gebhart/patrepeval huggingface dataset:
Genetic Manipulation of Isoflavone 7-<i>O</i>-Methyltransferase Enhances Biosynthesis of 4′-O-Methylated Isoflavonoid Phytoalexins and Disease Resistance in Alfalfa (2000)

4'-O-Methylation of an isoflavonoid intermediate is a key reaction in the biosynthesis of the phytoalexin medicarpin in legumes. However, isoflavone O-methyltransferase (IOMT) from alfalfa converts the isoflavone daidzein to 7-O-methyl daidzein (isoformononetin) in vitro as well as in vivo in unchallenged leaves of transgenic alfalfa ectopically expressing IOMT. In contrast, elicitation of IOMT-overexpressing plants with CuCl(2) or infecting these plants with Phoma medicaginis leads to greater accumulation of formononetin (4'-O-methyl daidzein) and medicarpin in the leaves than does elicitation or infection of control plants, and no isoformononetin is detected. Overexpression of IOMT results in increased induction of phenylpropanoid/isoflavonoid pathway gene transcripts after infection but has little effect on basal expression of these genes. IOMT-overexpressing plants display resistance to P. medicaginis. The apparently different regiospecificities of IOMT in vivo and in vitro are discussed in relation to potential metabolic channeling at the entry point into the isoflavonoid pathway.
Optimization of binding electrostatics: Charge complementarity in the barnase‐barstar protein complex (2001)

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand-charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase-barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (K(d) approximately 10(-14) M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild-type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins.
Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development. (1993)

The chromosomal genes fla and p93 and the ospA gene from a linear plasmid were sequenced from up to 15 isolates of Borrelia burgdorferi, which causes Lyme borreliosis in man. Comparison of the gene trees provides no evidence for genetic exchange between chromosomal genes, suggesting B. burgdorferi is strictly clonal. Comparison of the chromosomal gene trees with that of the plasmid-encoded ospA reveals that plasmid transfer between clones is rare. Evidence for intragenic recombination was found in only a single ospA allele. The analysis reveals three common clones and a number of rare clones that are so highly divergent that vaccines developed against one are unlikely to provide immunity to organisms from others. Consequently, an understanding of the geographic and genetic variability of B. burgdorferi will prove essential for the development of effective vaccines and programs for control. While the major clones might be regarded as different species, the clonal population structure, the geographic localization, and the widespread incidence of Lyme disease suggest that B. burgdorferi should remain the name for the entire array of organisms.
Neuronal nitric-oxide synthase localization mediated by a ternary complex with synapsin and CAPON (2002)

The specificity of the reactions of nitric oxide (NO) with its neuronal targets is determined in part by the precise localizations of neuronal NO synthase (nNOS) within the cell. The targeting of nNOS is mediated by adapter proteins that interact with its PDZ domain. Here, we show that the nNOS adapter protein, CAPON, interacts with synapsins I, II, and III through an N-terminal phosphotyrosine-binding domain interaction, which leads to a ternary complex comprising nNOS, CAPON, and synapsin I. The significance of this ternary complex is demonstrated by changes in subcellular localization of nNOS in mice harboring genomic deletions of both synapsin I and synapsin II. These results suggest a mechanism for specific actions of NO at presynaptic sites.
Laboratory Tests of Cable-Based Roof Moisture Detection System (1998)

The writers have devised a prototype cable-based roof moisture detection and location system (U.S. Patent 5,648,724) that was tested in simulated conditions. The detection system can use a variety of principles to monitor roofing for the presence of moisture. The location system uses a metallic time-domain reflectometer (MTDR) to locate a suspected wet area by sending an electromagnetic pulse or step signal down the sensor cable and looking for reflections caused by a change in the dielectric constant surrounding the cable due to the presence of a wet area. Tests revealed the MTDR technique to be sensitive and able to locate the position of less than 1 L (0.22 gal.) of water within 0.3 m (1 ft) over 30.5 m (100 ft) of cable. Where multiple regions of wetting were present along the length of the cable, it was possible to locate each boundary between wet and dry.
Learning from native defects on EUV mask blanks (2014)

Defects in the EUV mask blank are one of the largest hurdles to achieving manufacturing readiness of EUV masks. For defect-free masks, the obvious approach is to order blanks that do not have defects or to shift the pattern so that remaining defects do not create a printed defect on wafer. The approach during development should be different. At this learning phase, it is wise to study the defects as they occur naturally on the EUV mask blank. This paper outlines a comprehensive approach to building a mask specifically to showcase the native defects so that they can be studied and repairs can be attempted. The method applied to mask build, defect inspection and characterization will be reviewed in detail. Printability of the mask defects of interest are characterized using both wafer printing and EUV microscope data. Repairs are attempted and characterized. In the end, the impact of native defects is discussed along with the viability of various repair methods.
Investigation of Injection Strategies to Improve High Efficiency RCCI Combustion With Diesel and Gasoline Direct Injection (2012)

Experiments were performed to investigate injection strategies for improving engine-out emissions of RCCI combustion in a heavy-duty diesel engine. Previous studies of RCCI combustion using port-injected low-reactivity fuel (e.g., gasoline or iso-octane) and direct-injected high-reactivity fuel (e.g., diesel or n-heptane) have reported greater than 56% gross indicated thermal efficiency while meeting the EPA 2010 heavy-duty PM and NOx emissions regulations in-cylinder. However, CO and UHC emissions were higher than in diesel combustion. This increase is thought to be caused by crevice flows of trapped low-reactivity fuel and lower cylinder wall temperatures. In the present study, both the low- and high-reactivity fuels were direct-injected, enabling more precise targeting of the low-reactivity fuel as well as independent stratification of equivalence ratio and reactivity. Experiments with direct-injection of both gasoline and diesel were conducted at 9 bar IMEP and compared to results from experiments with port-injected gasoline and direct-injected diesel at matched conditions. The results indicate that reductions in UHC, CO, and PM are possible with direct-injected gasoline, while maintaining similar gross indicated efficiency as well as NOx emissions well below the EPA 2010 heavy-duty limit. Additionally, experimental results were simulated using multi-dimensional modeling in the KIVA-3V code coupled to a Discrete Multi-Component fuel vaporization model. The simulations suggest that further UHC reductions can be made by using wider injector angles which direct the gasoline spray away from the crevices.
IL-33 drives group 2 innate lymphoid cell-mediated protection during Clostridium difficile infection (2019)

Clostridium difficile (C. difficile) incidence has tripled over the past 15 years and is attributed to the emergence of hypervirulent strains. While it is clear that C. difficile toxins cause damaging colonic inflammation, the immune mechanisms protecting from tissue damage require further investigation. Through a transcriptome analysis, we identify IL-33 as an immune target upregulated in response to hypervirulent C. difficile. We demonstrate that IL-33 prevents C. difficile-associated mortality and epithelial disruption independently of bacterial burden or toxin expression. IL-33 drives colonic group 2 innate lymphoid cell (ILC2) activation during infection and IL-33 activated ILC2s are sufficient to prevent disease. Furthermore, intestinal IL-33 expression is regulated by the microbiota as fecal microbiota transplantation (FMT) rescues antibiotic-associated depletion of IL-33. Lastly, dysregulated IL-33 signaling via the decoy receptor, sST2, predicts C. difficile-associated mortality in human patients. Thus, IL-33 signaling to ILC2s is an important mechanism of defense from C. difficile colitis.
Pd-Catalyzed Aerobic Oxidative Coupling of Thiophenes: Synergistic Benefits of Phenanthroline Dione and a Cu Cocatalyst (2020)

Substituted bithiophenes are prominent fragments in functional organic materials, and they are ideally prepared via direct oxidative C-H/C-H coupling. Here, we report a novel Pd<sup>II</sup> catalyst system, employing 1,10-phenanthroline-5,6-dione (phd) as the ancillary ligand, that enables aerobic oxidative homocoupling of 2-bromothiophenes and other related heterocycles. These observations represent the first use of phd to support Pd-catalyzed aerobic oxidation. The reaction also benefits from a Cu(OAc)<sub>2</sub> cocatalyst, and mechanistic studies show that Cu promotes C-C coupling, implicating a role for Cu<sup>II</sup> different from its conventional contribution to reoxidation of the Pd catalyst.
Linear and nonlinear behavior of crystalline optical whispering gallery mode resonators (2004)

We demonstrate strong nonlinear behavior of high-Q whispering gallery mode (WGM) resonators made out of various crystals and devices based on the resonators. The maximum WGM optical Q-fact or achieved at room temperature exceeds 2×1010.
Additions and Corrections - Thiophene Systems. 3. Synthesis of Thieno[3,4-b][1,5]benzoxazepin-10-one and Thieno[3,4-b][1,5]benzothiazepin-10-one. (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditions and Corrections - Thiophene Systems. 3. Synthesis of Thieno[3,4-b][1,5]benzoxazepin-10-one and Thieno[3,4-b][1,5]benzothiazepin-10-one.Jeffery Press, Nancy Eudy, and Sidney SafirCite this: J. Org. Chem. 1980, 45, 26, 5433Publication Date (Print):December 1, 1980Publication History Published online9 October 2003Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/jo01314a615https://doi.org/10.1021/jo01314a615research-articleACS PublicationsRequest reuse permissionsArticle Views25Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A method for daily setup and quality checks of LSO:Ce based time of flight positron emission tomographs (2014)

The setup of PET scanners usually requires an external positron source. A correct setup procedure has to ensure that the detectors are calibrated for gain adjustments, photopeak locations, and positioning maps for individual detector crystals. In order to verify the quality of the setup on a daily basis, daily quality checks are performed where the variations are checked with an external source and flagged if a new setup should be performed. Performing equivalent checks and calibrations using the intrinsic radiation of LSO have successfully been studied previously. Using additional information given by the time of flight information, the intrinsic source originating from the isotope 176Lu can create very accurate setup data within time durations allowing daily scheduling of data collection. The addition of time of flight information also gives an intrinsic method to check the timing calibration essential to time of flight PET scanners. This intrinsic automated setup and quality checks are performed daily without the need of an operator or mechanical devices, creating a consistent condition that data is collected in.
Amplification of Optical Disk Readout Signals by Homodyne Detection (2009)

We experimentally demonstrated the amplification of optical disk readout signals by homodyne detection. This technique uses optical interference to amplify the signals. We further applied phase-diversity detection to reliably obtain the amplified readout signal. The optical system was carefully designed so that a sufficiently amplified readout signal can be obtained. In particular, we applied a corner cube prism as a reflection mirror to achieve sufficient stability of the interferometric optical system. We experimentally demonstrated a 3.6 times amplification of a Blu-ray Disc readout signal. The estimated signal-to-noise ratio (SNR) improvement for an assumed eight-layer optical disk readout signals by applying homodyne detection on the basis of the observed amplification was +7.9 dB, which significantly enables reliable readout of recorded signals. The present technique will be essential for the real commercialization of next-generation multilayer optical disk because of its outstanding ability of SNR improvement.
Process for coal desulfurization. [use of microwave energy] (1978)

A process for coal desulfurization generates extremely low amounts of heat from microwave energy to induce thermochemical, in-situ, reactions to liberate sulfur in the form of stable gaseous species, such as H/sub 2/S, COS and SO/sub 2/.
Testing the Efficacy of a Multi-Component DNA-Prime/DNA-Boost Vaccine against Trypanosoma cruzi Infection in Dogs (2011)

Overall, these results demonstrated that TcVac1 provided a partial resistance to T. cruzi infection and Chagas disease, and provide an impetus to improve the vaccination strategy against Chagas disease.
Tunable filtering balun with enhanced stopband rejection (2012)

For the first time a tunable balun with bandpass response by loading tunable capacitors in the split ring resonators is proposed. By tuning the capacitors’ values, the operating frequency of the balun can be tuned continuously. A shunt stub is employed to realise an additional transmission zero in the higher stopband without any influence on the bandpass response. Theoretical analysis of the filtering balun is conducted and presented. The fabricated balun indicates that the frequency-tuned range of the passband is more than 400 MHz with acceptable insertion loss, and the differences between the two output ports is 180°±5° in phase and within 0.5 dB in magnitude in this tuning range.
Novel GC/Py/GC/IRMS-Based Method for Isotope Measurements of Nitrate and Nitrite. I: Converting Nitrate to Benzyl Nitrate for δ<sup>18</sup>O Analysis (2020)

The <sup>18</sup>O/<sup>16</sup>O (and <sup>15</sup>N/<sup>14</sup>N) ratio of natural nitrate (NO<sub>3</sub><sup>-</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>) can be used to extract valuable information about their source and fate as environmental contaminants, their metabolism as macronutrients in plants and animals, and their behavior in the N biogeochemical cycle. We developed an accurate, precise, sensitive (minimum sample size: 0.2 μg NO<sub>3</sub><sup>-</sup>-equivalent), and reliable (minimal oxygen exchange, loss, or gain) method to selectively isolate and purify nitrate and nitrite from natural water, soil, air, and plant materials by strong anion exchange (SAX) for low- to normal-salinity samples or strong cation exchange (SCX) for high-salinity samples, followed by quantitative conversion to their respective benzyl esters, which can be separated and individually analyzed for δ<sup>18</sup>O (and potentially δ<sup>15</sup>N) by gas chromatography (GC)/pyrolysis/GC/isotope-ratio mass spectrometry (IRMS). The method compares favorably with the currently popular bacterial denitrification and chemical reduction methods, in terms of sensitivity and reliability, and has the potential to simultaneously measure δ<sup>15</sup>N and δ<sup>18</sup>O of nitrate and nitrite from natural samples of various origins.
Middleware Architecture for Ad-hoc Social Network (2016)

The aim of this study is to purpose architecture for middleware for Ad-hoc Social Networks. Many social relationships in a limited geographical area are ad-hoc, e.g., in conference or tourist locations where people meet each other for a specific purpose and may not have access to Internet via Wi-Fi or mobile connection. The Ad-hoc Social Network (ASN) helps to meet temporary location-based social needs by creating a social network where like-minded users participate in social communication connected by an infrastructure-less ad-hoc network. This study presents middleware architecture for ASNs that provides software developers a platform for developing mobile apps that enable social connections. The proposed architecture is a software suite that includes an application layer, transport layer, ad-hoc social layer and ad-hoc communication layer. This study also presents different functions and features required for each layer in ASN.
Cleanup of Organic and Inorganic Wellbore Deposits Using Microemulsion Formulations: Laboratory Development and Field Applications (2017)

Progressive reduction of the flow path of oil and/or gas in the near-wellbore region could cause a gradual decline in hydrocarbon production. The major parameters that influence the time-frame of this process are related to the properties of the crude oil and to the reservoir pressure and temperature. Failure to achieve expected well production could also occur, suddenly, after a well intervention or after the wellbore construction. In either case, changes in pressure, temperature, fluid composition, incompatibility of fluids and/or poor fluid-rock interaction can generate precipitation and deposits of asphaltenes and paraffins, scale formation, emulsions or sludge and wettability alteration. In general, traditional treatments do not target all possible causes of crude oil flow-path reduction at the same time, and a sequence of treatment fluids are pumped to clean up the multiple damages (e.g., treatment of organic deposits followed by an acid treatment to remove scale deposits). The long cleanup time and high volume of fluids used in a multi-step treatment could impact the economics of the projects, especially offshore. The present work discusses multifunctional treatments for production enhancement and flow assurance that can remove organic deposits (e.g., paraffins and asphaltenes), emulsion blockage, scale deposits and increase water-wet condition of the flow path surfaces in one step.
An approach to measuring RBC haemolysis and profiling RBC mechanical fragility (2016)

Red blood cells (RBC) can be damaged by medical products, from storage or from disease. Haemolysis (cell rupture and haemoglobin release) is often a key indicator, with mechanical fragility (MF) offering the potential to assess sub-haemolytic damage as well. This article reports on a unique approach to measuring haemolysis, without the need for centrifugation or other sample separation. It also reports on employing that in measuring blood fragility (susceptibility to haemolysis) under shear stress, utilising an electromagnet to cause a bead to oscillate within a cartridge that contains the sample. Cycling between stressing and optical measurement of induced haemolysis at progressively increasing durations of stress provides a fragility profile. Sub-system-level testing shows high accuracy for the haemolysis measurements and fair consistency for MF profiling. Improving accuracy and precision of profiling is a current focus and a fully integrated and automated version of this system is under development.
Optical interlayer coupling design for optical interconnects based on mirror enhanced grating couplers (2012)

We have designed new optical interlayer couplers based on grating couplers with post-processed mirrors to achieve low insertion loss on a 130nm SOI CMOS process. Optimized design shows an interlayer coupling loss of 2.2 dB.
A thermal model of polymer degradation during selective laser sintering of polymer coated ceramic powders (1996)

Reports that measurable amounts of polymer degradation occur during the fabrication of objects from polymer coated ceramic powders by selective laser sintering (SLS). Argues that because the binder is important in achieving strong green parts that can be handled with minimal breakage during post‐processing operations, it is essential to minimize the extent of binder losses. As the first step towards understanding the mechanisms of binder degradation, this paper presents a thermal model of the physical system, noting that the agreement between theory and experiment are good. The model is used to help determine the most influential parameters affecting binder losses during fabrication from polymer coated powders. Predicts that adjustments to laser beam diameter, laser scanning distance and gaseous environment will strongly affect polymer binder degradation during processing. Further predicts correctly that polymer degradation during SLS processing is not sensitive to the inherent degradation kinetics of the polymer.