gebhart/patrepeval huggingface dataset:
Inhibition of the p66/p51 form of human immunodeficiency virus reverse transcriptase by tRNA<sup>Lys</sup> (1990)

Human immunodeficiency virus (HIV) reverse transcriptase (RT) uses host tRNA(Lys) partially annealed to the primer binding site (PBS) as primer for the initiation of cDNA synthesis. When assaying cDNA synthesis with a template-primer complex formed by an RNA fragment carrying the PBS site and bovine tRNA(Lys) we noticed that an excess of primer tRNA inhibited strongly the DNA polymerase activity of a recombinant HIV RT (p66-p51 heterodimeric form) produced in transformed yeast cells. The same inhibitory effect was observed with animal DNA polymerase alpha, while avian retrovirus RT was neither affected by tRNA(Lys) nor by its specific primer tRNA(Trp). Although the strongest inhibition was observed with tRNA(Lys), other tRNas like tRNA(Phe) and tRNA(Trp) inhibited also the HIV RT, whereas tRNAs specific for valine, proline and glycine had no effect on enzyme activity. Digestion of tRNA(Lys) with pancreatic RNase abolished the inhibition; on the other hand T1 RNase digestion had no effect on the inhibition suggesting a role of the anticodon region in this effect. The 12- and 14-mers corresponding to the anticodon regions of the three bovine tRNA(Lys) isoacceptors inhibited RT activity, indicating that at least an important part of the inhibitory effect could be ascribed to this tRNA region. A strong stimulation of DNA polymerase activity was observed when the effect of tRNA(Lys) was assayed on a recombinant HIV reverse transcriptase produced in a protease deficient yeast strain, which leads to the production of an active p66 enzyme. The same tRNAs that inhibited strongly the heterodimeric form stimulated the p66 form of HIV reverse transcriptase. The results suggest that although both enzymatic forms are able to interact with tRNA(Lys) the topography, as well as the functional implications of the interaction between the precursor and the mature form of HIV reverse transcriptase with the tRNA(Lys) primer, are different.
Identification of Regions of the <i>Escherichia coli</i> Chromosome Specific for Neonatal Meningitis-Associated Strains (2000)

Specific virulence factors associated with the pathogenesis of Escherichia coli strains causing neonatal meningitis (ECNM), such as the K1 capsular polysaccharide, the S fimbriae, and the Ibe10 protein, have been previously identified. However, some other yet unidentified factors are likely to be involved in the pathogenesis of ECNM. To identify specialized unique DNA regions associated with ECNM virulence, we used the representational difference analysis technique. The genomes of two strains belonging to nonpathogenic phylogenetic group A of the ECOR reference collection were subtracted from E. coli strain C5, isolated from a case of neonatal meningitis. Strain C5 belongs to the phylogenetic group B2 as do the majority of ECNM. We have isolated and mapped 64 DNA fragments which are specific for strain C5 and not found in nonpathogenic strains. Of these clones, 44 were clustered in six distinct regions on the chromosome. The sfa and ibe10 genes were located in regions 2 and 6, respectively. A group of genes (cnf1, hra, hly, and prs) known to be present in a pathogenicity island of the uropathogenic strain E. coli J96 colocalized with region 6. The occurrence of these DNA regions was tested in a set of meningitis-associated strains and in a control group composed of non-meningitis-associated strains belonging to the same B2 group. Regions 1, 3, and 4 were present in 91, 82, and 81%, respectively, of the meningitis strains and in 40, 13, and 47% of the control strains. Together, these data suggest that regions 1, 3, and 4 code for factors associated with the ability of E. coli to invade the meninges of neonates.
Troubleshooting the refinery desalter operation (1986)

The increasing oil weight, sulfur content, and addition of impurities in production challenge the basic design of the chem-electric desalter and complicate its functioning as a pressurized-heater, gravitational settling, and oil-water resolution device. The increasing oil weight leads to greater oil carry-under and the increased impurities act as emulsion stabilizers, making the resolution of the oil-water emulsion more difficult. These problems call for a better understanding of the basic factors affecting successful desalter operations, e.g., mechanical, electrical, gravitational, and chemical variables and their interactions with one another. A clearer understanding of these variables better equip the refiner to handle the problems associated with charging difficult-to-desalt feedstocks.
CDMA-Based UHF-RFID System with Semi-Passive UHF Transponders (2011)

Abstract—RFID systems, in general, increase the efficiency of logistic systems, e.g., inventory of stocks. Unfortunately, present existing systems come fast to their limits if a certain number of RFID transponders must be inventoried in a limited period of time, as the channel access method of current RFID systems is based on Time Division Multiple Access. To shorten the inventory process, this work shows an implementation of an UHF RFID system based on semi-passive UHF transponders, using Code Division Multiple Access as anti-collision method. The work focuses on the uplink channel (tag to reader) that covers the transponders ’ backscattered signals. This channel access method enables simultaneous transfer of transponder data; i.e., all transponders in the field may respond at the same time within the same frequency band. The data transfer realized for the uplink channel uses a set of orthogonal spreading sequences (Gold codes) being different for every transponder. The RFID reader designed in this work despreads the backscattered signals and decodes the data of the different transponders. This work shows, in principle, the opportunity for a simultaneous data transfer on the uplink channel in RFID systems, which in turn may reduce the time needed for a complete inventory round. The entire system is build upon dedicated hardware, which is, also, a new aspect of this paper. Keywords-Radio frequency identification; cdma; uhf; transponder; digital signal processors. I.
A comparative study of swelling properties of hydrogels based on poly(acrylamide‐<i>co</i>‐methyl methacrylate) containing physical and chemical crosslinks (2003)

Abstract Poly (acrylamide‐ co ‐methyl methacrylate) hydrogels of different ratios were prepared by using chemical and physical crosslinks to study the effect of nature of crosslinks on swelling behavior of hydrogels. The chemically crosslinked gels were prepared by using NN ′‐methylene bis acrylamide, while physically crosslinked hydrogels were prepared by precipitation polymerization method, using dioxane as solvent. Detailed swelling kinetics such as swelling ratio, transport exponent n , diffusion coefficient D and the effect of pH on equilibrium swelling studies. The study revealed that the nature of crosslinks alter the swelling characteristics of the hydrogel. In chemically crosslinked hydrogels the water transport is Fickian in nature, while in the case of the physically crosslinked hydrogels the water transport mechanism is anomalous indicating major change in relaxation mechanism due to nature of crosslinks. The results also indicate that with increasing acrylamide content the swelling ratio of the hydrogels were also increased, but the transport exponent n remains nearly constant. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 779–786, 2003
Internalization of Near‐Infrared Fluorescently Labeled Activatable Cell‐Penetrating Peptide and of Proteins into Human Fibrosarcoma Cell Line HT‐1080 (2014)

The internalization of near-infrared fluorescently labeled cargos into living cells and tissues allows a highly sensitive detection without interference from skin, porphins or other fluorescent cell and tissue compounds. In this study, the uptake of labeled bovine serum albumin and an antibody, into fibrosarcoma (HT-1080) cells was triggered by the formation of non-covalent complexes with different cell-penetrating peptides; uptake efficiency and intracellular localization were determined. To improve selectivity of internalization into tumor cells, a fluorescent activatable cell-penetrating peptide (ACPP) was synthesized and functionally characterized. This 25-mer peptide was designed to be activatable by Matrix-Metallo-Proteases (MMPs). Its uptake selectivity was estimated using cells with different MMP activities.
Waveform-Diversity-Based Millimeter-Wave UAV SAR Remote Sensing (2009)

To integrate a synthetic aperture radar (SAR) into an operational unmanned airborne vehicle (UAV), it should be as small as possible to meet stringent limitations of size, weight, and power consumption. It appears that the novel combination of millimeter-wave frequency-modulated continuous-wave (FMCW) technology and SAR techniques can provide an optimal solution. However, some efficient techniques should be applied to resolve range/Doppler ambiguities in FMCW UAV SAR systems. As such, a technique of waveform-diversity-based millimeter-wave UAV SAR imaging is presented in this paper. Along with the described system concept and signal model, the performance of the diversified waveforms evaluated by their cross correlations is detailed. As the conventional stop-and-go approximation is not valid for FMCW SAR, a modified wavenumber-domain algorithm with a consideration of continuous antenna motion during transmission and reception is derived. This imaging algorithm is validated with computer simulations. Furthermore, one parallel direct-digital-synthesizer-driven phase-locked-loop synthesizer with adaptive nonlinearity compensation, which has been validated by the experimental results, is proposed to obtain a millimeter-wave FMCW signal with fine frequency linearity.
Modeling Library Dependencies and Updates in Large Software Repository Universes (2017)

Popular (re)use of third-party open-source software (OSS) is evidence of the impact of hosting repositories like maven on software development today. Updating libraries is crucial, with recent studies highlighting the associated vulnerabilities with aging OSS libraries. The decision to migrate to a newer library can range from trivial (security threat) to complex (assessment of work required to accommodate the changes). By leveraging the `wisdom of the software repository crowd' we propose a simple and efficient approach to recommending `consented' library updates. Our Software Universe Graph (SUG) models library dependency and update information mined from super repositories to provide different metrics and visualizations that aid in the update decision. To evaluate, we first constructed a SUG from 188,951 nodes of 6,374 maven unique artifacts. Then, we demonstrate how our metrics and visualizations are applied through real-world examples. As an extension, we show how the SUG can compare dependencies between different super repositories. From a sample of 100 GitHub applications, our method found that on average 79% similar overlapping dependencies combinations exist between the maven and github super repository universes.
Controlled drug delivery vehicles for cancer treatment and their performance (2018)

Although conventional chemotherapy has been successful to some extent, the main drawbacks of chemotherapy are its poor bioavailability, high-dose requirements, adverse side effects, low therapeutic indices, development of multiple drug resistance, and non-specific targeting. The main aim in the development of drug delivery vehicles is to successfully address these delivery-related problems and carry drugs to the desired sites of therapeutic action while reducing adverse side effects. In this review, we will discuss the different types of materials used as delivery vehicles for chemotherapeutic agents and their structural characteristics that improve the therapeutic efficacy of their drugs and will describe recent scientific advances in the area of chemotherapy, emphasizing challenges in cancer treatments.
Improved large-signal performance of paralleled DC-DC converters current sharing (1999)

This paper introduces fuzzy logic control as a technique for significantly improving the large-signal performance of paralleled DC-DC power converters with master-slave current sharing control. The control design for such systems is challenged by its high modeling complexity, and present approaches which come only from a small-signal perspective unable to give a good response for wide load and line transients. The fuzzy logic approach, by dealing naturally with nonlinearities, offers a good and parameter-insensitive transient response for the current sharing loop. The design methodology of the fuzzy compensator, simulation results, and a comparison with existing classical designs are shown.
Core-Shell Structured Ni@SiO2 Catalysts Exhibiting Excellent Catalytic Performance for Syngas Methanation Reactions (2017)

In this study, we prepared core-shell structured Ni@SiO2 catalysts using chemical precipitation and modified Stöber methods. The obtained Ni@SiO2 samples exhibited excellent catalysis performances, including high CO conversion of 99.0% and CH4 yield of 89.8%. Moreover, Ni@SiO2 exhibited excellent catalytic stability during a 100 h lifetime test, which was superior to that of the Ni/SiO2 catalyst. The prepared samples were characterized using a series of techniques, and the results indicated that the catalytic performance for syngas methanation reaction of the Ni@SiO2 sample was markedly improved owing to its nanoreactor structure. The strong interaction between the Ni core and the SiO2 shell effectively restrained the growth of particles, and the deposition of C species.
An efficient and recyclable heterogeneous palladiumcatalyst utilizing naturally abundant pearl shell waste (2010)

An efficient and recyclable ligand-free heterogeneous catalyst has been prepared by the immobilization of palladium onto ground pearl shell powders (Pd/shell powders, Pd/SP). The catalytic activity and recyclability of the prepared Pd/SP along with the charcoal and calcium carbonate supported palladium (Pd/C and Pd/CaCO3) catalysts have been evaluated using the reductive homocoupling of aromatic halides. Pd/SP not only has higher catalytic activity, but also exhibits much stronger stability than Pd/C and Pd/CaCO3. The remarkable Pd/SP stability has been attributed to the chelation of palladium species with the surface chitin and protein molecules of the supported pearl shell powders. The X-ray photoelectron spectroscopy (XPS) studies show that the reductive Pd0 species can be regenerated in situ from the oxidative Pd2+ species for the Pd/SP catalyzed reductive homocoupling of aromatic halides in ethanol/DMSO solution, suggesting that the heterogeneous and homogeneous palladium catalysis proceeds through a similar Pd0/Pd2+ cycle catalytic mechanism.
<i>In vivo</i>x-ray phase contrast analyzer-based imaging for longitudinal osteoarthritis studies in guinea pigs (2010)

Over the last two decades phase contrast x-ray imaging techniques have been extensively studied for applications in the biomedical field. Published results demonstrate the high capability of these imaging modalities of improving the image contrast of biological samples with respect to standard absorption-based radiography and routinely used clinical imaging techniques. A clear depiction of the anatomic structures and a more accurate disease diagnosis may be provided by using radiation doses comparable to or lower than those used in current clinical methods. In the literature many works show images of phantoms and excised biological samples proving the high sensitivity of the phase contrast imaging methods for in vitro investigations. In this scenario, the applications of the so-called analyzer-based x-ray imaging (ABI) phase contrast technique are particularly noteworthy. The objective of this work is to demonstrate the feasibility of in vivo x-ray ABI phase contrast imaging for biomedical applications and in particular with respect to joint anatomic depiction and osteoarthritis detection. ABI in planar and tomographic modes was performed in vivo on articular joints of guinea pigs in order to investigate the animals with respect to osteoarthritis by using highly monochromatic x-rays of 52 keV and a low noise detector with a pixel size of 47 × 47 µm(2). Images give strong evidence of the ability of ABI in depicting both anatomic structures in complex systems as living organisms and all known signs of osteoarthritis with high contrast, high spatial resolution and with an acceptable radiation dose. This paper presents the first proof of principle study of in vivo application of ABI. The technical challenges encountered when imaging an animal in vivo are discussed. This experimental study is an important step toward the study of clinical applications of phase contrast x-ray imaging techniques.
Influence of Dietary Zinc on Hepatic Collagen and Prolyl Hydroxylase Activity in Alcoholic Rats (1992)

The effects of dietary zinc on hepatic collagen and prolyl hydroxylase activity in normal and alcoholic rats has been investigated in four groups of pair-fed male Wistar rats given either liquid ethanol or a control diet for 12 wk. Each group of pair-fed animals received a diet with a different zinc concentration (standard diet, 7.6 mg/L; low-zinc diet, 3.4 mg/L; zinc-supplemented diet, 76 mg/L; and zinc-extrasupplemented, 300 mg/L. There were no significant differences in hepatic collagen concentration and prolyl hydroxylase activity between alcoholic and normal rats receiving a standard diet (collagen, 77 +/- 5 and 73 +/- 6 micrograms/mg protein; and prolyl hydroxylase; 37 +/- 26 and 36 +/- 22 cpm/mg protein). Alcoholic rats fed a low-zinc diet showed increased prolyl hydroxylase activity (75 +/- 10 cpm/mg protein, p less than 0.05), although no changes in hepatic collagen (77 +/- 10 micrograms/mg protein) were observed in comparison with rats fed a standard alcoholic diet. By contrast, hepatic collagen was significantly lower in alcoholic rats fed a zinc-supplemented diet (66 +/- 4 and 63 +/- 3 micrograms/mg protein, p less than 0.05 and p less than 0.01, respectively), and hepatic prolyl hydroxylase activity was particularly lower in rats receiving zinc 300 mg/L (18 +/- 20 cpm/mg protein). Similar effects were observed in normal rats. We conclude that dietary zinc influences hepatic prolyl hydroxylase activity and collagen deposition in alcoholic rats, and in consequence, the control of dietary zinc is necessary to assess the effects of alcohol on collagen metabolism in rats.
Improving Light‐Curing Instruction in Dental School (2013)

Delivering an inadequate amount of light to a light-cured resin will result in a resin that is inadequately cured. This study measured the radiant exposure that students delivered to a simulated restoration to determine if instruction with immediate feedback increased the amount of light they delivered. The amount of light (radiant exposure in J/cm(2)) delivered to a simulated restoration by sixty-three dental students using the same curing light for twenty seconds was recorded. The experiment was repeated after the students had been given detailed light-curing instructions together with immediate feedback using the MARCPS system. Initially, the students delivered between 1.4 and 17.5 J/cm(2) (mean±SD: 9.8±3.5 J/cm(2)). After receiving instructions and feedback on their light-curing technique, they delivered between 6.7 J/cm(2) and 17.8 J/cm(2) (mean±SD: 13.2±3.3 J/cm(2)). ANOVA and Fisher's post hoc multiple comparison tests showed that providing immediate feedback on the students' light-curing technique made a significant improvement in the radiant exposure they delivered (p<0.05). It was concluded that many dental students in this study were not using the curing light properly. After the students had received one session of additional instruction and immediate feedback using the MARC-PS, they delivered 35 percent more light energy to the same simulated restoration. Students who were closer to graduation showed a greater improvement in their light-curing technique (p=0.0091).
The effect of gingival wall location on the marginal seal of class ii restorations prepared with a flowable bulk-fill resin-based composite. (2019)

SureFil SDR is a flowable resin-based composite that allows a single incremental bulk placement. The marginal seal of SureFil SDR at the gingival margins of class II restorations located apical to the cemento-enamel-junction (CEJ) has not been adequately evaluated compared to those located occlusal to the CEJ. Forty class II cavities were prepared in human molars. The gingival margins of 20 preparations were located 0.5 mm occlusal to the CEJ, and the other 20 preparations were located 0.5 mm apical to the CEJ. The cavities surfaces were bonded with XenoV dental adhesive and filled with SDR in one bulk increment up to 4 mm, after which they were covered with CeramX. The teeth were subjected to thermo-and load-cycling, and their gingival margins were exposed to 0.5% basic-fuchsin solution. The specimens were sectioned mesio-distally and scored for microleakage. A Wilcoxon test for pairwise comparison was performed to determine significance. Dye penetration was observed in 30% of the 20 restorations with cavo-surface margins located occlusal to the CEJ and in 55% of the 20 restorations with cavo-surface margins located apical to the CEJ. The bulk-fill flowable resin base SureFil SDR with XenoV dental adhesive provided a better marginal seal in class II restorations with gingival margins above the CEJ compared to restorations with gingival margins below the CEJ. SDR should not be recommended for class II cavity preparations with gingival margins located below the CEJ.
RF-Powered Transceiver With an Energy- and Spectral-Efficient IF-Based Quadrature Backscattering Transmitter (2015)

This study introduces a 5.8 GHz RF-powered transceiver that includes a transmitter using an IF-based quadrature backscattering (IFQB) technique. The IFQB transmitter can produce a quadrature modulated signal without active RF circuits, such as PLL, local generation, and local distribution circuits. Thus, the IFQB technique can significantly reduce the power consumption while achieving denser constellations by the quadrature modulation. The RF-powered transceiver consists of the IFQB transmitter, an OOK receiver, and a power management unit (PMU) for RF powering. The transmitter and receiver operate under a 0.6 V power supply provided by the PMU to further reduce the power consumption. We fabricated a prototype RF-powered transceiver using a 65 nm Si CMOS process to confirm the validity of the proposed technique. During the measurements, the transmitter achieved 2.5 Mb/s with a 32-QAM modulation while consuming 113 μW. In addition, a wireless temperature sensing demonstration was conducted using the prototype sensor node with the presented RF-powered transceiver.
Square-QAM adaptive modulation/TDMA/TDDsystems using modulation level estimationwith Walsh function (1995)

The authors propose a square-QAM adaptive modulation/time division multiple access/time division duplex (TDMA/TDD) system for land mobile communications to achieve high quality and high bit rate transmission in both flat and frequency selective fading environments. To further improve performance, a new modulation level estimation scheme using the Walsh function and maximum likelihood (MS) estimation is also proposed. Computer simulation confirms that the proposed system gives 8 dB better performance and four times larger delay spread immunity than that of conventional QPSK systems at BER = 10-3.