4‐Monooxygenase Activity (2023)

Monooxygenases, an important class of enzymes, have been the subject of enzyme engineering due to their high activity and versatile substrate scope. Reactions performed by these biocatalysts have long been monitored by a colorimetric method involving the coupling of a dye precursor to naphthalene hydroxylation products generated by the enzyme. Despite the popularity of this method, we found the dye product to be unstable, preventing quantitative readout. By incorporating an extraction step to solubilize the dye produced, we have improved this assay to the point where quantitation of enzyme activity is possible. Further, by incorporating spectral deconvolution, we have, for the first time, enabled independent quantification of the two possible regioisomeric products: 1-naphthol and 2-naphthol. Previously, such analysis was only possible with chromatographic separation, increasing the cost and complexity of analysis. The efficacy of our improved workflow was evaluated by monitoring the activity of a toluene-4-monooxygenase enzyme from Pseudomonas mendocina KR-1. Our colorimetric regioisomer quantification was found to be consistent with chromatographic analysis by HPLC. The development and validation of a quantitative colorimetric assay for monooxygenase activity that enables regioisomeric distinction and quantification represents a significant advance in analytical methods to monitor enzyme activity. By maintaining facile, low-cost, high-throughput readout while incorporating quantification, this assay represents an important alternative to more expensive chromatographic quantification techniques.
Prediction of 3D internal organ position from skin surface motion: results from electromagnetic tracking studies (2005)

An effective treatment method for organs that move with respiration (such as the lungs, pancreas, and liver) is a major goal of radiation medicine. In order to treat such tumors, we need (1) real-time knowledge of the current location of the tumor, and (2) the ability to adapt the radiation delivery system to follow this constantly changing location. In this study, we used electromagnetic tracking in a swine model to address the first challenge, and to determine if movement of a marker attached to the skin could accurately predict movement of an internal marker embedded in an organ. Under approved animal research protocols, an electromagnetically tracked needle was inserted into a swine liver and an electromagnetically tracked guidewire was taped to the abdominal skin of the animal. The Aurora (Northern Digital Inc., Waterloo, Canada) electromagnetic tracking system was then used to monitor the position of both of these sensors every 40 msec. Position readouts from the sensors were then tested to see if any of the movements showed correlation. The strongest correlations were observed between external anterior-posterior motion and internal inferior-superior motion, with many other axes exhibiting only weak correlation. We also used these data to build a predictive model of internal motion by taking segments from the data and using them to derive a general functional relationship between the internal needle and the external guidewire. For the axis with the strongest correlation, this model enabled us to predict internal organ motion to within 1 mm.
Optimisation de l'IIP3 des amplificateurs faible bruit par effet de substrat (2009)

National audience
Epigenetics of drought-induced trans-generational plasticity: consequences for range limit development (2015)

Genetic variation gives plants the potential to adapt to stressful environments that often exist beyond their geographic range limits. However, various genetic, physiological or developmental constraints might prevent the process of adaptation. Alternatively, environmentally induced epigenetic changes might sustain populations for several generations in stressful areas across range boundaries, but previous work on Boechera stricta, an upland mustard closely related to Arabidopsis, documented a drought-induced trans-generational plastic trade-off that could contribute to range limit development. Offspring of parents who were drought treated had higher drought tolerance, but lower levels of glucosinolate toxins. Both drought tolerance and defence are thought to be needed to expand the range to lower elevations. Here, we used methylation-sensitive amplified fragment length polymorphisms to determine whether environmentally induced DNA methylation and thus epigenetics could be a mechanism involved in the observed trans-generational plastic trade-off. We compared 110 offspring from the same self-fertilizing lineages whose parents were exposed to experimental drought stress treatments in the laboratory. Using three primer combinations, 643 polymorphic epi-loci were detected. Discriminant function analysis (DFA) on the amount of methylation detected resulted in significant combinations of epi-loci that distinguished the parent drought treatments in the offspring. Principal component (PC) and univariate association analyses also detected the significant differences, even after controlling for lineage, planting flat, developmental differences and multiple testing. Univariate tests also indicated significant associations between the amount of methylation and drought tolerance or glucosinolate toxin concentration. One epi-locus that was implicated in DFA, PC and univariate association analysis may be directly involved in the trade-off because increased methylation at this site on the genome decreased drought tolerance, but increased glucosinolate concentration.
Diffraction of Photoelectrons Emitted from Core Levels of Te and Na Atoms Adsorbed on Ni(001) (1978)

Azimuthal anisotropies in the photoemission from the Te $4d$ and Na $2p$ core levels have been measured for these atoms adsorbed in the $c(2\ifmmode\times\else\texttimes\fi{}2)$ configuration on Ni(001). The observed variations with photoelectron kinetic energy, polar angle of emission, and adsorbate species indicate that this is a very promising technique for surface-structure determination. Preliminary multiple-scattering calculations show encouraging agreement with experiments.
Effect of anti-miR-146a LNA or miR-146a mimic upon IL-1β-induced COX-2 protein and release of HMGB1. (2015)

&lt;p&gt;COX-2 protein expression 24 hours after exposure to IL-1β in U373 cells transfected with LNA-antimiR-146a (50 nM) or miR-146a mimic (pre-mir-146a, 50 nM). (&lt;b&gt;A&lt;/b&gt;) Representative immunoblot and (&lt;b&gt;B&lt;/b&gt;) densitometric analysis: values (optical density units relative to the optical density of β-actin) are mean ± SEM of two separate experiments performed and are expressed relative to the levels in unstimulated cells. (&lt;b&gt;C&lt;/b&gt;) HMGB1 immunoblot (1 control; 2, IL-1β; 3, IL-1β + mimic; 4, IL-1β + mimic scramble; 5 mimic; 6, IL-1β + LNA-antimiR-146a; 7, IL-1β + LNA-antimiR-146a scramble 8, LNA) and densitometric analysis (&lt;b&gt;D&lt;/b&gt;, optical density units of cellular HMGB1 relative to the optical density of β-actin). *p&lt;0.05, compared to control; **p&lt;0.05, LNA or mimic transfected cells stimulated with IL-1β compared to IL-1β alone.&lt;/p&gt;
ChemInform Abstract: SYNTHESIS OF 4‐AMINO‐6‐PHENYL‐3(2H)‐PYRIDAZINONES: A GENERAL PROCEDURE (1984)

Abstract Beim Behandeln mit Phosphorpentachlorid und Phosphoroxychlorid erhält man aus den Pyridazinonen (I) im wesentlicher eine Dichlorverbintlung (II) neben geringeren Anteilen des Chlorieruxngsproduktes IIIl).
Exploiting the Misalignment of the Serrated Trailing Edge for Improved Aerofoil Broadband Noise Reduction (2017)

This paper presents the experimental results of adding variable flap angles to the serrated trailing edges and their effects on the self-noise radiation of an aerofoil. The investigation included aeroacoustics and wake flow measurements on an NACA 65-(12)10 aerofoil. This paper explores further combinations of positive and negative serration flap angles,  U and  L respectively, across the spanwise extent of the trailing edge. A new parameter, the serration oscillation wavelength (λ), was also included. The study investigates five individual cases, Baseline (B), Straight-Serration (SS), sIngle-Flapped-Serration (IFS), Multi-FlappedSerration (MFS), Split-Flapped-Serration (SFS) and Spanwise-Wavy-Serration (SWS). The serration amplitude and wavelength remained consistent as 30 mm and 3.3 mm respectively. It is clear that all the “misaligned” trailing edges produce different noise characteristics compared to the conventional SS trailing edge. At low-to-mid frequency range, the conventional SS trailing edge still outperforms both the MFS and SFS trailing edges. However, from mid-to-high frequency, both the MFS and SFS trailing edges can achieve higher noise reduction than the SS trailing edge considerably. At very high frequency, where the SS trailing edge would otherwise experience noise increase, there is no noise increase for both the MFS and SFS trailing edges because the periodic misalignment reduces the crossflow component in the space between adjacent members of the serration. The SWS trailing edge produces the same level of noise reduction as the SS trailing edge across the low-to-mid frequency range. From mid-to-high frequency range, the SWS trailing edge outperforms the SS trailing edge, but the level of further noise reduction it can achieve is less than those of MFS and SFS trailing edges. At very high frequency, the SWS begins to experience slightly noise increase over the baseline, B, trailing edge. However, the increase in noise level by the SWS trailing edge at this high frequency range is still less than that by the SS trailing edge. The near-wake flow measurement results provide some explanations for the mechanisms underpinning the broadband noise reduction and high frequency noise suppression by these trailing edge devices.
Density Functional Theory-Based Molecular Modeling: Verification of Decisive Roles of Van der Waals Aggregation of Triiodide Ions for Effective Electron Transfer in Wet-Type N3-Dye-Sensitized Solar Cells (2020)

Density functional theory-based molecular modeling (DFT/MM) validates that KI and I2 undergo exothermic van der Waals (vdW) aggregation in acetonitrile (AN) or in the presence of 4-tert-butylpyridine (TBP), forming potassium triiodide (KI3) and, further mutual vdW aggregation leads to the formation of (KI3)2 and AN, (KI3)2 and (AN)2 and (KI3)2 and TBP in the AN-based Dye sensitized solar cells (DSSC) electrolytes. All KI3 aggregates have a very low energy gap, 0.17 eV, 0.14 eV and 0.05 eV of lowest unoccupied molecular orbital (LUMO) + 1 and LUMO, respectively, verifying efficient electron diffusion in μm-thick DSSC electrolytes. Hydrogen-bonding aggregation of anatase TiO2 model, Ti9O18H and OH, with N3 (proton) dye is also validated by DFT/MM, and the energy structure verifies unidirectional electron flow from highest occupied molecular orbital (HOMO) on thiocyanide (SCN) groups of N3 dye to LUMO on the TiO2 model at the aggregates. Further, DFT/MM for the aggregation of K+I3− with N3 verifies the most exothermic formation of the aggregate of N3 (proton) and K+I3−. The UV-Vis spectra of N3 (proton) and K+I3− is consistent with reported incident photocurrent efficiency (IPCE) action spectra (λ = 450–800 nm) of N3-sensitized DSSC, verifying that the N3 dye of N3 (proton) and K+I3− becomes an effective sensitizer in the anode / TiO2 / N3 (proton) / KI/I2 / acetonitrile (AN) / cathode structured DSSC. The energy structure of LUMO and LUMO + 1 of the aggregates, Ti9O18H and OH and N3 (proton), N3 and K+I3−, (KI3)2 and AN and (KI3)2 and TBP verifies high IPCE photocurrent and effective electron diffusion via KI3-aggregates in the DSSC of Ti9O18H and OH and N3 (proton) and K+I3−.
Electrocoagulation (1982)

Intra-arterial electrolysis was performed in the renal arteries of 10 pigs with platinum electrodes. Direct current was used and with correct technique firmly adherent thromboses in the arteries could regularly be made. The method is somewhat time-consuming and with unsuitable electrodes, too much current or too high current strength, vessel perforations occurred. Further experiments are under way to improve the method.
A tunable, nonsubsampled, non-uniform filter bank for multi-band audition and level modification of audio signals (2005)

The need for investigation and (possibly non-linear) modification (e.g. dynamic range compression) of the components of an audio signal corresponding to different spectral bands is widespread. Two examples of present focus include multi-band dynamic range compression of a musical signal and frequency-dependent gain control in a hearing aid. We present a technique we call sub-band audition, which enables the user to listen to individual sub-bands of an audio signal, and thus better determine required modifications. The filter bank requirements of such an application are presented. Finally, the design of a tunable, nonsubsampled, non-uniform filter bank, based on allpass-complementary filter banks and elliptic minimal Q-factor (EMQF) filters, is presented.
Histone deacetylase inhibitors improve antisense-mediated exon-skipping efficacy in mdx mice (2022)

Antisense-mediated exon skipping is one of the most promising therapeutic strategies for Duchenne muscular dystrophy (DMD), and some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA despite their low efficacy. The potential of this therapy is still limited by several challenges, including the reduced expression of the dystrophin transcript and the strong 5′-3′ imbalance in mutated transcripts. We therefore hypothesize that increasing histone acetylation using histone deacetylase inhibitors (HDACi) could correct the transcript imbalance, offering more available pre-mRNA target and ultimately increasing dystrophin rescue. Here, we evaluated the impact of such a combined therapy on the Dmd transcript imbalance phenomenon and on dystrophin restoration levels in mdx mice. Analysis of the Dmd transcript levels at different exon-exon junctions revealed a tendency to correct the 5′-3′ imbalance phenomenon following treatment with HDACi. Significantly higher levels of dystrophin restoration (up to 74% increase) were obtained with givinostat and valproic acid compared with mice treated with ASO alone. Additionally, we demonstrate an increase in H3K9 acetylation in human myocytes after treatment with valproic acid. These findings indicate that HDACi can improve the therapeutic potential of exon-skipping approaches, offering promising perspectives for the treatment of DMD. Antisense-mediated exon skipping is one of the most promising therapeutic strategies for Duchenne muscular dystrophy (DMD), and some antisense oligonucleotide (ASO) drugs have already been approved by the US FDA despite their low efficacy. The potential of this therapy is still limited by several challenges, including the reduced expression of the dystrophin transcript and the strong 5′-3′ imbalance in mutated transcripts. We therefore hypothesize that increasing histone acetylation using histone deacetylase inhibitors (HDACi) could correct the transcript imbalance, offering more available pre-mRNA target and ultimately increasing dystrophin rescue. Here, we evaluated the impact of such a combined therapy on the Dmd transcript imbalance phenomenon and on dystrophin restoration levels in mdx mice. Analysis of the Dmd transcript levels at different exon-exon junctions revealed a tendency to correct the 5′-3′ imbalance phenomenon following treatment with HDACi. Significantly higher levels of dystrophin restoration (up to 74% increase) were obtained with givinostat and valproic acid compared with mice treated with ASO alone. Additionally, we demonstrate an increase in H3K9 acetylation in human myocytes after treatment with valproic acid. These findings indicate that HDACi can improve the therapeutic potential of exon-skipping approaches, offering promising perspectives for the treatment of DMD.
ChemInform Abstract: Role of Arginine in Development of Biopharmaceuticals (2010)

Abstract Review: 32 refs.
Silicon Photonics Circuit Design: Methods, Tools and Challenges (2018)

Abstract Silicon Photonics technology is rapidly maturing as a platform for larger‐scale photonic circuits. As a result, the associated design methodologies are also evolving from component‐oriented design to a more circuit‐oriented design flow, that makes abstraction from the very detailed geometry and enables design on a larger scale. In this paper, the state of this emerging photonic circuit design flow and its synergies with electronic design automation (EDA) are reviewed. The design flow from schematic capture, circuit simulation, layout and verification is covered. The similarities and the differences between photonic and electronic design, and the challenges and opportunities that present themselves in the new photonic design landscape, such as variability analysis, photonic‐electronic co‐simulation and compact model definition are discussed.
Evaluation of Rock/Fracture Interaction: During Steam Injection Through Vertical Hydraulic Fractures (1997)

Summary The design, results, and analysis of a steamdrive pilot in the South Belridge diatomite, Kern County, California, are reviewed. Pilot results demonstrate that steam can be injected across a 1,000-ft-tall diatomite column using hydraulically fractured wells and that significant oil is produced in response to steaming. A computationally simple numerical model is proposed and used to analyze reservoir heating and volumetric sweep by steam. Results from the analysis show that hydraulic fractures undergoing steam injection can be dynamic and asymmetrical.