gebhart/patrepeval huggingface dataset:
Sources of Organic Compounds Required for Primitive Life (2019)

Carbon compounds on the early Earth were not the simple mixture previously referred to as a “prebiotic soup.” Instead, there was a continuing input of organic material synthesized by geochemical and photochemical reactions in the volcanic crust and atmosphere; organic compounds were also being delivered during late accretion by the infall of interplanetary dust particles (IDPs), impacting comets, and asteroid-sized bodies. Compounds from both sources (terrestrial and not) then underwent chemical processing by volcanism, photochemistry, and mineral-driven oxidation–reduction reactions. Some of these processes were synthetic reactions that led to increasing complexity, but this was balanced by other processes such as hydrolysis and pyrolysis that degraded organic material into simpler compounds or tar-like polymers. Because the atmosphere contained no molecular oxygen, the organic compounds that formed were relatively stable as a dilute solution in the global ocean, but were also dissolved in freshwater hydrothermal pools in contact with mineral surfaces of volcanic land masses. In either case, a process was required by which the organic compounds could become sufficiently concentrated to undergo chemical reactions. Questions to be addressed: What are plausible sources of organic compounds? What is their composition and abundance? How would organic material be chemically processed on the early Earth? How can dilute organic solutes become sufficiently concentrated to undergo chemical reactions? Chapter 1 described how virtually all of the carbon now circulating in the biosphere as organic and inorganic compounds was delivered during accretion of planetesimals as the Earth formed, and it is reasonable to assume that Mars had a similar addition of carbon compounds and water after it cooled from primary accretion. On the Earth, organic substances delivered during primary accretion would have been destroyed by the heat of impacts and the moon-forming event, so the carbon compounds necessary for the origin of life were necessarily added after the Earth had cooled sufficiently for a global ocean to appear.
Influence of salinity exposure on wheat root metabolism in the context of tissue tolerance and susceptibility (2019)

Salinity is responsible for large yield losses of crops around the world. Wheat is a staple food crop, and its early growth is particularly salt sensitive. Salinity stress causes adverse effects on plant growth and development at both physiological and biochemical levels. To date, numerous studies have focused on plant metabolic responses to salinity in above ground tissues, however surprisingly little is known about the metabolic responses of wheat roots exposed to salt. Within the plant, roots are most vulnerable to salinity as they are directly exposed to salt in the soil. Previous research identified the key role that Gamma Aminobutyric Acid (GABA) metabolism plays in the salt responses of shoots. This project will investigate the regulation of GABA metabolism in salt stressed roots as well as the impact of salt stress on root physiology and respiration. We exposed Scepter wheat variety to 150mM NaCl for 3 days and 6 days through gradual increment of salt and assessed biomass, chlorophyll content, Na+ and K+ levels using flame photometry, and root respiration by Q2 oxygen sensor. Scepter showed significant reduction in fresh weight and dry weight at the whole plant level and organ level after 3 days of treatment with 150 mM NaCl, salt treatment caused a reduction in relative growth rate, chlorophyll content and an increase in root to shoot ratio in salt treated plants compared to the controls. A significant increase of Na+ content was observed in both roots and shoots after 3 days and 6 days of 150 mM NaCl treatment, but K+ levels significantly declined after 3 days of salt treatment in both roots and shoots. The Na+/K+ ratio significantly increased in both shoots and roots after 3 days and 6 days of salt treatment, but roots have higher Na+/K+ ratio compared to shoots. Experiments on oxygen consumption of roots with externally added GABA showed that capacity of roots to use GABA under salt stress to drive respiration increases with salt exposure. The results highlight the implication of salt stress on plants at physiological level and suggest a possible role of GABA in root responses to salinity, further this project will use high throughput mass spectrometry based metabolomics and proteomic approaches to elucidate the metabolic and proteomic changes in roots of wheat varieties which differ in salt tolerance based on the shoot characteristics under salinity.
Benzimidazole-derived Compounds Designed for Different Targets of Alzheimer’s Disease (2019)

Benzimidazole scaffold has been efficiently used for the design of various pharmacologically active molecules. Indeed, there are various benzimidazole drugs, available today, employed for the treatment of different diseases. Although there is no benzimidazole moiety containing a drug used in clinic today for the treatment of Alzheimer's Disease (AD), there have been many benzimidazole derivative compounds designed and synthesized to act on some of the validated and non-validated targets of AD. This paper aims to review the literature to describe these benzimidazole containing molecules designed to target some of the biochemical cascades shown to be involved in the development of AD.
Synthesis of [11C]levofloxacin (2001)

Abstract Levofloxacin, the pure S enantiomer of the fluoroquinolone antibiotic ofloxacin, was labeled via methylation of the corresponding, des ‐methyl, secondary amine with N.C.A. [ 11 C]methyl iodide. The methylation reaction was regioselective, giving predominantly the preferred methyl amine at high temperature in DMF, while otherwise giving predominantly the methyl ester of a free carboxylic acid also present in the molecule. Levofloxacin was obtained in 80% chemical yield after a 45 min synthesis. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Closed-Loop Pressure Feedback Control of a Pressure-Driven Microdroplet Generator (2016)

To predict the size of droplets formed by pressure-driven flows, the droplet size as a nonlinear function of the pressure ratio is measured experimentally. The mathematical model of the pressure-driven microfluidic device is established, and by varying the volume of a container, comparative and quantitative measurements of the response speed and control accuracy of pressure-driven flows are presented. In particular, a closed-loop control system with feedback of the driven pressure is demonstrated, and the deviation between the measured and the predicted value of the driven pressure can be eliminated by using a PI controller. As a result, by accurately controlling the driven pressure of pressure-driven flows, monodisperse droplets with a desired size can be formed for pressure-driven microdroplet generators.
Dual-beam photoconductivity modulation spectroscopy in a-Si: H (1982)

Abstract D.c. photoconductivity and dual-beam photoconductivity modulation measurements on intrinsic a-Si: H are reported. The dual-beam technique is used to elucidate the recombination mechanisms which affect d.c. photoconductivity. In the dual-beam photoconductivity technique two light beams are used, a steady pump beam with hv > 1·5 eV and a chopped monochromatic beam with 0·6 eV hv < 2·0 eV. The pump beam creates free electrons and holes and thus changes the occupation of the semiconductor gap states through which recombination occurs. The second, monochromatic, beam is used to probe recombination processes by altering the occupation of selected gap states, thereby modulating the photoconductivity. The photoconductivity modulation spectrum, which is dependent on temperature and the intensity of the pump beam, is rich in information about gap states that act as recombination centres. Infrared quenching of photoconductivity is observed below T = 200 K. Analysis of this effect in terms of two classes of gap state allows the identification of a distribution of gap states with a small electron capture coefficient of ∼ 4 × 10−13 cm3 s−1 and with a low-energy cut-off at an optical energy of ∼ 0·6 eV above the valence band edge. Above 220 K, the infrared quenching signal disappears and a slow-response positive modulation effect appears which has a low hv cut-off of 0·8–0·9 eV and peaks at ∼ 1·1 eV. The origin of this effect is as yet unclear. Above 250 K a new signal appears with a higher hv threshold energy of ∼ 0·9–1·0 eV. The appearance and growth of this signal with increasing temperature may be due to a temperature-dependent majority-carrier capture coefficient for the gap state involved.
Analysis and Experimental Kinematics of a Skid-Steering Wheeled Robot Based on a Laser Scanner Sensor (2015)

Skid-steering mobile robots are widely used because of their simple mechanism and robustness. However, due to the complex wheel-ground interactions and the kinematic constraints, it is a challenge to understand the kinematics and dynamics of such a robotic platform. In this paper, we develop an analysis and experimental kinematic scheme for a skid-steering wheeled vehicle based-on a laser scanner sensor. The kinematics model is established based on the boundedness of the instantaneous centers of rotation (ICR) of treads on the 2D motion plane. The kinematic parameters (the ICR coefficient , the path curvature variable and robot speed ), including the effect of vehicle dynamics, are introduced to describe the kinematics model. Then, an exact but costly dynamic model is used and the simulation of this model's stationary response for the vehicle shows a qualitative relationship for the specified parameters and . Moreover, the parameters of the kinematic model are determined based-on a laser scanner localization experimental analysis method with a skid-steering robotic platform, Pioneer P3-AT. The relationship between the ICR coefficient and two physical factors is studied, i.e., the radius of the path curvature and the robot speed . An empirical function-based relationship between the ICR coefficient of the robot and the path parameters is derived. To validate the obtained results, it is empirically demonstrated that the proposed kinematics model significantly improves the dead-reckoning performance of this skid-steering robot.
Dissociative electron transfer of copper(ii) complexes of glycyl(glycyl/alanyl)tryptophanin vacuo: IRMPD action spectroscopy provides evidence of transition from zwitterionic to non-zwitterionic peptide structures (2020)

We report herein the first detailed study of the mechanism of redox reactions occurring during the gas-phase dissociative electron transfer of prototypical ternary [Cu<sup>II</sup>(dien)M]˙<sup>2+</sup> complexes (M, peptide). The two final products are (i) the oxidized non-zwitterionic π-centered [M]˙<sup>+</sup> species with both the charge and spin densities delocalized over the indole ring of the tryptophan residue and with a C-terminal COOH group intact, and (ii) the complementary ion [Cu<sup>I</sup>(dien)]<sup>+</sup>. Infrared multiple photon dissociation (IRMPD) action spectroscopy and low-energy collision-induced dissociation (CID) experiments, in conjunction with density functional theory (DFT) calculations, revealed the structural details of the mass-isolated precursor and product cations. Our experimental and theoretical results indicate that the doubly positively charged precursor [Cu<sup>II</sup>(dien)M]˙<sup>2+</sup> features electrostatic coordination through the anionic carboxylate end of the zwitterionic M moiety. An additional interaction exists between the indole ring of the tryptophan residue and one of the primary amino groups of the dien ligand; the DFT calculations provided the structures of the precursor ion, intermediates, and products, and enabled us to keep track of the locations of the charge and unpaired electron. The dissociative one-electron transfer reaction is initiated by a gradual transition of the M tripeptide from the zwitterionic form in [Cu<sup>II</sup>(dien)M]˙<sup>2+</sup> to the non-zwitterionic M intermediate, through a cascade of conformational changes and proton transfers. In the next step, the highest energy intermediate is formed; here, the copper center is 5-coordinate with coordination from both the carboxylic acid group and the indole ring. A subsequent switch back to 4-coordination to an intermediate IM1, where attachment to GGW occurs through the indole ring only, creates the structure that ultimately undergoes dissociation.
Class II transactivator expression in melanoma cells facilitates T-cell engulfment. (2015)

The results suggest a possible mechanism for HLA class II-positive melanoma cells in blunting an anti-tumor response and suggest a possible target for melanoma therapy.
Birefringence Measurement Techniques Applied to Stress Evaluation in Optical Devices (2005)

Residual stress affects the reliability and the performance of optical devices. The Two-Waveplate Compensator (TWC) and the Brace-Köhler techniques are implemented for full-field retardation measurements. Stress profiles are computed in various optical fibers.
Generation of technology-portable flexible analog blocks (2003)

This paper introduces a complete methodology for retargeting of analog blocks to different sets of specifications, even to different technology processes. By careful integration of the tuning process of design parameters with layout generation, fully functional designs are generated in a few minutes of CPU time.
Power Optimization for Low Interference and Throughput Enhancement for 5G and 6G systems (2021)

While the first 5G releases have been defined, it is expected that future Beyond 5G (B5G) and 6G networks will further reduce inter-site distances between access points. Accordingly, ensuring co-existence and controlling interference in such scenarios is pivotal for the success of future wireless systems. In this work all the unused wireless time-frequency resources in non-congested cells are leveraged to propose a novel Link Adaptation (LA) scheme, whose paradigm is to maximize resource utilization and reduce transmit power as much as possible. Note that this contrasts currently considered mechanisms that simply maximize spectral efficiency, demanding power optimization with long-term updates from other procedures. The proposed scheme does not require inter-cell coordination and is transparent to other MAC procedures, making its practical implementation trivial. We analytically establish that the mechanism achieves at least the same capacity in all cells and reduces transmit power when compared to state of the art LA mechanisms. In addition, extensive 3GPP-compliant system level simulations are conducted to assess the performance of the proposal, showing substantial gains in terms of achievable cell throughput in congested cells and overall transmit power reduction.
Switching between “On” and “Off” states of persistent activity in lateral entorhinal layer III neurons (2007)

Persistent neural spiking maintains information during a working memory task when a stimulus is no longer present. During retention, this activity needs to be stable to distractors. More importantly, when retention is no longer relevant, cessation of the activity is necessary to enable processing and retention of subsequent information. Here, by means of intracellular recording with sharp microelectrode in in vitro rat brain slices, we demonstrate that single principal layer III neurons of the lateral entorhinal cortex (EC) generate persistent spiking activity with a novel ability to reliably toggle between spiking activity and a silent state. Our data indicates that in the presence of muscarinic receptor activation, persistent activity following an excitatory input may be induced and that a subsequent excitatory input can terminate this activity and cause the neuron to return to a silent state. Moreover, application of inhibitory hyperpolarizing stimuli is neither able to decrease the frequency of the persistent activity nor terminate it. The persistent activity can also be initiated and terminated by synchronized synaptic stimuli of layer II/III of the perirhinal cortex. The neuronal ability to switch "On" and "Off" persistent activity may facilitate the concurrent representation of temporally segregated information arriving in the EC and being directed toward the hippocampus.
Maternal Dioxin Exposure Combined with a Diet High in Fat Increases Mammary Cancer Incidence in Mice (2020)

BackgroundResults from previous studies have suggested that breast cancer risk correlates with total lifetime exposure to estrogens and that early-life 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure or diets high in fat can also increase cancer risk.ObjectivesBecause both TCDD and diet affect the estrogen pathway, we examined how TCDD and a high-fat diet (HFD) interact to alter breast cancer susceptibility.MethodsWe exposed pregnant female FVB/NJ mice (12.5 days postcoitus) to 1 μg/kg TCDD or vehicle; at parturition, the dams were randomly assigned to a low-fat diet (LFD) or a high-fat diet (HFD). Female offspring were maintained on the same diets after weaning and were exposed to 7,12-dimethylbenz[a]anthracene on postnatal days (PNDs) 35, 49, and 63 to initiate mammary tumors. A second cohort of females was treated identically until PND35 or PND49, when mammary gland morphology was examined, or PND50, when mammary gland mRNA was analyzed.ResultsWe found that maternal TCDD exposure doubled mammary tumor incidence only in mice fed the HFD. Among HFD-fed mice, maternal TCDD exposure caused rapid mammary development with increased Cyp1b1 (cytochrome P450 1B1) expression and decreased Comt (catechol-O-methyltransferase) expression in mammary tissue. Maternal TCDD exposure also increased mammary tumor Cyp1b1 expression.ConclusionsOur data suggest that the HFD increases sensitivity to maternal TCDD exposure, resulting in increased breast cancer incidence, by changing metabolism capability. These results provide a mechanism to explain epidemiological data linking early-life TCDD exposure and diets high in fat to increased risk for breast cancer in humans.
Coordination of replication and transcription along a Drosophila chromosome (2004)

The mechanisms by which metazoan origins of DNA replication are defined, regulated, and influenced by chromosomal events remain poorly understood. To gain insights into these mechanisms, we developed a systematic approach using a Drosophila high-resolution genomic microarray to determine replication timing, identify replication origins, and map protein-binding sites along a chromosome arm. We identify a defined temporal pattern of replication that correlates with the density of active transcription. These data indicate that the influence of transcription status on replication timing is exerted over large domains (>100 kb) rather than at the level of individual genes. We identify 62 early activating replication origins across the chromosome by mapping sites of nucleotide incorporation during hydroxyurea arrest. Using genome-wide location analysis, we demonstrate that the origin recognition complex (ORC) is localized to specific chromosomal sites, many of which coincide with early activating origins. The molecular attributes of ORC-binding sites include increased AT-content and association with a subset of RNA Pol II-binding sites. Based on these findings, we suggest that the distribution of transcription along the chromosome acts locally to influence origin selection and globally to regulate origin activation.
Flux displacement in rectangular iron sheets and geometry-dependent hysteresis loss (2014)

This paper suggests a possible explanation to the geometry-dependence of core loss by solving Maxwell's equations for the flux distribution inside a magnetic conductor carrying eddy currents. The solution reveals a displacement of flux towards the edges of the magnetic sheet. Core loss with and without the displacement effect are compared for the tooth of a highly excited and high-frequency electric machine. A significant difference from standard calculation methods is obtained.
Measurement of 1–10 Hz 3D vibration modes with a CT-scanner (2020)

Abstract A new in situ vibration mode measurement method within a tomograph is proposed based on Projection-based Digital Volume Correlation techniques. Several projection angles are selected and a large number of radiographs of the vibrating sample are acquired at random instants with a small exposure time in order to ‘freeze out’ the displacement and avoid motion blurring. Based on an initial reconstruction acquired in a static configuration, the displacement field measurement is performed using a Proper Generalized Decomposition technique. All projections are analyzed as being due to a few vibration modes deforming the known reference volume. The different projection directions are related to each other assuming that the modal amplitude probability distribution functions are statistically similar. A synthetic test case, mock-up of a liver, is used to illustrate and validate the approach. In this case, 5 projection angles were chosen, 300 radiographs per angle, and the first three vibration modes could be recovered with a good accuracy.
Vaccination of cattle with binary ethylenimine-treated bovine leukemia virus (1983)

SUMMARY Eighteen adult cattle were vaccinated 3 times, at 2-week intervals, with bovine leukemia virus ( blv ) antigen that had been treated with binary ethylenimine. Two weeks after the last vaccination, 14 vaccinated and 8 nonvaccinated cattle were inoculated (challenge-exposed) with blv -infected lymphocytes. The serologic and virologic responses of all cattle were monitored for 1 year. Serologic examinations included a virus-neutralization test and an agar-gel immunodiffusion test for antibody to the glycoprotein antigen of blv . Of the 3 virologic examinations conducted on isolated blood lymphocytes, 2 detected infective blv —namely, a syncytium-induction assay ( sia ) and a sheep bioassay. The 3rd examination was a competition radioimmunoassay ( cria ) for the viral p24 antigen. All of the 8 nonvaccinated cattle became seropositive within 4 weeks after challenge exposure and they remained positive thereafter. At the time of challenge exposure, the 18 vaccinated cattle had blv -specific antibody. Twelve of the 14 challenge-exposed vaccinated cattle and 1 of the 4 nonchallenge-exposed vaccinated cattle remained seropositive throughout the experiment. The results of virologic examinations indicated that the 8 nonvaccinated cattle, 12 of the 14 challenge-exposed vaccinated cattle, and 1 of the 4 nonchallenge-exposed vaccinated cattle became infected with blv . Sheep bioassay was the most sensitive indicator of infection. In the in vitro assays, there were fewer positive results in vaccinated than in nonvaccinated cattle. In the sia , 21.8% of the samples from challenge-exposed vaccinated cattle were positive, whereas 87.5% of the samples from nonvaccinated cattle were positive. In the cria , samples from 38.5% of the challenge-exposed vaccinated cattle were positive as compared with those from 75% of the nonvaccinated cattle. All sia and cria tests on nonchallenge-exposed vaccinated cattle gave negative results.